title: A BRCA1 coiled-coil domain variant disrupting PALB2 interaction predisposes to mammary tumors with a targetable defect in homologous recombination repair [RNA-seq]

first: Roebi

last: Bruijn

first: Emilia

last: Pulver

first: Chirantani

last: Mukherjee

first: Gerarda

last: van de Kamp

first: Stefan

last: Roobol

first: Magdalena

last: Rother

first: Hanneke

last: van der Gulden

last: de Bruijn

first: Maria

last: Lattanzio

middle: P

middle: C


title: CYFIP1 dosages exhibit divergent behavioral impact via diametric regulation of NMDAR complex translation in mouse models of psychiatric disorders

status: Public on Feb 02 2022

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

country: Germany

institute: Ludwig Maximilian University of Munich

type: Expression profiling by high throughput sequencing

summary: Gene dosage imbalance caused by copy number variations (CNVs) are prominent contributors to brain disorders. 15q11.2 CNV duplications and deletions have been associated with autism spectrum disorder (ASD) and schizophrenia (SCZ), respectively. The mechanism underlying these diametric contributions remain unclear. Here we established both loss-of-function and gain-of-function mouse models of Cyfip1, one of four genes within 15q11.2 CNVs and these mice exhibited both distinct and shared behavioral abnormalities related to ASD and SCZ. RIP-seq analysis identified mRNA targets of CYFIP1 in vivo, including postsynaptic NMDAR complex components. These mouse models showed diametric changes in levels of postsynaptic NMDAR complex components at synapses due to dysregulated protein translation, resulting in bidirectional alteration of NMDAR-mediated signaling. Importantly, pharmacological balancing of NMDAR signaling in mouse models with diametric CYFIP1 dosages rescues behavioral abnormalities. Our integrated analyses provide insight into how gene dosage imbalance caused by CNVs may contribute to divergent neuropsychiatric disorders.

overall_design: Examination of Cyfip1 mRNA binding targets in mouse hippocampus by RNA immunoprecipitation sequencing (RIP-seq).

first: Nam-shik

last: Kim

middle: R

last: Ringeling

first: Ki-jun

last: Yoon

first: Guo-li

last: Ming

first: Hongjun

last: Song


title: Critical role of FGF, RA, and WNT signaling for otic lineage specification from human PSCs in a 2D/3D-combined differentiation system

status: Public on Feb 01 2022

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

summary: The otic placode, from which the inner ear develops, initially forms as a thickened ectodermal patch adjacent to the dorsolateral hindbrain. Induction of otic placodal cells from human pluripotent stem cells (hPSCs) provides a robust approach to investigation of otic development. However, attempts to recapitulate otic lineage specification from hPSCs by stepwise differentiation methods have had limited success. One possible reason is that the role of signaling pathways in otic cell differentiation is not fully understood. Here, we developed a novel differentiation system involving use of suspension culture (3D floating culture) in combination with signaling factors for generating otic placodal cells via stepwise differentiation of hPSCs. We demonstrate that hPSC-derived pre-placodal cells acquired the potential to differentiate into posterior placodal cells after fibroblast growth factor 2 (FGF2) and retinoic acid (RA) treatment. Subsequent activation of WNT signaling following posterior placode specification induced differentiation of SIX1+/PAX8+/SOX2+ otic placodal cells. qPCR analysis showed that WNT activation increased expression of otocyst markers, including PAX8, PAX2, DLX5 and FBXO2. Moreover, induced otic cells exhibited similar gene expression patterns to the ventral and medial portions of the otocyst that give rise to the sensory epithelium of the inner ear. Collectively, our results indicate a critical role for FGF2, RA, and WNT signaling for the in vitro differentiation of the otic cell lineage from hPSCs. Our new culture system paves the way for improved modeling of early human inner ear development and will be of value to studies on the further differentiation of sensory epithelial cells.

overall_design: RNA seq of human placodal cells

first: Tsubasa

last: Saeki

first: Hideyuki

last: Okano


title: Partial resistance to HDAC inhibitors in FAPs of dystrophic muscles at late stages of disease is associated to epigenetic and transcriptional features of cellular senescence

city: La Jolla

first: Pier Lorenzo

last: Puri

state: CA

address: 10901 N Torrey Pines Rd

country: USA

institute: Sanford Burnham Prebys

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chromatin accessibility profiling by ATAC-seq

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

summary: An updated protocol for ATAC-seq, including wet-lab library preparation and guidelines about sequencing and data analysis.

overall_design:
ATAC-seq was performed on the cell lines at a variety of different input cell numbers,to test the scaling of Tn5 on data quality.
Please note that processed data was not generated for the samples used to quality control concentrations of Tn5; the final TSS scores and library metrics will given in tables in the manuscript.

first: Hailey

last: Modi

first: Lucas

last: Kampman

first: Ryan

middle: M

last: Corces


title: PAX7::GFP hESC-derived myogenic progenitor(MPC) cell gene expression profile change after primary transplantation into murine muscle

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

summary: To understand the mechanism of why in vivo PAX7::GFP+ cells having better engraftment capability

overall_design: RNA sequencing experiment was performed with the in vivo PAX7::GFP+ cells that were isolated from primary recipient mice and cultured in vitro for 4 days (right before 2nd transplantation) in comparison to PAX7::GFP MPC maintained in vitro (before 1st transplantation)

first: Gabsang

last: Lee

first: Congshan

last: Sun


title: Metabolic Regulations by ceRNA under Grass-fed and Grain-fed regimens in Angus Beef Cattle [miRNA-Seq]

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

country: China

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: To clarify the mechnism that  grass-fed and grain-fed regimens inducing the different characteristics of Wyu Angus cattle, we used high-throughput sequencing and metabolomics analysis to explore differentially expressed genes , differentially expressed miRNAs and lnRNAs,  meanwhile constructed importantly regulatory networks.

overall_design: Liver samples of steers with grass-fed and grain-fed from Wye Angus farm were  collected, sequenced and analyzed with each group 3 individuals when they reached market weight (about 14 months old for steers with grain-fed and 21 months old for steers with grass-fed).

first: Jiuzhou

last: Song'lab


title: Dual Chromatin Repressors Regulate Hippocampal Development

first: Kai-Chun

last: Chang

department: Bioengineering

institute: University of California, San Francisco

summary: The cell fate transition from radial glial-like (RGL) cells to neurons and astrocytes is crucial for development and pathological conditions. Two chromatin repressors- the enhancer of zeste homolog 2 and suppressor of variegation 4-20 homolog, are highly associated with RGL cells in the hippocampus, implicating hippocampal cell fate commitment underlying these epigenetic regulations. Using a double knock-out mouse model, we demonstrated that loss of both chromatin repressors in the RGL population leads to deficits in hippocampal development. At the molecular level, single nuclei RNA-Seq revealed differential gene expression and provided mechanistic insight that dual chromatin repressors are critical for the maintenance of cycling cells in the dentate gyrus as well as the balance of cell trajectories between neuronal and astroglial lineages.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Linked flow cytometry and single-nuclei RNAseq datasets from wild-type and double knock-out of Ezh2 and Suv4-20h mice brains

first: Christopher

middle: T

last: Rhodes

first: Adam

last: Abate

first: Chin-Hsing

middle: A

last: Lin


title: Partial resistance to HDAC inhibitors in FAPs of dystrophic muscles at late stages of disease is associated to epigenetic and transcriptional features of cellular senescence [RNA-seq]

summary: Pharmacological treatment of Duchenne Muscular Dystrophy (DMD) with histone deacetylase inhibitors (HDACi) is currently being tested in clinical trials. Pre-clinical studies performed in mdx mice - the mouse model of DMD - have shown that HDACi promote compensatory muscle regeneration, while inhibiting fibro-adipogenic degeneration, by targeting fibro-adipogenic progenitors (FAPs); however, these beneficial effects are restricted to early stages of disease progression. We show here that FAPs from late stage mdx mice exhibit epigenetic and transcriptional features of senescence that could not be fully reversed by HDACi. In particular, genome-wide increase in H3K9/14 acetylation at gene promoters of Senescence Associated Secretory Phenotype (SASP) genes was associated with their upregulation in late stage mdx FAPs. Treatment with the HDACi Trichostatin A (TSA) could inhibit SASP gene activation in FAPs, by decreasing H3K9/14 acetylation. Conversely, combinatorial decrease of H3K27 and/or H3K9/14 acetylation at promoters of genes required for cycle activation and progression was associated with their downregulation in FAPs from late stage mdx mice. However, these epigenetic and transcriptional alterations could not be reversed by TSA, due to a general resistance exhibited by FAPs from late stage mdx mice to HDACi-induced H3K9/14 hyperacetylation. Overall, this data reveal that disease-associated features of senescence develop in FAPs of DMD muscle through epigenetically distinct and pharmacologically dissociable events, and suggests that HDACi might at least retain anti- fibrotic and inflammatory activity at late stages of DMD, by repressing FAP-derived SASP.

overall_design: Integrative analysis of 2 different histone modifications (H3K9/14ac and H3K27ac ChIP-seq) and expression profiling (RNAseq) in FAPs derived from mdx mice at early and late stages of disease progression in response to TSA treatment. Comparative analysis of FAP transcriptome to other muscle-derived cells (MUSCs and Macrophages) to evaluate cell-specific features.

first: S

last: Consalvi

first: L

last: Tucciarone

first: E

last: Macrì

first: M

last: De Bardi

last: Picozza

first: I

last: Salvatori

first: A

last: Renzini

last: Valente

last: Mai

first: V

last: Moresi

first: P

middle: L


title: Oocyte developmental competence is instructed by H3.3 chaperone Hira complex

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Reproductive success begins with a healthy egg (a competent oocyte). An oocyte acquires its developmental competence during oogenesis in preparation for accomplishing the critical developmental transition from completion of meiosis to initiation of early embryogenesis. Here we comprehensively characterised the maternal role of major subunits of Hira (i.e. Hira, Cabin1 and Zscan4) during oocyte-to-embryo transition.

overall_design: GV oocytes from Hira or Cabin1 Het and KO mice, 2 cell embryos from Cabin 1 Het and KO mice, 2 cell embryos with Zscan4 overexpression were pooled for RNA sequencing analysis. GV oocytes from Cabin1 Het and KO mice (C57BL/6) were pooled for ATAC sequencing analysis.

first: Lance


title: Transcriptome profiling of H3K27me3 demethylase deficient B cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To assess how H3K27me3 demethylases, UTX and JMJD3, regulate B cell and plasma cell trasncriptomes. RNA-seq was performed on the following populations from control (CreCtrl) and double knockout (dKO) mice: 1) naïve marginal zone B (MZB) cells and follicular B (FOB) cells from control (CreCtrl) and double knockout (dKO) mice, 2) PC generated after three days of ex vivo culture of MZB or FOB cells, 3) PC generated at three days post in vivo stimulation with LPS

overall_design: RNAseq on margnizal zone B cells, follicular B cells and plamsa cells, from CreCtrl and UTX- and JMJD3-deficient dKO mice

first: C

middle: D

first: J

last: Boss


title: The effect on p53-induced gene transactivation by ARVCF knockdown.

