title: Developmental Programming: Impact of Prenatal Bisphenol-A Exposure On Liver and Muscle Transcriptome of Female Sheep [RNA-Seq]

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: Gestational Bisphenol A (BPA) exposure leads to peripheral insulin resistance, and hepatic and skeletal muscle oxidative stress and lipotoxicity during adulthood in the female sheep offspring. To investigate transcriptional changes underlying the metabolic outcomes, coding and non-coding (nc) RNA in liver and muscle from 21-month-old control and prenatal BPA-treated (0.5mg/kg/day from days 30 to 90 of gestation; Term: 147days) female sheep were sequenced. Prenatal BPA-treatment dysregulated:1) expression of 194 genes (138 down, 56 up) in liver and 112 genes (32 down, 80 up) in muscle; (2) 155 common gene pathways including mitochondrial-related genes in both tissues; 3) 1415 gene pathways including oxidative stress and lipid biosynthetic process specifically in the liver; (4) 192 gene pathways including RNA biosynthetic processes in muscle; (5) 77 lncRNA (49 down, 28 up), 14 microRNAs (6 down, 8 up), 127 snoRNAs (63 down, 64 up) and 55 snRNAs (15 down, 40 up) in the liver while upregulating 6 lncRNA and dysregulating 65 snoRNAs (47 down, 18 up) in muscle. Multiple ncRNA correlated with LCORL, MED17 and ZNF41 in liver but none of them in the muscle. OPLS-DA plots identified mRNAs PECAM, RDH11 and ABCA6, and miRNAs MIR200B and MIR30B in liver and mRNAs CAST, NOS1 and FASN and miRNAs MIR26B and MIR29A in muscle as gene signatures of gestational BPA exposure. These findings provide mechanistic clues into the development and/or maintenance of the oxidative stress and lipid accumulation and potential for development of mitochondrial and fibrotic defects contributing to the prenatal BPA-induced metabolic dysfunctions.

overall_design: 4 control and 4 BPA treated animals, with two tissue samples (liver and muscle) from each

first: Muraly

last: Puttabyatappa

first: Nadia

last: Saadat

first: Venkateswaran

last: Elangovan

first: John

last: Dou

first: Vasantha

last: Padmanabhan


title: Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [ChIP-seq]

status: Public on Jul 08 2022

city: Napoli

first: Pietro

last: Zoppoli

state: Napoli

address: via S.Pansini,5

department: DMMBM

country: Italy

institute: Università degli Studi di Napoli Federico II

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hmga2 KO pluripotent stem cells fail to develop into epiblast-like stem cells (EpiLCs). By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in stabilized epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. As nuclear lamina is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of HiC data in wt and Hmga2 KO cells allowed us to observe that inter-TAD interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina.

overall_design: Genome binding/occupancy profiling of Hmga2 in EpiLCs by high throughput sequencing.

first: Silvia

last: Parisi


title: Developmental Programming: Impact of Prenatal Bisphenol-A Exposure On Liver and Muscle Transcriptome of Female Sheep

country: USA

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Type I Interferon Signaling Mediates Microglial Dysfunction and Senescence in Human-Mouse Chimeric Brain Models of Down Syndrome and Alzheimer’s Disease [single-cell RNA-seq]

city: Piscataway

first: Mengmeng

last: Jin

state: NJ

address: 604 Allison Rd

institute: Rutgers University

summary: Microglia are critical for brain development and play a central role in Alzheimer’s disease (AD) etiology. Down syndrome (DS), also known as trisomy 21, is the most common genetic origin of intellectual disability and the most common risk factor for AD. Surprisingly, little information is available on the impact of trisomy of human chromosome 21 (Hsa21) on microglia in DS brain development and AD in DS (DSAD). Using our new induced pluripotent stem cell (iPSC)-based human microglia-containing cerebral organoid and chimeric mouse brain models, here we report that DS microglia exhibit enhanced synaptic pruning function during brain development. Consequently, electrophysiological recordings demonstrate that DS microglial mouse chimeras show impaired synaptic neurotransmission, as compared to control microglial chimeras. Upon being exposed to human brain tissue-derived soluble pathological tau, DS microglia display dystrophic phenotypes in chimeric mouse brains, recapitulating microglial responses seen in human AD and DSAD brain tissues. Further flow cytometry, single-cell RNA-sequencing, and immunohistological analyses of chimeric mouse brains demonstrate that DS microglia undergo cellular senescence and exhibit elevated type I interferon signaling after being challenged by pathological tau. Mechanistically, we find that shRNA-mediated knockdown of Hsa21-encoded type I interferon receptor genes, IFNARs, rescues the defective DS microglial phenotypes both during brain development and in response to pathological tau. Our findings provide in vivo evidence supporting a paradigm shifting theory that human microglia respond to pathological tau with accelerated senescence. Our results further suggest that targeting IFNARs may improve microglial functions during DS brain development and prevent human microglial senescence in DS individuals with AD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA-seq for 4 different human microglia cell samples from chimeric mouse brain.

first: Ziyuan

last: Ma

first: Peng

last: Jiang


title: The trichloroethylene metabolite S-(1,2-dichlorovinyl)-l-cysteine inhibits lipopolysaccharide-induced inflammation transcriptomic pathways and cytokine secretion in a macrophage cell model

summary: Macrophage cells play a critical role in the innate immune response during infection. Previous studies have reported that the trichloroethylene (TCE) metabolite S-(1,2-dichlorovinyl)-l-cysteine (DCVC) inhibits cytokine secretion in pathogen stimulated placental membranes, but little is known about the mechanism for these effects, including which cell types or transcriptomic pathways are impacted. We tested the hypothesis that DCVC inhibits lipopolysaccharide (LPS) stimulated inflammation pathways in differentiated (macrophage like) THP-1 cells. THP-1 cells were differentiated with phorbol 12-myristate 13-acetone (PMA) for 24 h and then treated with 1, 5, or 10 µM DCVC for 24 h. After an additional 4 h incubation with lipopolysaccharide (LPS), RNA was harvested, and RNA sequencing and cytokine analysis was performed. There were 1,399 differentially expressed genes in the cells co-treated with DCVC and LPS compared to LPS alone. Major pathways impacted include the inflammatory response, response to cytokines, and leukocyte activation. Finally, DCVC significantly reduced LPS-stimulated IL-1β, IL-6, and TNF-α secretion. These findings suggest that TCE could potentially modify important macrophage functions during infection.

overall_design: 4 treatment groups with 6 replicates: Control, LPS (100ng/mL), DCVC (5µM), and LPS (100ng/mL) + DCVC (5µM)

first: Sean

last: Harris

first: Ethan

last: Houskamp

first: Eleanor

middle: C

last: Sheeres

first: Emily

last: Schellenboom

first: Olivia

last: Harlow

first: Rita

last: Loch-Caruso

first: Erica

last: Boldenow


title: Impaired myocardial contractility underlies an Rbfox-mediated zebrafish model of hypoplastic left heart syndrome

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

summary: Here, we report that zebrafish lacking two orthologs of the RNA binding protein RBFOX2, which was previously linked to HLHS in newborns, display cardiovascular defects overlapping those in HLHS patients. In contrast to current models, we demonstrate that co-existing ventricular, valve, and aortic deficiencies in rbfox mutant zebrafish arise secondary to impaired myocardial contractility. On a molecular and cellular level, we find diminished expression and alternative splicing of sarcomere and mitochondrial components that compromise sarcomere assembly and mitochondrial respiration, respectively. Injection of human RBFOX2 rescues ventricular structure and function in rbfox mutant zebrafish, demonstrating conservation of molecular function between humans and zebrafish Rbfox proteins. However, injection of RBFOX2 variants previously identified in newborns with HLHS do not. Taken together, our data suggest that mutations in RBFOX2 are causal for HLHS and challenge the obligate multigenic etiology of the disease. Instead, we provide a complimentary paradigm where HLHS can arise from a single gene mutation where ventricular, valve, and aortic deficiencies manifest secondary to a primary myocardial defect.

overall_design: Heart mRNA profiles of 48hpf wild type (WT) and DKO (rbfox1l-/-; rbfox2-/-) zebrafish

last: Huang

first: Alexander

middle: A

last: Akerberg

first: Willam

middle: T

last: Pu

first: CGeoffrey

last: Burns

first: Caroline

middle: E


title: Auxin biosynthesis drives developmental reprogramming of differentiated cells

status: Public on Jul 07 2022

city: Tsurumi-ku, Yokohama

first: Yuki

last: Sakamoto

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: CSRS

country: Japan

institute: RIKEN

summary: Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis leaf cells. We demonstrate that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits the transcriptional activation of PLETHORAs (PLTs), leading to the induction of their downstream target gene YUCCA1 (YUC1) encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.

overall_design: Expression profiling for fresh and cultured mesophyll protoplasts from Arabidopsis leaves

first: Keiko

last: Sugimoto


title: Construction of the whole animal at a single cell resolution

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

sample_organism:
Drosophila melanogaster
Danio rerio
Eisenia andrei


title: Developmental Programming: Impact of Prenatal Bisphenol-A Exposure On Liver and Muscle Transcriptome of Female Sheep [ncRNA-Seq]

first: Kelly

last: Bakulski

first: Muraly

last: Puttabyatappa

first: Nadia

last: Saadat

first: Venkateswaran

middle: R

last: Elangovan

first: John

last: Dou

first: Vasantha

last: Padmanabhan


title: Antiviral function and viral antagonism of the rapidly evolving dynein activating adapter NINL

city: La Jolla

first: Matthew

last: Daugherty

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

summary: Viruses interact with the intracellular transport machinery to promote viral replication. Such host-virus interactions can drive host gene adaptation, leaving signatures of pathogen-driven evolution in host genomes. Here we leverage these genetic signatures to identify the dynein activating adaptor, ninein-like (NINL), as a critical component in the antiviral innate immune response and as a target of viral antagonism. Unique among genes en¬¬coding for dynein subunits, subunits of its co-factor dynactin, and dynein activating adaptors, NINL has evolved under recurrent positive selection, specifically in its carboxy-terminal cargo binding region. Consistent with a role for NINL in host immunity, NINL knockout cells are more permissive to viral replication as a result of a severe attenuation of interferon stimulated gene (ISG) production following interferon treatment. Moreover, we show that proteases encoded by diverse picornaviruses and coronaviruses cleave and disrupt NINL function in a host- and virus-specific manner.  Our work reveals the importance of NINL in the antiviral response and the utility of using signatures of host-virus conflicts to uncover new components of antiviral immunity and targets of viral antagonism.

