title: Redundancies in low K signaling of neo-tetraploids leads in increased shoot K [RNA-seq_2]

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

institute: University of Nottingham

summary: Whole Genome Duplication (WGD) events occurred frequently during land plant evolution and their long term benefits to neo-functionalization of genes and speciation is well known (Baduel et al., 2018). However short term benefits, important for the establishment of a new population, are more difficult to observe until Chao et al., 2013 described a fitness advantage under high salinity. Additionally shoot K levels were higher in neo-tetraploids, an important feature since K uptake becomes increasingly more difficult on highly saline soil. The molecular basis for these phenotypes was not known. Here we analyze neo-tetraploid Arabidopsis thaliana plants using RNAseq and ICP-MS to evaluate the effect of mutations and ploidy on the gene expression and shoot ionome. We are able to show that neo-tetraploid plants induce low-potassium (K) signaling to increase their shoot K content. However, we also show that this low-K signaling is distinct form previously studied, externally applied low-K signaling. In this way, we are able to identify new components of the K homeostasis network, which are required to regulate K demand. Additionally we are able to show that while individual components of the K uptake system are not sufficient to increase shoot K, a loss of root hairs abolished the ploidy K phenotype (PPP) as does a defective Casparian strip. Root hairs are the site of entry of K into the root and neo-tetraploids increase their root hair length and density (RHI) to facilitate their higher K demand. The Casparian strip on the other hand enables higher K concentration in the stele of the root, which is required for the increased K content in neo-tetraploids.

overall_design: RNAseq of Arabidopsis thaliana wild type Col-0 and mutants esb1-1, sos3-2 and rhd6-3/rsl1-1 after whole genome duplication, grown on soil and plates. Roots and shoots of soil grown plants and roots of plate grown plants were assessed for gene expression differences between diploids and neo-tetraploids. Three replicates were analyed.

first: Paulina

last: Flis

first: Fang-Jie

last: Zhao

last: Salt


title: miR-196b-TLR7/8 signaling axis regulates innate immune signaling and myeloid maturation in DNMT3A-mutant AML

status: Public on Jul 31 2022

city: Philadelphia

first: Sara

middle: E

last: Meyer

state: PA

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: microRNA in DNMT3A-mutant AML [miRNA-Seq]

summary: microRNA (miRNA or miR) are aberrantly expressed in acute myeloid leukemia (AML), and clinically may have diagnostic, prognostic, and therapeutic value. We identify miR-196b, is overexpressed in high-risk subset of DNMT3A-mutant AML and its activity is important to maintain a differentiation block and limit innate immune signaling pathways in AML. We interrogated previously published experimentally defined and computationally predicated miR-196b targets demonstrating that miR-196b regulates Toll-like Receptor Signaling. This work uncovered that miR-196b represses TLR7/8 activation and innate immune signaling in AML and that TLR7/8 activates a Stat1 transcriptional response associated with induced co-stimulatory molecule expression on the surface of AML-derived monocytes and dendritic-like cells.

overall_design: To identify the small non-coding RNA expression changes in murine Dnmt3a/Flt3ITD-mutant AML compared to Flt3ITD control MPN.

first: Holly

middle: A

last: Gamlen

first: Jennifer

middle: S

last: Romer-Seibert

first: Michael

last: Lawler

first: Amanda

middle: M

last: Versace

first: Yang

last: Feng

first: Olga

last: Guryanova

first: Neil

last: Palmisiano


title: Redundancies in low K signaling of neo-tetraploids leads in increased shoot K [RNA-seq_1]

country: United Kingdom

overall_design: RNAseq of Arabidopsis thaliana wild type Col-0 lines after whole genome duplication, under control conditions and salt stress. Roots and shoots of plate grown plants were assessed for gene expression differences between diploids and neo-tetraploids. Three replicates were analyed.

first: David


title: Redundancies in low K signaling of neo-tetraploids leads in increased shoot K


title: BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer

status: Public on Jul 30 2022

city: Houston

first: Xubin

last: Li

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: To explore the mechanisms of EGFR/HER2 activation by BET inhibition, we analyzed the mRNA changes in response to BET inhibition.

overall_design: Transcriptomic responses were profiled with BETi (JQ1) treatment in HCC1954, BT474 and SKOV3 cells using mRNA sequencing.

first: Anil

last: Korkut


title: RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 III

status: Public on Aug 07 2022

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

summary: Here we analyze the transcriptional profiles of homogenized lungs resected from young female APOE2, APOE3, and APOE4 knock-in mice on day 4 post infection with SARS-CoV-2 MA10. Weighted gene co-expression analysis identified gene modules enriched for genes implicated in T and B cell activation to be downregulated in APOE2 and APOE4 mice during COVID-19 progression.

overall_design: Weighted gene co-expression network analysis and pathway analysis of RNA-sequencing data.

first: B


title: The effect of insulin treatment versus insulin resistance on microRNA expression in the hypothalamic neuronal cell line mHypoE-46.

city: Toronto

first: Denise

middle: D

last: Belsham

state: ON

address: 1 Kings College Circle MSB3346

department: Physiology

country: Canada

institute: University of Toronto

summary: The goal of this study was to determine the microRNAs altered upon the development of insulin resistance in a murine hypothalamic Neuropeptide Y/Agouti-related Peptide expressing cell line mHypoE-46

overall_design: Twelve samples were analyzed.  This included two time points 4 and 24 hours post treatment with either vehicle (Phosphate Buffered Saline, PBS) or 100 nM of Insulin. The experiment was replicated three times independently.

last: Chalmers

first: Ana

last: Nazarians-Armavil


title: Identification of the factor to lead human mesenchymal stem cell line into decellularized bone

status: Public on Jul 29 2022

city: Tokyo

first: Anri

last: Koyanagi

state: Bunkyo, Yushima

department: Comprehensive pathology

country: Japan

institute: Tokyo medical and dental university

summary: Enhanced migration ability due to overexpression of SHC4 was firmly confirmed in UE7T-9 cells.

overall_design: UE7T-9 cell clones of SHC4 OE were established with the infection with lentivirus containing plasmids of SHC4 and conducted in the following  experiment.

first: Iichiroh

last: Onishi


title: Proteolysis resistant huntingtin isoform induced by antisense oligonucleotide maintains normal huntingtin function in mouse

city: Leiden

first: Pontus

last: Klein

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

summary:
Huntington’s disease (HD) is a late onset neurological disorder for which no neuroprotective therapies efficiently delay onset or progression. A key pathological mechanism in disease involves the proteolysis of polyglutamine (polyQ)-expanded mutant huntingtin (mHTT) generating polyQ-containing N-terminal fragments that are crucial contributors to HD pathogenesis since inhibition of the cleavage at the putative caspase-6 site reduces pathology in a HD mouse model. Interestingly, a naturally occurring alternative spliced form of HTT lacking exon12 (HTTΔ12) leads to a protein with an internal deletion of the caspase-6 N-terminal cleavage site. Here, we have taken a multidisciplinary approach to characterize the therapeutic potential of targeting exon12 of HTT. We show that HTTΔ12 is fully resistant to caspase-6 cleavage in both cell-free and tissue lysate assays, while maintaining overall biochemical and structural properties similar to wild-type (wt)-HTT. We generated mouse deleted for exon12 and found that exon12 is dispensable for HTT main physiological functions including embryonic development and intracellular trafficking such as BDNF transport. Finally, we pharmacologically induced HTTΔ12 using an antisense oligonucleotide (ASO). QRX-704 ASO efficiently distributes in the whole brain, is stable several months, and reduces pathogenic proteolysis. Thus, ASO-induced exon12 deletion of HT
We performed gene expression profiling analysis using data obtained from RNA-seq of brain tissue (cortex and striatum) samples originating from mouse littermates from HttΔ12 (Δ12;KI) and HttKO (KO) lines at 3 month of age.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for c57BL/6N mouse adult HttΔ12 brain.

first: Hyeongju

last: Kim

first: Sophie

last: Lenoir

first: Angela

last: Helfricht

first: Taeyang

last: Jung

first: Zhana

last: Karneva

first: Yejin

last: Lee

first: Wouter

last: Beumer

first: Geert

last: van der Horst

first: Herma

last: Anthonijsz

first: Levi

last: Buil

first: Frits

last: van der Ham

first: Gerard

last: Platenburg

first: Pasi

last: Purhonen

first: Hans

last: Hebert

first: Sandrine

last: Humbert

first: Frédéric

last: Saudou

first: Ji-Joon

last: Song


title: Real-time quantitative PCR analysis of cytokines and chemokines in C57BL/6 mouse liver ischemic-reperfusion injury (IRI) model.

city: Washington, DC

first: Alexander

last: Kroemer

state: DC

address: 3800 Reservoir Road NW, Pasquerilla Healthcare Center (PHC), 2nd Floor,

department: Center for Translational Transplant Medicine (CTTM)

institute: MedStar Georgetown Transplant Institute

summary: We assessed mouse cytokines and chemokines gene expression in fatty liver ischemic-reperfusion injury (IRI). C57BL/6 mice were fed with a normal chow diet (ND, 4.09 kcal/gram,13.4% kJ/fat) or a high-fat diet (HFD, 5.10 kcal/gram, 60% kJ/fat) and further grouped to treat with orally administered N-acetylcysteine (NAC, 10g/L). To induce liver ischemic-reperfusion injury in mice, an atraumatic micro clip was placed across the hepatic hilus, which interrupted the blood supply to the left and median lobes of the liver for 45-minutes partial warm ischemia time. After 24 hours of liver IRI, the affected left lobe of the liver was harvested and stored in Allprotect Tissue Reagent (Qiagen). We used Qiagen RT² Profiler™ PCR Array for mouse cytokines & chemokines to distinguish immunologically related gene signatures specific to the liver IRI in mice and characterize the effect of NAC treatment in HFD mice.

overall_design: qPCR gene expression profiling. Liver tissue specimens from IRI and sham group from mice (n=3) were used and treated separately as indicated in the summary. An equal amount of total RNA from mice was pooled prior to gene expression analysis.


title: Cytoglobin dependent transcriptomic changes determine sensitivity of melanoma to ferroptopsis

city: Antwerpen

first: Joey

last: De Backer

state: Antwerpen

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

summary: In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contributes to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor suppressive role for CYGB. Remarkably, CYGB knockdown also triggered activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via modulation of ferroptosis and pyroptosis cell death signalling pathways.

