title: Regulatory response of methanogen cells to different forms of iron and sulfur

city: Bozeman

first: Rachel

middle: L.

last: Spietz

state: MT

institute: Montana State University

summary: We used comparative transcriptomics to explore cellular responses to growth on pyrite (FeS2) or aqueous iron (Fe(II)) and sulfur (cysteine or sulfide). Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study. Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study.

overall_design: Methanosarcina barkeri strain MS cells were grown with three different sources of iron and sulfur: 20 uM ferrous iron and 2mM cysteine, 20 uM ferrous iron and 2 mM sulfide, or 2 mM pyrite (FeS2). Total mRNA from mid-log phase cells from four replicate for each condition were sequenced.

first: Devon

last: Payne

first: Eric

last: Boyd


title: Functional role of SERPINA1 in trophoblasts

status: Public on Mar 10 2022

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

type: Expression profiling by high throughput sequencing

summary: Analysis of the effect of SERPINA1 siRNA experiment

overall_design: RNA-seq analysis of silenced SERPINA1 (n = 3) and negative control (n=3) samples

first: Heli

last: Tiensuu

first: Pinja

last: Tissarinen


title: Acute lymphoblastic leukemia displays a distinct highly methylated genome

status: Public on Mar 03 2022

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is tightly regulated during development and is stably maintained in normal cells. In contrast, the methylome of cancer cells is commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data examining large cohorts at genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing of leukemic cells across multiple subtypes of ALL, leukemia cell lines and normal hematopoietic cells, and show that in contrast to most cancers, ALL samples only exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T-ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients that is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome, and provide insights into the deregulation of methylation in cancer.

overall_design: Genome-wide DNA methylation profiling of B-ALL and T-ALL cell lines as well as DNA methylation and expression profiling of Jurkat cells with TET2 knockout.

first: Alexandra

middle: L

last: Mattei

first: Helene

last: Kretzmer

first: Chunxu

last: Qu

first: Xiang

last: Chen

first: Yiping

last: Fan

first: Gang

last: Wu

first: Kathryn

middle: G

last: Roberts

first: Selina

last: Luger

first: Mark

last: Litzow

first: Jacob

last: Rowe

first: Elisabeth

last: Paietta

first: Wendy

last: Stock

first: Elaine

middle: R

last: Mardis

first: Richard

middle: K

last: Wilson

first: James

last: Downing

first: Charles

last: Mullighan

first: Alexander

last: Meissner


title: Alysiella filiformis DSM 16848 RNA-Seq

status: Public on May 10 2022

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: mRNA-Seq for differential gene expression analysis and delineation of chromosome interaction domains

overall_design: 3 conditions in biological triplicates (exponential growth (OD600 = 0.2) in mod. PY-medium ("B") and BSTSY+FBS ("Serum"), stationary growth (OD600 = 1) in mod. PY-medium ("B") and BSTSY+FBS ("Serum"), growth on solid medium for 24h, exponential growth (OD600 = 0.2) in mod. PY-medium + 25 ug/ml rifampicin for 30 min)

first: Tobias

last: Viehboeck


title: Single-cell intracellular epitope and transcript detection revealing signal transduction dynamics

city: Nijmegen

first: Francesca

last: Rivello

address: Heyendaalseweg 135

department: Physical-Organic Chemistry

country: Netherlands

institute: Radboud University

summary: To further our understanding of how biochemical information flows through cells upon external stimulation, we require single-cell multi-omics methods that concurrently map changes in (phospho)protein levels across signaling networks and the associated gene expression profiles. Here, we present Quantification of RNA and Intracellular Epitopes by sequencing (QuRIE-seq), a droplet-based platform for single-cell RNA and intra- and extracellular (phospho)protein quantification through sequencing. We applied QuRIE-seq to quantify cell-state changes of 6976 cells, at both the signaling and transcriptome level following 2, 4, 6, 60, and 180-minute stimulation of the B-cell receptor pathway (BCR) in Burkitt lymphoma cells (BJABs). Using the recently developed multi-factor omics analysis (MOFA+) framework we delineated changes in single-cell (phospho)protein and gene expression patterns over multiple timescales and revealed the effect of an inhibitory drug (Ibrutinib) on signaling and gene expression landscape.

overall_design: We used our novel technology QuRIE-seq for simultaneous quantification of RNA and (phospho) proteins at a single-cell level. The deposited data contains the quantification of gene expression profiles as well as a set of 80 proteins for individual BJAB cells upon different durations of aIg stimulation (0, 2, 4, 6, 60, 180 min) with previous ibrutinib inhibition (for 6, 180 min)

middle: M

first: Erik

last: van Buijtenen

first: Kinga

last: Matuła

first: Jessie

middle: A

last: van Buggenum

first: Paul

last: Vink

first: Hans

last: van Eenennaam

first: Klaas

middle: W

last: Mulder

first: Wilhelm

middle: T

last: Huck


title: Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy [snRNA-Seq]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

country: USA

institute: Weill Cornell Medicine

summary: Activation of microglia is a prominent pathological feature in tauopathies, including Alzheimer’s disease. How microglia activation contributes to tau toxicity  remains largely unknown. Here we show that nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, activated by tau, drives microglial-mediated tau propagation and toxicity. Constitutive activation of microglial NF-κB exacerbated, while inactivation diminished, tau seeding and spreading in young PS19 mice. Inhibition of NF-B activation enhanced the retention while reduced the release of internalized pathogenic tau fibrils from primary microglia and rescued microglial autophagy deficits. Remarkably, inhibition of microglial NF-κB in aged PS19 mice rescued tau-mediated learning and memory deficits, restored overall transcriptomic changes while increasing neuronal tau inclusions. Single cell RNA-seq revealed that tau-associated disease states in microglia were diminished by NF-B inactivation and further transformed by constitutive NF-B activation. Our study establishes a central role for microglial NF-B signaling in mediating tau spreading and toxicity in tauopathy.

overall_design: Droplet-based single nuclear RNA sequencing of cortical tissues from Ikbkb+/+ (n=4),  Ikbkb+/+;P301S+(n=3),  Ikbkb-/-;P301S+ (n=2) and IkbkbCA;P301S+ (n=2) mice

first: Chao

last: Wang

last: Fan

first: Rabia

last: Khawaja

first: Bangyan

last: Liu

first: Lihong

last: Zhan

first: Lay

last: Kodama

first: Marcus

last: Chin

first: Yaqiao

last: Li

first: David

last: Le

first: Yungui

last: Zhou

first: Carlo

last: Condello

first: Lea

last: Grinberg

first: William

last: Seeley

first: Bruce

last: Miller

first: Sue-Ann

last: Mok

first: Jason

middle: E

last: Gestwicki

first: Ana

last: Cuervo

first: Wenjie

last: Luo


title: Immunomodulatory effects of PI3Kδ inhibition in murine and human solid tumors [mouse]

status: Public on Mar 02 2022

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: Phosphoinositide 3-kinase δ (PI3Kδ) plays key roles in lymphocytes and inhibitors targeting this PI3K have been approved for hematological malignancies. While preclinical data in hematological and solid tumor models have demonstrated that PI3Kδ inhibitors (PI3Kδi) can induce anti-tumor immunity, the impact of PI3Kδi in human solid tumors remains unknown. Here, we assessed the effects of the PI3Kδi AMG319 in patients with early stage head and neck cancer in a neoadjuvant, double-blind and placebo-controlled randomised phase-II trial. We find that PI3Kδ inhibition decreases tumor-infiltrating TREG cells and causes heightened cytotoxic potential of tumor-infiltrating CD8+ and CD4+ T cells. Loss of intratumoral TREG cells and an increase in the frequency of activated TREG cells in the blood post-treatment are indicative of systemic effects on TREG cell tissue retention and maintenance. At the chosen AMG319 dosing, the occurrence of immune-related adverse events caused treatment discontinuation in 43% of drug-treated patients, further suggestive of systemic effects on TREG cells. Consistent with this notion, in a murine syngeneic tumor model, PI3Kδi caused a decrease in TREG cells in both tumor and non-malignant tissues and affected TREG subtype composition, maintenance and functionality.

overall_design: Single-cell RNA-seq was performed from FoxP3+CD4+ T cells isolatied from Murine spleen, tumor, and colon in PI3Kdi-treated (n = 3) and placebo-control treated (n = 3) animals

first: Simon

last: Eschweiler

first: Ciro

last: Ramírez-Suástegui

first: Emma

last: King

first: Lindsey

last: Chudley

first: Jaya

last: Thomas

first: Oliver

last: Wood

first: Adrian

last: von Witzleben

first: Divya

last: Singh

first: Danielle

last: Jeffrey

first: Katy

last: McCann

first: Hayley

last: Simon

first: Monalisa

last: Mondal

first: Alice

last: Wang

first: Elena

last: Lopez-Guadamillas

first: Yingcong

first: Nicola

last: Dobbs

first: Louisa

last: Essame

first: Gary

last: Acton

first: Fiona

last: Kelly

first: Gavin

last: Halbert

first: Joseph

middle: J

last: Sacco

first: Andrew

last: Schache

first: Richard

last: Shaw

first: James

last: McCaul

first: Claire

last: Paterson

middle: H

last: Davies

first: Peter

last: Brennan

first: Rabindra

middle: P

first: Paul

last: Loadman

last: Wilson

first: Khalid

last: Ali

first: Alan

last: Hackshaw

first: Gareth

first: Terry

last: Jones

first: Ferhat

last: Ay

first: Klaus

last: Okkenhaug

first: Bart

last: Vanhaesebroeck

first: Vijayanand

last: Pandurangan

first: Christian

last: Ottensmeier


title: Differentially expressed genes in undifferentiated spermatogonia at single cell level following a low dose of busulfan

status: Public on Mar 04 2022

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: Spermatogonial stem cells are responsible for sustaining gametes production and male fertiliy in men. However, germ cells including SSCs are highly sensitive to chemotherapies and radiations, placing male cancer patients at high risk of treatment-induce infertility. We have previously shown that the undifferentiated spermatogonial population of mouse testis is  functionally heterogeneous and contain both stem cells and committed progenitor cells. Using mouse model of chemotherapy-induced germline damage and recovery, we aim to define  molecular charactersitics, dynamics and heterogeneity of undifferentiated spermatogonia during germline regeneration compared to homeostatic undifferentiated spermatogonia.

overall_design: Undifferentiated spermatogonia were isolated by flow sorting from adult WT untreated controls and busulfan-treated adult mice at D10. Cells were pooled for each treatment group, 3 mice per group, 2 independent experiments.