city: Sapporo

first: Masashi

last: Idogawa

institute: Sapporo Medical University

summary: To explore the effect of ARVCF on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in ARVCF knockdown or control U2OS cells.

overall_design: Osteosarcoma U2OS cells stably expressing shRNA-ARVCF or negative control shRNA were treated with nutlin-3a which activates endogenous p53. The change of p53-induced gene transactivation was analyzed.


title: Redistribution of EC-SOD due to the R213G SNP reveals differential RNA-seq profile of recruited alveolar macrophages and accelerated apoptosis in response to bleomycin

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: A known human SNP in the matrix-binding domain of extracellular superoxide dismutase (EC-SOD), with an arginine to glycine substitution at position 213 (R213G), redistributes EC-SOD from the matrix into extracellular fluids. We reported that, following bleomycin (bleo), knock-in mice harboring the human R213G SNP (R213G mice), compared to wild-type (WT) littermates exhibit enhanced resolution of inflammation and protection against fibrosis. We tested the hypothesis that the EC-SOD R213G SNP promotes resolution via accelerated apoptosis of recruited alveolar macrophage (recAM).

overall_design: RNA-seq of alveolar macrophages  populations in response to bleomycin

first: Ayed

last: Allawzi

first: Jay

last: Hesselberth

first: Eva

last: Nozik-Grayck


title: Single-cell RNAseq analysis of kidney glomerular injury in IgA nephropathy

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: We applied scRNAseq analysis to investigate the mouse kidney glomerular injury in IgA nephropathy

overall_design: Mouse kidney glomerular single cells from control and IgAN samples were sorted into 384-well-plates and RNA-sequenced using the SmartSeq2 method

first: Sonia

last: Zambrano

first: Jaakko

last: Patrakka


title: SPARCLE, a p53-induced lncRNA, controls apoptosis after genotoxic stress by promoting PARP-1 cleavage

city: Cuernavaca

first: Karla

middle: F

last: Meza-Sosa

state: Morelos

address: Av. Universidad

department: Institute for Biotechnology

country: Mexico

institute: UNAM

summary: p53, master transcriptional regulator of the genotoxic stress response, controls cell cycle arrest and apoptosis following DNA damage. Here we identify a p53-induced lncRNA SPARCLE (Suicidal PARP-1 Cleavage Enhancer) adjacent to miR-34b/c required for p53-mediated apoptosis. SPARCLE is a ~770 nucleotide, nuclear lncRNA induced one day after DNA damage. Despite low expression (<15 copies/cell), SPARCLE deletion increases DNA repair and reduces DNA damage-induced apoptosis as much as p53 deficiency, while its over-expression restores apoptosis in p53-deficient cells. SPARCLE does not alter gene expression. SPARCLE causes apoptosis by acting as a caspase-3 cofactor for PARP-1 cleavage, which separates its N-terminal (NT) DNA binding domain from PARP-1 catalytic domains. NT-PARP-1 binds to DNA breaks but, lacking its PARylation domains, does not initiate DNA repair. In fact, expressing NT-PARP-1 in SPARCLE-deficient cells increases unrepaired DNA damage and restores apoptosis after DNA damage. Thus, as a PARP-1 cleavage cofactor, SPARCLE enhances p53-induced apoptosis.

overall_design: Strand-specific RNA-seq of HCT116 cells treated with doxorubicin (1 uM) or control media for 48h. Cells are WT, KO or Over-express SPARCLE. Two biological replicates per condition are sequenced

first: Judy

last: Lieberman


title: Small RNA profiling of WT E14, Dgcr8_KO, Drosha_KO, Dicer_KO and Ago1&2_Double_KO mouse embryonic stem cells

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

summary: Purpose: The goals of this study was to obtain the profile of miRNAs and endogeneous siRNAs of RNAi mutant mESCs

overall_design: small RNA profiling of different RNAi mutant mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Transcriptome of WT, Dgcr8_KO, Drosha_KO, and Ago1&2_double KO mouse embryonic stem cells cultured in 2i

summary: Purpose: The goals of this study was to assess the impact of different RNAi-mutant proteins on mESC transcriptome in 2i condition.

overall_design: mRNA profiles of different RNAi-mutant mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Transcriptome of AGO1&2 double KO mouse embryonic stem cells

summary: Purpose: The goals of this study was to obtain the trasncriptome of WT mESCs to compare it with the transcriptome of all RNAi mutant mESCs (deposit separately).

overall_design: mRNA profiles of AGO1&2 double KO mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Lactate rewires lipid metabolism and sustains a metabolic-epigenetic interplay in prostate cancer

status: Public on Jan 31 2022

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

institute: IOR

summary: Lactate is abundant in the tumor environment as the secreted product of fermentative cells. In prostate cancer (PCa), cancer-associated fibroblasts are the major contributors and this secreted lactate is uptaken by cancer cells to sustain their mitochondrial metabolism. However, how lactate controls the metabolic and transcriptional regulation in tumors is far to be elucidated. Here, we identify an innovative lactate-driven mechanism able to increase the expression of genes involved in lipid metabolism in PCa cells. This regulation enhances intracellular lipid accumulation in lipid droplets (LDs) and provides acetyl moieties for histone acetylation, establishing a regulatory loop between metabolites and epigenetic control. Interestingly, inhibition of this loop by targeting bromodomains histone acetylation readers suppresses the expression of perilipin-2 (PLIN2), a crucial component of LDs, disrupting the lactate-dependent lipid metabolic rewiring. Since this metabolic-epigenetic regulatory loop sustains PCa metastatic potential, its targeting is of clinical relevance as demonstrated by the inhibition of PCa invasive potential in vivo. Overall, our findings show that lactate has both a metabolic and an epigenetic role in promoting PCa progression.

overall_design: RNA-seq analysis of 16 samples: 4 DU145 control cells; 4 DU145 treated with Lactate; 4 DU145 treated with I-BET762; 4 DU145 trated with Lactate and I-BET762

first: Luigi

last: Ippplito

first: Paola

last: Chiarugi

first: Carlo

middle: V

last: Catapano


title: IL-9 is required for multi-cytokine producing tissue-resident memory CD4+ T cell-dependent allergic airway recall responses

city: Indianapolis

first: Rakshin

last: Kharwadkar

state: Indiana

address: 635 Branhill Dr., 418 MS building

institute: Indiana University School of Medicine

summary: Asthma is a chronic inflammatory lung disease with intermittent flares predominately mediated through memory T cells.  Yet, the identity of long-term memory cells that mediate allergic recall responses are not well defined. In this report, using a mouse model of chronic allergen exposure followed by an allergen-free rest period, we have characterized a sub-population of Th2 cells that secretes IL-9 as an obligate effector cytokine. IL-9-secreting cells have a resident memory T cell phenotype and blocking IL-9 during a recall challenge significantly diminishes airway inflammation and airway hyperreactivity. T cells secrete IL-9 in response to allergen recall and secretion is amplified by IL-33. Using scRNA-seq and scATAC-seq, we define the cellular identity of a distinct populations of T cells with pro-allergic cytokine patterns. Thus, in a recall model of allergic airway inflammation, IL-9 secretion from a multi-cytokine producing cell population is required for an allergen recall response.

overall_design: 1. To compare transcriptional profile of ST2+CD4 T cells and ST2- CD4 T cells in the lung, ST2+ and ST2- CD4 T cells were isolated from the lung in a recall model and pooled together to generate replicates of ST2+ CD4 T cells and ST2- CD4 T cells, with a total of 4 samples for scRNA-seq and snATAC-seq analysis. 2. To examine to the function of IL-9 in allergic recall response, single suspension of total viable cells from the lung were generated from the mice that were treated with anti-IL-9 or isotype (100 μg/ml) during the recall challenge. For this experiment three replicates of total lung cells after anti-IL-9 or isotype treatment were used for scRNA-seq analysis.

first: Mark

middle: H

last: Kaplan

first: Benjamin

middle: J

last: Ulrich

first: Hongyu

last: Gao


title: Single-cell RNA analyses of cattle PBMC

city: Beltsville

first: Yahui

state: Maryland

address: 10300 Baltimore Ave Bldg 306

institute: ARS, USDA

summary: Comprehensive analyses of tissues at the single-cell level will benefit our understanding of genetic bases for complex traits. We performed single-cell RNA sequencing (scRNA-seq) analyses of peripheral blood mononuclear cells (PBMCs) from Holstein cattle, investigating their cell types and responses to lipopolysaccharide (LPS) treatment in vitro. The responses to LPS treatment include innate immunity activation of monocytes, macrophages, and dendritic cells, as well as B cell proliferation. The innate immunity responses are featured with CCL2 and CXCL2 proinflammatory cytokines. We detected trait-relevant cell types and found that DEGs induced by LPS were significantly associated with many complex traits of economic value in Holstein.

overall_design: Four samples from cattle PBMC

first: Jianbin

last: Li

first: Gaozhan

last: Cai

first: Yujiao

last: Wang

first: Wenjing

last: Yang

first: Yanqin

first: Xinxin

last: Zhao

first: Rongling

first: Yundong

first: Ransom

last: Baldwin VI

first: Congjun

first: Lingzhao

last: Fang

first: George

middle: E

last: Liu


title: Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model

city: Melbourne

first: Stephanie

middle: Louise

last: Neville

state: Victoria

address: 792 Elizabeth Street

country: Australia

institute: University of Melbourne

summary: This study reports on the co-administration of a zinc ionophore (PBT-2) and ampicillin to break antibiotic resistance of Streptococcus pneumoniae in a murine pneumonia model. The molecular mechanism for this heightened antimicrobial activity was identified through transcriptomic and metabolomic analyses of a wild type strain and a zinc efflux mutant to identify cellular targets of zinc intoxication. This revealed that zinc intoxication induces numerous cellular disruptions, which when combined with frontline antibiotics, can break antibiotic resistance and potentially preclude further resistance from emerging.

overall_design: Purified RNA from four biological replicates of untreated S. pneumoniae D39, D39 treated with 100 µM zinc and D39 ∆czcD treated with 100 µM zinc were pooled for RNA sequencing. Data were used to compare gene expression in the untreated cells to the WT treated cells and the ∆czcD treated cells.

first: Christopher

last: McDevitt


title: Human glioma stem cell GS5: Control vs. ZNF117 knockout

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

summary:
Glioblastoma (GBM) is a deadly disease without effective treatment. Because glioblastoma stem cells (GSCs) contribute to tumor resistance and recurrence, improved treatment of GBM can be achieved by eliminating GSCs through inducing their differentiation. Prior efforts have been focused on studying GSC differentiation towards the astroglial lineage.
We used microarrays to detail the global programme of gene expression underlying ZNF117 knockout and identified distinct classes of up-regulated genes during this process.