overall_design: Differential gene expression analysis of CYGB knockdown G361 melanoma cells under basal conditions (untreated) and upon treatment with ferroptosis inducer RSL3.

first: David

last: Hoogewijs


title: The Deciphering of Mouse Uterine Microenvironment during Early Pregnancy [spatial transcriptomics]

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: The mouse uterine microenvironment at pregnancy D7.5 was investigated by Visium spatial transcriptome. Ten distinct uterine microenvironments were identified with diverse biological functions, different endocrine regulations and intensive interactions. The single cell RNA-seq of D7.5 mouse uterus has been intergrated with the spatial visium results and predicted the presence of mutiple types of cells in each microenvironment.

overall_design: The mosue uterus were collected at D7.5, either sectioned for Visium spatial transcriptome, or isolated into single cell for scRNA-Seq.

first: Rong

last: Li

first: Tianyuan

last: Wang

first: Xin

last: Xu

first: Olivia

last: Emery

first: Myeongjin

last: Jin

first: San-Pin

last: Wu

first: Francesco

middle: J

last: DeMayo


title: Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

type: Genome binding/occupancy profiling by high throughput sequencing


title: Gene expression of depletion of lncRNA Miat in mouse stem-like MB cells [miRNA-Seq]

city: New York

first: Adam

last: Schmitt

state: New York

address: 417 E 68th St

institute: MSKCC

summary: To investigate the effect of gene alteration of Miat and Mtdh in mouse stem-like MB cells.  by canonical oncogenic signaling to maintains the self-renewal capacity of a population of  tumorigenic stem-like medulloblastoma cells that are resistant to cytotoxic therapy.  by canonical oncogenic signaling to maintains the self-renewal capacity of a population of  tumorigenic stem-like medulloblastoma cells that are resistant to cytotoxic therapy. Miat and  Mtdh cooperate to promote medulloblastoma tumorigenesis and treatment resistance by  regulating the biogenesis of a subset of microRNAs that target genes involved in these processes.

overall_design: CRISPR/sgGal4-4 and sgMiat in stem-like MB cells

first: Kai-Lin

last: Peng


title: Gene expression of depletion of lncRNA Miat in mouse stem-like MB cells [RNA-Seq]

summary: To investigate the effect of gene alteration of Miat in mouse stem-like MB cells.  by canonical oncogenic signaling to maintains the self-renewal capacity of a population of  tumorigenic stem-like medulloblastoma cells that are resistant to cytotoxic therapy.  by canonical oncogenic signaling to maintains the self-renewal capacity of a population of  tumorigenic stem-like medulloblastoma cells that are resistant to cytotoxic therapy. Miat and  Mtdh cooperate to promote medulloblastoma tumorigenesis and treatment resistance by  regulating the biogenesis of a subset of microRNAs that target genes involved in these processes.


title: RNA-seq profiling of colon and ileum tissues from the UC Davis Type 2 Diabetes Mellitus Rat Model

city: Little Rock

first: Brian

last: Piccolo

state: AR

address: 15 Children's Way

institute: Arkanssa Children's Nutrition Center

summary: The RNA-seq analysis continues our work profiling the the gastrointestinal tract of the UC Davis Type 2 Diabetes Mellitus (UCD-T2DM) Rat. Male UCD-T2DM rats (age ~170 days) were included in this study if either recently diagnosed as diabetic (n=6, RD, nonfasting glucose > 300 mg/dl) or 3-month post-onset of diabetes (n=6, D3M). A set of younger non-diabetic UCD-T2DM rats were also studied as a non-diabetic comparison (n=6, ND, age ~70 days).

overall_design: Comparison of transcriptome between UCD-T2DM rat that are non-diabetic (ND), < 1 month post-onset diabetes (RD), and 3 month post-onset diabetes (D3M)


title: Gene expression of depletion of lncRNA Miat in mouse stem-like MB cells


title: Effects of two-component system NarQ/P deletion on gene expression of Actinobacillus pleuropneumoniae in nitrate-rich anaerobic growth

city: Wuhan

first: Qiuhong

last: Zhang

address: No. 1, Shizishan Street

country: China

institute: Huazhong Agricultural University

summary: Nitrate metabolism is an adaptation mechanism used by many bacteria for survival under anaerobic environments. As a by-product of inflammation, nitrate is used by the intestinal bacterial pathogens to enable gut infection. However, the responses of bacterial respiratory pathogens to nitrate are less well understood. Actinobacillus pleuropneumoniae is an important bacterial respiratory pathogen of swine. Previous studies have suggested that adaptation of A. pleuropneumoniae to anaerobiosis is important for infection. In this work, A. pleuropneumoniae growth and pathogenesis in response to the nitrate were investigated. Nitrate significantly promoted A. pleuropneumoniae growth under anaerobic condition in vitro and lethality in mice. By using narQ and narP deletion mutants, and single-residue mutation complementary strains of ΔnarQ, the two-component system NarQ/P were confirmed to be critical for nitrate induced growth, with Arg50 in NarQ as an essential functional residue. Transcriptome analysis showed that nitrate up-regulated multiple energy-generating pathways, including nitrate metabolism, mannose and pentose metabolism and glycerolipid metabolism via the regulation of NarQ/P. Furthermore, narQ, narP and its target gene encoding the nitrate reductase Nap contributed to the pathogenicity of A. pleuropneumoniae. The Nap inhibitor tungstate significantly reduced the survival of A. pleuropneumoniae in vivo, suggesting that Nap is a potential drug target. These results give new insights into how the respiratory pathogen A. pleuropneumoniae utilizes alternative electron acceptor nitrate to overcome the hypoxia microenvironment, which can occur in the inflammatory or necrotic infected tissues.

overall_design: Comparative gene expression profile analysis of RNA-seq data of Actinobacillus pleuropneumoniae serovar 1 str. 4074 wild type strain and deletion strains (ΔnarP, ΔnarQ) in anaerobic culture and anaerobic culture supplemented with 5mM nitrate, respectively

first: Lu


title: Indel profiling of primary hepatocytes by deep sequencing

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: CRISPR/Cas9 has proven to be an efficient tool for gene editing both in vitro and in vivo. The aim of this study is to evaluate editing efficiency of various genes targted in Rosa26-Cas9 knock-in mice.

overall_design: Efficiency of in vivo genome editing was assessed using for hepatocytes isolated from the livers of Cas9-EGFP mice to which adeno-assocaited viruses (AAVs) packaged with sgRNAs targeting various genes were injected. Genemic regions containing each cut site were amplified by PCR, and libraries were prepared for deep sequencing.

first: Jonathan

last: Sussman

first: Ben

middle: Z

last: Stanger


title: DLGAP1-AS2-Mediated Phosphatidic Acid Synthesis Activates YAP Signaling and Confers Chemoresistance in Squamous Cell Carcinoma [ATAC-Seq]

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences


title: RNA-Seq analysis of the gene expression profile of wild type and dRassf mutant flies after infection by Flock House Virus

city: Xiamen

first: Bo

last: Liu

address: Xiang'an South Rd 4221-120

institute: Xiamen University

summary: Our study identifies an important role for the tumor suppressor RASSF in maintaining proper antiviral responses in Drosophila.

overall_design: Examination of the transcriptional alterations in wild type and dRassf mutant flies after infection by Flock House Virus


summary: Squamous cell carcinomas (SCC) constitute a group of human malignancies that originate from the squamous epithelium. Most SCC patients experience treatment failure and relapse and have a poor prognosis due to de novo and acquired resistance to first-line chemotherapeutic agents. To identify chemoresistance mechanisms and explore novel targets for chemosensitization, we performed whole-transcriptome sequencing of paired resistant and parental SCC cells. We identified DLGAP1 antisense RNA 2 (D-AS2) as a crucial noncoding RNA that contributes to chemoresistance in SCC. Mechanistically, D-AS2 affected chromatin accessibility around the histone mark H3K27ac of FAM3 metabolism regulating signaling molecule D (FAM3D), reducing FAM3D mRNA transcription and extracellular protein secretion. FAM3D interacted with the Gαi-coupled G protein-coupled receptors (GPCRs) formyl peptide receptor 1 (FPR1) and FPR2 to suppress phospholipase D (PLD) activity, and reduced FAM3D increased PLD signaling. Moreover, activated PLD promoted phosphatidic acid (PA) production and subsequent nuclear translocation of yes-associated protein (YAP). Accordingly, in vivo administration of a D-AS2-targeting antisense oligonucleotide sensitized SCC to cisplatin treatment. In summary, this study shows that D-AS2/FAM3D-mediated PLD/PA lipid signaling is essential for SCC chemoresistance, suggesting D-AS2 can be targeted to sensitize SCC to cytotoxic chemotherapeutic agents.

overall_design: ATAC-seq of DLGAP1-AS2 silenced and control NCI-H1703 cells

first: Yabing

first: Qingyu

last: Luo

first: Xiaowei


title: Targeting the unwindosome by mebendazole is a vulnerability of chemoresistant hepatoblastoma

status: Public on Jul 28 2022

city: Munich

first: Roland

last: Kappler

address: Lindwurmstr. 2a

department: Pediatric Surgery

institute: University Munich

summary: We identified mebendazole as a drug to circumvent chemoresistance in hepatoblastoma cell lines that are resistant to cisplatin. In order to identify the mechanistic basis of mebendazole function, we performed gene expression analysis of three mebendazole-treated hepatoblastoma cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mebendazole-treated hepatoblastoma cell lines


title: DLGAP1-AS2-Mediated Phosphatidic Acid Synthesis Activates YAP Signaling and Confers Chemoresistance in Squamous Cell Carcinoma [RNA-Seq]

overall_design: RNA-seq of DLGAP1-AS2 overexpressed and control KYSE450 cells


title: 3' droplet-based single cell RNA sequencing of a mouse large intestinal epitherlium

city: Shinjuku

first: Mayumi

last: Oda

address: 35 Shinanomachi.

department: School of Medicine

institute: Keio University

summary: Using 3' droplet-based single-cell sequencing, we performed the transcriptional profiling of mouse large intestinal epithelial cells at the single-cell level.

overall_design: For scRNA-seq of the mouse colonic epithelium, we isolated mouse colonic crypts from three female 12-week-old C57BL/6 mice. For purification of epithelial cells and removal of immune cells and dead cells, the cells were suspended in 200 ml of cold PBS and stained with 5 ml of APC anti-mouse CD326 (EpCAM) antibody (118213, BioLegend), PE anti-CD45 antibody (BD Biosciences, 1:500) and DAPI (1:1000) for 20 min. Live CD45– EpCAM+ single cells were sorted into a 1.5 mm tube using a cell sorter.

first: Koji

last: Taniguchi

first: Keiko

last: Ishikawa


title: Single-cell expression profiling of visceral adipose tissue and splenic  CD4+ T cells from Treg-bmal1WT and Treg-bmal1KO mice at ZT0 and ZT12.

