title: Cancer coopts differentiation of B-cell precursors into macrophages [human]

last: De

summary: We recently reported that some cancers induce accumulation of bone marrow (BM) B-cell precursors in the spleen to convert them into metastasis-promoting, immunosuppressive B cells. Here, using various murine tumor models and samples from humans with breast and ovarian cancers, we provide evidence that cancer cells also coopt differentiation of the extranodal B-cell precursors to generate macrophages (termed B-MF). We link the trans-differentiation to a small subset of CSF1R+ Pax5Lo cells within BM pro-/pre-B and immature B cells and cancer-secreted M-CSF that downregulates Pax5 via CSF1R signaling. Thus, cancer generates tumor-associated macrophages (TAM) from B-cell precursors besides their primary source, monocytes. Based on their differences from monocyte-derived TAM, such as a superb ability to induce FoxP3+ Tregs, suppress proliferation of T cells and more efficiently phagocytize apoptotic cells, we propose that cancer generates B-MF to mediate cancer escape.

overall_design: This gene expression microarray study examines differences between PBMC-derived B cells from breast cancer (BC, N=8) and non-diseased (ND, N=7) patients

first: Chen

first: Emeline

last: Ragonnaud

first: Monica

last: Bodogai

first: Le

last: Zong

first: Jung-Min

last: Lee


title: Cancer coopts differentiation of B-cell precursors into macrophages [mouse]

status: Public on Sep 20 2021

city: Baltimore

first: Supriyo

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

overall_design: This study compares gene expression in bone marrow (BM)-derived  B cells cultured in B cell media (BMBC_BCM, N=3), BM B-cell derived macrophages cultured in cancer-conditioned media (BMBC_C4T1.2_CM, N=3), BM pre-B cell-derived macrophages, cultured in macrophage media (BMF4_80M_MM, N=3), and BM pre-B cell-derived macrophages, cultured in cancer-conditioned media (BMF4_80M_C4T1.2_CM, N=3).

last: Chen

first: Bongsoo

last: Park

first: Isabel

last: Beerman

first: Arya

last: Biragyn


title: Distinct Functional Properties of Perinatal vs Adult Adipose Progenitors

status: Public on Aug 23 2021

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: We previously identified functional distinct sub-popultions in adult male gWAT Pdgfrb+ cells utilizing the MuralChaser lineage tracking system and Single-cell RNA-seq. To examine the cellular altas and developmental aspects of male gWAT, we performed Single-cell RNA-seqs on different developing stage of gWAT (P3,P7 and 5-week). To examine the mesothelial origin hypothesis of gWAT, we also performed  Single-cell RNA-seq on P7 gWAT associated mesothelial cells.

overall_design: We isolated Stromal Vascular Fraction (SVF) from epidydimal white adipose tissue (eWAT) of Postnatal Day 3 (n=10)/ Psotnatal Day 7 (n=5) / 5-week (n=5) male mice respectively. We also isolated Postnatal Day 7 eWAT associated mesothelial cells. Single cell library preparation was performed using the 10X Genomics Single Cell 3 v3 according to the manufacturers instructions.

first: Qianbin

last: Zhang

first: Lei

last: Guo


title: Distinct, opposing functions for CFIm59 and CFIm68 in mRNA alternative polyadenylation of Pten and in the PI3K/Akt signalling cascade

status: Public on Sep 10 2021

city: Montreal

first: Thomas

middle: F.

last: Duchaine

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

summary: The precise maintenance of PTEN dosage is crucial for tumor suppression across a wide variety of cancers. Post-transcriptional regulation of Pten heavily relies on regulatory elements encoded by its 3’UTR. We previously reported the important diversity of 3’UTR isoforms of Pten mRNAs produced through alternative polyadenylation (APA). Here, we reveal the direct regulation of Pten APA by the mammalian cleavage factor I (CFIm) complex, which in turn contributes to PTEN protein dosage. CFIm consists of the UGUA-binding CFIm25 and APA regulatory subunits CFIm59 or CFIm68. Deep sequencing analyses of perturbed (KO and KD) cell lines uncovered the differential regulation of Pten APA by CFIm59 and CFIm68 and further revealed that their divergent functions have widespread impact for APA in transcriptomes. Differentially regulated genes include numerous factors within the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signalling pathway that PTEN counter-regulates. We further reveal a stratification of APA dysregulation among a subset of PTEN-driven cancers, with recurrent alterations among PI3K/Akt pathway genes regulated by CFIm. Our results refine the transcriptome selectivity of the CFIm complex in APA regulation, and the breadth of its impact in PTEN-driven cancers.

overall_design: 3'UTR-seq to study changes alternative polyadenylation upon CFIm knockdown in mouse NIH3T3 cells

first: Hsin-Wei

last: Tseng

middle: F


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse [scRNA-seq]

status: Public on Aug 17 2021

city: Tampere

first: Sinja

last: Taavitsainen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.

overall_design: Single-cell RNA sequencing of parental LNCaP cells (DMSO treated, the control), LNCaP cells treated with 10µM enzalutamide for 48 hours, and LNCaP-derived enzalutamide-resistant RES-A and RES-B cells.