overall_design: Comparative gene expression analysis of RNA-seq data for A549 cells and its gene knockout derivatives (NINL KO, NIN KO) with or without interferon alpha treatment

first: D

last: Stevens

first: C

last: Beierschmitt

first: S

last: Mahesula

first: M

last: Corley

first: J

last: Salogiannis

first: B

middle: V

last: Tsu

last: Cao

first: A

middle: P

last: Ryan

middle: L

last: Reck-Peterson

middle: D


title: Type I Interferon Signaling Mediates Microglial Dysfunction and Senescence in Human-Mouse Chimeric Brain Models of Down Syndrome and Alzheimer’s Disease [bulk RNA-seq]

first: Mengmeng

last: Jin

overall_design: RNA-seq of 6 primitive macrophage progenitor (PMP) cell lines

first: Ziyuan

last: Ma

first: Peng

last: Jiang


title: key histone modifications in porcine oocytes and early embryos

city: Wuhan

first: Wei

last: Zhu

address: No.1,Shizishan Street , Hongshan District

institute: Huazhong Agricultural University

summary: Conservation and species specificity are both unveiled in the reprogramming process of epigenetic modifications in early embryos. Pig is important agricultural livestock that closely related to human life and understanding the mechanisms of epigenetic reprogramming in porcine embryos could be assistive to the pig breeding industry and also informative to human embryo research. Nevertheless, current knowledge of epigenetic reprogramming in porcine embryos is elusive. We profile H3K4me3, H3K27me3, and H3K27ac modifications in porcine oocytes and preimplant embryos. Our data reveal the existence of unusual broad H3K4me3 domains not only in oocytes but also expanded in pre-ZGA embryos and demonstrates the extensive transitions of unusual broad H3K4me3 domains and their roles during embryogenesis. Notably, broad H3K27me3 and H3K27ac enriched domains are found to be preferably colocalized in these broad H3K4me3 domains when comparing to it in mice and human. By knocking down KDM5B in pig embryos, cleavage and developments were disrupted as demonstrated in mouse.

overall_design: Oocytes (GV and MII stages) and IVF embryos (zygote, 2-cell, 4-cell, 8cell, morula and blastocyst) were collected and H3K4me3  (Abcam, ab8580) and H3K27me3 (Millipore, 07449) were profiled with ULI-NChIP protocol. In addition, to investigate the functions of KDM5B/C during pig embryogenesis, siRNA targeting pig KDM5B/C were injected into zygotes and then embryos at 4-cell stages were collected for H3K4me3 ChIP-seq experiments. For each developing stage or condition, two replicates were performed for each histone modification.

first: Guowei

last: Bu

first: Xin

last: Liu

first: Yi-Liang

last: Miao


title: The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling [ATAC-seq]

city: Shenzhen

first: Huanhuan

last: Cui

state: Guangdong

address: Southern University of Science and Technology, No.1088, Xueyuan Avenue, Xili Street, Nanshan District

department: Department of Biology

summary: DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remained unknown.  In this study, we demonstrated that DPF3a, the short isoform of DPF3, could promote kidney cancer cell migration both in vitro and in vivo, consistent with the clinical observation that DPF3a was significantly upregulated in ccRCC patients with metastasis. Mechanistically, DPF3a specifically interacted with  SNIP1, via which it formed a complex with SMAD4 and p300 histone acetyltransferase (HAT), the major transcriptional regulators of TGF-β signaling pathway. Moreover, the binding of DPF3a could release the repressive effect of SNIP1 on p300 HAT activity, leading to increased local histone acetylation and activation of cell movement related genes. In summary, our findings uncovered a novel link between chromatin remodeling and tumor metastasis, whose inhibition is a key therapeutic goal for ccRCC treatment.

overall_design: ATAC-seq in 786-O cells

last: Chen


title: Immunologically active phenotype is associated with response to PD-1/PD-L1 inhibitors in patients with advanced non-small cell lung cancer

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

summary: Immunotherapy in immunologically active tumors may improve prognosis of non-small cell lung carcinomas (NSCLC). Our objective was to develop a reliable and stable scoring system for the identification of immunologically active HNSCC and to evaluate its association with response to immunotherapies. A Hot Oral Tumor (HOT) score was developed using data from The Cancer Genome Atlas in human-papillomavirus negative head and neck squamous cell carcinomas; it was computed in 92 patients with early stage NSCLC treated with surgery to evaluate the prognostic impact of the HOT score.

overall_design:
In 92 patients with surgically treated NSCLC, gene expression profiles were generated using formalin-fixed paraffin embedded biopsies or surgically resected specimens collected prior to treatment initiation. Gene expression profiles were generated using HTG EdgeSeq technology and the Oncology Biomarker Panel (OBP).

>>>Submitter states that raw data are currently unavailable. They are working with the sequencing company to retrieve  the raw files<<<

first: Valery

last: Attignon

first: Christine

last: Caux

first: Lucas

last: Michon

first: Christophe

first: Sylvie

last: Lantuejoul

first: Pierre

last: Saintigny


title: The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling [ChIP-seq]

institute: Southern University of Science and Technology

overall_design:
ChIP-seq in 786-O cells;
Please note that each NARROWPEAK processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.


title: Construction the larval and adult zebrafish cell atlas at single cell resolution

first: Guoji

last: Guo

summary: Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

overall_design: Over 550,000 cells derived from zebrafish whole-body single-cell dissociation and profiling at the larval stage (72 hpf, 3 replicates, 10 fish for each replicate) and adult (90 day, 6 replicates, 1 fish for each replicate).

first: Xiaoping

last: Han

first: Renying

last: Wang

first: Jiaqi

last: Li

first: Jingjing

first: Peijing

last: Zhang


title: Gene expression profiles of paired endoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimens.

summary: Ongoing immunomodulatory strategies in tumors characterized by an overall hot immune phenotype may improve prognosis of head and neck squamous cell carcinomas (HNSCC). Our objective was to develop a reliable and stable scoring system for the identification of immunologically hot HNSCC and to evaluate its association with response to immunotherapies. A Hot Oral Tumor (HOT) score was developed using data from The Cancer Genome Atlas. HOT score was then computed in 27 patients with HNSCC in paired perendoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimen. None of the patients was treated with neoadjuvant therapy. Concordance and correlation of the HOT score was high in paired samples.

overall_design: In 27 patients,  paired endoscopic biopsies  and subsequent surgically resected head and neck squamous cell carcinomas (HNSCC) were analyzed for gene expression profiles using formalin-fixed paraffin embedded tissues and HTG EdgeSeq technology (Oncology Biomarker Panel (OBP).

first: Jean-Philippe

last: Foy

first: Geneviève

last: Hervé

first: Chloé

last: Bertolus


title: Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment

first: Pietro

last: Zoppoli


title: Construction the adult Drosophila cell atlas at single cell resolution

summary: Single-cell mRNA sequencing (mRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

overall_design: Over 270,000 cells derived from Drosophila whole-body single-cell dissociation and profiling at 11 day (D11) and 16 day (D16) after laying eggs (nearly 25-30 fruit flies per timepoint).


title: Ribosome profiling and RNA-seq of human corneal epithelial cells upon mild osmotic stress

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

summary: We present ribosome profiling(for activaly translated RNA) and RNA-seq (for total RNA) data for human corneal epithelial cells exposed to mild osmotic stress (500 mOsm) for 1h and 6h (additionally torin1 (mTOR inhibitor) or MeAIB (SNAT2 inhibitor were added for the last hour of treatment.

overall_design: Ribosomal profiling and RNA-seq of human corneal epithelial cells. There are 4 replicates for each of the following conditions: control, 1h exposure to 500 mOsm, 6h exposure to 500 mOsm, 6h exposure to 500 mOsm + Torin1 for the last hour of treatment, 6h exposure to 500 mOsm + MeAIB for the last hour of treatment

first: D

last: Krokowski

first: R

last: Jobava

first: K

middle: J

first: C

middle: W

first: X

last: Fu

first: S

last: Venus

first: B

last: Guan

first: J

last: Wu

first: Z

last: Gao

first: W

last: Banaszuk

first: M

last: Tchorzewski

first: T

last: Mu

first: P

last: Ropelewski

last: Merrick

first: Y

last: Mao

first: A

middle: I

last: Sevval

first: H

last: Miranda

middle: B

last: Qian

last: Manifava

first: N

last: Ktistakis

last: Vourekas

first: E

last: Jankowsky

first: I

last: Topisirovic

first: O

last: Larsson

last: Hatzoglou


title: ICOS-deficient Treg cells can prevent spontaneous autoimmunity but are impaired in controlling acute inflammation

city: Montreal

first: Woong-Kyung

last: Suh

state: QC

address: 110 Pine avenue, SuhLab

country: Canada

institute: institut de Recherche Clinique de Montreal (IRCM)

summary: ICOS is induced in activated T cells and its main role is to boost differentiation and function of effector T cells. ICOS is also constitutively expressed in a subpopulation of Foxp3+ regulatory T cells under steady-state condition. Studies using ICOS germline knockout mice or ICOS-blocking reagents suggested that ICOS has supportive roles in regulatory T (Treg) cell homeostasis, migration, and function. To avoid any compounding effects that may arise from ICOS-deficient non-Treg cells, we generated a conditional knockout system in which ICOS expression is selectively abrogated in Foxp3-expressing cells (ICOS FC mice). Compared to Foxp3-Cre control mice, ICOS FC mice showed a minor numerical deficit of steady-state Treg cells but did not show any signs of spontaneous autoimmunity, indicating that tissue-protective Treg populations do not heavily rely on ICOS costimulation. However, ICOS FC mice showed more severe inflammation in oxazolone-induced contact hypersensitivity, a model of atopic dermatitis. This correlated with elevated numbers of inflammatory T cells expressing IFN-γ and/or TNF-α in ICOS FC mice compared with the control group. In contrast, elimination of ICOS in all T cell compartments negated the differences, confirming that ICOS has a dual positive role in effector and Treg cells. Single-cell transcriptome analysis suggested that ICOS-deficient Treg cells fail to mature into T-bet+CXCR3+ “Th1-Treg” cells in the draining lymph node. Our results suggest that regimens that preferentially stimulate ICOS pathways in Treg cells might be beneficial for the treatment of Th1-driven inflammation.