first: Jinyue

last: Liao

first: Julien

middle: D

last: Legrand

first: Fernando

last: Rossello

first: Ai-Leen

last: Chan

first: Antonella

last: Papa

first: TinLap

last: Lee


title: Embryonic neural crest cell derivatives release pro-metastatic cues driving neuroblastoma dissemination in an avian disease model

status: Public on Mar 09 2022

city: LYON

first: Olivier

last: IMBAUD

state: Rhône-Alpes

address: Faculty of Medicine and Pharmacy - 3rd floor 8 Rockefeller Avenue

department: NeuroMyoGene Institut (INMG)

country: France

institute: UCBL | CNRS UMR 5310 | INSERM U1217

summary: Embryonic malignant transformation is concomitant to organogenesis, often affecting multipotent and migratory progenitors. Neuroblastoma (NB) is an emblematic example, arising from neural crest progenitors and characterized by a high heterogeneity and a widely disseminated clinical presentation. Metastatic triggers from the embryonic environment are suspected but yet unknown due to limited investigation access in patients and current models. Using combinations of ex vivo and in vivo models mimicking the embryonic context coupled to proteomic and transcriptomic analyses, we identify Olfactomedin1 (OLFM1) released by sympathetic derivatives at the core of a gene program promoting NB cells decohesion, primary tumor escape and dissemination. This OLFM signature discriminates metastatic from localized stages in NB patient cohorts. Finally, we report an extended tumor cell escape gene signature of disseminated forms specifically shared by cancers with neural-crest origin, revealing a sustained embryonic imprint of the lineage of origin, manifested in the metastatic properties of malignant cells.

overall_design: We harvested IGR-N91 cells cultivated with the hanging drop protocol for 24 hours in E8-cSGcm, E8-cDRGcm or in E15.5-mSGcm and performed whole RNASeq analyses. For each condition, the number of significantly upregulated and downregulated transcripts as compared to control medium were homogeneously distributed. Each condition is in duplicates.

first: Dounia

last: Ben Amar

first: Karine

last: Thoinet

last: Imbaud

first: Clélia

last: Costechareyre

first: Loraine

last: Jarrosson

first: Benjamin

last: Villalard

first: Julia

last: Novion Ducassou

first: Yohann

last: Couté

first: Valérie

last: Combaret

first: Nadège

last: Corradini

first: Céline

last: Delloye-Bourgeois

last: Castellani

first: Florie

last: Reynaud

first: Jean-François

last: Brunet


title: Quantitative Analysis of PPARD mRNA-Seq Transcriptomes of Mouse KRAS Mutant Pancreatic Tissues by Next Generation Sequencing (NGS)

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: Pancreatic cancer is the most highly lethal disease with an increasing incidence. Accumulating evidence shows that as an initiating event of pancreatic tumorigenesis, mutant KRAS requires additional factors to promote pancreatic cancer progression. Peroxisome proliferator-activated receptor-delta/beta (PPAR-d) is a ligand-activating transcription factor that modulates many critical cellular functions and is upregulated in human pancreatic cancer tissues. To study PPAR-d's effects on mutant KRAS-initiated pancreatic tumorigenesis, we have generated a novel transgenic mouse model with simultaneously targeted PPAR-d overexpression and KrasG12D mutation (KRASmu) in pancreatic epithelial cells (called KC/Pd mice). Our preliminary data showed that PPAR-d ligand GW501516 strongly promoted pancreatic tumorigenesis in KRASmu mice (KC), and PPAR-d upregulation dramatically enhanced these effects in KC/Pd mice. However, molecular mechanisms by which PPAR-d and its synthetic ligand GW501516 promote KRASmu-initiated pancreatic tumorigenesis remains largely unknown. We have therefore performed genome-wide mRNA seq profiling analysis for pancreatic tissues from KC [WT] and KC/Pd (PD) mice fed GW501516 diet to discover the critical genes/pathways directly regulated by PPAR-d overactivation that accelerate pancreatic cancer progression. Pancreatic tissues of GW-treated KC/Pd (PD-GW) and KC (WT-GW) mice had distinctive differential expression patterns with 1498 differentially expressed genes (DEGs) according to a cut-off of p(Adj)<.05, including 709 upregulated DEGs and 789 downregulated DEGs. Furthermore, Gene set enrichment analyses of these 1498 DEGs using the ?Hallmark gene sets? category showed that the top enriched pathways included IL6-JAK-STAT3, inflammatory response, and KRAS signaling. Thus, the RNA-seq profiling analyses provide us important clues for molecular mechanisms by which PPAR-d overactivation promotes pancreatic cancer progression.

overall_design: The mRNA-seq transcriptome profile of mouse pancreatic tissues from KC (WT) mice and  KC/PD (PD) mice fed a GW501516 diet for 3 days (3 mice per group) was generated by deep sequencing using Illumina HiSeq3000

first: Imad

last: Shureiqi

first: Xiangsheng

last: Zuo

first: Jing

last: Wang


title: Comparison of transcriptional profile of CHO cells cultured in different media.

status: Public on Mar 01 2022

city: Gunma

first: Hiroki

last: Tanemura

address: 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Ohra-gun

country: Japan

institute: Daiichi sankyo co., LTD.

summary: Two clones of Chinese hamster ovary (CHO) cells were cultured in 2 different chemical difined custom media. Transcriptional profile were compeared between clones and media.

overall_design: Examination of 2 different CHO cell clones and media. Cells were cultured for 14 days and sampled on day 4, 7, 9, 11, 14.

first: Kenji

last: Masuda

first: Takeshi

last: Okumura

first: Koichi

last: Nonaka


title: Patient-derived brain organoids uncover reversible cellular abnormalities in Pitt-Hopkins Syndrome II

city: Campinas

first: Fabio

last: Papes

state: SP

address: Rua Carl Von Linaeus

country: Brazil

institute: University of Campinas

summary: We evaluate cellular phenotypic abnormalities and alterations in molecular pathways due to mutations in the gene TCF4 in cells derived from Pitt-Hopkins patients, in comparison with respective controls (parents).

overall_design: Comparison between RNA-Seq libraries of neural progenitor cells of low passage from Pitt-Hopkins Syndrome patients and respective parents of matching sex. Libraries for each individual include three biological replicates.

first: Antonio

last: Camargo


title: the RNA binding property of FSCN1

status: Public on Mar 05 2022

city: jilin

first: Hongfei

last: cai

address: No.1 Xinmin Street, Chaoyang District, Changchun City, Jilin Province

department: Ddepartment of Thoracic Surgery

country: China

institute: The First Hospital of Jilin University

summary: To investigate the RNA binding property of FSCN1 in ESCC, RNA immunoprecipitation (RIP) was performed using an FSCN1 monoclonal antibody in ECA-109 cell lysate

last: Cai


title: Single-cell RNA-seq of total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- and Pou2f3+/+, Pou2f3+/- mice

city: San Francisco

first: Richard

last: Locksley

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: UCSF

summary: Total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- (KO) and Pou2f3+/+, Pou2f3+/- (heterozygous and homozygous WT mice together in WT sample) littermated mice were sorted for live cells on Moflo XDP cell sorter (singlets, FSCAxSSCA, DAPI-). Immediately post-sorting, cells were run on 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry). Libraries were run on the NovaSeq 6000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (Cell Ranger Version 3.0.2, 10X Genomics). Primary assessment with this software for WT DC sample reported 2,441 cell-barcodes with 7,651 median unique molecular identifiers (UMIs, transcripts) per cell and 2,004 median genes per cell sequenced to 61.4% sequencing saturation with 48,559 mean reads per cell. Primary assessment with this software for MARCH1-/- DC sample reported 681 cell-barcodes with 6,309 median unique transcripts per cell and 1,774 median genes per cell sequenced to 73.1% sequencing saturation with 202,410 mean reads per cell.

overall_design: Total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- (KO) and Pou2f3+/+, Pou2f3+/- (WT) littermated mice were sorted for live cells on Moflo XDP cell sorter (singlets, FSCAxSSCA, DAPI-) and subjected to single cell sequencing using 10X Chromium platform.

first: Claire

last: O'Leary

first: Andrew

last: Schroeder


title: A novel high throughput screen to identify candidate molecular networks that regulate spermatogenic stem cell functions

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

institute: University of Newcastle

summary: To understand the role of the transcription factor ZSCAN2 in regulating spermatogonial stem cell function, we performed single cell RNA-sequencing on testis cells enriched for spermatogonia, comparing control populations with populations from a CRISPR-generated Zscan2-knockout mouse line. Transcriptome profiling revealed that ZSCAN2 deficiency alters key cellular processes in undifferentiated spermatogonia such as translation, chromatin modification, and ubiquitination. These findings are cohesive with the decline in regenerative capacity that is experienced by spermatogonial stem cells in the Zscan2-knockout mouse testis following exposure to clastogens.

overall_design: Comparison of testicular cell populations (speramatogonia enriched) from a control and Zscan2-knockout mouse line

first: Jon

last: Oatley


title: Tissue specific gene expression of epithelial tuft cells from small intestine and gallbladder in mouse

summary: Rare chemosensory epithelial cells called tuft cells have known roles in small intestinal regulation of type 2 cytokine producing Group 2 innate lymphoid cells. To understand the phenotype of tuft cells in another tissue, the extrahepatic biliary tree, we performed RNAseq analysis on tuft cells and non-tuft epithelial cells from small intestine and gallbladder of the mouse.

overall_design: IL-25+ and IL-25- epithelial cells were sorted from reporter mice into Dynabead mRNA Direct Micro Purification kit lysis buffer (Thermofisher); mRNA was isolated according to the manufacturer’s protocol. Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit according to the manufacturer’s protocol (NuGen Technologies). Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers according to manufacturer’s protocol (Illumina). Library fragment size distributions were assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent Technologies). Library sequence quality was assessed by sequencing single-end 50 bp reads using the Illumina MiSeq platform and pooled for high-throughput sequencing on the Illumina HiSeq 4000 by using equal numbers of uniquely mapped reads (Illumina). Twelve samples per lane were multiplexed. Sequencing yielded a median read depth of 89.2 million reads per sample.


title: A Combination of Chemotherapy and Oncolytic Virotherapy Sensitizes Colorectal Adenocarcinoma to Immune Checkpoint Inhibitors in a cDC1-Dependent Manner

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

summary: Comparison of transcriptome data in tumors from mice treated with combinations of mitomycin C, oncolytic HSV-1, anti-PD-1 and anti-CTLA-4.

overall_design: RNA was extracted from tumors and transcriptome data was assessed using a Clariom S assay.