first: Alfonso

last: Urbanucci

first: Matti

last: Nykter

first: Gerhardt

last: Attard

first: Frank

last: Claessens

first: Nikolai

last: Engedal

first: Florian

last: Handle


title: Kidney VISTA prevents IFNγ-IL-9 axis-mediated tubulointerstitial fibrosis after acute glomerular injury

status: Public on Aug 04 2021

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

summary:
Backgrounds: The present study addressed whether V-domain Ig suppressor of T cell activation (VISTA), constitutively expressed in kidney macrophages, has a protective role in tubulointerstitial fibrotic transformation after acute antibody-mediated glomerulonephritis.
Methods: Wild-type (WT) and VISTA-deficient (Vsir-/-, KO) mice were treated with nephrotoxic serum to induced acute antibody-mediated glomerulonephritis, and their cytokine and fibrosis profiles were compared.
Results: VISTA was highly expressed in kidney macrophages (resident more than infiltrating subset). If VISTA was depleted, tubules suffered further damage after glomerular injury. In damaged Vsir–/– mice, the contact frequency of macrophages with infiltrated T cells increased, and then the immunometabolic characteristics of T cells changed to overproduction of interferon-γ. The Vsir–/– parenchymal tissue cells responded to this altered milieu as more producing interleukin-9, which augmented tubulointerstitial fibrosis and irreversible kidney dysfunction. The blocking antibodies against interferon-γ and interleukin-9 protected above pathological process by VISTA depletion.
Conclusions: VISTA is a sentinel protein of kidney macrophages, which prevents tubulointerstitial fibrosis via interferon-γ-interleukin-9 axis after acute antibody-mediated glomerular injury.

overall_design: single-cell RNA sequencing data of 8 weeks old C57BL/6 mice (Vsir-/-)

first: SeungSeok

last: Han

first: Min-Gang

last: Kim

last: Yun


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Development of Specific Therapy Against Right Ventricular Failure (in vitro analysis)

status: Public on Sep 07 2021

city: Tokyo

first: Shogo

last: Ito

email: itoshogo@keio.jp, itopap122@icloud.com

address: 35 Shinanomachi Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

summary: Right ventricular (RV) failure plays a critical role in any type of heart failure. However, there is no specific therapy developed for RV failure. To understand RV failure, we focused on the RV specific genes. Global gene expression analysis showed that alternative complement pathway-related genes including C3 and Cfd were significantly upregulated in right ventricle in murine heart. We generated the RV failure by right ventricle-specific pressure overload model mice, pulmonary artery constriction (PAC), which induces RV failure around 14 days. After administration of C3a receptor (C3aR) antagonist, RV function was dramatically improved PAC-induced RV dysfunction in wild type mice. To investigate the role of C3a to cardiomyocyte, C3a recombinant protein was administerd to neonatal rat ventricular myocytes (NRVMs), the results that several MAP kinesis were phosphorylated by C3a. In turn, to identify the key expressed genes as downstream of C3a in NRVMs, global gene expression analysis was performed in vitro.

overall_design: Rat neonatal ventricular myocytes (NRVMs) were cultured by culture medium and C3a recombinant protein was adminsterd for 12 hours. The cells were lysed with Trizol reagent (Invitrogen) and whole RNA were extracted.

first: Tomohisa

last: Seki

first: Shinsuke

last: Yuasa


title: Investigation of SNHG1 functions  in neuroblastoma

status: Public on Aug 01 2021

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: The gene expression profiles of SK-N-BE(2)C cell lines with CRISPR/Cas9-mediated depletion of SNHG1 were perfomed to investigate the role of SNHG1 in neuroblastoma

overall_design: RNA were extracted from SK-N-BE(2)C cell lines with CRISPR/Cas9-mediated depletion of SNHG1and then profiled by sequencing.

first: H

last: Juan

first: S

middle: H

last: Lin

first: C

middle: L


title: Murine colonic tumor single-cell RNA-seq

status: Public on Jul 01 2021

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: WT normal, Adjacent normal, and tumor from the colon of mice (C57BL/6) generated from different conditions

overall_design: AOM/DSS tumor vs. Lrig1creERT2/+ tumor;Apc-fl/+ vs. adjacent normal vs. WT normal

first: Alan

last: Simmons

first: Wei

last: Li


title: Molecular characterization of chronic liver disease dynamics: from liver fibrosis to acute-on-chronic liver failure