overall_design: Comparing ICOS WT and ICOS-deficient (ICOS FC) Tregs in steady-state and inflammation conditions.

first: Jinsam

last: Chang

first: Antoine

last: Bouchard

first: Yasser

last: Bouklouch

first: Vincent

last: Panneton

first: Joanna

last: Li

first: Nikoletta

last: Diamantopoulos

first: Saba

last: Mohammaei

first: Roman

last: Istomine

first: Fernando

last: Alvarez

first: Ciriaco

last: Piccirillo


title: Immunologically hot phenotype is associated with response to PD-1/PD-L1 inhibitors in patients with advanced head and neck squamous cell carcinoma.

first: PIERRE

last: SAINTIGNY

summary: Ongoing immunomodulatory strategies in tumors characterized by an overall hot immune phenotype may improve prognosis of head and neck squamous cell carcinomas (HNSCC). Our objective was to develop a reliable and stable scoring system for the identification of immunologically hot HNSCC and to evaluate its association with response to immunotherapies. A Hot Oral Tumor (HOT) score was developed using data from The Cancer Genome Atlas. HOT score was computed in 102 patients with HNSCC treated with immunotherapy targeting PD-1/PD-L1 in the context of clinical trials. High HOT score was associated with a statistically significant improved clinical outcome.

overall_design: in 102 patients with advanced head and neck squamous cell carcinomas (HNSCC) treated with immunotherapy targeting PD-1/PD-L1 in the context of clinical trials, gene expression profiles were generated using formalin-fixed paraffin embedded biopsies or surgically resected specimens collected prior to treatment initiation. Gene expression profiles were generated using HTG EdgeSeq technology and the Oncology Biomarker Panel (OBP).

first: Andy

last: Karabajakian

first: Valery

last: Attignon

first: Lucas

last: Michon

first: Jérôme

last: Fayette

first: Carole

last: Crozes

first: Pierre

last: Saintigny


title: Analysis of porcine blastocyst from oocyte exposed to the high level of NEFAs

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

type:
Expression profiling by array
Methylation profiling by array

overall_design: Refer to individual Series


title: The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling.

first: Huanhuan

last: Cui


title: Immunologically hot phenotype is associated with response to second-line PD-1/PD-L1 inhibition in patients with advanced non-small cell lung cancer

summary: Ongoing immunomodulatory strategies in tumors characterized by an overall hot immune phenotype may improve prognosis of patients with non-small cell lung cancer (NSCLC). Our objective was to develop a reliable and stable scoring system for the identification of immunologically hot NSCLC and to evaluate its association with response to immunotherapies. A Hot Oral Tumor (HOT) score was developed using data from The Cancer Genome Atlas. HOT score was computed in 82 patients with NSCLC treated with second-line immunotherapy targeting PD-1/PD-L1. High HOT score was associated with a statistically significant improved clinical outcome.

overall_design: In 82 patients with advanced non-small cell lung cancer (NSCLC) treated with second-line immunotherapy targeting PD-1/PD-L1, gene expression profiles were generated using formalin-fixed paraffin embedded biopsies or archival surgically resected specimens collected prior to treatment initiation. Gene expression profiles were generated using HTG EdgeSeq technology and the Oncology Biomarker Panel (OBP).

first: Sandra

last: Ortiz-Cuaran

first: Maxime

last: Boussageon

first: Sylvie

last: Lantuejoul

first: Maurice

last: Pérol


title: Development of an improved inhibitor of Lats Kinases to promote regeneration of mammalian organs

status: Public on Jul 06 2022

city: New York City

first: Nathaniel

last: Kastan

state: NY

address: 1305 York Ave

institute: Tri-institutional MD-PHD program, Weill Cornell

summary: To confirm that treatment with TDI‑011536 activates Yap in vivo, we collected liver and heart tissue for RNA sequencing four hours after IP injection at 200 mg/kg

overall_design: Three control mice and three experimental mice were used for the study. Each one was IP injected with 200mg/kg of LKI-2, and after four hours, liver and hearts were collected for RNA extraction and sequencing.

first: Jim

last: Hudspeth

first: Matthew

last: Paul


title: Gene expression in untreated and TGF-b2-treated equine bone marrow-derived mesenchymal stem cells

city: Raleigh

first: Alix

middle: Kay

last: Berglund

state: NC

address: 1060 William Moore Dr

department: Clinical Sciences

institute: North Carolina State University

summary: To investigate the transcriptome level changes in gene expression in equine mesenchymal stem cells following treatment with TGF-b2, we used RNA-sequencing to compare gene expression between mesenchymal stem cells from the same donor horses cultured in standard media and media containing TGF-b2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for equine bone marrow-derived mesenchymal stem cells cultured in standard media and media containing 1 ng/ml human recombinant TGF-b2.

middle: K

first: Lauren

last: Schnabel


title: Construction the adult earthworm cell atlas at single cell resolution.

first: Guoji

last: Guo

summary: Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio), fruit fly (Drosophila melanogaster) and earthworm (Eisenia andrei) are still lacking. Here, we construct the zebrafish, Drosophila and earthworm cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish, Drosophila and earthworm, and studying difference between vertebrates and Invertebrates at single cell level.

overall_design: Over 30,000 cells derived from earthworm whole-body single-cell dissociation and profiling at adult (6 and 8 months, 2 for each time point).

first: Xiaoping

last: Han

first: Renying

last: Wang

first: Jiaqi

last: Li

first: Jingjing

first: Peijing

last: Zhang


title: The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling [RNA-seq]

overall_design: RNA-seq in 786-O cells

first: Wei

last: Chen


title: Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis

city: New York

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: High-throughput methodologies are the cornerstone of screening approaches to identify novel compounds that regulate immune cell function. To identify novel targeted therapeutics to treat immune disorders and haematological malignancies, there is a need to integrate functional cellular information with the molecular mechanisms that regulate changes in immune cell phenotype. We facilitate this goal by combining quantitative methods for dissecting complex simultaneous cell phenotypic effects with genomic analysis. This combination strategy we term Multiplexed Analysis of Cells sequencing (MAC-seq), a modified version of Digital RNA with perturbation of Genes (DRUGseq). We applied MAC-seq to screen compounds that target the epigenetic machinery of B cells and assess altered humoral immunity by measuring changes in proliferation, survival, differentiation and transcription. This approach revealed that polycomb repressive complex 2 (PRC2) inhibitors promote antibody secreting cell (ASC) differentiation in both murine and human B cells in vitro. This is further validated using T cell-dependent immunization in mice. Functional dissection of downstream effectors of PRC2 using arrayed CRISPR screening uncovered novel regulators of B cell differentiation, including Mybl1, Myof, Gas7 and Atoh8. Together, our findings demonstrate that integrated phenotype-transcriptome analyses can be effectively combined with drug screening approaches to uncover the molecular circuitry that drives lymphocyte fate decisions.

overall_design: To examine the effect of EMCs on B cells, DRUGseq was performed on purified naive murine B cells stimulated with LPS (15ug/mL) with 1µM of various EMCs. To examine the changes in transcriptome and epigenome as a result of GSK126 treatment, purified B cells were stimulated with LPS (15ug/mL) and cultured with various concentrations of GSK126. The samples are harvested at indicated timepoints for RNA-seq and ChIP-seq (H3K27me3).

middle: Y

first: Stephin

last: Vervoort

first: Edwin

last: Hawkins


title: Sox8 reprograms ectoderm into ear vesicles and associated neurons [Lmx1aE1_rnaseq]

city: London

first: Andrea

last: Streit

address: Guys Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: Kings College London

summary: The vertebrate inner ear arises from a pool of progenitors with the potential to give rise to all the sense organs and cranial ganglia of the head1-6. Here we explore the molecular mechanisms that control ear specification from these progenitors. Using a multi-omics approach combined with loss-of-function experiments we identify a core transcriptional circuit that imparts ear identity, along with non-coding elements that integrate this information. This analysis places the transcription factor Sox8 at the top of the ear determination network. Introducing Sox8 into cranial ectoderm not only converts non-ear cells into ear progenitors, but also activates the cellular programmes for ear morphogenesis and neurogenesis. Thus, Sox8 emerges as a master regulator of ear identity and may be a key factor for sense organ cell reprogramming.

overall_design: Chick embryos were electroporated at ss3-6 with either Lmx1aE1- or Sox3U3-EGFP reporter constructs. Embryos were collected at somite stage (ss) 18-21 and processed for cell dissociation. For each sample, 2000 EGFP+ cells were collected by FACS and RNA libraries generated and send for PE 75bp sequencing with HiSeq4000.

first: Ailin

last: Buzzi

first: Jingchen

first: Alexandre

last: Thiery

first: Julien

last: Delile


title: Sox8 reprograms ectoderm into ear vesicles and associated neurons [ATAC-seq]

overall_design: 30 pieces OEP tissue from ss8-9 chick embryos was manually dissected, dissociated and processed for ATACseq library preparation.


title: Sox8 reprogram ectoderm into ear vesicles and auditory neurons [smartseq2]

overall_design: Chick embryos were electroporated at head fold stages with Pax2E1-EGFP reporter constructs. Embryos were grown at 38°C until the desired somite stages (ss8-9, ss11-12, ss14-15). Heads were cut rostral to the first somite and processed for dissociation. EGFP+ single cells were collected by FACS into 96 well plates containing 2.3ul of lysis buffer. Single cell RNA libraries were generated and submitted for PE 75bp sequencing with the HiSeq4000.


title: Sox8 reprograms ectoderm into ear vesicles and associated neurons [Sox8OE_rnaseq]

overall_design: Chick embryos were electroporated at head fold stages with a combination of either pCES-Sox8-mCherry + pTK-Lmx1aE1-EGFP or pCES-mCherry + pCES-EGFP constructs. Embryos were incubated at 38°C for 16-24 hrs, and processed for cell dissociation. For each sample, 4000 mCherry+EGFP double positive cells were collected by FACS and RNA libraries generated and send for PE 75bp sequencing with HiSeq4000.