first: Nader

last: El-Sayes


title: Capturing early gene expression dynamics during wood decay by brown rot fungus Rhodonia placenta

city: Saint Paul

first: Jonathan

last: Schilling

state: MN

address: 1500 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota

summary: Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step, itself, might require induction. To capture this early gene regulation event, here we integrated fine-scale cryo-sectioning with whole transcriptome sequencing to dissect gene expression at the single hyphal cell scale (tens of μm). We improved spatial resolution 50x, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. By comparing the first 100-μm section with a 100-μm from a later decay stage, it was clear that the early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation, LOX) that were previously and incorrectly assumed to be constitutively expressed. However, this delayed pattern was not universal, with a handful of genes upregulated immediately at the hyphal front.

overall_design: To compare gene expression at different stages of decay, we used a space-for-time experimental design, during which Rhodonia placenta grew directionally along a wood wafer. We sampled each wafer at four locations (0-100 μm, 4900-5000 μm, 15000-15100 μm, and 19900-20000 μm) yielding a 100-μm section for each sample from which RNA was extracted and sequenced. Two replicates from each wafer (n=6) were sampled for each location.

last: Anderson

first: Jiwei

last: Zhang

first: Lye

last: Markillie

first: Hugh

last: Mitchell

first: William

middle: B

last: Chrisler

first: Matthew

last: Gaffrey

first: Galya

last: Orr

middle: S


title: Immunomodulatory effects of PI3Kδ inhibition in murine and human solid tumors [human]

first: Pandurangan

last: Vijayanand

overall_design: Smart-seq2 single-cell RNA-seq was performed from isolated T cells from paired Human tumor samples PRE (n = 6) and POST (n = 6) PI3Kδi AMG319 treatment.

first: Simon

last: Eschweiler

first: Ciro

last: Ramírez-Suástegui

first: Emma

last: King

first: Lindsey

last: Chudley

first: Jaya

last: Thomas

first: Oliver

last: Wood

first: Adrian

last: von Witzleben

first: Divya

last: Singh

first: Danielle

last: Jeffrey

first: Katy

last: McCann

first: Hayley

last: Simon

first: Monalisa

last: Mondal

first: Alice

last: Wang

first: Elena

last: Lopez-Guadamillas

first: Yingcong

last: Li

first: Nicola

last: Dobbs

first: Louisa

last: Essame

first: Gary

last: Acton

first: Fiona

last: Kelly

first: Gavin

last: Halbert

first: Joseph

last: Sacco

last: Schache

last: Shaw

first: James

last: McCaul

last: Paterson

last: Davies

first: Peter

last: Brennan

first: Rabindra

first: Paul

last: Loadman

last: Wilson

first: Khalid

last: Ali

first: Alan

last: Hackshaw

first: Gareth

first: Terry

last: Jones

first: Ferhat

last: Ay

first: Klaus

last: Okkenhaug

first: Bart

last: Vanhaesebroeck

first: Vijayanand

last: Pandurangan

first: Christian

last: Ottensmeier


title: Transcriptional analysis on the impact of anti-PD-L1 mAb on murine lung tumor sorted myeloid populations.

city: Jette

first: Kirsten

last: De Ridder

state: Brussel

address: Laarbeeklaan 103

department: Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences

country: Belgium

institute: Vrije Universiteit Brussel

summary: Targeted gene expression on Lewis lung carcinoma (LLC) sorted MHC-IIlow macrophages (M2), Ly6Chigh inflammatory (IM) and Ly6Clow residential (RM) monocytes to investigate the effect of anti-PD-L1 mAb on specific myeloid subsets in the lung tumor microenvironment performed using the nCounter Myeloid Innate Immunity Panel by Nanostring .

overall_design: C57BL/6  mice were challenged intravenously with LLC cells and treated every 3 days with anti-PD-L1 or isotype control mAbs for 4 times in total. On week three lungs were isolated and  MHC-IIlow macrophages, Ly6Chigh and Ly6Clow monocytes were sorted for RNA isolation (3-4 biological replicates).

first: Hanne

last: Locy

first: Stefaan

last: Verhulst

first: Cleo

last: Goyvaerts


title: Distinct SARS-CoV-2 sensing pathways in pDCs driving TLR7-antiviral vs. TLR2-immunopathological responses in COVID-19

city: Aarhus C

first: martin

last: Jakobsen

address: Høegh-Guldbergs Gade 10, Bygn. 1115

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: In this study, we broadly investigated the nature and timing of SARS-CoV-2-induced changes in pDC gene expression, therefore we profiled 789 selected genes using NanoString nCounter technology after 4, 24 and 48 hrs in two individual donors found to be high (Dhigh) and low (Dlow) responders in terms of IFN production

overall_design: Total RNA was purified from pDC cells from two individual donors infected with SARS-CoV-2 after 4, 24 and 48 hrs

first: Ulvi

last: Ahmadov

first: Lasse

last: Kristensen

first: Martin


title: Fungal mycobiome drives IL33 secretion and type 2 immunity in pancreatic cancer

city: Buffalo

first: Prasenjit

last: Dey

address: Elm & Carlton Sts. CGP/BLSC-L5 307

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

summary: TH2 and innate lymphoid cells 2 (ILC2) can stimulate tumor growth by secreting pro-tumorigenic cytokines such as IL4, IL5 and IL13. However, the mechanisms by which type 2 immune cells traffic to the tumor microenvironment (TME) are unknown. Here, in pancreatic ductal adenocarcinoma (PDAC), we show that oncogenic KrasG12D (Kras*) increases the expression of IL33 in cancer cells, which upon secretion recruits and activates the TH2 and ILC2. Correspondingly, cancer cell-specific deletion of IL33 reduces TH2 and ILC2 recruitment and promotes tumor regression. Unexpectedly, we discovered that the cellular release of IL33 into the TME is dependent on the intratumoral fungal mycobiome. Genetic deletion of IL33 or anti-fungal treatment decreases TH2 and ILC2 infiltration and increases survival. Consistent with these murine data, high IL33 expression is observed in approximately 20% of human PDAC, and expression is mainly restricted to cancer cells. These data expand our knowledge of the mechanisms driving PDAC tumor progression and identifies therapeutically targetable pathways involving intratumoral mycobiome-driven secretion of IL33.

overall_design: Single-cell RNAseq of PDAC tumor. CD45+ FACS sorted cells were used for the analysis.


summary: We report the RNAseq of mouse pancreatic cancer cell lines with Kras ON vs Kras OFF. TH2 and innate lymphoid cells 2 (ILC2) can stimulate tumor growth by secreting pro-tumorigenic cytokines such as IL4, IL5 and IL13. However, the mechanisms by which type 2 immune cells traffic to the tumor microenvironment (TME) are unknown. Here, in pancreatic ductal adenocarcinoma (PDAC), we show that oncogenic KrasG12D (Kras*) increases the expression of IL33 in cancer cells, which upon secretion recruits and activates the TH2 and ILC2. Correspondingly, cancer cell-specific deletion of IL33 reduces TH2 and ILC2 recruitment and promotes tumor regression. Unexpectedly, we discovered that the cellular release of IL33 into the TME is dependent on the intratumoral fungal mycobiome. Genetic deletion of IL33 or anti-fungal treatment decreases TH2 and ILC2 infiltration and increases survival. Consistent with these murine data, high IL33 expression is observed in approximately 20% of human PDAC, and expression is mainly restricted to cancer cells. These data expand our knowledge of the mechanisms driving PDAC tumor progression and identifies therapeutically targetable pathways involving intratumoral mycobiome-driven secretion of IL33.

overall_design: Four mouse pancreatic cancer cell lines were continuously treated with Dox or without Dox for 2 days and 4 days respectively. These treated cells were then RNA sequenced


title: Whole blood DNA methylation arrays of individuals with Sotos syndrome and healthy control subjects

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: To understand how NSD1 inactivation deregulates DNA methylation, and to explore how these abnormalities affect human development, we profiled DNA methylation in SS patients and healthy control individuals using the Illumina Infinium EPIC Beadchip array.

overall_design: Genome-wide DNA methylation was profiled in whole blood samples of three individuals with Sotos syndrome (n=3), and age- and sex-matched healthy control subjects (n=3). Control subjects represent anonymous blood donors that were matched to probands by age and sex.  We also profiled a pooled blood DNA sample of the unaffected parents of the three probands (n=5 parents).

first: Kevin

last: Brennan

first: Olivier

last: Gevaert


title: Inhibition of histone readers bromodomain extra-terminal proteins alleviates scleroderma fibrosis

city: Ann Arbor

first: Pei-Suen

last: Tsou

address: 109 Zina Pitcher Pl. 4025 BSRB

institute: University of Michigan

summary: We assessed transcriptomic changes in fibroblasts isolated from skin biopsies from diffuse cutaneous scleroderma patients before and after BET inhibitor JQ1 treatment

overall_design: RNA-seq analysis of fibroblasts in diffuse cutaneous systemic sclerosis patients after JQ1 treatment


title: Single cell RNA sequencing from organoid stroma derived from E16 salivary glands.

city: Albany

first: Nicholas

last: Moskwa

state: New York

address: 1400 Washington Avenue

institute: University at Albany

summary:
Purpose: Use scRNA Seq to find stromal subpopulations and define how these subpopulations contribute to salivary gland proacinar differentiation.
Method: scRNA Seq on stromal enriched cells from E16 salivary organoids. Model closely related cells using PCA and UMAP regressions. Find genes that broadly and specifically define cell subpopulations.
Results: The stromal fibroblasts have multiple subpopulations. Stromal cells can be subdivided by their expression of Pdgfra, Pdgfrb, Thy1, and Acta2.
Conclusions: Organoids grown with FGF2 selects for Pdgfra expressing stroma and without FGF2 Acta2 stroma dominates.

overall_design: Transcriptome analysis of stromal cell subpopulations

first: Deirdre

last: Nelson

first: Paolo

last: Forni

first: Melinda

last: Larsen


title: Genome-wide maps of chromatin state in HepG2 cells

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in HepG2 cells.

overall_design: ChIP-seq were performed with antibodies against acetylated H3K27 (H3K27ac), H3K4me1, and H3K4me3 and evaluated the open chromatin regions by assay for transposase-accessible chromatin with sequencing (ATAC-seq) to detect the genome-wide maps of chromatin state in HCC cells.

first: Zhiao

last: Chen


title: RNA helicase DHX37 facilitates liver cancer progression by cooperating with PLRG1 to drive super enhancer-mediated transcription of cyclin D1

summary: We provide evidence highlighting a close cooperative mechanistic interaction between DHX37 and PLRG1 that regulates CCND1 expression and promotes liver cancer progression, advancing our understanding of epigenetic and transcriptional dysregulations mediated by RNA helicases and super-enhancers in HCC, possibly facilitating cancer diagnosis and treatment.