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: we reported single-cell gene expression of  CD4+ T cells  from the visceral adipose tissue of from male Foxp3-Cre.YFP bmal1WT or Foxp3-Cre.YFP bmal1flox/flox mice, and from spleen from bmal1WT mice,  at ZT0 or ZT12. We found that VAT Tregs could be subdivided into five subtypes: p1 ST2+, p2 ST2+, Tbet+, IL18r+ and resting clusters. We found diurnal variation within the ST2+ subgroups, where the more activated p1 ST2+ Tregs were more represented at ZT0 in WT VAT Tregs. Such variations were not observed in splenic Tregs. In contrast, bmal1KO VAT Tregs were were enriched in the ST2+ Tregs, and had a constitutively high proportion of the p1 ST2+ subtype at ZT0 and ZT12.

overall_design: Animals were housed in reverse-light cycle rooms. 34,000 VAT and 32,000 splenic CD4+ T cells were single-sorted. Cells from each genotype, time-point and tissue were multiplexed using TotalSeq hashing antibodies separately and then pooled.. Cell encapsulation, RNA isolation, and hash library construction and sequencing were performed using the 10X Genomics platform.

first: Tianli

last: Xiao

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Ablation of ER stress-linked kinase PERK in cancer cells elicits protective T cell immunity by paraptosis immunogenic cell death-induced Type-I IFN

city: Tampa

first: Paulo

last: Rodriguez

state: Florida

address: 3011 W. Holly Drive, MRC, 2067

institute: H. Lee Moffitt Cancer Center

summary: C57BL6 wildtype mice were injected with B16F10 melanoma transduced with either untargeted sgRNA (Scramble) or PERK (EIF2AK3) knockout (KO) sgRNA. At day 17, tumors were harvested to isolate cKit+ (CD117) precursors via magnetic bead enrichment. These cKit expressing precursors were then sequenced.

overall_design: Comparison of RNA expression in tumor infiltration cKit expressing precursors from B16F10 Scramble and B16F10 PERK knockout melanoma tumor implanted in wildtype immunocompetent C57BL6 mice

first: Jessica

last: Mandula

first: Timothy

last: Shaw

first: Darwin

last: Chang

first: Ling

last: Cen


title: GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway

city: Ann Arbor

first: Ming

last: Li

state: Michigan

address: Rm 3220, Biological Sciences Building, 1105 North University Ave

department: MCDB

institute: The University of Michigan

summary:
To investigate the expression profilings after knocking out TMEM251.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different TMEM251 sgRNA knockout cells compared to WT

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and 251KO HEK293 cells

first: Xi

last: Yang

first: Weichao

last: Zhang


title: Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary:
We performed RNA-seq on pre-treatment endoscopic biopsies from 114 patients, including 97 patients treated with NAT that qualified for outcome analyses
We then performed gene expression profiling analysis using data obtained from RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data between CR/iCR patients and ssgsea analysis

first: Francisco

last: Sanchez-Vega

first: Julio

last: Garcia-Aguilar


title: Transcriptional profiling of visceral adipose tissue from Foxp3.YFP-Cre Bmal1WT and Foxp3.YFP-Cre Bmal1KO mice after 16 weeks of high-fat diet

summary: We profiled the transcriptome of visceral adipose tissue from Foxp3.YFP-Cre Bmal1WT or Foxp3.YFP-Cre bmal1flox mice after 16 weeks of high-fat diet. We found that adipose tissue with Bmal1-deficient Tregs showed an increased enrichment of inflammatory pathways and a loss of metabolic pathways after high-fat diet feeding.

overall_design: Mice were fed a low-fat diet for 14 weeks followed by 16 weeks of high-fat diet. 50 to 100mg of visceral adipose tissue was excised, snap frozen and stored in trizol for RNA extraction


title: Transcriptional profiling of Visceral Adipose Tissue (VAT) and splenic Tregs over circadian time

summary: We isolated VAT and splenic Tregs every four hours over twenty-four hours and reported their transcriptome. We found that the expression of core clock genes was upregulated and rhythmic in VAT Tregs compared with splenic Tregs. Additionally, we described hundreds of other genes with rhythmic expression over time.

overall_design: The retired B6 male breeders (>35 weeks old) were housed under strict 12:12 light:dark cycle. CD4+ CD25+ Tregs were double sorted every four hours from the spleen and VAT and processed for RNA-Seq.


title: Transcriptional profiling of Bmal1WT and Bmal1KO Tregs

summary: We isolated visceral adipose tissue (VAT) Tregs from Foxp3.YFP-Cre Bmal1WT or Foxp3.YFP-Cre bmal1flox mice fed a normal lean diet or a high-fat diet. VAT Tregs were also sorted after adoptive transfer. We found that Bmal1KO Tregs are more activated in lean mice, after 4 weeks HFD and after adoptive transfer, but loseVAT Treg signature after 16 weeks of high-fat diet feeding.

overall_design: Foxp3YFP+ Tregs were double-sorted from the visceral adipose tissue of 18-to-30-week-old male at ZT0. For high-fat diet experiments, mice were fed a lean diet for 14 weeks followed by high fat diet of indicated length. For adoptive transfer experiments, Foxp3YFP+ Tregs were double-sorted 9 weeks after adoptive transfer. For the adoptive transfer, the mice were 20 weeks old when they were sacrificed.


title: WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome

city: Hong Kong

first: Wai- Yee

last: Chan

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

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

overall_design: Refer to individual Series


title: WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome [ChIP-seq]

summary: Werner Syndrome (WS) is an autosomal recessive disorder characterized by premature aging due to mutations of the WRN gene. A classical sign in WS patients is short stature, but the underlying mechanisms are not well understood. Here we report that WRN is indispensable for chondrogenesis, which is the engine driving the elongation of bones and determines height.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for WRN protein in human embryonic stem cells (hESCs).

first: Tian

last: Yuyao

first: Chan

last: Wai-Yee


title: Identifying DAP5 mRNA translation and direct-binding targets in human embryonic stem cells (hESCs) using Ribo-seq and CLIP-seq.

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: The eIF4G1 DAP5 homolog is involved in several non-canonical translation initiation mechanisms. We applied ribosome profiling and found that DAP5 translationally activated mRNAs are enriched with translated uORFs. We also performed a genome-wide UV-cross linking immunoprecipitation screen (CLIP-seq) for identifying mRNAs that directly interact with DAP5 in hESCs. We found 959 bound mRNAs common to both Abs (out of 1073 and 2152 enriched mRNAs identified by CS and MBL antibodies, respectively).

overall_design:
To asses DAP5 translation profile we performed ribosome profiling on DAP5-KD and NT control hESCs. The libraries were prepared from cells treated with the translation elongation inhibitor cycloheximide (CHX). In parallel, we used a tailored RNA-seq protocol to quantify RNA levels.
For the CLIP-seq profiling H9 cells were UV cross-linked, lysed and treated with DNase. DAP5-RNA complexes were pulled down using 2 specific antibodies (Cell Signaling, 5169 or MBL, RN003P). The DAP5 bound mRNAs as well as the total RNA were used for libraries preparation.

first: Maya

last: David

first: Orel

last: Mizrahi

first: Gilgi

last: Friedlander

first: Adi

last: Kimchi


title: WRN promotes bone development and growth by unwinding SHOX-G-quadruplexes via its helicase activity in Werner Syndrome [RNA-seq]

overall_design: RNA-sequencing (RNA-seq) for WRN protein in human embryonic stem cells (hESCs).


title: DDX17 modulates expression and alternative splicing of genes involved in cell apoptosis in lung adenocarcinoma cells

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Accumulating evidence indicates that RNA-binding proteins (RBPs) are involved in tumorigenesis. As a member of DEAD-box RBPs, DDX17 has a significant role in various contexts, such as mRNA translation, pre-mRNA splicing, ribosome biogenesis, and DNA repair. However, whether DDX17 is involved in the regulation of gene expression and alternative splicing in  lung adenocarcinoma (LUAD) remains unclear. Methods: CCK-8 assay was used to evaluate cells proliferation. Cell apoptosis was evaluated by an Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) apoptosis detection kit. We used high-throughput RNA sequencing (RNA-seq) to determine differentially expressed genes (DEGs) and alternative splicing (AS) events in DDX17 knockdown LUAD cells. Functional and pathway enrichment analysis was also performed. Results: Knockdown of DDX17 by siRNA significantly inhibited the proliferation and induced apoptosis in A549 cells. 5243 DEGs were identified. Functional enrichment analyses indicated that these genes were mainly enriched in biological processes including regulation of transcription, regulation of cell growth, DNA repair. DDX17 knockdown increased the level of pro-apoptotic gene expression and decreased the expression of pro-proliferation genes. We also showed that DDX17-regulated AS events revealed by computational analysis using ABLas software in A549 cells were highly validated by RT-qPCR, and also validated by TCGA-LUAD dataset. Functional enrichment analyses showed regulated alternatively spliced genes (RASGs) were mainly enriched in biological processes related to apoptotic process, DNA repair, positive regulation of translation, positive regulation of apoptotic process. Conclusion: The present findings suggest that DDX17 may function as an oncogene by regulating both the expression and the alternative splicing of genes associated with proliferation, invasion and apoptosis in LUAD cells. Our findings may bring new insights into understanding the molecular mechanisms of LUAD and provide a new direction for LUAD treatment.

first: Cheng

last: He

first: Yanhong

last: Lu

first: Gang

first: Jingyue

last: Zhou


title: Gene expression profiles affected by Sam68-knockdown in oral squamous cell carcinoma cells

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

institute: University of tsukuba

summary:
The changes in the transcriptome via Sam68-knockdown were investigated in oral squamous cell carcinoma cells.
The candidate genes which are regulated by Sam68 were demonstrated.

overall_design: Oral squamous cell carcinoma cells with Sam68 siRNA or control siRNA were analysed using mRNA-sequencing.