title: Sox8 reprograms ectoderm into ear vesicles and associated neurons [ChIP-seq]

overall_design: 200 pieces OEP tissue from ss8-9 chick embryos was manually dissected, dissociated and processed for ChIPseq library preparation using antibodies for H3K27Ac, H3K27me3 and H3K4me3.


title: Sox8 reprogram ectoderm into ear vesicles and auditory neurons

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


title: The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia

status: Public on Jul 05 2022

city: Johnson City

first: Lev

last: Yampolsky

state: Tennessee

address: 811 Lazywood Dr

department: Biological sciences

institute: East Tennessee State University

summary: Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 hours of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis,   showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.

overall_design: Daphnia magna from four clones (FI-FSP1-16-2, IL-M1-8, GB-EL75-69,  HU-K-6, Daphnia stock collection, Basel, Switzerland) were reared either in normoxia (dissolved oxygen (DO) concentration adjusted twice daily to 8 mg/L) or in chromic mild intermittent hypoxia (DO concentration adjusted twice daily to 4 mg/L). Daphnia from both treatments were then either exposed to acute hypoxia (DO <1 mg/L) for 12 hours, or taken directly form the 8 mg/L or 4 mg/L treatments without acute hypoxia exposure.  Thus the four treatments formed a 2x2 full factorial fashion with respect to chronic and acute hypoxia: Daphnia reared at normoxia; Daphnia reared at normoxia and exposed to acute hypoxia for 12 hours; Daphnia reared in chronic mild hypoxia; and Daphnia reared in chronic mild hypoxia and exposed to acute hypoxia for 12 hours. Each sample consisted of two adult females pooled together. RNA was extracted using Qiagen RNAeasy kit (Cat ID: 74134) and quantified using a Qubit (ThermoFisher) fluorometer. Following extraction, RNAs were reverse transcribed and sequencing libraries were constructed from the cDNAs as prescribed by the Oxford Nanopore Technology (Oxford, UK) PCR-cDNA Barcoding kit protocol (SQK-PCB109), with 3 biological replicates per clone per treatment, each replicate consisting of RNA extracted from two Daphnia individuals. Barcoded samples from the 4 treatments within each clone were pooled together into 3 replicate libraries, purified separately, and pooled together immediately before adding the sequencing adapter. Libraries were then sequenced using Oxford Nanopore MinION for 24-48 hours per sequencing run, obtaining 2-4 Gb of reads in each run.

first: Millicent

middle: N

last: Ekwudo

first: Morad

middle: C

last: Malek

first: Cora

last: Anderson


title: A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals distinct transcriptional properties and context-dependent binding and regulation of target genes (RNA-Seq)

city: Shanghai, China

first: Yifan

address: Ruijin Hospital

institute: Shanghai Institute of Hematology

summary: The ETO-family transcriptional corepressors, including ETO, ETO2 and MTGR1, are all involved in leukemia-causing chromosomal translocations. In every case, an ETO-family corepressor acquires a DNA-binding domain (DBD) to form a typical transcription factor – the DBD binds to target genes, while the ETO moiety contributes essentially to its transcriptional property. A direct comparative study of these “homologous” fusion transcription factors may clarify their similarities and differences in regulating transcription and leukemogenesis. Here, we performed a side-by-side comparison between AML1-ETO and ETO2-GLIS2, the most common fusion proteins in the M2 and M7 subtypes of acute myeloid leukemia, respectively, by inducible expression of them in U937 leukemia cells. We found that, although AML1-ETO and ETO2-GLIS2 can use their own DBDs (i.e., the Runt domain of AML1 and the zinc finger domain of GLIS2) to bind DNA, they actually share a large proportion of genome-wide binding regions dependent on other cooperative transcription factors such as ETS- and CEBP-family proteins. Functionally, AML1-ETO acts as either transcriptional repressor or activator, whereas ETO2-GLIS2 mainly acts as an activator. The repressor-versus-activator functions of AML1-ETO is determined by the abundance of cooperative transcription factors/cofactors on the target genes. Through these mechanisms, AML1-ETO and ETO2-GLIS2 differentially regulate several key transcription factors that are essential for myeloid differentiation. Indeed, AML1-ETO inhibits myeloid differentiation of U937 cells, whereas ETO2-GLIS2 facilitates it. Taken together, this study is the first direct comparative study between AML1-ETO and ETO2-GLIS2 in the same cellular context, and the results provide new insights into the context-dependent transcriptional regulatory mechanisms that may underlie how these seemingly “homologous” fusion transcription factors exert distinct functions to drive different subtypes of leukemia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U937-CTR cells and its inducible over-expressed derivatives (U937-AE, U937-EG).

first: Xiaojian

last: Sun


title: Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB driven gliomas

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary: Here we describe the use of a high-throughput pipeline coupled to the commonly used tissue-specific retroviral RCAS-TVA mouse tumor model system. Utilizing next generation sequencing, we show that retroviral integration sites can be reproducibly detected in malignant stem cell lines generated from RCAS-PDGFB-driven glioma biopsies.

overall_design: 63 cell lines and 14 biopsies were analyzed for RCAS integrations. In addition, one control sample was sequenced.

first: Holger

last: Weishaupt

first: Matko

last: Čančer

first: Gabriela

last: Rosén

first: Karl

middle: O

last: Holmberg

first: Susana

last: Häggqvist

first: Ignas

last: Bunikis

first: Yiwen

last: Jiang

first: Smitha

last: Sreedharan

first: Ulf

last: Gyllensten

first: Oren

last: Becher

first: Lene

last: Uhrbom

first: Adam

last: Ameur


title: A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals distinct transcriptional properties and context-dependent binding and regulation of target genes

last: Zhang


title: Pf4 infection alters P. aeruginosa virulence

city: Evreux

first: Sylvie

last: Chevalier

address: 55 rue Saint Germain

institute: Normandie Université

summary: Pf4 is a filamentous bacteriophage integrated as a prophage into the genome of Pseudomonas aeruginosa PAO1. Pf4 virions can be produced without killing P. aeruginosa. Cell lysis can however occur during superinfection when Pf virions successfully infect a host lysogenized by a Pf superinfective variant. We have previously shown that infection of P. aeruginosa PAO1 with a superinfective Pf4 variant led to abolish twitching motility and to alter biofilm’s architecture. More precisely, the cells embedded into the biofilm were showing for most of them a filamentous morphology, that could be related to the activation of the cell envelope stress response involving both the AlgU and SigX extra cytoplasmic function sigma factors. Herein, we show that Pf4 variant-infection resulted also into a drastic dysregulation of 3,360 genes representing about 58% of P. aeruginosa’s genome, of which about 43% of the virulence factors encoding genes showing a down-regulation. Accordingly, Pf4 variant infection (termed Pf4*) causes in vivo reduction of P. aeruginosa virulence, decreased production of N-acyl-homoserine lactones and 2-alkyl-4-quinolones quorum sensing molecules, and related virulence factors, such as pyocyanin, elastase, and pyoverdine. In addition to virulence encoding genes, expression of genes involved in metabolism, including energy generation and iron homeostasis, was affected, suggesting further relationships between virulence and central metabolism. Altogether, these data suggest that Pf4 phage variant infection results in complex networks dysregulations, leading to reducing acute virulence in P. aeruginosa. This work contributes to the comprehension of the bacterial response to filamentous phage infection.

overall_design: Comparative gene expression profiling analysis of RNA-Seq data for Pseudomonas aeruginosa H103 (PAO1 derivative) treated or not by a superinfective Pf4 phage.

first: Damien

last: Tortuel

first: Ali

last: Tahrioui

first: Audrey

last: David

first: Mélyssa

last: Cambronel

first: Flore

last: Nilly

first: Thomas

last: Clamens

first: Olivier

last: Maillot

first: Magalie

last: Barreau

first: Marc

last: Feuilloley

last: Lesouhaitier

first: Alain

last: Filloux

first: Emeline

last: Bouffartigues

first: Pierre

last: Cornelis


title: APRIL drives a co-ordinated but diverse response as a foundation for plasma cell longevity

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

institute: The University of York


title: Transcriptomic analyses of the effects of hepatic insulin signaling on hepatic gene expression in the PiZ mouse model of alpha-1-antitrypsin deficiency liver disease

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

summary: RNA-Seq data on livers from 4-5 month old male PiZ mice with or without genetic disruption of insulin receptor and FOXO1 hepatic expression

overall_design: Analyses of WT, Z, and ZZ mice, WT v LIRKO v LIRKO-FOXO1-KO

first: David

middle: A

last: Rudnick

middle: F

middle: H

last: Perlmutter


title: Nanostring profiling of urothelial cells intracellularly infected with UPEC

status: Public on Jul 04 2022

city: Nashville

first: Maria

last: Hadjifrangiskou

state: TN

address: 1211 Medical Center Drive

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary: The primary goals of this study are to: determine how intracellular infection of urothelial cells with uropathogenic Escherichia coli influences urothelial cell metabolism, and determine the influence of cytochrome bd on the urothelial cell response to infection

overall_design: HTB-9 urothelial cells were propagated and infected in RPMI (Gibco) supplemented with 10% fetal bovine serum (Gibco). Cells were mock infected or infected either with UPEC isolate UTI89 or an isogenic mutant lacking cytochrome bd (∆cydAB). Bacteria were added to urothelial cell monolayers at a multiplicity of infection (MOI) of 5-10, centrifuged at 600 x g for 5 minutes to facilitate and synchronize attachment, and incubated for two hours at 37˚C in 5% CO2. Monolayers were washed thoroughly with PBS, and fresh RPMI containing 100 µg/mL gentamicin (Gibco) was added to each well to kill extracellular bacteria. Monolayers were incubated another two hours and washed with PBS prior to RNA extraction. RNA was extracted was intracellularly infected urothelial cells using TRIzol Reagent (Invitrogen) according to manufacturer’s protocols. 20 µg nuclease free glycogen (Sigma) was added to facilitate RNA precipitation. 100 ng purified RNA (20 ng/µL) was hybridized for 20 hours and analyzed using the nCounter Human Metabolic Pathways Panel (NanoString Technologies) according to manufacturer’s protocols. RNA was analyzed from at least three biological replicates per condition. Raw data were normalized and subjected to background thresholding using default settings. Normalized data were analyzed using the nCounter Advanced Analysis platform (v2.0.134) plugin for nSolver using default settings (Benjamini-Yekutieli method).