overall_design: Huh 7 cells were transfected with siRNA targeted indicated genes using Lipofectamine RNAiMAX or were transfected with Flag-DHX37 targeted indicated genes lentivirus. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed using indicated antibodies to study the H3K27ac status and binding sites of transcription factor in Huh 7 cell. Cleavage Under Targets and Tagmentation (CUT&Tag) was performed to explore whether super-enhancers are directly regulated by DHX37 or PLRG1. Whole-transcriptome sequencing (RNA-Seq) was perfemed to identify the downstream target genes regulated by DHX37 through silenced DHX37 by siRNA in Huh 7 cells.

first: Zhen

last: Liu


title: Expression data from E16 mouse embryonic organoids - grown with epithelium and stroma in the presence or absence of FGF2 [Epi]

summary: FGF2 signals BMP7 expression and TGFB/myofibroblast gene inhibition that promotes proacinar differentiation. We have characterized these stromal factors affecting the epithelium using a combination of scRNA Sequencing of whole tissue and transcriptional profiling of the organoid cell compartments.

overall_design: Gene expression changes and GSEA was performed using gene expression microarrays. Organoids made from embryonic mouse cells were grown then different cell types were separated and their transcriptomes were analyzed based on their response to growth conditions with or without FGF2.

first: Ayma

last: Mahmood


title: The Alzheimer’s gene SORL1 is a key regulator of endosomal recycling in human neurons

city: Seattle

first: Jessica

last: Young

state: Washington

address: 850 Republican St

department: Pathology

institute: University of Washington

summary: Loss of the Sortilin-related receptor 1 (SORL1) gene seems to act as a causal event for Alzheimer’s disease (AD). Recent studies have established that loss of SORL1, as well as mutations in autosomal dominant AD genes APP and PSEN1/2, pathogenically converge by swelling early endosomes, AD’s cytopathological hallmark. Acting together with the retromer trafficking complex, SORL1 has been shown to regulate the recycling of the amyloid precursor protein (APP) out of the endosome, contributing to endosomal swelling and to APP misprocessing. We hypothesized that SORL1 plays a broader role in neuronal endosomal recycling and used human induced pluripotent stem cell derived neurons (hiPSC-Ns) to test this hypothesis. In SORL1 deficient (SORL1KO) cell lines, we map the trafficking of the glutamate receptor and the BDNF neurotrophic receptor, two kinds of transmembrane proteins that depend on endosomal recycling and that are linked to AD pathophysiology. We find that as with APP, SORL1 is required for efficient endosomal recycling of the glutamate receptor AMPA1 (GLUA1) and the BDNF receptor Tropomyosin-related kinase B (TRKB). Next, we used cell lines engineered to overexpress SORL1 and find that increased SORL1 expression enhances recycling for APP and GLUA1. Finally, we performed an unbiased transcriptomic screen of SORL1KO neurons and the data further support SORL1’s role in endosomal recycling.  We observed altered expression networks that regulate cell surface trafficking and neurotrophic signaling. Collectively, and together with other recent observations, these findings suggest that SORL1 is a key and broad regulator of retromer-dependent endosomal recycling in neurons, a conclusion that has both pathogenic and therapeutic implications.

overall_design: RNA was collected from 3 separate differentiations including a combination of two WT clones and two SORL1KO clones. Each sample includes 2-3 technical replicates. RNA was collected from 2 million purified neurons for each sample.

first: Swati

last: Mishra

first: Allison

last: Knupp

first: Marcell

last: Szabo

first: Charles

last: Williams

first: Chizuru

last: Kinoshito

first: Dale

last: Hailey

first: Yuliang

last: Wang

first: Olav

last: Andersen


title: Distinct molecular and immune hallmarks of inflammatory arthritis induced by immune checkpoint inhibitor therapy

first: Linghua

address: 1881 EAST ROAD

department: Genomic medicine

institute: MD Anderson Cancer Center

summary: We report globel transcriptomic landscane and TCR sequencing of synovial fluid cells and autologoug peripheral blood mononuclear cells.

overall_design: We performed single cell RNA sequencing and TCR sequencing of synovial fluid cells and matching peripheral blood samples from eight patients who developed arthritis after immune checkpoint inhibitor therapy.

first: Sang

last: Kim

first: Yanshuo

last: Chu


title: Gene expression signature in CAFs dependent on PGE2

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

institute: Goethe-University

summary: We studied the impact of a PGE2 signaling on tumor progression in the PyMT mammary carcinoma mouse model. To gain insight into the reasons underlying altered tumor development, whole transcriptome profiling of FACS-isolated cancer-associated fibroblasts (CAFs) from WT and mPGES-1 KO tumors were generated via next generation mRNA sequencing, in triplicates, on a NextSeq 550 high-throughput bench top sequencer.

overall_design: Cancer-associated fibroblast mRNA profiles of mice bearing polyoma middle T oncogene (PyMT)-induced tumors (WT or mPGES-1 KO) were generated after cell isolation by FACS-sorting in triplicates.

first: Eiman

last: Elwakeel

first: Kathi

last: Zarnack

first: Mirko

last: Brüggemann


title: Transcriptional profiles reveal deregulation of lipid metabolism and inflammatory pathways in neurons exposed to palmitic acid

city: Mexico City

first: Luis

middle: Alonso

last: Herrera Montalvo

state: Mexico City

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan

department: Unidad de Investigacion Biomedica en Cancer

country: Mexico

institute: Instituto Nacional de Cancerología / Instituto Nacional de Medicina Genómica

summary: The effects of the consumption of high-fat diets (HFD) have been studied to unravel the molecular pathways they are altering in order to understand the link between increased caloric intake, metabolic diseases, and the risk of cognitive dysfunction. The saturated fatty acid, palmitic acid (PA), is the main component of HFD and it has been found increased in the circulation of obese and diabetic people. In the central nervous system, PA has been associated with inflammatory responses in astrocytes, but the effects on neurons exposed to PA have not been largely investigated. Given that PA affect a variety of metabolic pathways, we aimed to analyze the genomic profile activated by this fatty acid to shed light on the mechanisms of neuronal dysfunction. In the current study, we profiled the transcriptome response after PA exposition at non-toxic doses in primary hippocampal neurons. Gene ontology and Reactome analysis revealed a pattern of gene expression which is associated with inflammatory pathways and, importantly, with the activation of lipid metabolism that is considered not very active in neurons. Validation by qRT-PCR of Hmgcs2, Angptl4, Ugt8 and Rnf145 confirmed the results obtained by RNAseq. Overall, these findings suggest that neurons are able to respond to saturated fatty acids changing the expression pattern of genes associated with inflammatory response and lipid utilization that may be involved in the neuronal damage associated with metabolic diseases

overall_design: Total RNA-seq in 2 control and 2 Palmitic acid treated primary hippocampal neurons cultures obtained from E17 wistar rats (rRNA-depleted)

first: Clorinda

last: Arias

first: Manuel

last: Flores-León

first: Nicolas

last: Alcaraz

first: Martha

last: Perez-Domínguez

first: Karla

last: Torres-Arciga

first: Rosa

last: Rebollar-Vega

first: Inti

last: De la Rosa-Velázquez

first: Cristian

last: Arriaga-Canon

last: Herrera

first: Rodrigo

last: González-Barrios


title: Single-cell RNA sequencing analysis of mouse cardiac tissues with myocardial infarction

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: To investigate the transcriotome alteration in myocardial infarction (MI)-associated cells, we performed RNA sequcening analysis with single cells derived from mouse infarcted cardiac tissues or normal left ventricle (LV). Particularly, cardiac endothelial cells (ECs) were traced using a Cdh5-Cre;LSL-tdTomatom system.

overall_design: Myocardial infarction (MI) was induced Cdh5-CreERT2;Rosa-LSL-tdTomato mice. 0, 1, 2, 3, 8 weeks after the surgery, infarcted tissues or normal left ventricle (LV) were harvested. Single-cell suspensions were analyzed by RNA sequencing.

first: Duo

last: Zhang


title: Impact of Ptdss1 knockdown in tumor cells and Mertk KO in macrophages on tumor-associated macrophage phenotype

last: Weigert

summary: We studied the impact of Ptdss1 knockdown in PyMT mouse mammary tumor cells and of Csf1-driven Mertk KO (macrophage-specfic) on tumor growth and the associated macrophage phenotype in an orthotopic tumor model. To gain insight into the reasons underlying tumor rejection once either Ptdss1 was deleted in tumor cells or Mertk was knocked out in macrophages, whole transcriptome profiling of FACS-sorted tumor-associated macrophages of WT or macrophage-specific Mertk KO mice receiving either control tumor cells or Ptdss1 knockdown tumor cells was performed via next generation mRNA sequencing, at least in triplicates, on a NextSeq 500 high-throughput bench top sequencer.

overall_design: FACS sorted macrophage mRNA profiles of WT or macrophage-specific Mertk KO mice bearing PyMT tumor cell orthografts with or without Ptdss1 knockdown in tumor cells were generated 5 weeks after tumor cell injection, at least in triplicates.

first: Christina

last: Dillmann


title: Molecular changes associated with biological aging of cochlear hair cells

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Age-related hearing loss (ARHL) is a progressive sensorineural hearing loss that occurs as people get older. As many as 35% to 50% of the population aged between 65 and 75 have ARHL. Although age-related changes in the central auditory system can contribute to hearing impairment, degeneration of the mechanosensitive hair cells in the cochlea is the prevalent cause of ARHL. The molecular mechanisms of hair cell aging are largely unknown. To provide a comprehensive dataset of age-related genes and pathways in hair cells, we individually collected inner and outer hair cells, the two types of sensory receptor cells in the cochlea, from 9- and 26-month-old CBA/J mice and performed cell type-specific transcriptomic analysis. Our analysis showed a significant reduction of the expression of genes related to hair cell structure and function such as Tmc1, Kcnq4, Kcnj13, Slc7a14, Slc17a8, Chrna9/Chrna10, and Slc26a5. Our hair cell-specific transcriptome analysis provides a rich resource for mechanistic studies of biological aging of cochlear hair cells.

overall_design: Individual inner hair cells and outer hair cells were manually and separately collected from cochleae of CBA mice aged 9 and 26 months based on their morphology using the pipette-aspiration technique. Each sample represents a biological replicate including ~1,000 hair cells collected from cochleae of 6 - 18 mice (both male and female).

middle: Z

first: Huizhan

last: Liu

first: Kimberlee

last: Giffen

first: Heidi

last: Henderson

first: Talia

last: Cao

last: Li

first: Shu

last: Tu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Endothelial cells and Magnesium-based alloy treated Endothelial cells Transcriptomes