overall_design: Two-condition experiment, Control vs.ZNF117 knockout. Biological replicates: 4 control, 3 transfected, independently grown and harvested. One replicate per array.

last: Zhou

first: Xingchun


title: Omics analyses of mouse constitutive androstane receptor (CAR) ligand TCPOBOP effects in humanized mice reveal off-target lipid metabolism disruption

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: In this study, we compared the metabolic effects of TCPOBOP using lipidomic, transcriptomic, and proteomic analyzes in wild-type and humanized CAR-PXR-CYP3A4/3A7 mice. In the humanized mouse model, human CAR retains its constitutive activity in metabolism regulation; however, it is not significantly activated by TCPOBOB. TCPOBOP elevated serum and liver levels of triglycerides and promoted hepatocyte hypertrophy in humanized CAR mice. Hepatic lipidomic analysis revealed a significant accumulation of triglycerides and downregulation of its metabolites in humanized CAR mice. RNA-seq analysis has shown gene expression changes mainly involved in lipid metabolic processes and in ppar, leptine, thyroid, and circadian clock pathways. In summary, we identify TCPOBOP as a lipid metabolism disruptor in humanized CAR mice

overall_design: RNA-seq was performed on C57BL/6 Ntac and humanized PXR-CAR-CYP3A4/3A7 mice liver harvested after 48 hours of TCPOBOP treatment (2 afministrations after 24 hour, 3mg/kg, n=4).

first: Josef

last: Skoda

first: Klara

last: Dohnalova

first: Karel

last: Chalupsky

first: Markus

last: Templin

first: Jana

last: Maixnerova

first: Stanislav

last: Micuda

first: Albert

last: Braeuning

first: Petr

last: Pavek


title: The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays

city: Columbus

first: Jeffrey

last: Parvin

state: Ohio

address: 250 Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University

summary: In this study, we used multiplexed  DNA repair assays of variants in the BRCA1 carboxy-terminus to functionally  characterize 2271 variants for homology-directed repair function (HDR) and 1427  variants for cisplatin resistance (CR). We found a high level of consistent results in the  two multiplexed functional assays with non-functional variants located within regions of  the BRCA1 protein necessary for its tumor suppression activity.

overall_design:
In this study, we have analyzed the BRCA1 carboxy-terminus for the functional impact of single missense substitutions using two multiplexed assays: homology directed repair of DNA double stranded breaks and resistance to cisplatin.
HDR is for homology-directed repair, CR is for the cisplatin treatment, and GL2 is for the control siRNA condition used.

first: Aleksandra

middle: I

last: Adamovich

first: Mariame

last: Diabate

first: Tapahsama

last: Banerjee

first: Gregory

last: Nagy

first: Nahum

last: Smith

first: Kathryn

last: Duncan

first: Erika

last: Mendoza

first: Gisselle

last: Prida

first: Michael

last: Freitas

first: Lea

last: Starita


title: Replicative history marks transcriptional and functional disparity in the memory T cell pool II

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

summary: To validate whether division history is linked to functional and transcriptional properties we established a CTV-based serial-transfer approach that allowes single cell transcriptional profiling of memory T cells that have undergone a high or low amount of prior division

overall_design: Naïve OT-I and GFP;OT-I T cells were transferred into primary recipients that were subsequently exposed to Lm-OVA infection. At day 30 post-infection, early memory T cells were harvested, CTV labeled and transferred into infection-matched secondary recipients. 75 days later, CTVHI (div0-2) and CTVLO (div5+) TCM were isolated from the GFP+ and GFP- pools, and the resulting TCM populations were then profiled by scRNAseq.

first: Lianne

last: Kok

first: Ton

last: Schumacher


title: Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex: RNA-Seq Data

city: Oklahoma City

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Sex differences in the brain as they relate to health and disease are often overlooked in experimental models. Many neurological disorders, like Alzheimer’s disease (AD), multiple sclerosis (MS), and autism, differ in prevalence between males and females. Sex differences originate either from differential gene expression on sex chromosomes or from hormonal differences, either directly or indirectly. To disentangle the relative contributions of genetic sex (XX v. XY) and gonadal sex (ovaries v. testes) to the regulation of hippocampal sex effects, we use the “sex-reversal” Four Core Genotype (FCG) mouse model which uncouples sex chromosome complement from gonadal sex. Transcriptomic and epigenomic analyses of hippocampal RNA and DNA from ∼12 month old FCG mice, reveals differential regulatory effects of sex chromosome content and gonadal sex on X- versus autosome-encoded gene expression and DNA modification patterns. Gene expression and DNA methylation patterns on the X chromosome were driven primarily by sex chromosome content, not gonadal sex. The majority of DNA methylation changes involved hypermethylation in the XX genotypes (as compared to XY) in the CpG context, with the largest differences in CpG islands, promoters, and CTCF binding sites. Autosomal gene expression and DNA modifications demonstrated regulation by sex chromosome complement and gonadal sex. These data demonstrate the importance of sex chromosomes themselves, independent of hormonal status, in regulating hippocampal sex effects. Future studies will need to further interrogate specific CNS cell types, identify the mechanisms by which sex chromosome regulate autosomes, and differentiate organizational from activational hormonal effects.

overall_design: RNA isolated from snap-frozen Four Core Genotype mouse hippocampus (n=5-6/group) using Qiagen AllPrep Mini Kit. Illumina’s TruSeq Stranded mRNA Library Prep Kit (#20020594, Illumina) was used on 500 ng of total RNA for the preparation of strand-specific sequencing libraries according to manufacturer’s guidelines. As previously described44, rRNA depletion was performed prior to library construction. Libraries were then normalized to 4 nM, pooled, denatured, and diluted for sequencing on Illumina Hiseq2500 in a 2x100 bp fashion.

first: Sarah

last: Ocanas

first: Victor

last: Ansere

first: Kyla

middle: B

last: Tooley

first: Niran

last: Hadad

first: Ana

last: Chucair-Elliott

first: David

last: Stanford

first: Shannon

last: Rice

first: Benjamin

last: Wronowski

first: Jessica

last: Hoffman

first: Steven

middle: N

last: Austad

first: Willard

last: Freeman


title: Small RNA-seq datasets of OsRDR4 transgenic plants

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

summary: In order to functionally characterize OsRDR4, a member of γ-clade RNA dependent RNA polymerase (RDR) in rice, transgenics were raised for the overexpression (OE) and knock-down (KD) of OsRDR4 in the background of Oryza sativa indica cultivar, Pusa Basmati 1. The knockdown lines showed developmental defects in terms of delayed flowering, short tillers, poor seed setting, etc.

overall_design: We have performed small RNA-seq analysis using Young panicle (5cm to 10cm) from wild type (WT), over-expression (OE) and knock-down (KD) transgenic lines. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

last: Shivaprasad

first: Chenna

last: Swetha

first: T

last: Sujith


title: Tig1 regulates proximo-distal identity during salamander limb regeneration

status: Public on Jan 30 2022

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

institute: TUD

summary: Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed ‘positional identity’. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/RARRES1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting HoxA13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.

overall_design: Transcriptomic changes elicited by Tig1-transfected vs. Non-transfected axolotl distal forelimb blastema cells (Hoxa13+).

first: Catarina

middle: R

last: Oliveira

first: Dunja

last: Knapp

first: Tobias

last: Gerber

first: Ahmed

last: Elewa

first: Sandra

middle: G

last: Gonzalez-Malagon

first: Phillip

last: Gates

first: Hannah

last: Walters

first: Andreas

last: Petzold

first: Hernan

last: Arce

first: Rodrigo

middle: C

last: Cordoba

first: Elaiyaraja

last: Subramanian

first: Osvaldo

last: Chara

first: Elly

last: Tanaka

first: Andras

last: Simon


title: Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex: Whole Genome OXBS-Seq Data

first: Michael

last: Stout

type: Methylation profiling by high throughput sequencing

overall_design: DNA isolated from snap-frozen Four Core Genotype mouse hippocampus (n=3/group) using Qiagen AllPrep Mini Kit. Whole genome oxidative bisulfite (WGoxBS) sequencing libraries were made from 1 ug of DNA and sequenced on NovaSeq6000.

first: Sarah

last: Ocanas

first: Victor

last: Ansere

first: Kyla

last: Tooley

first: Niran

last: Hadad

first: Ana

last: Chucair-Elliott

first: David

last: Stanford

first: Shannon

last: Rice

first: Benjamin

last: Wronowski

first: Jessica

middle: M

last: Hoffman

first: Steven

last: Austad

first: Willard

last: Freeman


title: RNA-seq data from human Caco-2 cells co-incubated with Giardia intestinalis WB cyst cells

first: Feifei

last: Xu

address: Husargatan 3

summary: In this study we compare at the transcriptomic level, how human gene expresion changes over time when Caco-2 cells co-incubated with Giardia cysts.

overall_design: Giardia trophozoites were grown in TYI-S33 until 80% confluency after that encystation was induced following the Uppsala encystation protocol reported by Einarsson et al. 2016. 2. Giardia cells were left to complete encystation for 32 hours and then collected and wash 3X in cold PBS and resuspended in sterile dH20 and left there for 3 days, on the third day cyst were collected and resuspended in DMEM (HI-FBS) and incubated with previously grown and differenatiated Caco2 cells for 1.5, 3 and 4.5 h. Prior interaction Caco-2 cells were collected.

first: Laura

last: Rojas


title: RNA-seq data from Giardia intestinalis WB trohozoites 7h into encysting Giardia cells infecting human Caco-2 cells

sample_organism:
Giardia duodenalis
Homo sapiens

platform_organism:
Giardia duodenalis
Homo sapiens

overall_design: In this study we compare at the transcriptomic level, how giardia and human gene expresion changes over time when encysting Giardia cells infect human Caco-2 cells.


title: RNA-seq time course analysis of potato WT and BRC1b-RNAi axillary buds in response to short-day conditions

city: Madrid

first: Rafael

last: Torres

state: Madrid

address: Darwin 3

department: Bioinformatics for Genomics and Proteomics (BioinfoGP)

country: Spain

institute: CNB

summary:
Purpose: observe the difference between potato (Solanum tuberosum ssp. andigena) WT and BRC1b RNAi axillary buds in response to the transition from long-day to short-day conditions. The time course includes four time points: Long days, after 2 days in short days, 1 week in short days and 2 weeks in short days.
Methods: stem were flash-frozen in N2(l) one hour after dawn and the axillary buds were dissected in the cold room. The four axillary buds bellow the third visible node counting from the apex (those most likely to produce tubers in RNAi line) were collected. RNA was extracted with FavorPrep™ Plant Total RNA Mini Kit from FAVORGEN. DNA was degraded in the column with RNase-free DNase I (Roche). Three biological replicates were used and each replicate is a pool of axillary buds from 4 plants.