first: Takehito

last: Sugasawa

first: Shin-ichiro

last: Fujita

first: Takuya

last: Komiyama

first: Takeshi

last: Kuroshima


title: The TBK1/IKKe Inhibitor Amlexanox Improves Dyslipidemia and Prevents Atherosclerosis

status: Public on Jul 27 2022

city: San Antonio

first: Xiaoli

last: Sun

state: TX

address: 7703 Floyd Curl Dr

department: Pharmacology

institute: University of Texas Health Science Center at San Antonio

summary: Cardiovascular diseases, especially atherosclerosis and its complications, are a leading cause of death. Inhibition of the non-canonical IkB kinases TBK1 and IKKe with amlexanox restores insulin sensitivity and glucose homeostasis in diabetic mice and human subjects. Here we report that amlexanox improves diet-induced hypertriglyceridemia and hypercholesterolemia in Western diet (WD)-fed Ldlr-/- mice, and protects against atherogenesis. Amlexanox ameliorates dyslipidemia, inflammation and vascular dysfunction through synergistic actions that involve upregulation of bile acid synthesis to increase cholesterol excretion. Transcriptomic profiling demonstrates an elevated expression of key bile acid synthesis genes. Furthermore, we found that amlexanox attenuates monocytosis, eosinophilia and vascular dysfunction during WD-induced atherosclerosis. These findings demonstrate the potential of amlexanox as a new therapy for hypercholesterolemia and atherosclerosis.

overall_design: Bulk RNA-seq of RNA isolated from vehicle or amlexanox treated Ldlr-/- mice fed Western diet.

first: Peng

last: Zhao


title: Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth-medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth-promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hyper methylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.

overall_design: BS-seq: soil-grown plants of ibm1-1 was compared with the Col-0, each genotype has 2 biological replicates; RNA-seq in soil: soil-grown plants of ibm1-1 was compared with the Col-0, and each genotype has 3 biological replicates; RNAseq in medium: MS-medium-grown seedlings of ibm1-1 was compared with Col-0, and each genotype has 2 biological replicates

first: Suhui

last: Lv

first: Yu

last: Yang

last: Yu

first: Kai

last: Tang

first: Hailing

last: Zi

first: Li

last: Peng

first: Juan

middle: I

last: Vílchez


title: An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish

city: kansas city

first: Tatjana

last: Piotrowski

state: MO

address: 1000 East 50th street

institute: Stowers institute for medical research

summary: Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo, 15min neomycin, 1hr post-neo, 3hr post-neo, 5hr post-neo, il10ra_sib_homeo, il10ra_sib_1hr, il10ra_sib_3hr, il10ra_mut_homeo, il10ra_mut_1hr and  il10ra_mut_3hr

overall_design: scRNA-seq

first: Nicolas

last: Denans

first: Nhung

middle: T

last: Tran

first: Daniel

middle: C

last: Diaz

first: Madeleine

last: Swall

first: Jillian

last: Blanck


title: Transcriptional Signatures of the BCL2 Family in Acute Myeloid Leukaemia Treatment

city: Seoul

first: Chansub

last: Lee

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

summary: We established BFSigs labeled as the BCL2, MCL1/BCL2, and BFL1/MCL1 signatures that identify key anti-apoptotic proteins. Unsupervised clustering based on BFSig information consistently classified AML patients into three robust subtypes across different AML cohorts, implying the existence of biological entities revealed by the BFSig approach. Lastly, we successfully confirmed the validity of BFSigs using NanoString technology.

overall_design: An AML NanoString dataset of 47 bone marrow samples was acquired from randomly chosen patients with AML diagnosed in Seoul National University Hospital (SNUH). We designed a custom NanoString nCounter expression panel with our 82 optimized genes and conducted an validation study using 47 AML samples.


title: PI3Kβ and β-Catenin mediate EZH2 removal from promoters controlling human ESC stemness and primitive streak gene expression

city: Cantoblanco

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: The mechanism governing the transition of human embryonic stem cells towards differentiated cells is only partially understood. To explore this transition, the activity and expression of the ubiquitous phosphoinositide-3-kinase (PI3K α and β) were modulated. This study reports a pathway that dismantles the repression imposed by the EZH2 polycomb repressor on an essential stemness gene, NODAL, and on transcription factors required at differentiation to trigger primitive streak formation. The primitive streak is the site where gastrulation begins to give rise to the three embryonic cell layers from which all human tissues derive. The pathway involves an essential PI3Kβ-non-catalytic action for control of active-RAC1 levels, c-Jun-Nterminal-kinase activation and nuclear β-CATENIN accumulation. β-CATENIN deposition at promoters triggers the release of EZH2 repressor permitting both stemness maintenance (through control of NODAL) and correct differentiation, by allowing primitive streak master genes expression. PI3Kβ -mediated epigenetic control of EZH2/β-CATENIN might be modulated to direct stem cell differentiation.

overall_design: Gene expression of three different human cell lines (three biological replicates each) was measured by single-channel Agilent DNA microarrays

first: Sudhanshu

last: Yadav

first: Antonio

last: Garrido

first: M

last: Hernández

first: Vicente

last: Pérez-García

first: Mario

middle: F

last: Fraga

first: Ana

last: Carrera


title: Thyroid hormone-mediated histone modificaiton protects primary mouse cortical neurons from the toxic effects of hypoxic injury.

city: Los Angeles

first: Kailtyn

middle: Yan-Yun

last: Liu

state: CA

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

summary: Epigenetic and genetic regulation mediates the response to stress at the cellular level and allows cells for adaptation and survival. Thyroid hormone has been shown to have a protective role in neuronal injury, although the mechanisms are not established. We hypothesized that the neuroprotective role of thyroid hormone was associated with epigenetic modifications of histone proteins. We used hypoxic neurons as a model system for hypoxia-induced brain injury. Mouse primary cortical neurons were exposed to 0.2% oxygen for 7 hours with or without treatment with 10 nM Triiodotyroxine (T3). We analyzed the mRNA expression of histone modifying enzymes by RNA-seq and the posttranslationally modified histone 3 proteins by ELISA assay and Western blot. We found that methylation of H3K27, associated with inactive promoters, was highly induced in hypoxic neurons, and this methylation was reduced by T3 treatment. H3K4 methylation is the hallmark of active promoters. Three (Set1db, Kmta2c and Kmt2e) out of six H3K4 methyltransferases were downregulated by hypoxia and restored by T3 treatment. H3K4me3 protein, by ELISA assay, was increased 76% in T3-treated hypoxic neurons, compared to without T3 treatment. H3K56ac, plays a critical role in transcription initiation, was markedly increased in T3-treaed hypoxic neurons, compared to those without T3 treatment, indicating that T3 treatment stimulated gene transcription. Additionally, T3 treatment restored hypoxia-induced downregulation of histone acetyltransferase, Kat6a, Kat6b and Crebbp, which function as transcription factors. These findings indicate that T3 treatment mitigates hypoxia-induced alteration of the histone modifications and protects neurons from hypoxia-induced injury.

overall_design: Modling hypoxia-induced neuron injury. Mouse primary cortical neuron cultures were used. There are three groups, control (normoxia), hypoxia (0.2% oygen) and hypoxia+10nM T3 treatment groups. Comparative gene expression profiling of each groups.

first: Kaitlyn

middle: Y

first: Gregory

last: Brent

first: Kiyomi

last: Abe

first: Jianrong

last: Li


title: Balanced Control of Thermogenesis by Nuclear Receptor Corepressors in Brown Adipose Tissue

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Brown adipose tissue (BAT) is a key thermogenic organ, whose expression of Uncoupling Protein 1 (UCP1) and ability to maintain body temperature in response to acute cold exposure requires histone deacetylase 3 (HDAC3). HDAC3 exists in tight association with nuclear receptor corepressors NCoR1 and NCoR2(also known as Silencing Mediator of Retinoid and Thyroid Receptors, or SMRT), butthe functions of NCoR1/2 in BAT have not been established.Here we report that, as expected, genetic loss of NCoR1/2 in BAT (NCoR1/2 BAT-dKO) leads to loss of HDAC3 activity. In addition, HDAC3 is no longer bound at its physiological genomic sites in the absence of NCoR1/2, leading to a shared deregulation of BAT lipid metabolism between the NCoR1/2 BAT-dKO and HDAC3 BAT KO mice. Despite these commonalities, however, loss of NCoR1/2 in BAT does not phenocopy the cold sensitivity observed in the HDAC3 BAT-KO, nor does loss of either corepressor alone. Instead, BAT lacking NCoR1/2 is inflamed, particularly with respect to the IL-17 axis that increases thermogenic capacity by enhancing innervation. Integration of BAT RNA-seq and ChIP-seq data revealed that NCoR1/2 directly regulate Mmp9, which integrates extracellular matrix remodeling and inflammation. These findings reveal pleiotropic functions of the NCoR/HDAC3 corepressor complex in BAT, such that HDAC3-independent suppression of BAT inflammation counterbalances their stimulation of HDAC3 activity in the control of thermogenesis.

overall_design:
RNA-Seq: There are 4 samples for each group: NCoR2  Control, NCoR2 BAT-sKO, NCoR1/2 Control, NCoR1/2 BAT-dKO, NCoR1 Control. 3 samples for NCoR1 BAT-KO
We analyzed an n of 4 for each group: NCoR2 Control, NCoR2 BAT-sKO, NCoR1/2 Control, NCoR1/2 BAT-dKO.  Isolated RNA from these groups was sequenced at Novogene using an Illumina Platform, PE150, with approximately 30 million reads per sample. For NCoR1 Control (n=4) and NCoR1 BAT-sKO (n=3), libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) and sequenced at the Next-Generation Sequencing Core at the University of Pennsylvania on the NextSeq 500 platform (Illumina) at 75SR for a total of 20-40 million reads per sample.
ChIP-Seq: There are 2 samples of HDAC3 in HDAC3-KO, used as background, and 3 samples each of HDAC3 in Control and NCoR1/2-dKO
An n=3 was sequenced for NCoR1/2 Control and NCoR1/2 BAT-dKO groups, n=2 for HDAC3 BAT-KO, and n=1 each for input and IgG. The sequencing was done at the Next-Generation Sequencing Core at the University of Pennsylvania on a NextSeq platform (Illumina) at 100SR for a total of 30 million reads per sample.

first: Hannah

last: Richter

first: Amy

middle: K

last: Hauck

first: Kirill

last: Batmanov

first: Shin-Ichi

last: Inoue

first: Bethany

last: So

first: Mindy

last: Kim

first: Matthew

last: Emmett

first: Ronald

last: Cohen


title: A retino-collicular mechanism segregates visual from somatosensory circuits at perinatal life in mice