first: Connor

last: Beebout


title: APRIL drives a co-ordinated but diverse response as a foundation for plasma cell longevity [I]

summary: Antibody secreting cells (ASCs) survive in niche microenvironments, but cellular responses driven by particular niche signals are incompletely defined. The TNF superfamily (TNFSF) member A proliferation-inducing ligand (APRIL) can support the maturation of transitory plasmablasts into long-lived plasma cells. Here we explore the biological programs established by APRIL in human plasmablast. Under conditions allowing the maturation of ex vivo or in vitro generated plasmablasts, we find that APRIL drives activation of ERK, p38 and JNK, accompanied by a classical NFκB response and activation of the AKT/FOXO1 pathway. Time course gene expression data resolve co-ordinated transcriptional responses propagated via immediate early genes and NFκB targets and converging onto modules of genes enriched for MYC-targets and metabolism and cell growth related pathways. This response is shared between APRIL and an alternate TNFSF member CD40L but is not a feature of alternative niche signals delivered by IFNα or SDF1. However, APRIL and CD40L responses also diverge. CD40L drives expression of genes related to the activated B-cell state while APRIL does not. Thus, APRIL establishes a broad foundation for plasma cell longevity with features of cellular refuelling, while being uncoupled from support of the B-cell state.

overall_design: mRNA profiles of 20 samples, 4 replicates for each time/condition

first: Sophie

last: Stephenson

first: Reuben

middle: M

last: Tooze

first: Gina

last: Doody


title: RNA sequencing of short time IL-4 stimulated bone marrow derived cells with or without Elp3

city: Liège

first: Dawei

last: Chen

address: Avenue de l'Hôpital,11

department: GIGA-Stem cells

country: Belgium

institute: University of Liège

summary: Comparison of transcriptome of 2 hours IL-4 treated bone marrow derived cells (BMDMs) from WT and Elp3 KO mice

overall_design: Bone marrow cells were isolated from Wildtype mice and myeloid Elp3 deficient mice, then the cells were cultured in L929 medium and treated or not by IL4 for 2 hours.

first: Arnaud

last: Lavergne

first: Manon

last: Deckers


title: INSM2 promotes the development of neuroblastoma by regulating lipid metabolism

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Lipid metabolism plays important roles in neuroblastoma. To explore INSM2-dependent gene regulation, RNA-seq analysis was performed. Compared with the control group, INSM2 knockdown SK-N-BE(2) cells showed differently expressed genes. We found that INSM2 regulates lipid metabolism to promote the development of neuroblastoma.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-Scb) or sh-INSM2 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Haibo

last: Cao

first: Jian

last: Wang

last: Pan


title: APRIL drives a co-ordinated but diverse response as a foundation for plasma cell longevity [II]

overall_design: mRNA profiles of 27 samples, 3 replicates for each time/condition


title: A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals distinct transcriptional properties and context-dependent binding and regulation of target genes (ChIP-Seq)

first: Yifan

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA-tag in U937 cells.

first: Xiaojian

last: Sun


title: Single Cell sequencing of human bronchial Brush cells in IPF and disease controls

status: Public on Jul 03 2022

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

summary: The study aimed to compare the gene expression profiles at a single cell level in bronchial brush cells between patients with idiopathic pulmonary fibrosis and disease controls.

overall_design: Single-cell RNA sequenceing data was generated from bronchial Brushes fo 9 IPF patients with UIP pattern and 6 nonUIP controls

first: Naftali

last: Kaminski

first: Antje

last: Prasse


title: RNASeq to investigate ETV4 and ETV5 function in human foetal lung tip progenitor cells

status: Public on Jul 02 2022

city: Cambridge

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: In order to understand transcription factor ETV4 and ETV5 function, we have knocked down ETV4 and ETV5 synergistically in human foetal lung tip progenitor organoids using an inducible CRISPRi system. We discovered that ETV double knockdown led to organoid cell self-renewal defects

overall_design: We used 2 independent organoid parental lines infected with an inducible CRISPRi system. 2 different non-targeting control (NT) gRNAs, which do not bind to anywhere of the genome, 2 gRNA combinations targeting for ETV4 and ETV5 double knockdown, were used to control non-specific effect from organoid lines, lentiviral infection and different gRNAs.

first: Emma

middle: L

last: Rawlins


title: DLL4 and VCAM1 enhance the emergence of T cell-competent hematopoietic progenitors from human pluripotent stem cells

city: Vancouver

first: Peter

last: Zandstra

state: British Columbia

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

summary: T cells show tremendous efficacy as cellular therapeutics. However, obtaining primary T cells from human donors is expensive and variable. Pluripotent stem cells (PSCs) have the potential to provide a renewable source of T cells, but differentiating PSCs into hematopoietic progenitors with T cell potential remains a significant challenge. Here, we report an efficient serum- and feeder-free system for differentiating human PSCs into hematopoietic progenitors and T cells. This fully-defined approach allowed us to study the impact of individual proteins on blood emergence and differentiation. Providing DLL4 and VCAM1 during the endothelial-to-hematopoietic transition enhanced downstream progenitor T cell output by ~80-fold. These two proteins synergised to activate notch signalling in nascent hematopoietic stem and progenitor cells and VCAM1 additionally promoted an inflammatory transcriptional program. We also established optimised media formulations that enabled efficient and chemically defined maturation of functional CD8αβ+, CD4-, CD3+, TCRαβ+ T cells with a diverse TCR repertoire.

overall_design: CD34+ cells derived from IPSCs were plated on one of four coating conditions (Uncoated plates, VCAM1 coated, DLL4 coated, or DLL4+VCAM1 coated plates) and were differentiated for 5 days in EHT media. We collected non-adherent cells at Day 5 of this process from each of the conditions and analyzed using scRNAseq.

first: Yale

middle: S

last: Michaels

first: John

last: Edgar

first: Matthew

last: Major

first: Elizabeth

last: Castle

first: Carla

last: Zimmerman

first: Ting

last: Yin

first: Andrew

last: Hagner

first: Charles

last: Lau

first: Han

last: Hsuan-Hsu

first: M

last: Ibañez-Rios

first: Lauren

last: Durland

first: David

middle: J

last: Knapp


title: NOTCH1 signaling during CD4+ T-cell activation alters transcription factor networks and enhances antigen responsiveness

city: Seattle

first: Scott

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

overall_design: Refer to individual Series


title: NOTCH1 signaling during CD4+ T-cell activation alters transcription factor networks and enhances antigen responsiveness [IN_VIVO_AW3]

summary: Adoptive transfer of T cells expressing chimeric antigen receptors (CAR-T) effectively treats refractory hematologic malignancies in a subset of patients but can be limited by poor T-cell expansion and persistence in vivo. Less differentiated T-cell states correlate with the capacity of CAR-T to proliferate and mediate antitumor responses, and interventions that limit tumor-specific T-cell differentiation during ex vivo manufacturing enhance efficacy. NOTCH signaling is involved in fate decisions across diverse cell lineages and in memory CD8+ T cells was reported to upregulate the transcription factor FOXM1, attenuate differentiation, and enhance proliferation and antitumor efficacy in vivo. Here, we used a cell-free culture system to provide an agonistic NOTCH1 signal during naïve CD4+ T-cell activation and CAR-T production and studied the effects on differentiation, transcription factor expression, cytokine production, and responses to tumor. NOTCH1 agonism efficiently induced a stem cell memory phenotype in CAR-T derived from naïve but not memory CD4+ T cells and upregulated expression of AhR and c-MAF, driving heightened production of interleukin-22 (IL-22), IL-10, and granzyme B. NOTCH1-agonized CD4+ CAR-T demonstrated enhanced antigen responsiveness and proliferated to strikingly higher frequencies in mice bearing human lymphoma xenografts. NOTCH1-agonized CD4+ CAR-T also provided superior help to cotransferred CD8+ CAR-T, driving improved expansion and curative antitumor responses in vivo at low CAR-T doses. Our data expand the mechanisms by which NOTCH can shape CD4+ T-cell behavior and demonstrate that activating NOTCH1 signaling during genetic modification ex vivo is a potential strategy for enhancing the function of T cells engineered with tumor-targeting receptors.

overall_design: 6 samples (3 controls)

first: Alec

last: Wilkens

first: Stanley

middle: R

last: Riddell


title: Transcriptomic analysis of CO2-treated strawberries with enhanced resistance to softening and oxidative stress

city: Fuencarral-El Pardo,  Madrid

first: Crisanto

last: Gutierrez

state: Madrid

address: C. Nicolás Cabrera, 1

department: Replicación del DNA, división celular y cromatina

country: Spain

institute: CBMSO-CSIC

summary: Identification of molecular determinants underlying the firming effect and  protection gainst senescence of high CO2 using diploid strawberries: One of the greatest threats to strawberries is rapid softening, however firmness increases during or following high CO2 levels. Firmness at consumption is an obvious target for preventing fruit loss and to gain eating quality. Therefore, we performed RNA-seq analysis, construcing a weighted gene co-expression network analysis (WGCNA) to identify which molecular determinants play a role in cell wall integrity , using strawberries under storage conditions. Differential gene expression (DEG) analysis showed that cell wall structural architecture of firmer CO2 -treated strawberries is characterised by xyloglucans stabilisation attributed mainly to a down-regulation of Csl-like E1, β-glc, XTH15 and maintenance of expression levels of FUT and GMP as well as improved lamella integrity linked to a down-regulation of RG-lyase and PL-like. The preservation of cell wall elasticity together with the up-regulation of LEA, EXPA4, and MATE transporters required to maintain cell turgor, are the mechanisms controlled by high CO2. In stressed air-cold stored strawberries, in addition to an acute softening, there is a preferential transcript accumulation of genes involved in lignin and raffinose pathways. The oxidative stress involving jasmonate and H2O 2 is characteristic of senescent non-cold stored samples. The results are fundamental and practical for breeding in strawberry industry.