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: mRNA-seq was conducted to validate the changed mRNA expression of Endothelial cells after contacting with Magnesium-based alloy discs compared with normal Endothelial cells.

overall_design: mRNA profiles of  Endothelial cells and Magnesium-based alloy treated Endothelial cells were generated by deep sequencing, sample is mixed by 3 dependent expiriments, using llumina HiSeq  4000

first: Hongchi

first: Rifang

last: Luo


title: Age-related changes of gene expression in stria vascularis

summary: Age-related hearing loss is a progressive sensorineural hearing loss that occurs as people get older. Degeneration of the organ of Corti and atrophy of the lateral wall of the scala media in the inner ear are the two primary causes. Transcriptome analysis has emerged as a powerful tool in revealing the genetic and molecular profile of a cell or a population of cells during aging in organism models, animals and humans. Comparison of transcriptomes between young and older animals have identified many common genes and pathways that are associated with aging and longevity. We used RNA-seq to examine changes in gene expression profiles of the stria vascularis between 9- and 26-month-old CBA mice.   Our transcriptome analysis provides a rich resource for mechanistic studies of biological aging of stria vascularis.

overall_design: CBA mice (1m, 9m, 26 m old) of either sex were used. The lateral wall of the cochlea was microdissected from the bony wall of the cochlea. The stria vascularis was microdissected from the spiral ligament using fine forceps. The stria was transferred to an enzymatic digestion medium in a small Petri dish. The enzymatic digestion medium contained 1 ml L-15 and 0.5 mg trypsin (Sigma). After 5 min incubation at room temperature, the tissue was transferred to a small plastic chamber (0.8 ml in volume) containing enzyme-free culture medium (Leibovitz's L-15, 7.35 pH, 300 mOsm). Cells from stria were separated after gentle trituration of the tissue with a small pipette. Mixed populations (marginal, intermediate and basal cells) from four cochleae from two mice were pooled to generate each sample for each age group, and three independent samples were prepared for triplicate.  It is estimated that 1,000 cells were contained in each sample.

first: Grant

last: Kozeny


title: Recycling of memory B cell supports affinity maturation to antigenic drift

city: Birmingham

first: Kai-Michael

last: Toellner

state: West Midlands

address: 4th Floor IBR, Wolfson Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

summary: This study aims to compare relative mRNA transcript levels between murine naïve B cells, germinal centre B cells, emigrating memory B cells in draining lymph node and circulating memory B cells in distal lymph nodes.

overall_design: Four B cell subsets were isolated by fluorescence activated cell sorting and processed for RNA sequencing. Mice used were C57BL/6J background. Germinal centre and emigrating memory B cells were isolated from mGFP-expressing cells in popliteal lymph nodes among IgHNP Cg1cre k-/- mTmG adoptive cell transfer recipients immunised with 4-hydroxy-3-nitrophenylacetyl (NP) conjugated to chicken gamma globulin (CGG) in alum 8 days prior to isolation of cells. Circulating memory B cells were isolated from the axillary and brachial lymph nodes of the same mice at d8 post-immunisation with NP-CGG. Naive B cells were isolated from the non-adoptively transferred cells demarcated as those expressing neither mGFP or mTomato  in axillary and brachial lymph nodes.

first: Jennifer

last: Mueller-Winkler

first: Yang

first: Cameron

last: Burnett

first: Victor

last: Tybulewicz


title: Expression data from E16 mouse embryonic organoids - grown with epithelium and stroma in the presence or absence of FGF2 [Mes]

first: Nicholas

last: Moskwa

first: Ayma

last: Mahmood

first: Deirdre

last: Nelson

first: Paolo

last: Forni

first: Melinda

last: Larsen


title: Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse [RRBS]

status: Public on Feb 28 2022

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: By integrative analysis of gene expression, DNA methylation, and chromatin accessibility in paired diagnosis/relapse primary samples and in the respective patient-derived xenografts (PDXs), we identify the polycomb repressive complex 2 (PRC2) as key epigenetic driver of this immune escape modality. We report that loss of expression of HLA class II molecules is accompanied by a PRC2-dependent reduction in chromatin accessibility. Pharmacological inhibition of PRC2 subunits rescues HLA class II expression in AML relapses in vitro and in vivo, with consequent recovery of leukemia recognition by CD4+ T cells.

overall_design: Analysis of methylation profile of primary and 3 post transplantation from PDXs relapse compared to their controls at diagnosis.

first: Valentina

last: Gambacorta

first: Davide

last: Cittaro

first: Ivan

last: Merelli

first: Raffaella

last: Di Micco

first: Luca

last: Vago


title: RNA-seq of N2, HBR2340 and PHX2193 worms in L1 arrest (48 hours)

city: Dresden

first: Anastasios

last: Koutsoumparis

address: Tatzberg 47-49

institute: TU Dresden

summary: We report the gene expression in L1 arrest (48 hours) of wild-type sleeping worms (N2) and RIS-manipulated worms (HBR2340 and PHX2193)

overall_design: There are 12 samples in total. 4 biological replicates of N2, 4 biological replicates of HBR2340 and 4 biological replicates PHX2193

first: Henrik

last: Bringmann


title: Serum proteome analysis of systemic JIA and related lung disease identifies distinct inflammatory programs and biomarkers

first: Scott

last: Canna

address: The Children’s Hospital of Philadelphia Department of Pediatrics Philadelphia

institute: Children's Hospital of Philadelphia

summary: We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases.

overall_design: We included 162 serum samples from 129 patients for proteomic profiling using SOMAscan. For samples from a patient belonging to different patient groups at different times (e.g., active MAS and inactive sJIA, sJIA-LDFCHi and sJIA-LDFCLo), the samples were assigned to the separate patient groups.   Serum samples were distributed by disease group equally between two plates and measured by SOMAscan assay, according to the manufacturer’s instructions, (SOMAlogic, Boulder, CO) in collaboration with the NIH Center for Human Immunology (CHI). SOMAscan data were first normalized to remove hybridization variation within the run, followed by median normalization across all samples to remove other assay biases within the run and finally calibrated to remove assay differences between runs. 187 of 1305 targets were flagged for between-plate calibrator variation but remained in the analysis. Flagged SOMAmers were not enriched in any differentially expressed target lists. Post-normalization, all samples met predefined acceptance criteria and were included in the analysis. A complete description of the normalization and calibration procedures is available at: www.somalogic.com/wp-content/uploads/2017/03/SSM-071-Rev-0-Technical-Note-SOMAscan-Data-Standardization.pdf. Quantitative assessment of target abundance was expressed as relative fluorescence units (RFU).

last: Cannas

first: Elizabeth

last: Mellins

first: Purvesh

last: Khatri

first: Guangbo

last: Chen


title: scRNAseq of co-culture of primary human oligodendrocytes and IL-23 polarized human CD4 T cells in direct contact (contact) versus separated by a porous membrane (insert, no contact)

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

institute: crCHUM

summary: Multiple sclerosis (MS) is characterized by the loss of myelin and of myelin-producing oligodendrocytes (OLs) in the central nervous system (CNS). Pro-inflammatory CD4+ Th17 cells are considered pathogenic in MS and are harmful to OLs. We investigated the mechanisms driving human CD4+ T cell-mediated OL cell death. Using single cell RNA sequencing, we assessed the transcriptomic profile of primary human OLs and Th17 cells in direct contact or separated by an insert. We showed that upon close interaction, OLs upregulate the expression of mRNA coding for chemokines and antioxidant/anti-apoptotic molecules, while Th17 cells upregulate the expression of mRNA coding for chemokines and pro-inflammatory cytokines such as IL-17A, IFN-γ and granzyme B. We found that secretion of CCL3, CXCL10, IFN-γ, TNFα and granzyme B is induced upon direct contact in co-cultures of human Th17 cells with human OLs. In addition, we validated by flow cytometry and immunofluorescence that granzyme B levels are upregulated in Th17 compared to Th2 cells, and are even higher in Th17 cells upon direct contact with OLs or MO3.13 cells compared to Th17 cells separated from OLs by an insert.

overall_design: Adult human oligodendrocytes in primary culture derived from the same brain sample (resection path of surgery for epilepsy) were exposed to IL-23-polarized CD4 T cells (Th17 cells) from the same donor at 1:1 ratio. They were either directly in contact (contact condition) or separated by a an insert with a porous membrane of 0.4 µm size (insert, no contact condition).

first: Catherine

last: Larochelle

first: JoAnne

last: Stratton

first: Jack

last: Antel

first: Qiao-Ling

last: Cui

first: Hélène

last: Jamann


title: Integrative Proteome, Transcriptome and DNA Methylome Analysis of Regulatory Networks During U937-derived Macrophage Polarization from an M2 to M1 Phenotype [MeDIP-Seq]

city: Nanning

first: Lequn

last: Li

state: Guangxi

address: Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, He Di Rd #71

institute: Guangxi Medical University

summary: We report the application of MeDIP sequencing technology for high-throughput profiling of M2 and M1 phenotype U937 cells. A total of 260 differentially methylated regions (DMRs) within promotor regions were identified, with 191 hyper-methylated and 69 hypo-methylated every chromosome. These DMRs were then further examined using GO analysis, with the top10 most enriched GO terms for both the hyper- and hypo-methylation groups isolated. The processes associated with hyper-methylation included the regulation of protein processes (targeting, processing, maturation and localization) and tyrosine phosphorylation of STAT5 protein, while the hypo-methylated processes included the regulation of epithelial to mesenchymal transition, mesenchymal cell differentiation and epithelial to mesenchymal transition. When further analyzing the regulation of tyrosine STAT5 phosphorylation, three associated genes (IL-31RA, IL-3, and NF2) previous shown to be associated with tumor or cancer development  were also identified, thus suggesting that hyper-methylation may be important during M2 polarization into M1 cells. The epithelial to mesenchymal transition (EMT) process has been long accepted to be associated with cancer metastasis and malignance. Herein, four genes (TGFB1I1, TWIST1, HPN, and PHLDB2) that have been previously reported to participate in cancer invasion and metastasis were hypo-methylated during the EMT process, thus suggesting that these hypo-methylation sites might be a potential therapeutic target to control cancer metastasis. Moreover, the hyper-methylation was found to be predominantly localized to membranes, including the leading edge membrane, whole membrane, endoplasmic reticulum-Golgi intermediate compartment membrane, recycling endosome membrane and ruffle membrane, whereas the hypo-methylation was predominantly localized to the cytoskeleton, cell junction and cell cortex. These findings also suggest a potential ability for epigenetic therapy due to both the membrane and cytoskeleton being feasible targets for therapeutic chemical or antibody targeting. When performing pathway enrichment analysis for the hyper-methylated genes, fatty acid biosynthesis, ubiquitin mediated proteolysis, mRNA surveillance and AMPK signaling pathways were enriched; while for the hypo-methylated genes, pathways associated with cancers, such as tight junction, VEGF signaling, cAMP signaling, proteoglycans and Ras signaling pathways were enriched during polarization from M2 to M1 cells

overall_design: Examination of 2 different phenotypes of U937 cells.