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av Ramon y Cajal s/n, Campus de San Juan

department: Instituto Neurociencias CSIC-UMH

institute: Universidad Miguel Hernández (UMH)

summary: Mature cortical sensory areas are specialized to process unique sensory stimuli. Recent evidence shows that in the mouse embryo sensory cortices are prepared to respond to an incoming input from the periphery. However, whether these sensory circuits originate as modality specific modules, or they are segregated over time remains unknown. Here, we demonstrate that visual and somatosensory circuits originate as functionally intermingled modules, as whisker-pad stimulations at prenatal life led to a multimodal response activating both primary visual and somatosensory cortices. This multimodal response is switched to unimodal at birth via the superior colliculus, a midbrain structure where both modalities converge. Retinal afferent to the superior colliculus prompts the gating of visual from somatosensory circuits achieving sensory modality specificity at birth. Blocking stage I retinal waves resulted in prolonged convergence of somatosensory and visual circuits at the superior colliculus, which led to long-term consequences in the molecular identity of the superior colliculus and caused defects in eye-specific segregation and retinotopy. Hence, the superior colliculus stands as a key developmental regulator of sensory circuits by channeling modality stimuli to their appropriate sensory pathway.

overall_design: Bulk RNA-seq of superficial and deep layers from superior colliculus at P6 after intraocular injections of 50 mM carbenoxolone (cbx, Merck, C4790) or saline into the vitreous humor of the eye at P0-P1. The bulk tissue were microdissected (three brains were pooled for each sample) and the total RNA was extracted as in previous publication (Moreno-Juan et al., 2017).

first: Lorenzo

last: Puche-Aroca

first: Teresa

last: Guillamón-Vivancos

first: Mar

last: Aníbal-Martínez


title: Effect of sex and brain region on gene expression within isolated microglia in adult C57Bl/6J mice.

city: Worcester

first: Ryan

last: Logan

address: 366 Plantation Street

institute: University of Massachusetts Chan Medical School

summary: We used mice that conditionally expressed a fluorescent reporter only in TMEM119 expressing cells to sort microglia for RNA-sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq of three different brain regions (prefrontal cortex, striatum, midbrain) in both male and female mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for microglia isolated from prefrontal cortex, striatum, and midbrain from both male and female mice.

first: Marianne

last: Seney

first: Xiangning

last: Xue


title: [eCLIP] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

city: New York

first: Soobeom

last: Lee

address: 550 First Avenue, Smilow 1307 New York NY

institute: NYU

summary: Recent improvements in relapse/refractory B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) outcome can be attributed, in part, to the emergence of CD19-directed immune-based therapies including chimeric antigen receptor (CAR)-T cell therapy and bi-specific T cell engager (BiTE) therapy. Longitudinal BCP-ALL studies have highlighted individual cases of progressive surface CD19 antigen reduction associated with disease persistence following CAR-T infusion. CD19 genomic deletions and mRNA alternative splicing have been previously shown to confer CAR-T and BiTE resistance, however gene regulatory programs that modulate BCP-ALL CD19 surface antigen abundance remains poorly understood. To address this, we performed genome-wide CRISPR/Cas9 screening to identify positive and negative regulators of surface CD19 abundance in human BCP-ALL as compared to mature B cell neoplasms, chronic lymphocytic leukemia and B cell lymphoma. Here, we show DNA binding protein, ZNF143, occupies the CD19 promoter and transcriptionally regulates CD19 mRNA expression in human B-cell malignancies. Conversely, we show that RNA-binding protein, NUDT21, limits surface CD19 abundance on BCP-ALL. NUDT21 acts to regulate CD19 3’ UTR length and CD19 mRNA stability. NUDT21 mRNA displays high concordance with CD19 mRNA expression in primary healthy and transformed human B cell progenitors. Using primary BCP-ALL patient single cell data, we show that reduction of CD19 mRNA expression following CAR-T therapy coincides with increased NUDT21 mRNA expression. Importantly, NUDT21 ablation sensitizes BCP-ALL to BiTE and CD19 CAR-T killing ex vivo. These findings reveal previously unknown modulators of CD19 antigen abundance that can be applied to therapeutically enhance or determine resistance to CD19-based therapies in B-cell leukemias.

overall_design: Enhanced crosslinking and immunoprecipitation (eCLIP) of three BCP-ALL cell lines (Reh, NALM6 and 697) and one mature B-cell neoplasm cell lines ( B Cell Lymphoma/BCL: TMD8).

last: Witkowski

first: Eric

last: Wang

first: Iannis

last: Aifantis


title: [RNA-seq] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

overall_design:
Bulk RNA profiling of three BCP-ALL cell lines (Reh, NALM6 and 697) and two mature B-cell neoplasm cell lines (Chronic Lymphocytic Leukemia/CLL: HG3; B Cell Lymphoma/BCL: TMD8) transduced with sgROSA (control), sgNUDT21, or sgZNF143.

The file format for each sample is as follows: [cellline-condition_replicate]
sgRNA expression condition is labeled as follows: ROSA/B11;sgROSA, NUDT21;sgNUDT21, C8/C9;sgNUDT21, B5/B6;sgZNF143


title: PIF7 is the master regulator of thermomorphogenesis in shade

status: Public on Jul 26 2022

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

institute: Volcani Institute


title: PIF7 is the master regulator of thermomorphogenesis in shade [RNA-seq]

summary: The size and shape of plant organs are highly responsive to the local environmental conditions. The embryonic stem, or hypocotyl, of the plant is one such organ that displays impressive phenotypic plasticity, and its length is affected by both light and temperature. After sensing surrounding vegetation, hypocotyls of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. A similar elongation response occurs when the plants are grown in high ambient temperatures. Previous studies have shown that this response is mediated by a family of transcription factors called PHYTOCHROME-INTERACTING FACTORS (PIFs). However, it is poorly understood how environmental light and temperature interact to affect plants at the morphological and molecular levels. Here, we examine the genetic and molecular basis of the response to low R/FR under warm ambient temperatures. We found that low R/FR combined with warm temperature dominantly regulate by PIF7 and exhibit a synergistic effect on hypocotyl growth, greater than either stimulus alone. While the synergistic response was dependent on PIF7 and the plant hormone auxin, we demonstrate that additional, yet unknown key factor/s must be involved, likely working downstream of the phyB-PIF-auxin module. As shade responses are known to affect crop yield and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs. In addition, we point out key factors in this response that can potentially be modulated to minimize the negative effect on yield.

overall_design: Two biological replicates of wild-type seedlings grown in constant LED white light (~70µE) at 21°C in white light (WL) for three days and moved to 21°C WL supplement with Far-red (21FR; R/FR=0.6), 30°C in white light (30WL), 30°C WL supplement with Far-red (30FR; R/FR=0.6) or left at 21WL. Samples (whole seedlings) were collected after one, three, six, or 24 hours and sequenced to analyze the genes regulated by each condition.

first: Joanne

last: Chory


title: Exploring the Mechanism of Adjuvant Treatment of Glioblas-toma Using Temozolomide and Metformin

city: Taipei

first: YAO FENG

last: LI

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Pathology

country: Taiwan

institute: National Defense Medical Center

summary: To investigate the changes of the transcriptome and relevent signalling between control and metformin treated glioblastoma cell line.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 control verus 6 metformin treated glioblatoma cell lines.

first: Yao

last: Li

first: Pei-Chi

last: Chang


title: [Hi-C] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

overall_design:
Three dimensional chromatin structure profiling of three BCP-ALL cell lines (Reh, NALM6 and 697) transduced with sgROSA (control) or sgZNF143.

B11;sgROSA, B6;sgZNF143

first: Matthew


title: [MACE-seq] Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

overall_design: Massive Analysis of cDNA Ends (MACE) sequencing of three BCP-ALL cell lines (Reh, NALM6 and 697) and one mature B-cell neoplasm cell lines ( B Cell Lymphoma/BCL: TMD8) transduced with sgROSA (control) or sgNUDT21.


title: Transcriptional regulation of CD19 antigen abundance in B-cell malignancy

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

overall_design: Refer to individual Series


title: PIF7 is the master regulator of thermomorphogenesis in shade [ChIP-seq]

summary: The size and shape of plant organs are highly responsive to environmental conditions. The plant's embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The, hypocotyl of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. Similar elongation occurs in high temperature. PHYTOCHROME-INTERACTING FACTORS (PIFs) family transcription  are known to be importenet players in these responses. However, it is poorly understood how environmental light and temperature interact to affect plants development. We found that low R/FR combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PIF7 and the hormone auxin. We demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. As shade responses are known to affect yield, susceptibility to pathogens, and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs.

overall_design: Plants were grown in constant LED white light (~70µE) at 21°C in white light (21WL) for four days and moved to 21°C WL supplement with Far-red (21FR; R/FR=0.6), 30°C in white light (30WL), 30°C WL supplement with Far-red (30FR; R/FR=0.6) or left at 21WL. Samples (whole seedlings) were collected after 2 hours and sequenced to analyze PIF7 binding.


title: RNA features governing zinc finger antiviral protein sensitivity enable attenuated virus design

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

institute: Imperial College London

summary: Synonymous recoding of viral genome can attenuate their replication, but can have pleiotropic effects, with multiple mechanisms contributing to attenuation. We set out to design recoded viral genomes whose attenuation was specific and conditional. The zinc finger antiviral protein (ZAP) recognizes CpG dinucleotides and targets CpG-rich RNAs for depletion, but RNA features such as CpG numbers, spacing and surrounding nucleotide composition that enable specific modulation by ZAP are undescribed. Using synonymously mutated HIV-1 genomes, we define several sequence features that govern ZAP sensitivity and stable attenuation. Using features defined using HIV-1, we then designed a mutant enterovirus A71 genome whose attenuation was also stable and strictly ZAP-dependent, both in cell culture and in mice. This conditionally attenuated enterovirus A71 elicited neutralizing antibodies that were protective against wild-type enterovirus 71 infection and disease. Elucidation of the determinants of ZAP sensitivity can thus enable the rational design of conditionally attenuated viral vaccines.

sample_organism:
Homo sapiens
synthetic HIV-1

platform_organism:
Homo sapiens
synthetic HIV-1

overall_design: The goal of the experiment was to analyze RNA sequences of the HIV-1 genome bound the Zinc Finger Antiviral Protein (ZAP). ZAP:RNA complexes were extracted and purified from 293T cells, reversed transcribed and analysed by NGS. Two repeated experiments are included; HIV-1 mutants include (1) one with 15 CpGs located ~11nt from each other; (2) one with 15 CpGs located ~32nt from each other and (3) one mutant with 0 CpGs.