overall_design: The ripe Mara des Bois strawberries (Fragaria vesca) immediately after harvest (2 hours) were used as the control (AH). Those placed directly in a chamber at 20 ºC and 80 % RH for two days were the non-cold stored (NCS), while the strawberries transferred at 20ºC for 1 day following the 7-day storage at 1ºC (conditions employed to simulate a time in transit) were used to analyse the air-cold stored fruit (ACS) or CO2 -cold stored fruit (CCS). CCS were pretreated for two days with a gas mixture containing 18 % CO2 + 18 % O2 + 64 % N2 and then air-ventilated for another five days (CCS).

first: I

last: del Olmo

last: Romero

first: MD

last: Alvarez

middle: T

last: Sanchez-Ballesta

middle: I

last: Escribano

first: C

last: Merodio


title: Super-Enhancer Hypermutation Alters Oncogene Expression in B-cell Lymphoma

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University


title: Single cell sequencing on pediatric sialoblastoma

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

summary: As a rare embryonal malignant tumor, sialoblastoma recapitulates primitive salivary gland anlage, usually locating in parotid or submandibular gland and diagnosed at birth or during infancy. The transcriptome profiles as well as intertumoral heterogeneity of sialoblastoma have not yet been investigated. Here, through single-cell RNA sequencing of tumor samples from the same patient before and after chemotherapy, we constructed the first cell transcriptomic atlas of sialoblastoma. By calculating differentially expressed genes and performing gene ontology analysis, we found downregulation of cell proliferation while upregulation of epidermic differentiation pathways after chemotherapy. In addition, we demonstrated distinct transcriptional programs embedded in tumor, including cycling cells, basaloid cells, ductular cells, myoepithelial-like cells and transitional states. The proportion of cycling cells and transitional state cells decreased after chemotherapy whereas the proportion of basaloid cells and myoepithelial cells increased. Taken together, we offered a valuable resource for deciphering cellular heterogeneity as well as adaptive change of tumor cells after chemotherapy, providing insights into clinical management of sialoblastoma.

overall_design: A 6-month-old infant with growing left-sided firm cheek mass was referred to our institution and diagnosed as sialoblastoma through fine needle biopsy and following pathological examination. After four cycles of neoadjuvant chemotherapy adopting intermediate-risk neuroblastoma regimen (carboplatin, cyclophosphamide/etoposide, and doxorubicin), the volume of tumor did not shrink significantly.  We obtained the tumor tissue from the same  patient before and after chemotherapy ,and performed single-cell sequencing.

first: Ran

last: Yang

first: Yong

last: Zhan

first: Jun

last: Li

first: Wei

last: Yao

first: Rui


title: Mechanism of tolerance improvement of Escherichia coli W against 3-hydroxypropionic acid by deletion of a less characterized transcription factor yieP   (ChIP-exo data)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: The mechanism of 3-HP tolerance related to YieP was elucidated. The genome-wide analysises were carried out to find out the genes reponsible for 3-HP tolerance.

overall_design: ChIP-exo of yieP myc-tagged cells

first: Thuan

middle: P

last: Nguyen-Vo

first: Seyoung

last: Ko

first: Jung

first: Sunghoon

last: Park


title: Comparative spatial transcriptomic and single-cell analyses of human nail units and hair follicles demonstrate transcriptional similarities between the onychodermis and follicular dermal papilla

city: Seoul

first: Dongyoun

last: Lee

address: 81, Irwon-ro, Gangnam-gu

institute: Samsung Medical Center

summary: The nail unit and hair follicle are both hard keratin-producing organs that share various biological features. In this study, we demonstrated the presence of a nail-specific mesenchymal population called onychofibroblasts within the onychodermis. Onychodermis and follicular dermal papilla (DP) both expressed WNT and bone morphogenetic protein (BMP) signaling molecules. To analyze the function of BMP5 in nail development, we treated cultured human nail matrix keratinocytes (NMKs) with BMP5, which are highly expressed by onychofibroblasts. We observed increased expressions of hard keratin and HOXC13.

overall_design: We evaluated the effect of BMP5, which is highly expressed by onychofibroblasts, in nail-specific epithelial cells in vitro through the RNAseq analysis.

first: Joonho

last: Shim


title: Effect of Hairy and Enhancer of Split 1 (HES1) activation on gene expression of mature osteoclasts

status: Public on Jul 01 2022

city: Farmington

first: Ernesto

last: Canalis

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

summary:
To investigate the role of HES1 in osteoclast differentiation and function, bone marrow-derived macrophages (BMMs) were derived from CtskCre/WT;RosaHes1 and control (Rosa[STOP]Hes1 ) mice and were differentiated into mature osteoclasts.
We then performed gene expression profiling analysis using data obtained from RNA-seq of conrol and HES1-overexpressing osteoclasts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and HES1 over-expressing osteoclasts

first: Jungeun

last: Yu


title: Examining the role of murine norovirus (MNV)-infection on intraepithelial lymphocytes (IELs).

city: New York

first: Ken

last: Cadwell

address: 430 East 29th Street Suite 424

institute: NYU Langone School of Medicine

summary: We examined how MNV-infection affects the population and function of IELs in vivo.

overall_design: We infected B6 naïve mice with 3x10^6 PFUs MNV-CR6. On day 10 post infection, we harvested their IELs and sorted CD45+CD103+ populations for single cell RNA-Seq analysis.

first: Yu

last: Matsuzawa-Ishimoto

first: Joseph

last: Devlin

first: Eugene

last: Rudensky


title: Transcriptional and immune landscape of cardiac sarcoidosis

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

summary: Cardiac involvement is an important determinant of mortality amongst sarcoidosis patients. While granulomatous inflammation is a hallmark finding in cardiac sarcoidosis, the precise immune cell populations that comprise the granuloma remain unresolved. Furthermore, it is unclear how the cellular and transcriptomic landscape of cardiac sarcoidosis differs from other inflammatory heart diseases. We leveraged spatial transcriptomics (GeoMx DSP) and single nucleus RNA sequencing (snRNAseq) to elucidate the cellular and transcriptional landscape of cardiac sarcoidosis. Using GeoMX DSP technology, we compared the transcriptomal profile of CD68+ rich immune cell infiltrates in human cardiac sarcoidosis, giant cell myocarditis, and lymphocytic myocarditis. We performed snRNAseq of human cardiac sarcoidosis to identify immune cell types and examined their transcriptomic landscape and regulation. Using multi-channel immunofluorescence staining, we validated immune cell populations identified by snRNAseq, determined their spatial relationship, and devised an immunostaining approach to distinguish cardiac sarcoidosis from other inflammatory heart diseases. Despite overlapping histological features, spatial transcriptomics identified transcriptional signatures and associated pathways that robustly differentiated cardiac sarcoidosis from giant cell myocarditis and lymphocytic myocarditis. snRNAseq revealed the presence of diverse populations of myeloid cells in cardiac sarcoidosis with distinct molecular features. We identified GPNMB as a novel marker of multinucleated giant cells and predicted that the MITF family of transcription factors regulated this cell type. We also detected additional macrophage populations in cardiac sarcoidosis including HLA-DR+ macrophages, SYTL3+ macrophages and CD163+ resident macrophages. HLA-DR+ macrophages were found immediately adjacent to GPMMB+ giant cells, a distinct feature compared with other inflammatory cardiac diseases. SYTL3+ macrophages were located scattered throughout the granuloma and CD163+ macrophages, CD1c+ dendritic cells, non-classical monocytes, and T-cells were located at the periphery and outside of the granuloma. Finally, we demonstrate mTOR pathway activation is associated with proliferation and is selectively found in HLA-DR+ and SYLT3+ macrophages. In this study, we identified diverse populations of immune cells with distinct molecular signatures that comprise the sarcoid granuloma. These findings provide new insights into the pathology of cardiac sarcoidosis and highlight opportunities to improve diagnostic testing.

overall_design: We performed snRNAseq of human cardiac sarcoidosis (4 samples) and ischemic cardiomyopathy (3 samples) to identify immune cell types and examined their transcriptomic landscape and regulation.

first: Jing

last: Liu

first: Lulu

last: Lai

first: Ana

last: Villanueva

first: Andrew

last: Koenig

first: Gregory

last: Bean

first: Dawn

middle: E

last: Bowles

first: Carolyn

last: Glass

first: Michael

last: Watson

first: Kory

last: Lavine

first: Chieh-Yu

last: Lin


title: RNA-seq of Tnpo3fl/fl pro-B cells

city: Freiburg im Breisgau

first: Marc

last: Bayer

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Gene expression analysis in Tnpo3fl/fl mb1Cre compared to Tnpo3+/+ mb1Cre pro-B cells.

overall_design: B220+CD43+HSA+ pro-B cells were sorted from the bone marrow of two Tnpo3fl/fl mb1Cre mice (51, 63) or two Tnpo3+/+ mb1Cre mice (55, 69) and subjected to RNA-seq analysis.

first: Senthilkumar

last: Ramamoorthy

first: Sören

last: Boller

first: Rudolf

last: Grosschedl


title: Gene expression analysis in Tyk2 deficient AOM/DSS colorectal tumors in mice

city: Vienna

first: Robert

last: Eferl

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

summary: The goal of this study was to determine differences in gene expression profiles in colonic tumors of AOM/DSS treated mice with a total (Tyk2KO) or conditional deletion of Tyk2 in the intestinal epithelium (Tyk2DIEC).

overall_design: Analysis gene expression profile from AOM/DSS induced colon tumors in Tyk2wt, Tyk2KO Tyk2fl and Tyk2DIEC mice.