first: Honglin

last: Luo


title: Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse [RNA-seq]

first: Stefano

last: Beretta

overall_design: Analysis of gene expression profile of 5 relapse post transplantation vs paired diagnostic samples and 5 relapse post chemotherapy vs paired diagnostic samples. 3 relapse post transplantation from PDXs were treated with EPZ-6438 and compared with DMSO controls.

first: Valentina

last: Gambacorta

first: Davide

last: Cittaro

first: Ivan

last: Merelli

last: Di Micco


title: Degradation of the E. coli essential proteins DapB and Dxr results in oxidative stress which contributes 2 to the lethality through incomplete BER

city: Dallas

first: Charley

last: Gruber

address: 6000 Harry Hines

department: Microbiology

institute: UTSW

summary: We identified two new lethal stresses whose depletion results in bacterial cell death at least partially through incomplete BER. We confirmed that this pathway is causal to cell death and compared the various physiological changes that occur as a consequence of depletion of these two essentially proteins.

overall_design: Gene expression comparison of DapB and Dxr depleted cells at two and three hours post induction of the protease

middle: C

first: Graham

last: Walker


title: Gene expression data of SPC25 KD in HCCLM3 cell line

city: Zhengzhou

first: Wen-Kai

last: Shi

state: Henan

address: Jianshedong Road No.1

department: Department of hepatopancreatobiliary surgery

institute: The first affiliated hospital of Zhengzhou university

summary: Recently, SPC25 was shown to be overexpressed in HCC, but the mechanisms whereby this occurs remain unknown. In this study, we found that SPC25 was significantly overexpressed in HCC tissues, with further analysis revealing that elevated SPC25 expression was associated with HCC prognosis and metastasis. To further explore the mechanism of SPC25 in HCC, we performed a cDNA microarray in SPC25 knockdown HCCLM3 cells.

overall_design: Analysis of RNA isolated from HCCLM3-shVector and HCCLM3-shSPC25 cell lines.

first: Wenkai


title: DENR controls JAK2 translation to induce PD-L1 expression for tumor immune evasion

city: shanghai

first: Baiwen

last: Chen

address: south  chongqing road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: To identify the potential signaling pathway involved in DENR KO cells upon PD-L1 production, we harvested IFNγ-treated control and DENR KO cells for RNA-seq. Bioinformatic analysis of the RNA-seq data showed that 114 genes, including PD-L1, were significantly downregulated in DENR KO cells, and multiple classical signaling pathways, including JAK-STAT, and PD-L1, were enriched.

overall_design: mRNA profiles of DENR KO and control MC38 cells

first: Huabing


title: Brap regulates liver morphology and hepatocyte turnover via modulation of the Hippo pathway

first: Lara

last: Bideyan

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

summary: Regulation of hepatocyte proliferation and liver morphology is of critical importance to tissue and whole-body homeostasis. However, the molecular mechanisms that underlie this complex process are incompletely understood. Here we describe a novel role for the ubiquitin ligase BRAP in regulation of hepatocyte morphology and turnover via regulation of MST2, a protein kinase in the Hippo pathway.  The Hippo pathway has been implicated in control of liver morphology, inflammation and fibrosis. We demonstrate here that liver-specific ablation of Brap in mice results in gross and cellular morphological alterations of the liver. Brap-deficient livers exhibit increased hepatocyte proliferation, cell death, and inflammation. We show that loss of BRAP protein alters Hippo pathway signaling, causing a reduction in phosphorylation of YAP and increased expression of YAP target genes, including those regulating cell growth and interactions with the extracellular environment. Finally, increased Hippo signaling in Brap knockout mice alters the pattern of liver lipid accumulation in dietary models of obesity. These studies identify a role for BRAP as a modulator of the hepatic Hippo pathway with relevance to human liver disease.  tissue and whole-body homeostasis. However, the molecular mechanisms that underlie this  complex process are incompletely understood. Here we describe a novel role for the ubiquitin  ligase BRAP in regulation of hepatocyte morphology and turnover via regulation of MST2, a  protein kinase in the Hippo pathway. The Hippo pathway has been implicated in control of liver  morphology, inflammation and fibrosis. We demonstrate here that liver-specific ablation of Brap  in mice results in gross and cellular morphological alterations of the liver. Brap-deficient livers  exhibit increased hepatocyte proliferation, cell death, and inflammation. We show that loss of  BRAP protein alters Hippo pathway signaling, causing a reduction in phosphorylation of YAP  and increased expression of YAP target genes, including those regulating cell growth and  interactions with the extracellular environment. Finally, increased Hippo signaling in Brap  knockout mice alters the pattern of liver lipid accumulation in dietary models of obesity. These  studies identify a role for BRAP as a modulator of the hepatic Hippo pathway with relevance to  human liver disease.

overall_design: RNA-Seq of Liver specific Brap knockout mice liver vs control. (Brap fl/fl; Alb Cre+ vs Brap fl/fl; Alb Cre-) (n=4).

first: Rohith

last: Nagari

first: Christina

last: Priest

first: Peter

last: Tontonoz


title: DENR controls JAK2 translation to induce PD-L1 expression for tumor immune evasion [CRISPR screen]

summary: RNA-binding proteins (RBPs) can recognize thousands of RNAs that help to maintain cell homeostasis, and RBP dysfunction is frequently observed in various cancers. However, whether specific RBPs are involved in tumor immune evasion by regulating programmed death ligand-1 (PD-L1) is unclear. We performed targeted RBP CRISPR/Cas9 screening and identified density regulated re-initiation and release factor (DENR) as a PD-L1 regulator. DENR-depleted cancer cells exhibited reduced PD-L1 expression in vitro and in vivo. DENR depletion significantly suppressed tumor growth and enhanced the tumor-killing activity of CD8+ T cells. Mechanistically, DENR antagonized the translational repression of three consecutive upstream open reading frames (uORFs) upstream of Janus kinase 2 (JAK2); thus, DENR deficiency impaired JAK2 translation and the IFNγ-JAK-STAT signaling pathway, resulting in reduced PD-L1 expression in tumors. Overall, we discovered that the RBP DENR is a novel regulator in PD-L1 expression and highlighted the potential of DENR as a therapeutic target for immunotherapy.

overall_design: Examination of single guide RNAs (sgRNAs) enrichment in sorted cell populations based on PD-L1 expression


title: The myokine Fibcd1 is an endogenous determinant of myofiber size and mitigates cancer-induced myofiber atrophy

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Decline in skeletal muscle cell size (myofiber atrophy) is a key feature of cancer-induced wasting (cachexia). In particular, atrophy of the diaphragm, the major muscle responsible for breathing, is an important determinant of cancer-associated mortality. However, therapeutic options are limited. Here, we have used Drosophila transgenic screening to identify muscle-secreted factors (myokines) that act as paracrine regulators of myofiber growth. Subsequent testing in mouse myotubes revealed that mouse Fibcd1 is an evolutionary-conserved myokine that preserves myofiber size via ERK signaling. Local administration of recombinant Fibcd1 (rFibcd1) ameliorates cachexia-induced myofiber atrophy in the diaphragm of mice bearing patient-derived melanoma xenografts and LLC carcinomas. Moreover, rFibcd1 impedes cachexia-associated transcriptional changes in the diaphragm. Fibcd1-induced signaling appears to be muscle selective because rFibcd1 increases ERK activity in myotubes but not in several cancer cell lines tested. We propose that rFibcd1 may help reinstate myofiber size in the diaphragm of patients with cancer cachexia.

overall_design: RNA-sequencing data from diaphragm skeletal muscle at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.

first: Flavia

last: Graca

first: Mamta

last: Rai

first: Liam

last: Hunt

first: Anna

last: Stephan

first: Brittney

last: Gordon

first: Ruishan

first: Giovanni

last: Quarato

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Myriam

last: Labelle

first: Fabio

last: Demontis


title: Effects of lenalidomide treatment on CAR-redirected T cells derived from CLL patients

city: Monza

first: Sarah

last: Tettamanti

address: via Pergolesi, 33

institute: M.Tettamanti Research Center

summary:
Significant response rates have been reported in patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL), diffuse large B-cell lymphomas (DLBCL), mantle cell lymphomas and follicular lymphomas. In contrast, in CTL019 trials, only 26% of CLL patients had durable antitumor responses with dramatic mechanisms of resistance to anti-CD19.CAR T-cell therapy. Low expression of programmed cell death protein 1 (PD1) has been identified as pre-treatment predictor of response in these trials, though the mechanisms responsible for a limited efficacy in CLL remain poorly understood. Additional studies have demonstrated that CD8+ anti-CAR T cells from patients with CLL exhibit impaired metabolic function compared to CD8+ T cells from healthy donors and that these features are associated with T-cell exhaustion and a reduction in T-cell activation and degranulation.
Several T-cell defects have been observed in patients with CLL and are mainly related to impaired immune synapse (IS) formation, and these defects could ultimately impact on the CAR T-cell activation and expansion upon antigen encounter.
Thus, the purpose of this study was to explore the possibility of using lenalidomide, an immunomodulatory agent that has induced significant, long-lasting responses in CLL patients, to enhance the therapeutic efficacy of CD23.CAR-redirected T cells.

overall_design: a total of 4 samples are analyzed, from the same CLL donor. Unmanipulated (NT) T cells and CD23.CAR redirected T cells, both untreated and treated with 1μM lenalidomide

first: Maria

last: Caterina Rotiroti

first: Greta

last: Giordano Attianese

first: Silvia

last: Arcangeli

first: Ronghua

last: Zhang

first: Priyanka

last: Banerjee

last: Galletti

first: Sheighlah

last: McManus

first: Massimiliano

last: Mazza

last: Nicolini

last: Martinelli

first: Cristina

last: Ivan

first: Tania

last: Veliz Rodriguez

first: Federica

last: Barbaglio

first: Lydia

last: Scarfò

first: Maurilio

last: Ponzoni

first: William

last: Wierda

first: Varsha

last: Gandhi

first: Michael

last: Keating

first: Andrea

last: Biondi

first: Federico

last: Caligaris-Cappio

first: Ettore

last: Biagi

first: Paolo

last: Ghia

last: Bertilaccio


title: Exposure of Anopheles gambiae larvae to a sub-lethal dose of an agrochemical mixture induces tolerance to Fludora® Fusion and to its neonicotinoid component in adults