first: Paul

last: Bieniasz


title: Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity

city: Ann Arbor

first: Kenneth

last: Kwan

state: MI

address: 4909 Buhl Building, 1241 E. Catherine St.

department: Human Genetics

institute: University of Michigan

summary: Histone variants, which can be expressed outside of S-phase and deposited DNA synthesis-independently, provide long-term histone replacement in postmitotic cells, including neurons. Beyond replenishment, histone variants also play active roles in gene regulation by modulating chromatin states or enabling nucleosome turnover. Here, we uncover crucial roles for the histone H3 variant H3.3 in neuronal development. We find that newborn cortical excitatory neurons, which have only just completed replication-coupled deposition of canonical H3.1 and H3.2, substantially accumulate H3.3 immediately post mitosis. Co-deletion of H3.3-encoding genes H3f3a and H3f3b from newly postmitotic neurons abrogates H3.3 accumulation, markedly alters the histone posttranslational modification (PTM) landscape, and causes widespread disruptions to the establishment of the neuronal transcriptome. These changes coincide with developmental phenotypes in neuronal identities and axon projections. Thus, preexisting, replication-dependent histones are insufficient for establishing neuronal chromatin and transcriptome; de novo H3.3 is required. Stage-dependent deletion of H3f3a and H3f3b from (1) cycling neural progenitor cells, (2) neurons immediately post mitosis, or (3) several days later, reveals the first postmitotic days to be a critical window for de novo H3.3. After H3.3 accumulation within this developmental window, co-deletion of H3f3a and H3f3b does not lead to immediate H3.3 loss, but causes progressive H3.3 depletion over several months without widespread transcriptional disruptions or cellular phenotypes. Our study thus uncovers key developmental roles for de novo H3.3 in establishing neuronal chromatin, transcriptome, identity, and connectivity immediately post mitosis that are distinct from its role in maintaining total histone H3 levels over the neuronal lifespan.

overall_design: We analyzed a total of 12 samples of rRNA-depleted RNA from P0 mouse cortex using UMI RNA-seq. Libraries were generated using Click-seq. 4 samples were controls, 4 samples were H3f3a/H3f3b Neurod6-Cre conditional knockouts (dKO-N), and 4 samples were H3f3a/H3f3b Emx1-Cre conditional knockouts (dKO-E). We analyzed a total of 5 samples P0 mouse cortex using H3K4me3 CUT&Tag. 3 samples were controls, 2 samples were H3f3a/H3f3b Neurod6-Cre conditional knockouts (dKO-N). We analyzed a total of 5 samples P0 mouse cortex using H3K27me3 CUT&Tag, 3 controls and 2 were H3f3a/H3f3b Neurod6-Cre conditional knockouts (dKO-N). We analyzed 6 samples of P0 mouse cortex using ATAC-seq, 3 controls and 3 H3f3a/H3f3b Neurod6-Cre conditional knockouts (dKO-N). For snRNAseq, corticies from embroynic or adult mice were dissected and flash frozen, followed by nuclei dissociation and processing on the 10x Genomics Chromium controller.

first: Owen

middle: H

last: Funk

first: Yaman

last: Qalieh

last: Doyle

first: Mandy

last: Lam


title: T-cell exhaustion induced by continuous bispecific antibody exposure is ameliorated by treatment-free intervals

city: Munich

first: Maryam

last: Kazerani

address: Feodor-Lynen-Strasse 25

institute: LMU Gene Center

summary: T-cell-recruiting bispecific antibody therapy has yielded promising results in patients with hematologic malignancies, however, resistance and subsequent relapse remains a major challenge. T-cell exhaustion induced by persistent antigen stimulation or tonic receptor signaling has been reported to compromise outcomes of T-cell based immunotherapies. The impact of continuous exposure to bispecifics on T-cell function, however, remains poorly understood. In relapsed/refractory B-cell precursor acute lymphoblastic leukemia patients, 28-day continuous infusion with the CD19xCD3 bispecific antibody blinatumomab led to declining T-cell function. In an in vitro model system, mimicking 28-day continuous infusion with the half-life-extended CD19xCD3 bispecific AMG 562, we identified hallmark features of exhaustion arising over time. Continuous AMG 562 exposure induced progressive loss of T-cell function (day 7 vs day 28 mean specific lysis: 88.4% vs 8.6%; n = 6; p = .0003). Treatment-free intervals (TFIs), achieved by AMG 562 withdrawal, were identified as powerful strategy for counteracting exhaustion. TFIs induced strong functional reinvigoration of T cells (continuous vs TFI specific lysis on day 14: 34.9% vs 93.4%; ± SEM; n = 6; p < .0001) and transcriptional reprogramming. Furthermore, use of a TFI led to improved T-cell expansion and tumor control in vivo. Our data demonstrate the relevance of T-cell exhaustion in bispecific antibody therapy and highlight that T cells can be functionally and transcriptionally rejuvenated with TFIs. In view of the growing number of bispecific molecules being evaluated in clinical trials, our findings emphasize the need to consider and evaluate TFIs in application schedules to improve clinical outcomes.

overall_design: T cells of three healthy donors stimulated continuously with AMG 562 or with a treatment-free interval (TFI) from day 7-14 were sorted and analyzed. Samples: Continuously stimulated= day 0, 7, 14, 21; TFI-stimulated= day 14, 21. Total number of samples=18.

first: Nora

last: Philipp

first: Tobias

last: Straub

first: Marion

last: Subklewe


title: Blood miR-144-3p: A Novel Diagnostic and Therapeutic Tool for Depression

status: Public on Jul 25 2022

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Major depressive disorder (MDD) is the leading cause of disability worldwide. There is an urgent need for objective biomarkers to diagnose this highly heterogeneous syndrome, assign treatment, and evaluate treatment response and prognosis. MicroRNAs (miRNAs) are short non-coding RNAs, which are detected in body fluids that have emerged as potential biomarkers of many disease conditions. The present study explored the potential use of miRNAs as biomarkers for MDD and its treatment. We profiled the expression levels of circulating blood miRNAs from mice that were collected before and after exposure to chronic social defeat stress (CSDS), an extensively validated mouse model used to study depression, as well as after either repeated imipramine or single-dose ketamine treatment. We observed robust differences in blood miRNA signatures between stress-resilient and stress-susceptible mice after an incubation period, but not immediately after exposure to the stress. Furthermore, ketamine treatment was more effective than imipramine at re-establishing baseline miRNA expression levels, but only in mice that responded behaviorally to the drug. We identified the red blood cell-specific miR-144-3p as a candidate biomarker to aid depression diagnosis and predict ketamine treatment response in stress-susceptible mice and MDD patients. Lastly, we demonstrate that systemic knockdown of miR-144-3p, via subcutaneous administration of a specific antagomir, is sufficient to reduce the depression-related phenotype in stress-susceptible mice. RNA-sequencing analysis of blood after such miR-144-3p knockdown revealed a blunted transcriptional stress signature as well. These findings identify miR-144-3p as a novel target for diagnosis of MDD as well as for antidepressant treatment, and enhance our understanding of epigenetic processes associated with depression.

overall_design: We profiled transcriptional changes in the blood of male mice exposed to chronic social defeat stress and classified as stress susceptible or control mice. The mice received a systemic injection of antisense oligonucleotide of microRNA 144-3p or scrambled control.

first: Yentl

last: van der Zee

first: Lars

last: Eijssen

first: Eric

last: Nestler

first: Orna

last: Issler


title: Genome-wide chromatin binding of YBX1 in nasopharyngeal carcinoma (NPC) cell line S18 (ChIP-Seq)

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

summary: The development of therapeutic resistance and metastatic dissemination takes place in 20-30% patients with nasopharyngeal carcinoma (NPC), resulting in poor survival. Hence, a better understanding of the underlying molecular mechanisms will help improve clinical outcome. We have identified a novel circRNA, circIPO7, as a promoter of metastasis and cisplatin chemoresistance in NPC cells. circIPO7 was found to bind to YBX1. Genome binding/occupancy profiling by high throughput sequencing were performed to explore the underlying molecular mechanisms.

overall_design: Chromatin Immunoprecipitation (ChIP) was performed in the human nasopharyngeal carcinoma cell line S18 using YBX1 antibody, and then subjected to ChIP sequencing.

first: X

last: Hong

first: J

last: Ma

first: Y

middle: Q


title: CircIPO7 Promotes Nasopharyngeal Carcinoma Metastasis and Cisplatin Chemoresistance by Regulating YBX1 Nuclear Localization

summary:
The development of therapeutic resistance and metastatic dissemination takes place in 20-30% patients with nasopharyngeal carcinoma (NPC), resulting in poor survival. Hence, a better understanding of the underlying molecular mechanisms will help improve clinical outcome. We have identified a novel circRNA, circIPO7, as a promoter of metastasis and cisplatin chemoresistance in NPC cells.
Expression profiling and Genome binding/occupancy profiling by high throughput sequencing were performed to explore  the underlying molecular mechanisms.

overall_design:
The RNA sequencing analysis of nasopharyngeal carcinoma (NPC) cell line S18 upon circIPO7 knockdown.
Genome-wide chromatin binding of YBX1 in nasopharyngeal carcinoma (NPC) cell line S18 (ChIP-Seq).


title: Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease [methylation]

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

type: Methylation profiling by genome tiling array

summary: We investigated the dynamics of DNA methylation in blood samples of IBD patients treated with infliximab and analyzed the predictive potential regarding therapy outcome.

overall_design: We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 timepoints (from baseline to 14 weeks after therapy induction).

first: Konrad

last: Aden

first: Nathan

last: Baran

first: Philip

last: Rosentiel


title: Effect of deletion of CPES on gene expression during spermatogenesis in Drosophila testes

city: Frederick

first: Jairaj

last: Acharya

state: MD

address: 1050 Boyle Street

department: Cancer and Developmental Biology Laboratory

institute: National Cancer Institute, NIH

summary:
To investigate the role of CPES in germ cell differentiation during spermatogenesis in Drosophila testis. We have generated cpes null mutants using ends-out homologus recombination and rescued with Bam-Gal4 and UAS-CPES in cpes mutant background.
We then dissected 200 pairs of testes for each of the 3 replicates from wild type, cpes mutant and Rescue (Bam-Gal4 and UAS-CPES) Drosophila males and total RNA was extracted using Trizol and RNA-Clean and concentrater column. About 1ug of RNA in 20ul was submitted for bulk RNAseq using Illumina machine (HWI-ST1276).