first: Stefan

last: Moritsch


title: Phenotyping tumor-immune microenvironment in vivo in skin cancer patients

first: Aditi

last: Sahu

address: 9207-B, Dermatology Service, MSKCC, 530E, 74th street

department: Dermatology Service

institute: Memorial Sloan Kettering Cancer Center

summary: Phenotyping of tumors into hot, altered, or cold based on assessment of only T-cell infiltration in static tumor biopsies provides suboptimal prediction of immunotherapy response. In vivo dynamic mechanisms within the tumor microenvironment such as tumor angiogenesis and leukocyte trafficking also play a central role in modulating anti-tumor immunity and therefore immunotherapy response. Here, we report novel tumor immune microenvironment (TiME) phenotyping in vivo in patients with non-invasive spatially-resolved cellular-level imaging based on endogenous contrast.  Investigating skin cancers as a model, with reflectance confocal microscopy (RCM) imaging, we determined four major phenotypes with variable prevalence of vasculature (Vasc) and inflammation (Inf) features: VaschiInfhi, VaschiInflo, VascloInfhi and Vascmed/hiInflo. The VaschiInfhi phenotype correlates with high immune activation, exhaustion, and vascular signatures while VaschiInflo with endothelial anergy and immune exclusion. Automated quantification of TiME features demonstrates moderate-high accuracy and correlation with corresponding gene expression. Prospectively analyzed response to topical immunotherapy show highest response in VascloInfhi, and reveals the added value of vascular features in predicting treatment response.

overall_design: 14 skin cancer (basal call carcinoma, BCC) tissues from human patients

first: Candice

last: Byers

first: Pratik

last: Chandrani

first: Teguru

last: Tembo

first: Milind

last: Rajadhyaksha


title: EBF1 ChIP-seq after NICD1 induction

summary: Quantitative EBF1 ChIP-seq analysis in EBF1wt- or EBF1E271A-expressing pro-B cells harboring doxycycline-inducible NICD1 expression after doxycycline treatment.

overall_design: Ebf1-/- c-kit+ lymphocyte progenitors isolated from fetal liver were first transduced with a doxycycline-inducible NICD1 expression system, selected for retroviral expression and then transduced with EBF1wt- or EBF1E271A-expressing retroviruses. Cells were sorted for retroviral expression, in vitro differentiated into pro-B cells and treated with doxycyline for 6 hours prior to EBF1 ChIP-seq analysis. Human B cell spike-in chromatin was used for spike-in normalization.


title: RNA-seq of EBF1E271A-transduced progenitors

summary: Gene expression analysis in Ebf1-/- lymphocyte progenitors complemented with EBF1wt or EBF1E271A and co-cultured with OP9-DL1 feeder cells.

overall_design: Ebf1-/- c-kit+ lymphocyte progenitors isolated from fetal liver were transduced with EBF1wt- or EBF1E271A-expressing retroviruses, sorted for retroviral expression and co-cultured with OP9-DL1 feeder cells. For RNA-seq analysis, either GFP+CD19- progenitors were sorted after 7 days, or GFP+ progenitors were sorted after 3 days. 3 independent experiments were analyzed for each progenitor population.


title: Next generation sequencing for quantitative analysis of wild type versus Sox9-conditionally deleted embryonic archicortex transcriptome

city: London

first: Alessia

last: Caramello

state: London

address: The Francis Crick Institute, 1 Midland Road

institute: The Francis Crick Institute

summary:
Purpose: identify potential downstream targets of SOX9 in the cortical hem (CH) and dentate neuroepithelium (DNE) of the developing archicortex, comparing control with Sox9-conditionally deleted tissue using either Sox1Cre (active in both DNE and CH) or NestinCre (active in the DNE only)
Methods: archicortex mRNA profiles of E12.5 and E13.5 control, Sox9fl/fl;Sox1Cre and Sox9fl/fl;NestinCre conditional embryos were generated by deep sequencing, in quadruplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed to identify differentially expressed genes (DEGs) between Sox9fl/fl;Sox1Cre and Sox9fl/fl;NestinCre conditional embryos, comnpared to their controls. DEGs where further analysed singularly or in pathway analysis. Hopx downregualtion was validated in vivo with immunostaining.
Results: DEGs found in Sox9fl/fl;Sox1Cre/+ but not in Sox9fl/fl;Nestin-Cre mutants might specifically indicate genes regulated by SOX9 in the CH. Conversely, genes commonly affected in both mutants, might focus on pathways regulated by SOX9 in the DNE. We screened these lists to identify pathways in which SOX9 is already known to be involved or that are relevant to this developmental context. We identified the neurogenic factor NeuroD4 to be upregulated in Sox9fl/fl;Sox1Cre/+ mutants, and conversely the astrocytic markers (Atp1a2, Vim) to be downregulated, potentially indicative of the role of Sox9 in gliogenesis induction, which, in its absence, is delayed in favour of neurogenesis (Kang et al. 2012; Martini et al. 2013). We also observed a reduction in components of the NOTCH and WNT pathways (Notch1, Wnt7b, Fzd1), and of genes involved in cell adhesion, migration, and epithelial to mesenchymal transition (EMT; Limk2, Arhgap35, Fn1, Col2a1, Myh14). These results are consistent with SOX9 being involved in or interacting with both NOTCH and WNT pathways (Leung et al. 2016; Martini et al. 2013), and with previously identified roles of SOX9 in gliogenesis induction (Kang et al. 2012) as well as EMT during neural crest cells development (Liu et al. 2013; Lincoln et al. 2007). The gene Hopx was idneitified to be affected by absence of SOX9 specifically in the CH. We validated this result with in vivo immunostaining and show that HOPX is indeed highly expressed in the CH, and only mildly in the DNE. However, its expression is downregulated in both regions in absense of SOX9.
Conclusions: Our study represents the first analysis of archicortex transcriptome at two consecutive developmental stages in both controls and Sox9-conditionally deleted embryos. The strategic comparison of two Sox9-conditional deletion allows dissection of SOX9 downstream targets in two adjacent regions of the developing archicortex, which we validated with immunostainings  in vivo. Our methods allows to overcome the limitations of bulk RNA sequecing which does not provide spatial resolution and could be applied in other contexts to permit the dissection of complex biologic functions.

overall_design: Bulk mRNA extracted from E12.5 and E13.5 embryonic archicortex manually dissected from controls, Sox9fl/fl;Sox1Cre and Sox9fl/fl;NestinCre conditional embryos

first: Miriam

last: Sopena


title: RNA-Seq analysis of DLBCL cell lines

first: Laura

last: Pasqualucci

summary: Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.

overall_design:
Total RNA was extracted from cells in log phase of growth using the TRIzol reagent and assessed for quality and quantified using the Bioanalyzer 2100 (Agilent). Samples (all with RIN > 9) were used to generate RNA-seq libraries with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus, followed by high throughput sequencing on the Illumina HiSeq 4000 (60 million reads, 2 × 100 bp mode) system.

Please note that the following updates have been made on Oct 17, 2022:

The processed data (linked to the Series records) and data processing description have been updated.
The GSM6285354 sample title has been updated from (incorrectly named) HOCI-LY1 to HLY1.
The (incorrectly-named) GSM6285354 raw files have been replaced with the (identical but correctly-named) files.

first: Antony

last: Baden Holmes


title: Pregestational Diabetes Alters Cardiac changes

city: GUWAHATI

first: SANJAY

middle: K

last: BANERJEE

state: ASSAM

address: CHANGSARI

country: India

institute: NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH

summary:
Objective: To evaluate the altered expression of genes due to hyperglycaemia during foetal development in heart.
Methods: To understand the molecular defects in the two-days old neonatal rats, diabetic female rats were bred with healthy male rats and collected two days old hearts from neonates. Heart mRNA profiles of two-day-old neonatal rats were generated by RNA sequencing, in quadruplicate, using Illumina HiSeq.
Results: Using an optimized data analysis workflow, we mapped about 27 million sequence reads per sample to the rat genome (build Rnor_6.0) and identified 25456 transcripts in the heart of the neonatal rats. Approximately 4% of the transcripts showed differential expression between the Control and PGDM (pregestational diabetes mellitus) heart, with a fold change ≥2 and p value <0.05.
Conclusions: Transcriptomic profiling of the RNA-seq data revealed that several of the altered genes were associated with cardiac pathogenesis in neonatal heart during PGDM.

overall_design: Neonatal heart mRNA profiles of two-day old rats

first: Md

last: Alam

first: Sanjay

last: Banerjee


title: Monocyte and macrophage lipid accumulation results in downregulated type-I interferon responses [RNA-seq]

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

summary: Macrophages are critical components of atherosclerotic lesions and their pro- and anti-inflammatory responses influence atherogenesis. Type-I interferons (IFNs) are cytokines that play an essential role in antiviral responses and inflammatory activation and have been shown to promote atherosclerosis. Although the impact of type-I IFNs on macrophage foam cell formation is well-documented, the effect of lipid accumulation in monocytes and macrophages on type-I IFN responses remains unknown. Here we examined IFN stimulated (ISG) and non-ISG inflammatory gene expression in mouse and human macrophages that were loaded with acetylated LDL (acLDL), as a model for foam cell formation. We found that acLDL loading in mouse and human macrophages specifically suppressed expression of ISGs and IFN-β secretion, but not other pro-inflammatory genes. The down regulation of ISGs could be rescued by exogenous IFN-β supplementation. Activation of the cholesterol-sensing nuclear liver X receptor (LXR) recapitulated the cholesterol-initiated type-I IFN suppression. Additional analyses of murine in vitro and in vivo generated foam cells confirmed the suppressed IFN signaling pathways and suggest that this phenotype is mediated via down regulation of interferon regulatory factor binding at gene promoters. Finally, RNA-seq analysis of monocytes of familial hypercholesterolemia (FH) patients also showed type-I IFN suppression which was restored by lipid-lowering therapy and not present in monocytes of healthy donors. Taken together, we define type-I IFN suppression as an athero-protective characteristic of foamy macrophages. These data provide new insights into the mechanisms that control inflammatory responses in hyperlipidaemic settings and can support future therapeutic approaches focusing on reprogramming of macrophages to reduce atherosclerotic plaque progression and improve stability.

overall_design: In total, 6 samples were analyzed: 3 biological replicates of DMSO (notx) treated BMDMs and 3 biological replicates of DMSO + GW3965 (17h) treated BMDMs.