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

institute: Grenoble-Alpes University

summary: The heavy use of pesticides in intensive agricultural areas often leads to the contamination of neighbouring mosquito larvae breeding sites. Such exposure to complex agrochemical mixtures can affect the tolerance of mosquitoes larvae to insecticides. The objective of this study was to determine whether agrochemical pollutants found in Anopheline larval breeding sites can affect the tolerance of adults to Fludora® Fusion, a novel vector control insecticide formulation combining two insecticides with distinct modes of action. An. gambiae larvae were exposed to a sub-lethal dose of a mixture of agrochemical pesticides representative of a region with an intense agricultural activity in Ivory Coast. Comparative bioassays with Fludora® Fusion and its two insecticide component (deltamethrine and clothianidin) were carried out between adult mosquitoes exposed or not to the agrochemicals at the larval stage. A transcriptomic analysis through RNA sequencing was subsequently performed in larvae and adults in order to highlight the molecular mechanisms underlying the phenotypic changes observed. Bioessais revealed a significant increased tolerance of adult females to clothianidin (2.5-fold) and Fludora® Fusion (2.2-fold) following larval exposure to agrochemicals. No significant increased tolerance to deltamethrin was observed suggesting that pesticide exposure affects the efficacy of the Fludora® Fusion mixture mainly through mechanisms acting on clothianidin tolerance. Transcriptomic analysis revealed the potential of agrochemicals to induce various resistance mechanisms including cuticle proteins, detoxifications activities and altered insecticide sequestration. These results suggest that though Fludora® Fusion has a good potential for vector control, its efficacy may be locally affected by the ecological context. The present study also suggests that, although the complex interactions between the use of agrochemicals and vector control insecticides are difficult to decipher in the field, they still must be considered in the frame of insecticide resistance management programmes.

overall_design: mRNAseq  from Anopheles gambiae  4th stage Larvae and and 4-day old non-blood fed adult females.

first: S

last: Reynaud


title: Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer

city: Galway

first: Afshin

last: Samali

address: Newcastle Road, Biosciences Research Building

department: Apoptosis Research Centre

country: Ireland

institute: NUIG Galway

summary: In this study transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1α revealed changes in lipid metabolism genes associated with an accumulation of triacylglycerols (TAGs). We identified DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Mechanistically, the DGAT2 transcript is cleaved by IRE1 at guanine 260 within a hairpin stem loop structure. Our results highlight the importance of IRE1 RIDD activity in reprograming cellular lipid metabolism

overall_design: Triple negative breast cancer MDA-MB-231 cells were treated with 20 μM MKC8866 or DMSO for 8 and 24 h after which RNA was extracted and transcriptomic profile determined with RNA sequencing (n=3).

first: Adrienne

last: Gorman

first: Aitor

last: Almanza


title: CD74-NRG1 fusion as an bona fide oncogene

city: Cologne

first: Lisa

last: Werr

address: Kerpener Str. 62

institute: University Hospital of Cologne

summary: 3' RNA sequencing results of Rosa26CD74-NRG1/Flp mice (murine embryonic fibroblasts, tumor and normal tissue)

overall_design: To test this newly generated mouse model, we crossed Rosa26FSF.CD74-NRG1 mice with an established FLP-deleter strain (Rosa26Flp), which results in early embryonic excision of the FRT-flanked stop cassette and in nearly subsequent ubiquitous expression of the CD74-NRG1 fusion protein in all tissues of the resulting Rosa26FSF.CD74-NRG1/Flp mice [20]. To generate murine embryonic fibroblasts (MEF) out of these Rosa26FSF.CD74-NRG1/Flp mice, Rosa26FSF.CD74-NRG1/Flp mice carrying the CD74-NRG1 transgene as well as the FLP deleter allele were mated. We then used embryos homozygous (Rosa26FSF.CD74-NRG1/FSF.CD74-NRG1) and heterozygous (Rosa26FSF.CD74-NRG1/Flp) for the transgene, as well as CD74-NRG1 negative embryos (Rosa26Flp/Flp) for MEF generation. To characterize the different tumors further by transcriptome sequencing we compared tumor tissue of  Rosa26CD74-NRG1/Flp mice to different normal tissue samples from individual animals.

first: Dennis

last: Plenker

first: H

last: Reinhard

first: Roman

middle: K

last: Thomas


title: Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse

first: Stefano

last: Beretta

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

overall_design: Refer to individual Series


first: Yong-Dong

last: Wang

overall_design: RNA-sequencing data from diaphragm muscles (Dia) from 4-month-old female NCI Ath/nude mice (n=10/group) bearing a cachectic (CAC) or a non-cachectic (NONCAC) melanoma, and RNA-sequencing data from tibilias anterior (TA) and soleus (SOL) muscles from 4-month-old female NCI Ath/nude mice (n=5/group) bearing a cachectic (CAC) or a non-cachectic (NONCAC) melanoma

first: Flavia

middle: G

last: Zuanazzi

first: Mamta

last: Rai

first: Liam

last: Hunt

first: Brittney

last: Gordon

first: Giovanni

last: Quarato

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Myriam

last: Labelle

first: Fabio

last: Demontis


title: RNA-seq of N2 and HBR227 worms in L1 arrest (48 hours)

first: Anastasios

last: Koutsoumparis

summary: We report the gene expression in L1 arrest (48 hours) of wild-type sleeping worms (N2) and aptf-1(gk794) mutant sleepless worms (HBR227)

overall_design: There are 8 samples in total. 4 biological replicates of N2 and 4 biological replicates of HBR227

first: Henrik

last: Bringmann


overall_design: RNA-sequencing data from diaphragm muscles from 4-month-old male C57BL/6J mice: control mice (n=5), control mice treated with rFibcd1 (n=5), mice with LLC tumors (n=3), and mice with LLC tumors and treated with rFibcd1 (n=4)


title: Transcriptome analysis of liver tumors derived from human induced liver cancer-forming cells (iLCCs)

status: Public on Feb 27 2022

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: We found that a set of six transcription factors, FOXA3, HNF1A, HNF1B, LIN28B, L-MYC, and KLF5, can induce direct conversion of human umbilical vein endothelial cells (HUVECs) into liver cancer-forming cells (LCCs). These induced LCCs (iLCCs)  efficiently give rise to tumors that closely resemble human combined hepatocellular cholangiocarcinoma after transplantation to immunodeficient mice. We conducted RNA-seq analyses to investigate the characteristincs of the tumors derived from iLCCs.

overall_design: RNA-Seq analyses for the tumors derived from iLCCs.

first: Yasuyuki

last: Ohkawa

first: Kenichi

last: Horisawa

first: Takeshi

last: Goya


title: Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse [ATAC-seq]

first: Stefano

last: Beretta

summary: By integrative analysis of gene expression, DNA methylation, and chromatin accessibility in paired diagnosis/relapse primary samples and in the respective patient-derived xenografts (PDXs), we identify the polycomb repressive complex 2 (PRC2) as key epigenetic driver of this immune escape modality. We report that loss of expression of HLA class II molecules is accompanied by a PRC2-dependent reduction in chromatin accessibility. Pharmacological inhibition of PRC2 subunits rescues HLA class II expression in AML relapses in vitro and in vivo, with consequent recovery of leukemia recognition by CD4+ T cells.

overall_design: Analysis of differential chromatin accessibility of 5 relapse post transplantation vs paired diagnostic samples and 5 relapse post chemotherapy vs paired diagnostic samples. 3 relapse post transplantation from PDXs were treated with EPZ-6438 and compared with DMSO controls.

first: Valentina

last: Gambacorta

first: Davide

last: Cittaro

first: Ivan

last: Merelli

first: Raffaella

last: Di Micco

first: Luca

last: Vago


title: Mll3/Mll4 catalytic activity is necessary for de novo enhancer-promoter contacts during embryonic stem cell differentiation [PLAC-seq]

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: PLAC-seq, mRNA-seq, and ChIP-seq experiments in mouse embryonic stem cells and neural progenitor cells in the presense or absence of  Mll3/4 catalytic activity.

overall_design: PLAC-seq experiments in mouse embryonic stem cells and neural progenitor cells in the presense or absence of  Mll3/4 catalytic activity.

first: Naoki

last: Kubo


title: Transcriptome analysis of human induced liver cancer-forming cells (iLCCs) , HepG2 cells, Huh6 cells, Huh7 cells, and HuCCT1 cells

summary: We found that a set of six transcription factors, FOXA3, HNF1A, HNF1B, LIN28B, L-MYC, and KLF5, can induce direct conversion of human umbilical vein endothelial cells (HUVECs) into liver cancer-forming cells (LCCs). These induced LCCs (iLCCs)  efficiently arise tumors that closely resemble human combined hepatocellular cholangiocarcinoma after transplantation. We conducted 3' untranslated region (UTR)-seq (RNA-seq) analyses to investigate the characteristincs of iLCCs, HepG2 cells, Huh6 cells, Huh7 cells, and HuCCT1 cells.

overall_design: 3' UTR-Seq analyses for HUVEC-derived iLCCs (iLCC196-12, iLCC196-9, and iLCC195-10), HepG2s (HepG2-1 and HepG2-2), Huh6, Huh7, and HuCCT-1s (HuCCT1-1 and HuCCT1-2).


title: Immunomodulatory effects of PI3Kδ inhibition in murine and human solid tumors

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Whole transcriptome bisufilte sequencing for multiple species [Mouse]

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary: We applied BS-seq to mouse GV and MII oocytes, and 1-Cell embryos.

overall_design: ~200 embryos were collected to build the library

first: Jianheng

last: Liu

first: Tao

last: Huang

first: Yusen

first: Tianxuan

last: Zhao

first: Xueni

first: Wanying

last: Chen


title: Expression profiling for wild type and maternal NSUN2 knockout fly

summary: We applied RNA-seq to examine the effect of NSUN2 knockout on gene expression changes

overall_design: Stranded RNA-seq of mRNA for multiple fly samples


title: Whole transcriptome bisufilte sequencing for multiple species [NSUN2 verification]

summary: (1) We cloned and transfected human xenogenic (zebrafish, mouse, etc.) NSUN2 into human NSUN2 knockout cells.(2) We treated wild-type human cells with nocodazole.

overall_design: Zebrafish NSUN2 overexpressed in HeLa NSUN2 knockout cells. We treated wild-type human cells with nocodazole.


title: Whole transcriptome bisufilte sequencing for multiple species [Drosophila]

summary: We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species.

overall_design: RNA BS-seq of mRNA for multiple species.