overall_design: Original RNAseq data was assessed and mapped to Drosophila genome. The  readcounts were taken input into DESeq r-package and using the function for variant stabilization transformation (vst) the counts were transformed for further analysis. The flybase IDs were mapped to gene symbols using org.dm.eg.db r-package. The vst ransformed counts file was used as one of the input file for Gene Set Enrichment Analysis (GSEA). Linux platform with GSEA v4.02 was used for anlysis. All the pathway sets were downloaded from http://www.go2msig.org/cgi-bin/prebuilt.cig?taxid=7227,  Drosophila melanogaster (Fruit fly- taxon 7227) genes identified by gene symbols. All Ontologies with high quality GO annotations only was further used in the analysis. Individual pathways were saved as .gmt file and used for analysis.

first: Govind

last: Kunduri

first: Usha


title: The RNA sequencing analysis of nasopharyngeal carcinoma (NPC) cell line S18 upon circIPO7 knockdown

summary: The development of therapeutic resistance and metastatic dissemination takes place in 20-30% patients with nasopharyngeal carcinoma (NPC), resulting in poor survival. Hence, a better understanding of the underlying molecular mechanisms will help improve clinical outcome. We have identified a novel circRNA, circIPO7, as a promoter of metastasis and cisplatin chemoresistance in NPC cells. High-throughput RNA sequencing analysis was performed in the human nasopharyngeal carcinoma cell line S18 after transfection with control siRNA or circIPO7 siRNA.


title: Coordination of nuclear and plastid transcription for chloroplast biogenesis requires H4 acetylation by the NuA4 complex

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

address: Autopista M-40, Km 38

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

summary: Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.

overall_design: Transcriptomic profiling through RNAseq of Arabidopsis plants grown on 1/2x Murashige & Skoog medium supplemented with 1% sucrose under long day photoperiod (16h light / 8h dark). Plants were grown at 22°C for 14 days, taking samples at Zeitgeber time (ZT) ZT8. Three libraries were generated using RNA from three independent experiments.

first: Javier

last: Barrero-Gil

first: Laura

last: Bouza-Morcillo

first: Loreto

last: Espinosa-Cores

first: José

middle: A

last: Jarillo

last: Piñeiro


title: STAT3 Inhibits Autocrine Interferon Signaling in Type I Conventional Dendritic Cells

city: Houston

first: LI

last: SHEN

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Type I conventional dendritic cells (cDC1s) are an essential antigen-presenting population, required for generating adaptive immunity against intracellular pathogens and tumors. While the transcriptional control of cDC1 development is well understood, the mechanisms by which extracellular stimuli affect cDC1 function remain unclear. Recently, we demonstrated that the cytokine IL-10 inhibits cDC1 maturation induced upon polyinosinic-polycytidylic acid (poly I:C) exposure via a STAT3-dependent mechanism. Furthermore, utilizing a tumor vaccine strategy, we found STAT3 restrains cDC1-mediated anti-tumor immunity. To understand the pathways by which IL-10 and STAT3 regulate cDC1s, we evaluated transcriptional responses by RNA-sequencing. Bioinformatic analyses indicated that many inflammatory pathways were enriched in cDC1s following poly I:C treatment, while interferon (IFN) signaling was uniquely inhibited by STAT3 upon concomitant exposure to IL-10. We found that poly I:C stimulated production of IFN-b and IFN-g from cDC1s. Concurrent exposure to IL-10 suppressed IFN-b and IFN-g secretion as well as accrual of phosphorylated STAT1 and expression of the IFN-response gene Cxcl10 in cDC1s. By contrast, Stat3-deficient cDC1s were refractory to IL-10, indicating STAT3 controls poly I:C-mediated IFN production and IFN transcriptional responses in cDC1s. Moreover, we found that maturation of cDC1s in response to poly I:C is dependent on the type I IFN receptor. Taken together, our data indicate STAT3 is essential for restraining autocrine type I IFN signaling in cDC1s elicited by poly I:C stimulation.

overall_design: STAT3fl/fl CD11c-Cre- and STAT3fl/fl CD11c-Cre+ in-vitro derived cDC1s were treated with PBS, IL-10 (10 ng/mL), poly I:C (20 ug/mL), or IL-10 + poly I:C for 6 hours. n = 3 per genotype and treatment condition

first: Taylor

last: Chrisikos

first: Li

last: Shen

first: Stephanie

middle: S

last: Watowich


title: Identification of Yox1 and Yhp1 target genes in S. cerevisiae

first: Jennifer

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School


title: Gene expression profile at single cell level of stromal vascular cells (SVC) from the subcutaneous adipose tissue (SAT) and the visceral adipose tissue (VAT) post-exposure to SARS-CoV-2 or mock conditions in vitro

city: Stanford

first: Kalani

last: Ratnasiri

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

summary: Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-19) outcomes, yet the underlying mechanism is unknown. To explore whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of adipose tissue contributes to pathogenesis, we evaluated COVID-19 autopsy cases and deeply profiled the response of adipose tissue to SARS-CoV-2 infection in vitro.

overall_design: SAT SVC and VAT SVC were isolated from 3 participants, exposed to either SARS-CoV-2 or mock conditions in vitro for 24 hours and analyzed using scRNAseq.

first: Giovanny

last: Martínez-Colón

first: Catherine

last: Blish

first: Tracey

last: McLaughlin


title: Identification of genes regulated by acute overexpression of Yox1 and Yhp1 in S. cerevisiae

summary: We report gene expression data for strains that overexpress the transcriptional repressors Yox1 or Yhp1 from a synthetic, estradiol-inducible promoter. Gene expression was also measured in strains that overexpress unphosphorylatable alleles of either Yox1 or Yhp1, to determine whether blocking phosphorylation of these proteins by Cdk1 changes the spectrum of regulated genes. Finally, gene expression was measured in corresponding control strains in which Yox1/Yhp1 proteins were expressed from their endogenous promoters. These data demontsrate that Yox1 is a stronger repressor than Yhp1, although they regulate the same genes. In addition, phosphodeficient alleles of each TF regulate the same genes as the wild type proteins.

overall_design: Gene expression was measured in asynchronous cells expressing wild type Yox1/Yhp1 proteins (YOX1, YHP1)  or Yox1/Yhp1 proteins mutations in Cdk1 phosphoryation sites (yhp1_13A or yox1_9A). RNA was collected before estradiol addition (0) and  20 minutes (20) and 60 minutes (60) after the addition of estradiol. Matched samples were collected from controls strains (ctrl) expressing the same Yox1/Yhp1 proteins from their endogenous promoters. Three biological replicates were performed (rep1-rep3).

first: Michelle

last: Conti

first: Rui

last: Li

first: Lihua

last: Zhu


title: MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Uveal melanoma (UM) is the most common primary malignancy of the eye in adults, but lacks any FDA-approved therapy for the deadly metastatic disease. Thus, there is great need to dissect the driving mechanisms for UM, and develop strategies to evaluate potential therapeutics. Using a zebrafish model, we previously identified MITF, the master melanocyte transcription factor, as a tumor suppressor in GNAQQ209L-driven UM. Here, we show that zebrafish mitfa-deficient GNAQQ209L-driven tumors significantly up-regulate neural crest markers, and higher expression of a melanoma-associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa-null state, as well as expression of GNAQQ209L, YAPS127A;S381A, or BRAFV600E oncogenes, impacts melanocyte lineage cells before they acquire the transformed state. Specifically, examination 5 days post-fertilization showed that mitfa-deficiency is sufficient to upregulate pigment progenitor and neural crest markers, while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co-expression. Finally, we show that this oncogene-induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall, this study establishes that a neural crest signature correlates with poor UM survival, and describes an in vivo assay for pre-clinical trials of potential UM therapeutics.

overall_design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild-type and null mitfa backgrounds compared to similar groups with added BRAF, GNAQ and YAP transgenes.

first: Grace

middle: B

last: Phelps

first: Hannah

middle: R

last: Hagen

first: Adam

last: Amsterdam

first: Nicole

last: García

first: Jacqueline

last: Lees


title: Single cell transcriptome mapping identifies a local innate B cell population driving chronic rejection after lung transplantation

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary:
Bronchiolitis obliterans syndrome (BOS) is the main reason for poor outcomes after lung transplantation (LTx). We and others have recently identified B cells as major contributors to BOS after LTx. The extent of B cell heterogeneity and the relative contributions of B cell subpopulations to BOS, however, remain entirely unclear. Here, we provide a comprehensive analysis of cell population changes and their gene expression patterns during chronic rejection after orthotopic LTx in mice. Out of a total of 11 major cell types, Mzb1-expressing plasma cells (PCs) were the most prominently increased population in BOS lungs. These findings were validated in two different cohorts of human BOS after LTx. A Bhlhe41, Cxcr3, Itgb1-triple positive-B cell subset, also expressing classical markers of the innate-like B-1 B cell population, served as the progenitor pool for Mzb1+ PCs. This subset accounted for the increase in IgG2c production within BOS lung grafts. A genetic lack of immunoglobulins decreased BOS severity after LTx. In summary, we
provide a detailed analysis of cell population changes during BOS. IgG-positive PCs and their progenitors – an innate B cell subpopulation – are the major source of local antibody production and a significant contributor to BOS after LTx.

overall_design: Single-cell RNA-seq of a mouse model of lymphocytic bronchiolitis/BOS after lung transplantation.

first: Natalia

last: Smirnova

first: Oliver

last: Eickelberg


title: Identification of genes regulated by Yox1 and Yhp1 in S. cerevisiae

first: Jennifer

last: Benanti

state: MA

summary: We report gene expression data for yeast strains expressing mutated versions of the transcriptional repressors Yox1 and Yhp1 that can't be phosphorylated by Cdk1. For comparision,  gene expression was also measured in cells with deletions in one or both repressors. Genes that are downregulatd in phosphomutant strains and upregulated in deletion strains are likely to be target genes of these transcriptional repressors.

overall_design: Gene expression was measured in asynchronous cells expressing Yox1/Yhp1 proteins with mutations in Cdk1 phosphoryation sites (yhp1_13A, yox1_9A and yox1_9A_yhp1_13A), and in strains deleted for one or both proteins (yhp1_del, yox1_del, and yox1_del_yhp1_del). Gene expression was also measured in matched wild type cells (WT) for comparision. Three biological replicates were performed (rep1-rep3). Although the same wild type strain was used for comparison, the WT_A replicates were collected alongside phosphorylation site mutant strains and  the WT_B replicates were collected alongside deletion strains.