overall_design: mRNA profiles of WT and BRC1b RNAi axillary buds in Long Days (LS), 2days in Short Days (SD), 1 week in SD, 2 weeks in SD.

last: Nicolas

first: Pilar

last: Cubas

last: Torres-Perez


title: RNA-seq of gastrocnemius (GA) muscle tissue from mice treated with extracellular vesicles (EV) from MCF-10A or MDA-MB-231 cells

city: La Jolla

first: Shizhen

last: Wang

address: 9500 Gilman Dr

institute: UCSD

summary: To compare gene expression changes in skeletal muscle caused by EVs from normal (MCF-10A) and cancer (MDA-MB-231) cells, we analyzed RNA isolated from the GA muscle of EV-treated female NOD scid gamma (NSG) mice. Mice had received tail-vein injections of EVs twice a week for 5 weeks (~10 ug EV per injection). Gene expression in muscle from mice treated with MDA-MB-231-derived EVs was compared to mice treated with MCF-10A-derived EVs.

overall_design: RNA-seq was used for transcriptomic profiling of GA muscle following a total of 10 times of intravenous EV injections (MCF-10A EVs or MDA-MB-231 EVs) in NSG mice. RNA-seq and data processing were performed by Novogene Co., Ltd.

first: Wei

last: Yan


title: CRISPRa screen for drivers of COL7A1 expression in keratinocytes

city: Minneapolis

first: Jakub

last: Tolar

state: Minnesota

address: 2001 6th St SE

department: Pediatrics

institute: University of Minnesota - Twin Cities

summary:
Background: Dystrophic epidermolysis bullosa (DEB) is a skin blistering disease caused by mutations in COL7A1, which encodes type VII collagen (C7). There is no cure for DEB, but previous work has shown potential therapeutic benefit in increasing production of even partially functional C7. Genome-wide screens using CRISPR-Cas9 have enabled the identification of genes involved in cancer development, drug resistance, and other genetic diseases, suggesting that they could be used to identify novel drivers of C7 production.
Methods: A keratinocyte C7 reporter cell line was created by integrating a tdTomato fluorescent marker into the last exon of the endogenous COL7A1 gene. A genome-wide CRISPR activation (CRISPRa) screen was performed with the C7_tdTomato reporter to identify genes and pathways that increase C7 expression. High tdTomato-expressing cells were sorted and sequenced to identify the single guide RNAs (sgRNAs) that became enriched relative to the starting material. Pathway analysis was performed on the corresponding genes to identify regulators and pathways that influence C7 expression. A targeted drug screen was performed in three different keratinocyte cell lines based on the CRISPRa screen results, and C7 upregulation was evaluated.
Results: The C7_tdTomato cell line was validated as an effective reporter cell line for detection of C7 upregulation. The CRISPRa screen identified two genes, DENND4B and TYROBP as top hits based on enrichment in the high fluorescence population and representation with multiple sgRNAs. Pathway analysis of the CRISPRa screen showed enrichment of toll-like receptor and interferon-related upstream regulators and functions related to calcium uptake and immune signaling. Several compounds in the targeted drug screen increased C7 expression in at least one keratinocyte line, but only kaempferol, a plant flavonoid, significantly increased C7 mRNA and protein in a DEB patient line.
Conclusions: The novel C7_tdTomato reporter cell line can be used to screen compounds for increased C7 expression. The CRISPRa screen combined with a fluorescent reporter cell line can be used to reveal mechanistic regulators of gene expression and therapeutic targets for rare genetic diseases. Kaempferol has shown promising results in increasing C7 production and should be further evaluated as a potential therapeutic for DEB patients.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: A CRISPRa screen was performed on N/TERT keratinocytes with tdTomato inserted into the COL7A1 locus. Relative abundance of each sgRNA was calculated based on the input material (plasmid DNA).

first: Michael

last: Pickett-Leonard

first: Elizabeth

last: Thompson

first: Frank

middle: W

last: Albert


title: Transcriptome of WT, Dicer_KO and Dicer-Complemented mouse embryonic stem cells

first: Constance

last: Ciaudo

summary: Purpose: The goals of this study was to assess the impact of different Dicer-mutant proteins on mESC transcriptome.

overall_design: mRNA profiles of different Dicer mutant mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Jumonji domain-containing protein-3 (JMJD3/Kdm6b) is critical for normal ovarian function and female fertility

status: Public on Jan 29 2022

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

summary: This study reports role of Jmjd3/kdm6b in female reproduction and provides a molecular insight of how Jmjd3/kdm6b regulates ovarian function and fertility in mice

overall_design: RNA-Seq of granulosa cell specific Jmjd3 knock out in female mice.

first: Sambit

last: Roy


title: Profiling immune network in regressing histiocytic dermatosis: a case report

city: Seoul

first: Kyung Bae

last: Chung

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University College of Medicine

summary: To understand the persistent inflammation even after 5 years of treatment of dapsone in Rosai-Dorfmann patient, we performed single cell RNA sequencing for persistent nodular lesions.

overall_design: We obtained 4-mm biopsies from nodular lesion and non-lesional skin. With dispase treatment, dermal tissue was only processed for single cell RNA sequencing. Compared single cell transcriptome between lesion and nonlesion.

first: Kyung

first: Ji-Hye

last: Hwang

first: Do-Young

last: Kim


title: Altered propionate metabolism contributes to tumor progression and aggressiveness

status: Public on Jan 28 2022

city: NEW YORK

first: John

last: Blenis

state: NY

address: 413 E 69TH ST FL 13

institute: Weill Cornell Medicine

summary: The alteration of metabolic pathways is a critical strategy for cancer cells to attain the traits necessary for metastasis in disease progression. We found that dysregulation of propionate metabolism occurs through TGFbeta- and ERK2-driven downregulation of methylmalonyl-CoA epimerase (MCEE). MCEE downregulation occurs through a transcription factor Sp1/EGR1 switch at its promoter region, resulting in reduced flux through this anapleurotic pathway and leading to accumulation of methylmalonic acid (MMA), a byproduct of the propionate metabolism. MMA accumulation through alteration of propionate metabolism produces a pro-aggressive signature in breast and lung cancer cells and increases their metastatic potential. Altogether, we present a previously uncharacterized dysregulation of propionate metabolism as a novel contributor to cancer and a valuable potential target in the therapeutic treatment of metastatic carcinomas.

overall_design: Global analysis of RNA levels to determine transcriptional reprogramming in A549 cells with shMUT expression for 3 days, in triplicate

first: Ana

middle: P

last: Gomes

first: Didem

last: Ilter


title: Combining cellular immunology with RNAseq to identify novel chlamydia T cell subset signatures

city: New Haven

first: HIROMITSU

last: ASASHIMA

state: CT

address: 114 Canner St, 3

institute: Yele School of Medicine

summary: Chlamydia trachomatis serovars A-L cause important diseases of the eyes and reproductive tract by infecting epithelium lining those organs. A major hurdle for vaccine trials is finding a surrogate biomarker for protective immunity.  Investigational data argues for T cell biomarker(s) reflecting mucosal adaption, cytokine polarization, B cell help, antibacterial effector mechanisms, or some combination thereof.  A human investigation and two mouse studies link IL-13 to protection from infection/immunopathology.  We performed RNAseq on T cells resident in spleens and genital tracts (gt) of naturally immune mice. CD4 signatures were consistent with helper function that differed by site including a gt specific Fgl2 signal.  The gt CD8 signature featured IL-10 and promotion of healing/scarring with a unique transcription of granzyme A.  The RNAseq data was used to refine previously published CD4γ13 and CD8γ13 transcriptomes derived from protective T cell clones, potentially identifying practicable T cell subset signatures for assessing chlamydia vaccine candidates.

overall_design: T cell profiles of spleen and genital tracts from mice after seconday infection of Chlamydia muridarum

first: Raymond

last: Johnson

first: Hiromitsu

last: Asashima

first: Subhasis

last: Mohanty

first: Albert

last: Shaw


title: Dataset of differentially expressed genes in mouse P12 testes in response to the loss of ATRX in Sertoli cells

city: Clayton

first: Vincent

last: Harley

state: VIC

address: 27-31 Wright Street

institute: Hudson Institute of Medical Research

summary: This dataset represents genes that are dysregulated in the postnatal day 12 (P12) mouse testis when ATRX is specifically inactivated in Sertoli cells (ScAtrxKO mice). The differentially expressed genes included in the dataset may play important roles in the testicular phenotypes observed in the ScAtrxKO mice, which were first reported in our previous work (Bagheri-Fam et al., 2011). In fetal ScAtrxKO mice, Sertoli cells undergo apoptosis due to cell cycle defects, resulting in smaller testes with reduced tubule volume. Adult ScAtrxKO mice show a wide range of spermatogenesis defects probably due to a failure of the dysfunctional ATRX protein to interact with the androgen receptor (AR). The chromatin remodeling protein ATRX is widely expressed in the human testis including Sertoli cells. In XY individuals, the loss of ATRX leads to ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome associated with a wide range of genital abnormalities such as hypospadias, ambiguous genitalia, and small testes with reduced tubule volume. Our dataset contributes towards understanding the mechanism underlying ATRX regulation of testis development and spermatogenesis.

overall_design: The Atrx gene was conditionally inactivated in the Sertoli cells by crossing Atrxflox/flox mice with AMH-Cre/+ mice. mRNA was extracted from testes at postnatal day 12 (P12) from wildtype or Atrx knockout (ScAtrxKO) male mice, prior to hybridizing to Illumina Sentrix MouseWG-6 v2.0 Expression BeadChip.

first: Stefan

last: Bagheri-Fam


title: Transcriptional response to loss of rab-11.1

city: Dallas

first: Peter

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: Loss of RAB-11.1 disrupts nuclear hormone receptor 49 association with endocytic vesicles and promotes its nuclear translocation and activation of the lipid surveillance response. Included in this dataset are the gene expression data in control and rab-11.1 RNAi conditions in C. elegans.

overall_design: mRNA profiling from whole worms treated with empty vector or rab-11.1 RNAi

first: Abigail

last: Watterson


title: Effects of TNF on 'starved' primary hepatocytes

status: Public on Jan 27 2022

city: Odense M

first: Anne

last: Loft

department: Biochemistry & Molecular Biology

summary: We generated transcriptional profiles of TNF-stimulated primary hepatocytes co-treated with PPARα and GR ligands to mimic a condition of starvation.

overall_design: Primary hepatocytes were cotreated with corticosterone (GR ligand), WY-14643 (PPARα ligand), and TNF for 8 hours to assess the effect of TNF on 'starved' hepatocytes.