title: Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]


title: Whole transcriptome bisufilte sequencing for multiple species

sample_organism:
Drosophila melanogaster
Danio rerio
Xenopus laevis
Xenopus tropicalis
Homo sapiens
Mus musculus


title: Whole transcriptome bisufilte sequencing for multiple species [Xenopus tropicalis]


title: Identification of microRNA transcriptome involved in bovine intramuscular fat deposition

status: Public on Feb 26 2022

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

type: Non-coding RNA profiling by high throughput sequencing

summary: Longissimus muscle samples were collected from angus-cross steers while being fed a high concentrate diet. Sample were collected on d 0, 92, and 124 of high concentrate feeding. Muscle samples were examined to evaluate the miRNA involved in bovine intramusclular fat deposition.

overall_design: The study is comprised of 12 samples, there are 3 groups (0, 92, and 124 d of high concentrate feeding) with 4 replicates each.

first: Maslyn

middle: A

last: Greene


title: Crosstalk between the diseased atherosclerotic aorta and the peripheral nervous system [Adventitia]

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

summary:
The goal of these studies was to delineate mechanisms of crosstalk between the atherosclerotic arterial wall of the aorta and the peripheral nervous system (PNS) in aged hyperlipidemic ApoE-deficient mice. We had observed by immunohistochemistry and morphometry that axon density of the PNS in adventitia segments that were located adjacent to advanced atherosclerotic plaques of aged hyperlipidemic ApoE-deficient mice were markedly higher than those adventitia segments that did not show adjacent atherosclerotic plaques in the intima layer. It is noteworthy in this connection that neither the media nor the intimal layer are innervated by axon endings. However, the adventitia layer of arteries is a conduit for axons and nerves of the PNS connecting the peripheral ganglia and peripheral organs including the spleen. In addition, we discovered (see references below) that atherosclerosis is sensed by the immune system of aged ApoE-deficient mice resulting in the formation of artery tertiary lymphoid organs in the adventitia layer of the arterial wall. To examine potential molecular mechanisms of the crosstalk between the disease aorta and the PNS, we isolated adventitia tissues and media tissues from aortas of ApoE-deficient mice and used wild-type mice as controls. Moreover, we observed that the sympathetic nervous system paraaortic and periaortic ganglia in aged ApoE-deficient but not of aged wild-type mice were infiltrated by leukocytes indicating that atherosclerosis is associated with major alterations of the PNS including axonogenesis and ganglionitis. To identify potential molecules involved in the crosstalk, we isolated respective tissues (media, adventitia, ganglia) by laser capture microdissection and generated large scale mRNA expression arrays to construct transcript maps that were assembled into transcript atlases.  Publications related to this approach: Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015. Artery tertiary lymphoid organs contribute to innate and adaptive immune responses in advanced mouse atherosclerosis. Mohanta SK, Yin C, Peng L, Srikakulapu P, Bontha V, Hu D, Weih F, Weber C, Gerdes N, Habenicht AJ. Circ Res. 2014 May 23;114(11):1772-87. doi: 10.1161/CIRCRESAHA.114.301137. Review. Control of dichotomic innate and adaptive immune responses by artery tertiary lymphoid organs in atherosclerosis. Weih F, Gräbner R, Hu D, Beer M, Habenicht AJ. Front Physiol. 2012 Jul 6;3:226. doi: 10.3389/fphys.2012.00226. Laser-capture microdissection of hyperlipidemic/ApoE⁻/⁻ mouse aorta atherosclerosis. Beer M, Doepping S, Hildner M, Weber G, Grabner R, Hu D, Mohanta SK, Srikakulapu P, Weih F, Habenicht AJ. Methods Mol Biol. 2011;755:417-28. doi: 10.1007/978-1-61779-163-5_35.
apoE-Adventitia arrays were submitted previously (GSM252007, GSM252008, GSM252009, GSM252010, GSM252011, GSM252014, GSM252015, GSM252016; GSE10000, GSE40156) and are now submitted together with new wild-type adventitia arrays not previously published in order to make all adventitia of ApoE-deficient mice and wild-type mice available in one new submission/location.

overall_design: A total number of 11 arrays were prepared: i) 4 replicates from mice with advanced lesions; ii) 4 replicates of mice without lesions; iii) 3 replicates from wild-type as controls.


title: Crosstalk between the diseased atherosclerotic aorta and the peripheral nervous system [Ganglion]

summary: The goal of these studies was to delineate mechanisms of crosstalk between the atherosclerotic arterial wall of the aorta and the peripheral nervous system (PNS) in aged hyperlipidemic ApoE-deficient mice. We had observed by immunohistochemistry and morphometry that axon density of the PNS in adventitia segments that were located adjacent to advanced atherosclerotic plaques of aged hyperlipidemic ApoE-deficient mice were markedly higher than those adventitia segments that did not show adjacent atherosclerotic plaques in the intima layer. It is noteworthy in this connection that neither the media nor the intimal layer are innervated by axon endings. However, the adventitia layer of arteries is a conduit for axons and nerves of the PNS connecting the peripheral ganglia and peripheral organs including the spleen. In addition, we discovered (see references below) that atherosclerosis is sensed by the immune system of aged ApoE-deficient mice resulting in the formation of artery tertiary lymphoid organs in the adventitia layer of the arterial wall. To examine potential molecular mechanisms of the crosstalk between the disease aorta and the PNS, we isolated adventitia tissues and media tissues from aortas of ApoE-deficient mice and used wild-type mice as controls. Moreover, we observed that the sympathetic nervous system paraaortic and periaortic ganglia in aged ApoE-deficient but not of aged wild-type mice were infiltrated by leukocytes indicating that atherosclerosis is associated with major alterations of the PNS including axonogenesis and ganglionitis. To identify potential molecules involved in the crosstalk, we isolated respective tissues (media, adventitia, ganglia) by laser capture microdissection and generated large scale mRNA expression arrays to construct transcript maps that were assembled into transcript atlases.  Publications related to this approach: Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015. Artery tertiary lymphoid organs contribute to innate and adaptive immune responses in advanced mouse atherosclerosis. Mohanta SK, Yin C, Peng L, Srikakulapu P, Bontha V, Hu D, Weih F, Weber C, Gerdes N, Habenicht AJ. Circ Res. 2014 May 23;114(11):1772-87. doi: 10.1161/CIRCRESAHA.114.301137. Review. Control of dichotomic innate and adaptive immune responses by artery tertiary lymphoid organs in atherosclerosis. Weih F, Gräbner R, Hu D, Beer M, Habenicht AJ. Front Physiol. 2012 Jul 6;3:226. doi: 10.3389/fphys.2012.00226. Laser-capture microdissection of hyperlipidemic/ApoE⁻/⁻ mouse aorta atherosclerosis. Beer M, Doepping S, Hildner M, Weber G, Grabner R, Hu D, Mohanta SK, Srikakulapu P, Weih F, Habenicht AJ. Methods Mol Biol. 2011;755:417-28. doi: 10.1007/978-1-61779-163-5_35.

overall_design: A total number of 11 arrays were prepared: i) 6 replicates from ApoE-deficient mice; ii) 5 replicates from wild-type mice.

first: Sarajo

last: Mohanta


title: Whole transcriptome bisufilte sequencing for multiple species [Xenopus laevis]


title: Human and mouse trigeminal ganglia cell atlas implicates multiple cell types in migraine

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

summary: The sensitization of trigeminal ganglion neurons contributes to primary headache disorders such as migraine, but the specific neuronal and non-neuronal trigeminal subtypes involved remain unclear. We thus developed a cell atlas in which human and mouse trigeminal ganglia are transcriptionally and epigenomically profiled at single-cell resolution. These data describe evolutionarily conserved and human-specific gene expression patterns within each trigeminal ganglion cell type, as well as the transcription factors and gene regulatory elements that contribute to cell-type-specific gene expression. We then leverage these data to identify trigeminal ganglion cell types that are implicated both by human genetic variation associated with migraine and two mouse models of headache. This trigeminal ganglion cell atlas improves our understanding of the cell types, genes, and epigenomic features involved in headache pathophysiology and establishes a rich resource of cell-type-specific molecular features to guide the development of more selective treatments for headache and facial pain.

overall_design: Single-nucleus RNA sequencing and Single-nucleus ATAC sequencing were performed on trigeminal ganglia from male and female naive mice or two models of headaches (IS or CSD)

first: Mengyi

last: Xu

first: Shamsuddin

last: Bhuiyan

first: William

last: Renthal


title: Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT474 breast cancer cell line

city: TORONTO

first: ELEFTHERIOS

last: DIAMANDIS

state: ONTARIO

address: 60 Murray St

institute: Mount Sinai Hospital

summary:
Accumulating evidence suggests that the androgen receptor (AR) and its endogenous ligands influence disease progression in breast cancer (BCa). However, AR-mediated changes in BCa differ among the various BCa subtypes according to their hormone receptor profile (i.e presence/absence of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2, (HER2)). Thus, we explored the androgen-regulated transcriptomic changes in the ER+PR+HER2+ BCa cell line, BT-474, and compared them with PR-mediated changes.
Methods: We performed RNA sequencing analysis, in treated BT-474 cells with dihydrotestosterone (DHT) and progesterone (PROG). Validation of the top ten differentially androgen-regulated genes and a number of other genes found in enriched signaling pathways was performed by qRT-PCR in BT-474 and other BCa cell lines. A parallel reaction monitoring targeted proteomic approach was developed for the verification of selected transcripts at the protein level.
Results: We detected 19,450 transcripts, of which 224 were differentially regulated after DHT treatment. The increased expression of two well-known androgen-regulated genes, KLK2 (p<0.05) and KLK3 (p<0.001), confirmed the successful androgen stimulation in BT-474 cells. The transcription factor, ZBTB16, was the most highly upregulated gene, with ~1000-fold change (p<0.001). Pathway enrichment analysis revealed downregulation of the DNA replication processes (p<0.05), and upregulation of the androgen signaling and fatty acid metabolism pathways (p<0.05). Changes related to PROG-treatment showed opposite effects in gene expression than DHT treatment. Similar expression profiles were observed among other BCa cell lines expressing high levels of AR (ZR75.1 and MBA-MB-453). The parallel reaction monitoring targeted proteomic analysis further confirmed that altered protein expression (e.g. KLK3, and ALOX15B) in the supernatant and cell lysate of DHT-treated BT-474 cells, compared to control cells.
Discussion: Collectively, our findings suggest that AR modulates the metabolism of BT-474 cells by affecting expression of a large number of genes and proteins. Based on further pathway analysis, we suggest that AR acts as a tumor suppressor in BT-474 cells.

overall_design: Examination of 3 different treatment conditions (control and two hormones), in triplicates. In total, 9 samples were analysed with RNA sequencing.

first: Stella

last: Vasiliou

first: Eleftherios

last: Diamandis