first: Hung-Jen

last: Chen

first: Cindy

last: van Roomen

first: Guillermo

last: Griffith

first: Ricky

last: Siebeler

first: Annette

last: Neele

first: Jeffrey

last: Kroon

first: Marten

last: Hoeksema

first: Menno

last: deWinther


title: Tnpo3 enables EBF1 function in conditions of antagonistic Notch signaling

first: Marc

last: Bayer

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

overall_design: Refer to individual Series


title: miR106b inhibition improves myogenic regenerative capacity of murine and human muscle stem cells and attenuates muscular dystrophy phenotype

city: Jaen

first: Francisco

last: Hernandez-Torres

address: Paraje Las Lagunillas s/n

department: Experimental Biology

institute: University of Jaen

summary: Satellite cells (SCs), the skeletal muscle stem cells, display functional heterogeneity linked to their regenerative potential. Dramatic changes in their behaviour are also associated to muscle wasting diseases. Therefore, understanding the mechanisms controlling satellite cell heterogeneous behaviour during muscle regeneration and diseases has become increasingly important for regenerative medicine. Here, we show that miR-106bis expressed in Myf5- quiescent SCs and downregulated during SC activation and muscle regeneration. In vitro and in vivo studies to show that miR106b inhibition enhances the regenerative capability of murine and human SCs by increasing myogenic precursors. miR106b is increased in dystrophic mice and intramuscular injection of antimiR enhances muscle regeneration accompanied by significant functional recovery. miR-106b is also elevated in human dystrophic SCs and its inhibition improves intrinsic proliferative defects, increasing their myogenic differentiation potential. Therefore, this study identifies miR-106b as compelling candidate to consider for potential clinical studies.

overall_design: In order to analyze expression profile changes as a result of miR106b inhibition during muscle regeneration in DMD mice model, cardiotoxin along either with anti-miR106b or  with anti-miR-Scrambled control were injected in tibialis anterior muscles. Samples were collected 3 or 5 days after injection. Each experimental point is represented by an animal tripilcate.  AD3 represents 3 days post-injection of anti-miR106b treatment experimetal points (n=3),  CD3 represents 3 days post-injection of anti-Scrambled control experimetal points (n=3), AD7 represents 7 days post-injection of anti-miR106b treatment experimetal points (n=3),  CD7 represents 7 days post-injection of anti-Scrambled control experimetal points (n=3). Therefore, the number of samples(experimental points)  is 12.

first: Hernandez-Torres

last: Francisco

first: Aranega

last: Amelia Eva


title: MEOX2 homeobox gene promotes growth of malignant gliomas [ACT-Seq & CUT&TAG]

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 460

institute: Heidelberg University Hospital

summary: Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10 and aberrantly activated RTK signaling pathways. Here, we identify mesenchymal homeobox 2 (MEOX2) as a salient oncogenic transcription factor candidate with increased expression in GBMs. Our results suggest that MEOX2 can enhance ERK signaling through a feed-forward mechanism. We show that MEOX2 overexpression can lead to increased growth in bona fide GBM implantation models and cooperates with loss of p53 and PTEN in cerebral organoid models of human malignant gliomas to induce cell proliferation. Furthermore, using high-throughput genomics, we identify transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor.

overall_design: Identification of MEOX2 binding sites and target genes in glioblastoma


title: MEOX2 homeobox gene promotes growth of malignant gliomas [RNA-Seq]

overall_design: Examination of transcriptomic alterations assciated with MEOX2 loss (using CRISPR/Cas9 in patient-derived GBM tumorspheres) or overexpression (in patient-derived GBM tumorspheres and immortalized human astrocytes).


title: Bulk RNA sequencing of Vegfr3 fl/fl (Ctrl) and Vegfr3 fl/fl;prox1creERT2 (Vegfr3iLKCko) mouse conjunctival tissue with or without allergic eye disease

status: Public on Jun 30 2022

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary:
To systematically evaluate the role of pro-lymphangiogenic VEGFR3 signal in allergic eye disease
we performed RNAseq analysis of unchallenged Ctrl (without allergic eye disease), OVA-challenged Ctrl (with allergic eye disease) and OVA-challenged Vegfr3iLECko (with allergic eye disease) mouse conjunctiva

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for unchallenged Ctrl, OVA-challenged Ctrl and OVA-challenged Vegfr3iLECko mouse conjunctiva tissue.

first: Feng

last: Zhang

first: Bingsheng

last: Lou

first: Wanwen

last: Wu


title: Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

institute: IMP

summary: Plasma cells (PCs) and their progenitors plasmablasts (PBs) are essential for the acute and long-term protection of the host against infections by providing high levels of highly specific antibodies. Several factors, like Blimp1 and Irf4, are already known to be essential for PC and PB differentiation and survival. We set out to identify additional genes, that are essential for PB development by CRISPR-Cas9 screening of 3,000 genes for the loss of PBs by employing the inducible GC B (iGB) culture system and Rosa26Cas9/+ mice. Among our hits in the screen were Mau2 and Nipbl, which are known to contribute to the loop extrusion function of the cohesin complex. Other examples of promising hits were Taf6, Stat3, Ppp6c and Pgs1. We thus provide a new set of genes, which are important for PB development.

overall_design:
We set out to identify genes that are essential for PB development by CRISPR-Cas9 screening of 3,000 genes for the loss of PBs by employing the inducible GC B (iGB) culture system and Rosa26Cas9/+ mice.
Four conditions, with two biological replicates each.

first: Theresa

last: Pinter

first: Maria

last: Fischer

first: Michaela

last: Fellner

first: Julian

last: Jude

first: Markus

last: Schäfer

first: Johannes

last: Zuber

first: Meinrad

last: Busslinger

first: Miriam

last: Wöhner


title: Next generation sequence of RNA in hematoma basal ganglia tissue of ICH mice model

city: Hangzhou

first: Yonghe

last: Zheng

state: Zhejiang

address: Jiefang Road 88th

institute: department of neurosurgery, Zhejiang University School of Medicine Second Affiliated Hospital

summary: To study the regulation of neuroinflammatory genes following an ICH insult, we induced ICH in C57 mice and analyzed the mRNA expression profile in the brain by RNA seq

overall_design: Expression profile of RNAs in hematoma basal ganglia tissue of ICH mice model

first: Xiongjie

last: Fu


title: MEOX2 homeobox gene promotes growth of malignant gliomas


title: Total RNA from wild-type, aar2-1 and aar2-2 mutant

city: Riverside

first: Xuemei

last: Chen

state: CALIFORNIA

address: 900 University AVe

institute: University of California

summary: We profiled total RNA from wild-type, aar2-1 and aar2-2 mutant

overall_design: Tota RNA from  wild-type, aar2-1 and aar2-2 mutant seedlings were examined. Three biological replicates were included.

first: Lusheng

last: Fan

first: Bin

last: Gao


title: RNA-seq analysis after overexpression of miR-148a in keratinocytes

city: Nottingham

first: Mohammed

last: Ahmed

address: Clifton Lane

institute: Nottingham Trent University

summary: Identification of the trasncriptional changes linked to over expression of miR-148a in kerratinocytes

overall_design: Control and overexpression of miR-148a (pro-miR-148a) in primary mouse epidermal keratinocytes

first: M


title: Multiomics analyses reveal the mechanical-stress-dependent changes in trabecular meshwork cytoskeletal-extracellular matrix interactions

city: Indianapolis

first: Padmanabhan

last: Pattabiraman

state: IN

address: Department of Ophthalmology, Room number 402, 1160 West Michigan Street

department: Ophthalmology

institute: Indiana University Purdue University Indianapolis

summary: The purpose of this study was to understand the response of trabecular meshwork under mechanical stretch using a multi-omics approach.

overall_design: Gene expression analysis of trabecular meshwork cells subjected to cyclic mechanical stretch compared to unstretched controls. Primary HTM cell cultures were subjected to 15% stretching at 0.69 Hz frequency for 8 h for mRNA sequencing analysis.

first: Avinash

last: Soundararajan

first: Ting

last: Wang

first: Aruna

last: Wijeratne

first: Amber

last: Mosley

first: Faith

middle: C

last: Harvey

first: Sanjoy

last: Bhattacharya


title: EBF1 contributes to the balance of lympho-myeloid fate in haematopoietic progenitors via B-lymphoid priming and Cebpa antagonism [10x]

city: Freiburg

first: Aurelie

last: Lenaerts

department: Cellular and Molecular Immunology

summary: Haematopoietic stem cells (HSC) and multipotent progenitor cells (MPP) generate all cells of the blood system, although cellular heterogeneity and bias in lineage potential have been observed. Here, we examined whether lineage-specific transcription factors, such as the B-lineage determinant EBF1, establish lineage bias in early progenitors. We detect low level EBF1 expression in myeloid-biased MPP3 and lymphoid-biased MPP4 cells, and show that Ebf1-deficient animals display reduced HSC quiescence and repopulation capacity, enhanced myelopoiesis and enhanced myeloid differentiation potential of MPP3 and MPP4 cells. Bulk and single-cell RNA-seq analysis revealed a CEBPa-driven myeloid transcriptome in Ebf1-deficient progenitors, and we find that EBF1 binds and potentially antagonizes the haematopoietic Cebpa enhancer. In MPP3 cells, EBF1 additionally primes enhancers associated with B-lymphoid genes that gain expression in common lymphoid progenitors. Thus, our study identifies EBF1 as an important determinant in regulating the balance of myeloid versus lymphoid potential in the earliest hematopoietic progenitors.

overall_design: Single-cell RNA seq of 10000 cells of LK and LSK populations/genotype were combined per sex, from Ebf1-wt Tie2Cre and Ebf1-flox Tie2Cre mice. 4 biological replicates per genotype.

first: Iwo

last: Kucinski

first: Rudolf

last: Grosschedl


title: EBF1 contributes to the balance of lympho-myeloid fate in haematopoietic progenitors via B-lymphoid priming and Cebpa antagonism

type: Genome variation profiling by high throughput sequencing


title: EBF1 contributes to the balance of lympho-myeloid fate in haematopoietic progenitors via B-lymphoid priming and Cebpa antagonism [ATAC-seq]

overall_design: Bulk ATAC seq from 5000 MPP3 and MPP4 cells, from Ebf1-wt Tie2Cre and Ebf1-flox Tie2Cre mice. 2 biological repliccates per genotype, per cell type.

first: Ward

last: Deboutte


title: EBF1 contributes to the balance of lympho-myeloid fate in haematopoietic progenitors via B-lymphoid priming and Cebpa antagonism [Bulk RNA-seq]

overall_design: Bulk RNA seq from sorted MPP3 and MPP4 cells, from Ebf1-wt Tie2Cre and Ebf1-flox Tie2Cre mice. 4 biological replicates per genotype, per cell type.