first: Søren

last: Schmidt

first: Stephan

last: Herzig


title: Cell Type-Specific Transcriptional Profiling of the Hepatic Fasting Response

summary: We generated time-resolved profiles of fasting-induced changes in the gene landscapes of hepatocytes and liver macrophages using the INTACT methodology

overall_design: We subjected female HEP-INTACT and MAC-INTACT mice to a fast starting at the onset of the mouse active phase, ZT12, and after 3, 8, 16, and 24h livers were collected for INTACT followed by RNA-seq analyses. Ad libitum fed controls were sacrificed at each time point to account for diurnal variations in gene expression.

last: Fisker Schmidt

first: Thomas

last: Schwarzmayr


title: RNA-seq analysis of Ralstonia solanacearum nitrosative stress response mutants

status: Public on Jan 26 2022

city: Madison

first: Alicia

last: Truchon

state: WI

address: 1630 Linden Drive

department: Plant Pathology

institute: University of Wisconsin - Madison

summary: Ralstonia solanacerum causes bacterial wilt disease on many important host crops, including tomato and potato. R. solanacearum cells enter a host from soil or infested water through the roots, then multiply and spread in the water-transporting xylem vessels. Despite the low nutrient and oxygen content of xylem sap, R. solanacearum grows extremely well inside the host, using denitrification to respire in this hypoxic environment. R. solanacearum growth in planta also depends successful mitigation of oxidative stress produced by both the bacterium and the host. We found that proteins encoded by norA and hmpX that are predicted to interact with nitric oxide (NO) and protect against cellular damage caused by NO. Reducing NO toxicity is especially important for Rs that generates NO via denitrifying respiration in planta, and encounters NO produced by plants as a defense and signaling molecule. By analyzing transcriptomes of mutants lacking these genes, we found that iron, sulfur, and nitrogen metabolism genes were consistently upregulated in mutants missing these genes. Our transcriptomic analysis suggests R. solanacearum mutants lacking norA and hmpX suffer oxidative stress from an increase in cellular toxicity caused by NO that leads to damage of iron, sulfur, and nitrogen metabolic proteins. Our results suggest that NorA and HmpX, contribute to oxidative stress mitigation in denitrifying cultures.

overall_design: We analyze gene expression of WT R. solanacearum strain GMI1000 and three GMI1000 mutant strains lacking genes involved in the nitrosative stress response. ∆norA and ∆hmpX missing NO binding protein, in denitrification promoting low-oxygen conditions to induce nitrosative stress in culture.  Each treatment or mutant included three biological replicates from separate overnight R. solanacearum cultures.

first: Connor

last: Hendrich

first: Beth

middle: L

last: Dalsing

first: Caitilyn

last: Allen


title: A Macrophage-Hepatocyte Glucocorticoid Receptor Axis Coordinates Fasting Ketogenesis

address: Campusvej 55

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

overall_design: Refer to individual Series


title: AXL targeting restores PD-1 blockade sensitivity of STK11/LKB1 mutant NSCLC through expansion of TCF1+ CD8 T cells

status: Public on Jan 24 2022

first: Huiyu

last: Li

institute: UT Southwestern Medical Center

summary: Mutations in STK11/LKB1 in non-small cell lung cancer (NSCLC) are associated with poor patient responses to immune checkpoint blockade (ICB) and introduction of a Stk11/Lkb1 (L) mutation into murine lung adenocarcinomas driven by mutant Kras and Trp53 loss (KP) resulted in an ICB refractory syngeneic KPL tumor. Mechanistically this occurred because KPL mutant NSCLCs lacked TCF1-expressing CD8 T cells, a phenotype recapitulated in human STK11/LKB1 mutant NSCLCs. Systemic inhibition of Axl results in increased type I interferon secretion from dendritic cells that expanded tumor-associated TCF1+ PD-1+ CD8 T cells, restoring therapeutic response to PD-1 ICB for KPL tumors. This was observed in syngeneic immunocompetent mouse models and in humanized mice bearing STK11/LKB1 mutant NSCLC human tumor xenografts. NSCLC patients with identified STK11/LKB1 mutations receiving bemcentinib and pembrolizumab demonstrated objective clinical response to combination therapy. We conclude that AXL is a critical targetable driver of immune suppression in STK11/LKB1 mutant NSCLC.

overall_design: scRNAseq paired with scTCRseq for immune cells sorted from KP tumors, KPL tumors undergone different treatment.

first: Zhida

last: Liu

first: Longchao

first: Hongyi

last: Zhang

first: Chuanhui

last: Han

first: Luc

last: Girard

first: Hyunsil

last: Park

first: Anli

first: Chunbo

last: Dong

first: Jianfeng

last: Ye

first: Austin

last: Rayford

first: Michael

last: Peyton

first: Xiaoguang

first: Kimberley

last: Avila

first: Xuezhi

last: Cao

first: Shuiqing

last: Hu

first: Md

last: Alam

first: Esra

last: Akbay

first: Luisa

last: Solis

first: Carmen

last: Behrens

first: Sharia

last: Hernandez-Ruiz

first: Lu

last: Wei

first: Ignacio

last: Wistuba

first: John

last: Heymach

last: Chisamore

first: David

last: Micklem

first: Hani

last: Gabra

first: Gro

last: Gausdal

first: James

last: Lorens

first: Bo

first: Yang-Xin

last: Fu

middle: D

last: Minna

first: Rolf

middle: A

last: Brekken


title: GPR56 (ADGRG1) and Transglutaminase (TG2) interaction in Regulation of Mesenchymal Transition in Glioblastoma

status: Public on Jan 25 2022

first: Nameeta

last: Shah

address: Bommasandra

institute: Mazumdar Shaw Center for Translational Research

summary: G protein-coupled receptor 56 (GPR56/ADGRG1) is an adhesion GPCR with an essential role in brain development and cancer. Elevated expression of GPR56 was observed in the clinical specimens of Glioblastoma (GBM), a highly invasive primary brain tumor. However, we found the expression to be variable across the specimens, presumably due to the intratumor heterogeneity of GBM. Therefore, we re-examined GPR56 expression in public domain spatial gene expression data and single-cell expression data for GBM, which revealed that GPR56 expression was high in cellular tumors, infiltrating tumor cells, and proliferating cells, low in microvascular proliferation and peri-necrotic areas of the tumor, especially in hypoxic mesenchymal-like cells. To gain a better understanding of the consequences of GPR56 downregulation in tumor cells and other molecular changes associated with it, we generated a sh-RNA-mediated GPR56 knockdown in the GBM cell line U373 and performed transcriptomics, proteomics, and phospho-proteomics analysis. Our analysis revealed enrichment of gene signatures, pathways, and phosphorylation of proteins potentially associated with mesenchymal (MES) transition in the tumor and concurrent increase in cell invasion and migration behavior of the GPR56 knockdown GBM cells. Interestingly, our analysis also showed elevated expression of Transglutaminase 2 (TG2) - a known interactor of GPR56, in the knockdown cells. The inverse expression of GPR56 and TG2 was also observed in intratumoral, spatial gene expression data for GBM and in GBM cell lines cultured in vitro under hypoxic conditions. Integrating all these observations, we infer a functional link between the inverse expression of the two proteins, the hypoxic niche, and the mesenchymal status in the tumor. Hypoxia-induced downregulation of GPR56 and activation of TG2 may result in a network of molecular events that contribute to the mesenchymal transition of GBM cells, and we propose a putative model to explain this functional and regulatory relationship of the two proteins.

overall_design: Examination of GPR56 Control and Knockdown in U373 GBM cell line.

first: Ravi

last: Sirdeshmukh


title: Arabidopsis LSM1 and DCP5 proteins aid evasion of translational repression during Cauliflower Mosaic Virus infection

city: Potsdam

first: Heinrich

last: Bente

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary: Processing bodies are tightly connected with the RNA silencing machinery. Deletion of processing body components leads to succeptibility of Cauliflower Mosaic Virus to translational repression. Here, we investigated if this succeptibility is mediated through differential sRNA targeting of the viral genome.

overall_design: 16 sRNA libraries from total RNA of Arabidopsis rosettes in duplicates of CaMV infected Col-0, lsm1, dcp5 and rdr6 plants with their respective double mutants. Controls include non-infected Col-0 and rdr6 plants.

first: Hoffmann

last: Gesa

first: Mahboubi

last: Amir

first: Bente

last: Heinrich

first: Garcia

last: Damien

first: Hanson

last: Johannes

first: Hafrén

last: Anders


title: Sequential enhancer state remodelling defines human germline competence and specification

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge


title: Improved maturity and yield of pluripotent stem cell-derived hepatocytes for 2D and 3D modeling of human liver pathophysiology

status: Public on Feb 03 2022

city: Montreal

first: Massimiliano

last: Paganelli

state: QC

address: 3175 Ch. Cote-Ste-Catherine

country: Canada

institute: CHU Sainte-Justine

summary: Robust and scalable differentiation of human pluripotent stem cells into high-quality hepatocyte-like cells (HLC) is achieved by acting on Wnt/b-catenin and TGFb pathways and taking advantage of latest knowledge on human liver development. Obtained HLC are comparable to primary human hepatocytes and superior to stem cell-derived hepatocytes generated with previously described protocols. As a proof of concept, such HLC were used to assess drug hepatotoxicity and study human ductal plate and bile duct morphogenesis in a complex liver organoid model.