first: Ana

last: Gil-Bona

middle: J


title: The genome wide mapping of H3K9 and H3K23 acetylation in Moz+/+ and Moz-/- MOZ-TIF2 AML cells

status: Public on Jul 24 2022

city: Tokyo

first: Takuo

last: Katsumoto

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

institute: National Cancer Center

summary: Monocytic leukemia Zinc finger protein (MOZ) is a MYST-type acetyltransferase involved in chromosomal translocation in acute myelogenous leukemia (AML) and myelodysplastic syndrome. MOZ is established as essential for hematopoiesis; however, the role of MOZ in AML has not been addressed. We propose that MOZ is critical for AML development induced by MOZ-TIF2 fusions. Moz-deficient hematopoietic stem/progenitor cells (HSPCs) expressing MOZ-TIF2 could form colonies in vitro but could not induce AML in mice. By contrast, Moz was dispensable for colony formation by HOXA9-transduced cells and AML development caused by HOXA9 and MEIS1, suggesting a specific requirement for MOZ in AML induced by MOZ/MLL-fusions. Expression of the of Meis1, but not Hoxa9, was reduced in Moz-deficient MOZ-TIF2 AML cells. AML development induced by MOZ-TIF2 was rescued by introducing Meis1 into Moz-deficient cells carrying MOZ-TIF2. Meis1 deletion impaired MOZ-TIF2-mediated AML development. Active histone modifications were also severely reduced at the Meis1 locus in Moz-deficient MOZ-TIF2 AML cells. These results suggest that endogenous MOZ is critical for MOZ-fusion-induced AML development and maintains active chromatin signatures at target gene loci.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-Seq) of genome wide H3K9 and H3K23 acetylation in Moz+/+ and Moz-/- MOZ-TIF2 AML cells

first: Issay

last: Kitabayashi


title: miRNA expression in human colitis-associated dysplasia

status: Public on Jul 23 2022

city: Philadelphia

first: Mariana

last: Franco Fragoso

address: 333 Cottman Avenue

department: Cancer Prevention and Control

institute: Fox Chase Cancer Center

summary: Patients with ulcerative colitis (UC) are at increased risk of colorectal cancer (CRC). Colitis-associated dysplasia (flat or polypoid) continues to be a reliable marker for CRC in these patients. However, flat lesions are often missed during endoscopy and can rapidly progress to high-grade dysplasia or cancer. microRNAs (miRs), small non-coding RNAs, have emerged as a valuable diagnostic biomarker of human cancer due to their ease of detection and stability. The goal of this study was to identify a miR signature that can serve as a reliable biomarker for the early detection of colitis-associated dysplasia in patients with long-standing colitis.

overall_design: The miR expression profiles of laser macrodissected colonic epithelial cells from non-dysplastic inflamed colon, flat and polypoid dysplasia was interrogated using the NanoString Human miRNA Platform (total of 22 patients).

last: Fragoso

first: Lisa

last: Vanderveer

first: Geysson

last: Fernandez

first: Harry

last: Cooper

first: Michael

last: Slifker

first: Karthik

last: Devarajan

first: Yan

last: Zhou

first: Eric

last: Ross

first: Walter

last: Koltun

first: Margie

last: Clapper


title: Mapping the zebrafish developmental and aging atlas by single cell mRNA-seq

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping current cell-type classification system. In previous studies, we constructed the Mouse Cell Atlas (MCA) and Human Cell Landscape (HCL) to catalog all cell types by collecting scRNA-seq data. Howerver, the systematic study for organism-level dynamic changes of cellular states across zebrafish life span are still lacking. Here, we constructed the zebrafish cell Landscape covering different development periods using Microwell-seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross-sepciess development, maturation and aging.

overall_design: Over 452,878 cells derived from zebrafish whole-body single-cell dissociation and profiling at the larval stage (21 day, 3 replicates, and 10 fish for each replicate) and adult (22 month, 6 replicates, 1 fish for each replicate).

first: Xiaoping

last: Han

first: Renying

last: Wang

first: Peijing

last: Zhang

first: Lifeng

last: Ma


title: RNAseq of CD8 T-cells stimulated with CXCR3 chemokines

city: Durham

first: Sudarshan

last: Rajagopal

state: NC

address: Box 102147, Duke University Medical Center

department: Biochemistry

institute: Duke University School of Medicine

summary: G protein-coupled receptors (GPCRs) interact with many transducers like G proteins and β-arrestins. Some GPCR agonists act as “biased agonists” which preferentially activate specific signaling transducers over others, leading to unique signaling profiles. The chemokine system, a subfamily of GPCRs that plays a critical role in inflammatory diseases, serves as an endogenous example of biased agonism where over 50 different chemokines ligands and 20 receptors interact promiscuously. In this study, we sought to determine the three different chemokines of the chemkoine receptor CXCR3 generate different transcriptional responses in primary CD8+ T cells. Using RNAseq on CD8+ T cells stimulated with either vehicle control, CXCL9, CXCL10, or CXCL11, the endogenous chemokines of CXCR3, we found that the CXCR3 chemokines promoted unique transcriptional responses that are predicted to differentially regulate inflammatory pathways. We observed significant changes in global transcriptional activation, detecting approximately 48000 transcripts, 887 of which varied by chemokine treatment. There was a high degree of replicability between biological replicates. The overwhelming majority of differentially expressed genes (DEGs) increased in transcript level following chemokine treatment. Compared to vehicle control, CXCL11 demonstrated the largest number of DEGs. Importantly, CXCL11 and CXCL10 demonstrate unique transcriptional profiles where the majority of DEGs were only found following treatment with each specific chemokine, rather than being shared across chemokines. These data contrast with that observed at CXCL9 – although it promoted a significant amount of transcriptional regulation, approximately 66% of CXCL9-induced DEGs were shared with CXCL11 and/or CXCL10.

overall_design: RNAseq on CD8+ T Cells stimulated with vehicle control, CXCL9, CXCL10 or CXCL11 for 2 hours

first: Dylan

last: Eiger

first: Noelia

last: Boldizsar

first: Christopher

last: Honeycutt

first: Julia

last: Gardner

first: Stephen

last: Kirchner

first: Chloe

last: Hicks

first: Issac

last: Choi

first: Uyen

last: Pham

first: Kevin

last: Zheng

first: Anmol

last: Warman

first: Jeffrey

last: Smith

first: Jennifer


title: Effect of hypoxic stress on Estrogen receptor alpha binding to chromatin

city: Basel

first: Charly

last: Jehanno

address: HebelStrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of basel

summary: This project aimed at assessing the influence of hypoxic stress on Estrogen receptor alpha genome wide binding to chromatin, in presence or absence of E2 ligand. I also aimed at assessing if a 1-month hypoxic stress followed by 1 month of normoxia imprints an epigenetic memory, therefore altering genome wide ER binding (rescue condition).

overall_design: 6 experimental conditions, with 1 technical replicate each 1) Normoxia : EtOH vs E2 (50 min); 2)Hypoxia: EtOH vs E2 (50 min); Rescue: EtOH vs E2 (50 min).

first: Raphael

last: Metivier


title: Self-reactivity of CD8 T-cell clones determines their differentiation status rather than their responsiveness in infections

status: Public on Jul 22 2022

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: The peripheral blood mononuclear cells (PBMCs) from young and old C57BL/6J mice were single cell RNA sequenced along with V(D)J sequences and cell surface protein markers that were used to demultiplex them from separate and unrelated experiment. The resulting data were then used to create an atlas of mouse peripheral CD8+ T cells. The analysis of this atlas has revealed two unconventional populations of antigen-inexperienced T cells and allowed for further examination of the steady-state phenotype of monoclonal T cells with various levels of self-reactivity.

overall_design: Peripheral CD8+ T cells from young (n = 3, age = 8 weeks) and old C57BL/6J(n = 3, age = 88 weeks) WT mice were sorted (Influx), scRNA sequenced and analyzed by for gene expression (two technical replicates), V(D)J and cell surface markers (used for demultiplexing of sequences from unrelated experiment).

first: Darina

last: Paprckova

first: Veronika

last: Niederlova

first: Ales

last: Neuwirth

first: Ondrej

last: Stepanek


title: A microbiome-produced metabolite drives immunostimulatory macrophages and boosts response to immune checkpoint inhibitors in pancreatic cancer [scRNA-seq]

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The composition of the gut microbiome controls innate and adaptive immunity and has emerged as a key regulator of tumor growth and the success of immune checkpoint blockade (ICB) therapy. However, the underlying mechanisms remain unclear. Pancreatic ductal adenocarcinoma (PDAC) tends to be refractory to therapy, including ICB. We found that the gut microbe-derived metabolite trimethylamine N-oxide (TMAO) enhances anti-tumor immunity to PDAC. Delivery of TMAO given intraperitoneally or via dietary choline supplement to PDAC-bearing mice reduces tumor growth and is associated with an immunostimulatory tumor-associated macrophage (TAM) phenotype and activated effector T cell response in the tumor microenvironment. Mechanistically, TMAO signals through potentiating type-I interferon (IFN) pathway and confers anti-tumor effects in a type-I IFN dependent manner. Notably, delivering TMAO-primed macrophages alone produced similar anti-tumor effects. Combining TMAO with ICB (anti-PD1 and/or anti-Tim3) significantly reduced tumor burden and improved survival beyond TMAO or ICB alone. Finally, the levels of trimethylamine (TMA)-producing bacteria and of CutC gene expression associate with improved survivorship and response to anti-PD1 in cancer patients. Together, our study identifies the gut microbial metabolite TMAO as an important driver of anti-tumor immunity and lays the groundwork for new therapeutic strategies.

overall_design: Single cell RNA-seq of CD45+ mouse cells under control or TMAO treatment

first: Rahul

last: Shinde

first: Gauri

last: Mirji


title: A microbiome-produced metabolite drives immunostimulatory macrophages and boosts response to immune checkpoint inhibitors in pancreatic cancer [RNA-seq]

overall_design: RNA-seq of bone marrow derived macrophages (BMDM) and tumor-associated macrophages (TAM) under different treatments


title: A microbiome-produced metabolite drives immunostimulatory macrophages and boosts response to immune checkpoint inhibitors in pancreatic cancer

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

overall_design: Refer to individual Series