overall_design: Comparison of liver-specific gene expression profile of our hepatocyte-like cells with previously described primary human hepatocytes (PHH: GSM2753380, GSM2753381 and GSM2753382 described in Gao et al. Stem Cell Rep. 2017;9:1813?1824) and stem cell-derived hepatocytes (HLC and hiHeps: GSM2411900, GSM2411902, GSM2411904 described in Warren et al. Cell Stem Cell 2017;20:547-557; GSM2753372, GSM2753373, GSM2753374 described in Gao et al. Stem Cell Rep. 2017;9:1813?1824). Prior to all analysis, the raw gene counts were normalized using the logCPM method by dividing each column by the total sum of its counts, multiply by a million and followed by the application of a log10-transform. Genes with the most variable expression were selected and transformed using the Z-score. Principal Component Analysis was generated using the Plotly's Python graphing library and sklearn Python module. Heatmap was created using Clustergrammer. We then compared HLC obtained with the new differentiation protocol with previously described HLC and PHH by performing an UMAP-based dimensionality reduction of the top 17 principal components obtained analyzing the 3000 most variable genes across datasets. For PHH, we used the following datasets: GSM2817112, GSM2815712, GSM2815717, GSM3146358, GSM3146359, GSM3067786, GSM3067787, GSM3067788, GSM3067804, GSM2753380, GSM2753381, GSM2753382 (described in Gao et al. Stem Cell Rep. 2017;9:1813?1824; Fu et al. Cell. Res. 2019;29:8?22; Xie et al. Cell. Res. 2019;29:696?710; Kim et al. J. Hepatol. 2019;70:97?107). For pluripotent stem cell-derived hepatocytes, we used the following datasets: GSM1817062, GSM2411900, GSM2411901, GSM2411902, GSM2411903, GSM2411904, GSM2411905, GSM2411906, GSM2411907, GSM2411908, GSM2411909, GSM2411910, GSM2411911, GSM2411912, GSM2411913, GSM2411914, GSM2411915, GSM2411916, GSM2411917, GSM2411918, GSM2411919, GSM2411920, GSM2411921, GSM2411922, GSM2411923, GSM2411924, GSM2411925, GSM2411926, GSM2411927, GSM2411928, GSM2411929, GSM2411930, GSM2411931, GSM2411932, GSM2411933, GSM2411934, GSM2411935, GSM2411936, GSM2411937, GSM2411938, GSM2411939, GSM2411940, GSM2411941, GSM2411942, GSM2411943, GSM2411944, GSM2411945, GSM2411946, GSM2411947, GSM2411948, GSM2411949, GSM2411950, GSM2411951, GSM2411952, GSM2411953, GSM2411954, GSM2411955, GSM2411956, GSM2411957, GSM2411958, GSM2411959, GSM2411960, GSM2411961, GSM2411962, GSM2411963, GSM2411964, GSM2411965, GSM2411966, GSM2411967, GSM2753372, GSM2753373, GSM2753374, GSM2753375, GSM2753376, GSM2753377, GSM2753378, GSM2753379, GSM3664948, GSM3664949, GSM3664950 (described in Warren et al. Cell Stem Cell 2017;20:547-557; Li et al. Nat. Commun. 2017;8:15166; Gao et al. Stem Cell Rep. 2017;9:1813?1824; Touboul et al. J. Hepatol. 2016;64:1315?1326). In brief, raw counts from different RNA-seq datasets were normalized (divided by the total count, multiplied by 1 million and natural-log transformed using log1p) and center-scaled. From the scaled data, the most variable genes (3,000) across datasets were used to conduct principal component analysis and the top principal components (17) were selected for dimensionality reduction and 2-dimention representation using the UMAP (Uniform Manifold Approximation and Projection) and DimPlot functions from the R Package Seurat.

first: Claudia

last: Raggi

first: Quang

middle: T

last: Pham


title: Sequential enhancer state remodelling defines human germline competence and specification [RNAseq_WildType]

summary: Germline-soma segregation is a fundamental event during mammalian embryonic development. Here we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced remodelling of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. Consistently, reducing the expression of the mesendodermal transcription factor OTX2 promotes the PGC fate. In hPGCs, SOX17 and TFAP2C initiate activation of enhancers to establish a core germline programme, including the transcriptional repressor PRDM1 and pluripotency factors POU5F1 and NANOG. We demonstrate that SOX17 enhancers are the critical components in the regulatory circuitry of germline competence. Furthermore, activation of upstream cis-regulatory elements by an optimized CRISPR activation system is sufficient for hPGC specification. We reveal an enhancer-linked germline transcription factor network that provides the basis for the evolutionary divergence of mammalian germlines.

overall_design: RNA-seq of hESC-derived cell types (two biological replicates for each cell type)


title: Cul5 regulates CD4+ T cell fate choice and allergic inflammation [RNA-seq]

city: Philadelphia

first: Paula

last: Oliver

state: PA

address: 816F ARC, 3615 Civic Center Blvd.

department: Department of Pathology, Perelman School of Medicine

institute: University of Pennsylvania

summary: Antigen encounter directs CD4+ T cells to differentiate into T-helper or -regulatory cells. This process focuses the immune response on the invading pathogen and limits tissue damage. Mechanisms that govern -helper versus -regulatory fate remain poorly understood. Here, we show that the E3 ubiquitin ligase Cul5 determines fate selection in CD4+ T cells by regulating IL-4 receptor signaling. Mice lacking Cul5 in T cells developed enhanced Th2 and Th9 inflammation and pathophysiological features of atopic asthma upon allergen exposure. Following T cell activation, Cul5 formed a complex with CIS and pJak1. Loss of Cul5 function resulted in reduced ubiquitylation and increased stability of pJak1, elevated STAT6 activity, and a reduced threshold for IL-4 receptor signaling. In accordance with this, Cul5-deficient T cells deviated from Treg to Th9 differentiation in low IL-4 conditions. These data support that Cul5 promotes a tolerogenic T cell fate choice and reduces susceptibility to allergic asthma.

overall_design: RNA-seq of Th9 polarized CD4 T cells from spleens/lymph nodes of WT vs. Cul5-/- CD4Cre mice.

first: Binod

last: Kumar

first: Natania

middle: S

last: Field

first: Dale

last: Kim

first: Asif

last: Dar

first: Yanqun

last: Chen

first: Aishwarya

last: Suresh

first: Nadia

last: Porter

first: Christopher

middle: F

last: Pastore

first: Li

middle: Y

last: Hung

first: Keisuke

last: Sawada

first: Palak

first: Omar

last: Elbulok

first: Emily

middle: K

last: Moser

first: De'Broski

last: Herbert


title: Sequential enhancer state remodelling defines human germline competence and specification [TF ChIP-seq]]

first: Walfred

last: Tang

overall_design: ChIP-seq of HA-SOX17 and Myc-PRDM1 in  hPGCLCs and DE (two biological replicates)


title: Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo

status: Public on Jan 23 2022

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM


title: AM in vivo and ex vivo RNAseq

summary: Here we show that alveolar macrophages maintain their core AM transcriptomic identity through culture expansion but show adaptations during culture expansion that are transient, reversible and fully restored upon transplantation into the alveolar niche.

overall_design: For expanded AMs (exAM), total RNA was extracted from exAMs after 2 months of culture. exAM were transplanted into 2 months old CD45.1 mice and analyzed 4 months post transplantation. In vivo AM subsets were sorted (Live, Singlets, SiglecF+, CD11c+, CD45.2+ or CD45.1+) from total lung homogenates directly into RNA lysis buffer (RLT buffer, Qiagen) for RNA extraction. RNA-seq samples were generated from a pool of 3 mice or exAM cultures in duplicates.

first: Sethuraman

last: Subramanian

first: Clara

middle: J

last: Busch

first: Kaaweh

last: Molawi

first: Laufey

last: Geirsdottir

first: Stephanie

last: Vargas-Aguilar

first: Hassiba

last: Belahbib

first: Gimenez

last: Gregory

first: Michael

middle: H

last: Sieweke


title: Sequential enhancer state remodelling defines human germline competence and specification [TF overexpression RNA-seq]]

overall_design: RNA-seq of PreME aggregates 12 hour after SOX17 or PRDM1 overexpression (two biological replicates)


title: Transcriptional Profiling in macrophage-specific GR KO mice

first: Anne

last: Loft

institute: University of Southern Denmark

summary: We generated transcriptional profiles in fasted GRflox; LysM-Cre+/- (GRMAC) mice and littermate controls (GRflox).

overall_design: We subjected female GRflox; LysM-Cre+/- (GRMAC) mice and littermate controls (GRflox) to a fast starting at the onset of the mouse active phase, ZT12, and after 8h livers were collected for RNA-seq analyses.

first: Søren

last: Fisker Schmidt

first: Stephan

last: Herzig


title: Spheroid culture differentially affects cancer cell sensitivity to drugs in melanoma and RCC models

status: Public on Jan 20 2022

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

summary: 2D culture as a model for drug testing often turns to be clinically futile. Therefore, 3D cultures (3Ds) show potential to better model responses to drugs observed in vivo. In preliminary studies, using melanoma (B16F10) and renal (RenCa) cancer, we confirmed that 3Ds better mimics the tumor microenvironment. Here, we evaluate how the proposed 3D mode of culture affects tumor cell susceptibility to anti-cancer drugs, which have distinct mechanisms of action (everolimus, doxorubicin, cisplatin). Melanoma spheroids show higher resistance to all used drugs, as compared to 2D. In RCC model, such modulation was only observed for doxorubicin treatment. As drug distribution was not affected by the 3D shape, we assessed the expression of MDR1 and mTor. Upregulation of MDR1 in RCC spheroids was observed, in contrast to melanoma. In both models mTor expression was not affected by the 3D cultures. By NGS, 10 genes related with metabolism of xenobiotics by cytochrome p450 were deregulated in renal cancer spheroids; 9 of them were later confirmed in melanoma model. The differences between 3D models and classical 2D cultures point to the potential to uncover new non canonical mechanisms to explain drug resistance set by the tumor in its microenvironment.

overall_design: RNA-Seq for 2D culture (2 replicates) and 3D cultured cells (2 replicates)

first: Aleksandra

last: Filipiak-Duliban

first: Arkadiusz

last: Kajdasz

first: Claudine

last: Kieda


title: A High-Resolution Route Map Reveals Distinct Stages of Chondrocyte Dedifferentiation (ATAC-Seq)

city: Hangzhou

first: Yishan

last: Chen

address: #866 Yuhangtang Road

institute: Zhejiang University

summary:
Objectives: Articular cartilage damage has become a universal health burden. Despite the recent progresses in cell-based cartilage regeneration, chondrocyte dedifferentiation has compromised the clinical outcomes, which is frequently seen in chondrocyte expansion and osteoarthritis, involving functional phenotype loss. However, its concept remains elusive with unknown intermediate process and mechanisms. Here we demonstrated a time-lapse atlas of chondrocyte dedifferentiation, to provide molecular details and informative biomarkers for clinical chondrocyte evaluation.
Methods:  Single-cell RNA sequencing (scRNA-seq) was employed to dissect the chondrocyte dedifferentiation and identify distinct cellular subpopulations. To validate the findings, live-cell metabolic assay, high-resolution imaging and ¡°assay for transposase-accessible chromatin with high throughput sequencing¡± (ATAC-seq) were conducted. Using a chemical inhibitor BTB06584 affecting on mitochondrial F1F0ATPase, we revealed the recovery potential of early and late dedifferentiated chondrocytes.
Results:Our findings shape a biphasic model consist of early and late dedifferentiation stages. Early dedifferentiated chondrocytes uniquely obtained a transient glycolytic phenotype with an activation of metabolic and anti-oxidant genes; late dedifferentiated chondrocytes exhibited ultrastructural changes including mitochondrion damages and stress-associated chromatin remodeling. Using a chemical inhibitor BTB06584, we revealed that early and late dedifferentiated chondrocytes possessed distinguished recovery potential from functional phenotype loss. BTB06584 treatment ameliorated early phenotype loss through inhibiting MAPK pathway. Notably, this two-stage transition was validated in human chondrocyte culture. An image-based approach was established for clinical utilization, to efficiently predict chondrocytes plasticity with stage-specific biomarkers.
Conclusion: Thus this study lays a foundation for future clinical chondrocyte quality regulation and provides insights for deeper understanding of chondrocyte dedifferentiation.

overall_design: We employed ATAC-seq of serial-passaged murine chondrocytes (P0 and 8) to reconstruct a time-lapse atlas of chondrocyte dedifferentiation.

first: Yeke

last: Yu


title: BHLHE40 Regulates T Cell Effector Function Required for Tumor Microenvironment Remodeling and Immune Checkpoint Therapy Efficacy

status: Public on Jan 19 2022

city: Houston

first: Alexander

middle: Sergeyevich

last: Shavkunov

address: 7455 Fannin St

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

summary: Using both global and conditional knockout mice, we demonstrated that the transcription factor Basic Helix-Loop-Helix Family Member E40 (BHLHE40/DEC1) is required in T cells for rejection of mouse syngeneic tumors upon immune checkpoint therapy (ICT) with anti-PD-1 or anti-CTLA-4 monoclonal antibody (mAb) treatment. Using single cell RNA sequencing (scRNAseq) we profiled intratumoral CD45+ cells from syngeneic mouse sarcomas that (a) grow progressively with control treatment in either Bhlhe40+/+ or Bhlhe40-/- tumor-bearing mice, (b) reject following anti-PD-1 or anti-CTLA-4 ICT in Bhlhe40+/+ tumor-bearing mice, or (c) grow progressively following anti-PD-1 or anti-CTLA-4 in Bhlhe40-/- mice. We performed two separate scRNAseq experiments with the same conditions but harvested tumors on either day 9 post-tumor transplant or day 11 post-tumor transplant. The groups were as follows: (1) Control mAb Bhlhe40+/+, (2) Control mAb Bhlhe40-/-, (3) anti-PD-1 Bhlhe40+/+, (4) anti-PD-1 Bhlhe40-/-, (5) anti-CTLA-4 Bhlhe40+/+, and (6) anti-CTLA-4 Bhlhe40-/-. scRNAseq of intratumoral immune cells in BHLHE40-deficient mice revealed differential ICT-induced immune cell remodeling. These BHLHE40-dependent gene expression alterations were associated with altered metabolism, NF-kB signaling, and IFN- response in subpopulations of intratumoral CD4+ and CD8+ T cells. Intratumoral T cells from tumor-bearing Bhlhe40-/- mice also had higher transcript expression of the inhibitory receptor gene Tigit, along with altered transcript expression of chemokine/chemokine receptor granzyme family members. Bhlhe40-/- CD4+ and CD8+ T cells also had reduced ICT-driven IFN- production. Furthermore, BHLHE40 was required for ICT-induced remodeling of macrophages from a CX3CR1+ CD206+ subpopulation to an iNOS+ subpopulation. While anti-PD-1 or anti-CTLA-4 ICT in tumor-bearing Bhlhe40-/- mice led to tumor outgrowth—several BHLHE40-dependent changes were specific to the ICT treatment that was administered.

overall_design: Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live intratumoral CD45+ cells into droplets and preparing libraries using Chromium Single Cell 5′ Reagent Kits following the manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using a NovaSeq 6000 Sequencing System (Illumina).

first: Avery

last: Salmon

first: Qi

last: Miao

first: Nicholas

middle: N

last: Jarjour

first: Sunita

last: Keshari

first: Ekaterina

last: Esaulova

first: Charmelle

last: William

first: Jeffrey

last: Ward

first: Anna

last: Highsmith

first: Josué

middle: E

last: Pineda

first: Reshma

last: Taneja

first: Ken

first: Brian

last: Edelson

first: Matthew

last: Gubin


title: Modeling the effects of acute and chronic oxidative stress on blood-brain barrier phenotype and function in 2D and 3D

status: Public on Jan 21 2022

city: Baltimore

first: Peter

middle: C

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: We report changes in gene expression of iPSC-derived brain microvascular endothelial cells (iBMECs) exposed to chronic (100 µM continuously) and acute (500 µM for 1 h) hydrogen peroxide over the course of seven days.

overall_design: 24 total samples collected; n =4 samples of acute oxidative stress at day 0 and its corresponding control, acute oxidative stress at day 4 and its corresponding control, and chronic oxidative stress at day 7 and its corresponding control

first: Tracy

last: Chung


title: Lateral mesoderm-derived mesenchymal stem cells with robust osteochondrogenic potential and hematopoiesis supporting ability

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, hiPSCs were induced to differentiate to mesenchymal stem cells (MSCs) through the intermediate stage of lateral mesoderm (LM). We sequenced mRNA samples of LM and LM-MSCs  to generate the gene expression profiles of these cells.

overall_design: 2 samples from LM stage (including LM 1 and LM 2), 2 samples from LM-MSCs (LM-MSCs 1 and LM-MSCs 2), and 2 samples of BMSCs (BMSCs 1 and BMSCs 2) were analyzed.

first: Yili

last: Wei

first: Bing

last: Wang

first: Weijun

last: Huang


title: SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal

status: Public on Jan 18 2022

city: San Francisco

first: Pauline

middle: Anne Catherine

last: Marangoni

state: CA

address: 513 Parnassus Avenue, HSE15

department: OFS

institute: UCSF

summary: Alternative splicing generates distinct mRNA variants and is essential for development, homeostasis, and renewal. Proteins of the serine/arginine (SR)-rich splicing factor family are major splicing regulators that are broadly required for organ development as well as cell and organism viability. However, how these proteins support adult organ function remains largely unknown. Here, we used the continuously growing mouse incisor as a model to dissect the functions of the prototypical SR-family protein SRSF1 during tissue homeostasis and renewal. We identified an SRSF1-governed alternative splicing network that is specifically required for dental proliferation and survival of progenitors but dispensable for the viability of differentiated cells. We also observed a similar progenitor-specific role of SRSF1 in the small intestinal epithelium, indicating a conserved function of SRSF1 across adult epithelial tissues. Thus, our findings define a regulatory mechanism by which SRSF1 specifically controls progenitor-specific alternative splicing events to support adult tissue homeostasis and renewal.

overall_design: 7 samples were spread across 4 conditions (3 controls, 4 mutants). Sequencing provided was 648 million estimated total reads aligning uniquely to mouse cDNA. Reads uniquely mapped to known mRNAs were used to assess expression changes between transcripts. Pairwise combinations were made between mutant and control cervical loops. QC was performed, before samples were ran through JuncBASE to identify and quantify AS events

first: Tingsheng

last: Yu

first: Oscar

last: Cazares

first: Alison

last: Tang

first: Hyun-Yi

last: Kim

first: Tomas

last: Wald

first: Adya

last: Verma

first: Qi

last: Liu

first: Mary

last: Barcellos-Hoff

first: Stephen

last: Floor

first: Han-Sung

last: Jung

first: Angela

last: Brooks

first: Ophir

last: Klein


title: A stress-reduced passaging technique improves the viability of human pluripotent cells

city: Kyoto

first: Kazutoshi

last: Takahashi

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

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Xeno-free culture systems have expanded the application of human pluripotent stem cells (PSCs). Here we describe an improved method for the subculture of human PSCs. The new method significantly facilitated the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications. Furthermore, the method did not alter the PSC characteristics after long-term culture and attenuated the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and improves the quality control of human PSC research and applications.

overall_design: Examination of 2 different human iPSC lines (WTB6 and WTC11) in early passages and later passages.

first: K

first: C

last: Okubo


title: Sequential enhancer state remodelling defines human germline competence and specification [ATAC-seq]

first: Walfred

overall_design: ATAC-seq of hESC-derived cell types and in vivo human primordial germ cells (two biological replicates for each cell type)

middle: W


title: Sequential enhancer state remodelling defines human germline competence and specification [ULI-NChIP-seq]

overall_design: Histone modifications ULI-NChIP-seq of hESC-derived cell types and human primordial germ cells (two biological replicates for each cell type and each chromatin mark)


title: FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons

city: New York

first: Caryn

middle: R

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

overall_design: Refer to individual Series


title: Mosaic loss of chromosome Y leads to clonal hematopoiesis and promotes leukemogenesis in mice

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

summary: Mosaic loss of chromosome Y (mLOY) is the most frequent chromosome alternation in the blood cells of aging adult male and is closely associated with AML, so we designed experiments to explore the mechanism. Bulk RNA sequencing was performed with AML1-ETO;sgSsty2/sgScramble;Trp53-/- Bone Marrow in vivo and sgSsty2/sgSsty1/sgScramble;Trp53-/- c-kit+ HSPCs in vitro. And our study demonstrates that mLOY is a functional driver for clonal hematopoiesis and leukemogenesis. KDM5D, a gene mediated H3K4 demethylation and located on both human and mouse chromosome Y, we wondered whether KDM5D could be a critical gene responsible for the pathology of mLOY. So bulk RNA sequencing was performed with sgKdm5d/sgScramble;Trp53-/- Bone marrow in vivo and Trp53-/- c-kit+ HSPCs in vitro to explore the mechanism of Kdm5d in mLOY.

overall_design: Bulk RNA-seq of sgSsty2/sgSsty1(mLOY) sgKdm5d and sgScr(control) in blood cells.

last: Zhang

first: Lei

last: Zhao

first: Shujun

last: Li

first: Yu

first: Chong

last: Chen


title: Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer [array]

status: Public on Jan 17 2022

city: Pamplona

first: Fernando

last: Lecanda

address: Avda. Pio XII 55

institute: CIMA

summary: Locoregional failure (LRF) in breast cancer patients post-surgery and post-irradiation (IR) is linked to a dismal prognosis. In a refined new model, we identified Enpp1 (Ectonucleotide pyrophosphatase /phosphodiesterase 1/CD203a) to be closely associated with LRF. Enpp1high circulating tumor cells (CTC) contribute to relapse by a self-seeding mechanism. This process requires the infiltration of PMN-MDSC and neutrophil extracellular traps (NET) formation. Genetic and pharmacological Enpp1 inhibition or NET blockade extend relapse-free survival. Furthermore, in combination with fractionated irradiation (FD), Enpp1 abrogation obliterates LRF.  Mechanistically, Enpp1-generated adenosinergic metabolites enhance Haptoglobin (Hp) expression. This inflammatory mediator elicits myeloid invasiveness and promotes NET formation. Accordingly, a significant increase in ENPP1 and NET formation is detected in relapsed human breast cancer tumors. Moreover, high ENPP1 or HP levels are associated with poor prognosis. These findings unveil the ENPP1/HP axis as an unanticipated mechanism exploited by tumor cells linking inflammation to immune remodeling favoring local relapse.

overall_design: Three cell lines were studied and triplicates were performed for each cell line for a total of 9 samples. Parental (ANV5) was used as control.

first: Rafael

last: Martínez-Monge


title: Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer [shENPP]

summary: Locoregional failure (LRF) in breast cancer patients post-surgery and post-irradiation (IR) is linked to a dismal prognosis. In a refined new model, we identified Enpp1 (Ectonucleotide pyrophosphatase /phosphodiesterase 1/CD203a) to be closely associated with LRF. Enpp1high circulating tumor cells (CTC) contribute to relapse by a self-seeding mechanism. This process requires the infiltration of PMN-MDSC and neutrophil extracellular traps (NET) formation. Genetic and pharmacological Enpp1 inhibition or NET blockade extend relapse-free survival. Furthermore, in combination with fractionated irradiation (FD), Enpp1 abrogation obliterates LRF.

overall_design: 2 cell lines with two shRNA for Enpp1 abrogation were studied and triplicates were performed for each cell line for a total of 18 samples. Non-targeting plasmid (shGFP) were used as control.


title: Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

first: Diep

last: Ganguly

address: 433 S University Ave

department: Department of Biology

summary: Photo-inhibitory high-light stress induces damage to photosystems and changes a myriad of metabolic processes in plants. In Arabidopsis it leads to increased abundance of markers of protein degradation and transcriptional upregulation of proteases and proteolytic machinery, but proteostasis is largely maintained. To identify specific enzymes degrading at a faster rate under high light conditions, we developed a 13C partial labelling approach to measure rates of turnover of specific proteins in Arabidopsis rosettes. We identified 73 proteins with rates of protein degradation enhanced by high-light. In addition to the expected increase in degradation rate of the photosystem II (PSII) D1 subunit, we discovered significant increases in degradation rate for specific molecular chaperones, nitrate reductase, glyceraldehyde-3 phosphate dehydrogenase, and phosphoglycerate kinase. Significant increases in degradation of 65 other plastid, mitochondrial, peroxisomal, and cytosolic enzymes were also found, including factors involved in redox shuttles within and between organelles and the cytosol. Coupled analysis of protein degradation rate, transcriptional rate, and protein abundance revealed that 57% of the nuclear-encoded enzymes with higher degradation rates also had high light-induced transcriptional responses, ensuring proteostasis. In contrast, plastid-encoded proteins with enhanced turnover rates showed decreased transcript abundances and must maintain protein abundance by other processes. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of PSII D1 subunit and the function of PSII, to replace key protein degradation targets in plants and ensure proteostasis under high-light stress.

overall_design:
Arabidopsis thaliana accession Columbia-0 plants were grown under 16/8-h light/dark conditions with cool white T8 tubular fluorescent lamps 4000K 3350 lm (Osram, Germany) with intensity of 100–125 μmol m-2 s-1 at 22 °C. Arabidopsis plants were grown in soil pots for 21 days until they reached leaf production stage 1.10 (Boyes et al., 2001). Shoots of Arabidopsis at the leaf production stage 1.10 were positioned into the sealed growth chamber with the soil pots kept underneath. Six tandem growth chambers were supplied with air at a continuous flow rate 6 L/min and kept overnight before the labelling experiment (T0). A homemade water column was connected to the air hose to keep the air humidity inside the growth chamber. A commercial LED (Heliospectra) were used as the light source for the labelling experiment and the light spectra was set as (420nm-250, 450nm-638, 530nm-750, 630nm-1000, 660nm-250 and 735nm-25). Normal and high light intensity at 100 and 500 µE was achieved by adjusting the distance between the growth chamber and the light source.

Shoot tissues were harvested in biological triplicate after differing light transitions from dark: T0D - end of night (dark control), T2H - 2 hours high light, T2L - 2 hours standard light, T5H - 5 hours high light, T5L - 5 hours standard light, T8H - 8 hours high light, and T8L - 8 hours standard light. Total RNA was isolated using TRI reagent based on an adapted protocol (Crisp et al., 2017). Full details are available at protocols.io: dx.doi.org/10.17504/protocols.io.bt8wnrxe. Total RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit (RS-122-2402, Illumina, CA, USA) as per manufacturer’s instructions but with input RNA and reaction volumes adjusted by one-third. PCR amplified libraries were pooled equal-molar and sequenced (75 bp, single-end) on one lane of the NextSeq500.

first: Barry

last: Pogson

first: A

last: Millar


title: Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer

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


title: Transcriptome profile changes during differentiation of avian satellite cells.

city: Poznan

first: Karol

last: Jopek

address: Swiecicki 6

department: Department of Histology and Embryology.

institute: Poznan University of Medical Sciences

summary: This study focused on a complex transcriptomic comparison of undifferentiated, differentiated and suspension cultured myosatellite cells, aiming to determine the effects of different culture methods on their transcriptome. Modern next-generation sequencing (RNAseq) was used to determine the levels of transcripts in cultures cell samples. Then differential expression and pathway analyses were performed using bionformatical methods. Differential regulation of gene expression, as well as significant enrichment and modulation of pathway activity, suggested that suspension culture potentially promotes the ex vivo associated loss of physiological characteristics and gain of plasticity.

overall_design: Examination of 3 samples: undifferentiated, differentiated and suspended satellite cells.

first: Afsaneh

last: Golkar-Narenji

first: Paweł

last: Antosik

first: Shelly

last: Nolin

first: Marcin

last: Ruciński

first: Agnieszka

last: Zok

first: Jarosław

last: Sobolewski

first: Maurycy

last: Jankowski

first: Maciej

last: Zdun

first: Dorota

last: Bukowska

first: Katarzyna

last: Stefańska

first: Jędrzej

middle: M

last: Jaśkowski

first: Hanna

last: Piotrowska-Kempisty

first: Paul

last: Mozdziak

first: Bartosz

last: Kempisty


title: Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer [oeENPP]

first: Fernando

last: Lecanda

overall_design: 4 cell lines were studied and triplicates were performed for each cell line for a total of 12 samples. Parental ANV5 or 4T1 were used as control.

first: Rafael

last: Martinez-Monge


title: CITE-seq of SUMOi treated C57Bl6 mice

status: Public on Jan 15 2022

city: Berlin

first: Schayan

last: Yousefian

address: Hannoversche Str. 28

country: Germany

institute: Berlin Institute of Health at Charité Berlin

summary: In our study, we investigated the effect of inhibition of SUMOylation on murine splenocytes. Mice were treated with 7,5 mg/kg SUMOi (TAK-981) on day 1 and day 4 and analysed on day5.

overall_design: Single-cell gene expression data are presented for SUMOi treated and control treated mice.

first: Markus

last: Schick

first: Dominik

last: Vonficht

first: Uta

last: Demel


title: An efficient simplified method for the generation of corneal epithelial cells from human pluripotent stem cells

city: Shiga

first: RODI

middle: KADO

last: ABDALKADER

address: 1-1-1 Noji-Higashi, Kusatsu

country: Japan

institute: Ritsumeikan University

summary: Corneal epithelial cells derived from hPSCs provides an important cells source for the construction of the in vitro preclinical models aimed for ophthalmic drugs tests. However, the recent differentiation protocols lack the optimal culturing conditions that hinder the robustness and the quality of cells as well as the scale-up application of cells production. Here we introduce a simplified, yet efficient small molecules-based corneal induction method (SSM-CI) for the generation of corneal epithelial cells from hPSCs. SSM-CI provides the advantage of minimization the cells culturing time and steps using only two defined xenobiotic-free and serum-free culturing mediums in combination with the TGFß pathway, Wnt/ß-catenin pathway signaling chemical inhibitors, and human bFGF growth factor for a period of 25 days. Compared to both conventional human corneal epithelial cell line (HCE-T) as well as the human primary corneal epithelial cells (hPCEpC), human embryonic stem cells derived corneal epithelial cells generated by SSM-CI has highly expressed major differentiation as well as maturation markers such as PAX6 and CK12. RNA-seq analysis indicated the genuine diversion of hPSCs into the corneal epithelium lineage where corneal progenitor and adult corneal epithelial phenotypes were significantly upregulated. Furthermore, despite the inhibition of TGF-β and Wnt/β-catenin at the early stage of differentiation, an upregulation of the TGF-β and Wnt/β-catenin pathways related transcripts we noticed in the late stage which indicated the necessity of these pathways in the generation of mature corneal epithelial cells. Moreover, there was a shift in gene signatures associated with the metabolic characteristics of mature corneal epithelial cells where a decrease of glycolysis related transcripts and an increase in fatty acid oxidation related one was noticed. That was also corresponded by the overexpression of metabolic enzymes and transporters related transcripts that were mainly responsible for the metabolism of fatty acids. Thus SSM-CI provide a comprehensive method for the generation of functional corneal epithelial cells that has the potential for the employment in future preclinical models.

overall_design: Next generation sequencing  starting with RNA-seq library construction (TruSeq stranded mRNA LT Sample Prep Kit)  from RNAs in Human embryonic stem cells KhES1 (K1) , Human embryonic stem cells derived corneal epithelial cells (K1-CEC) at day 10 and day 20, and human primary corneal epithelial cells (hPCEpC) using NovaSeq 6000.

first: Rodi

last: Abdalkader

first: Kamei

last: Ken-ichiro


title: Epigenetic Memory of AM in vivo and ex vivo

first: Julien

last: Maurizio

summary: Here we show that alveolar macrophage (AM) identity were conserved through culture expansion as determined by the analysis of epigenetic chromatin accessibility of core AM specific transcription markers and surface markers. Further, the adaptations to the culture environment were transient, reversible and fully restored to the in vivo status upon transplantation into the alveolar niche.

overall_design: BAL AM pooled from 3 mice were expanded ex vivo for 2 months and i.t transplanted into lungs of 2-3 WT CD45.1 mice. The lungs were collected at 4 months post transplantation and sorted for CD45.2+ exAM or CD45.1+ host AM. 3 mice each of BAL AM, exAM and 2-3 mice each for texAM or Host AM were pooled and used for ATAC-seq. The ATAC-seq was done in technical triplicate transposase reactions, from pools of 2-3 mice for each replicate, again controlling for biological variation. Triplicates were then further pooled bioinformatically for the analyses shown in Fig. 5.

first: Sethuraman

last: Subramanian

first: Clara

last: Busch

first: Hassiba

last: Belahbib

first: Bérengère

last: de Laval

first: Michael

last: Sieweke


title: Arabidopsis thaliana FIBRILLIN6 is involved in acclimation to moderate light stress and cadmium tolerance

status: Public on Jan 14 2022

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: By mining public co-expression databases, we have identified FBN6 as a photosynthesis-associated gene. FBN6 is located in thylakoids and plastoglobules, and its knock-out results in stunted plants characterized by slightly reduced chlorophyll contents, shorter roots and late flowering under long-day conditions. The delayed growth phenotype of fbn6-1 cannot be attributed to altered basic photosynthesis parameters or a reduced CO2 assimilation rate. FBN6 is also co-expressed with redox/ROS-associated genes, and we show that under moderate light stress, the primary leaves of fbn6 plants begin to bleach and contain enlarged plastoglobules. Furthermore, anthocyanin accumulation is reduced in fbn6 mutants. RNA-Seq and metabolomics analyses point to an altered sulfate assimilation leading to accumulation of reduced glutathione which in turn confers cadmium tolerance of fbn6 seedlings.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana fbn6-1 mutant compared to wild type in three replicates