status: Public on Sep 11 2021

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: BACKGROUND: The molecular mechanisms driving the progression from early chronic liver disease (eCLD) to cirrhosis and, finally, acute-on-chronic liver failure (ACLF) are largely unknown. Thus, the aim of this work is to develop a network-based approach to investigate molecular pathways driving progression from eCLD to ACLF. We created 9 liver-specific biological networks capturing key pathophysiological processes potentially related to CLD. We used these networks as framework to perform gene set enrichment analyses(GSEA) and create dynamic profiles of disease progression.  RESULTS: Principal component analyses revealed that samples clustered according to the disease stage. GSEA analyses of the defined processes showed an up-regulation of inflammation, fibrosis and apoptosis networks throughout disease progression. Interestingly, we did not find significant gene expression differences between CC and DC, while ACLF showed acute expression changes in all the defined liver-related networks. The analyses of disease progression patterns identified ascending and descending expression profiles associated to ACLF onset. Functional analyses showed that ascending profiles were associated to inflammation, fibrosis, apoptosis, senescence and carcinogenesis networks, while descending profiles were mainly related to oxidative stress and genetic factors. We confirmed by qPCR the up-regulation of 4 genes of the ascending profile CXCL-6, KRT-18, SPINK-1, and ITGA2, and validated our findings on an independent patient’s cohort.  CONCLUSION: ACLF is characterized by a specific hepatic gene expression pattern related to inflammation, fibrosis, apoptosis, senescence and carcinogenesis processes. Moreover, the observed profile is significantly different from that of compensated and decompensated cirrhosis, supporting thus the hypothesis that ACLF should be considered a distinct entity.

overall_design: Transcriptome analysis on liver biopsies from patients at different liver disease stages, including 5 fibrosis(eCLD), 8 compensated cirrhosis, 12 decompensated cirrhosis, 8 ACLF, and 6 control healthy livers was performed.

first: I

last: Graupera

first: L

last: Isus

first: J

middle: J

first: P

last: Sancho-Bru

last: Ginès

last: Aloy


status: Public on Jul 26 2021

city: Wuhan

first: cao

last: lu

state: Hubei

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

country: China

institute: Institute of Hydrobiology

summary: CD44 is a transmembrane adhesion molecule and the major receptor for hyaluronan. The function of CD44 has been implicated in numerous biological processes. Our study finds that zebrafish CD44a variants function as positive regulators in antibacterial response. In order to reveal the possible antibacterial mechanism of CD44a, the wild-type and CD44a-/--14del zebrafish larvaes infected with E. piscicida collected at 24 and 48 hpi were used for transcriptome sequencing. Our data demonstrate that zebrafish CD44a functions as a regulator of p53 signaling, apoptosis and autophagy in the antibacterial immune response.

overall_design: The hatched larvae (4 dpf) from wild-type and CD44a mutants (CD44a-/--14del) were infected with E. piscicida, the infection was performed in triplicate with a parallel group with 50 fish per group. At 24hpi and 48hpi; the larvae in each group was collected for cDNA Library Construction and Illumina Deep Sequencing.

first: Lu

last: Cao

first: Ming

middle: X

last: Chang


title: SPOROS: A pipeline to analyze DISE/6mer Seed Toxicity

status: Public on Aug 22 2021

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: The SPOROS pipeline is a read-based sequence analysis pipeline for studying 6mer Seed Toxicity in mouse and human RNA-seq data.

overall_design: Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Elizabeth

last: Bartom


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse [FAIRE-seq]

first: Sinja

last: Taavitsainen

overall_design: Formaldehyde-assisted isolation of regulatory elements (FAIRE) sequencing of parental LNCaP and LNCaP-derived, enzalutamide-resistant RES-A cells in biological triplicate. Both sublines were treated with DMSO (control), DHT (10nM; Sigma Aldrich), enzalutamide (10µM, Selleckchem), or a combination of DHT and enzalutamide.

first: Alfonso

last: Urbanucci

first: Matti

last: Nykter

first: Gerhardt

last: Attard

first: Frank

last: Claessens

first: Nikolai

last: Engedal

first: Stefan

last: Prekovic

first: Florian

last: Handle


title: A CRISPRi/a platform in iPSC-derived microglia uncovers regulators of disease states

status: Public on Jun 17 2021

city: San Francisco

first: Martin

last: Kampmann

state: CA

address: 675 Nelson Rising Ln

institute: UCSF

summary: Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform that enables the systematic elucidation of functional consequences of genetic alterations in human iPSC-derived microglia. We developed a protocol based on the inducible expression of six transcription factors, which generates microglia-like cells in an efficient eight-day protocol which was confirmed by bulk RNA sequencing. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the “druggable genome” that uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identifies regulators of these states. A disease-associated state characterized by SPP1 expression is selectively depleted by CSF1R inhibition.Thus, our platform can systematically uncover regulators of microglia states, enabling their functional characterization and therapeutic targeting.

overall_design: QuantSeq bulk RNA-sequencing of iTF-Microglia (Day 0, Day 8 (non-targeting and PFN1 CRISPRa sgRNAs), Day 9 +/- LPS treatment, Day 15) and Brownjohn-iMicroglia (Brownjohn et al., 2018, Day 9 +/- LPS treatment); Paired-end RNA-sequencing of iTF-Microglia (D14 +/- LPS treatment); and CROP-seq, single cell RNA-sequencing of Day 8 iTF-Microglia infected with a library of sgRNAs targeting 38 genes performed on four lanes of the 10X platform.

first: Sydney

last: Sattler

first: Nina

last: Draeger

first: Huang

last: Cindy

first: Gan

last: Li


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse [scATAC-seq]

overall_design: Single-cell ATAC sequencing of parental LNCaP cells (DMSO treated, the control), LNCaP cells treated with 10µM enzalutamide for 48 hours, and LNCaP-derived enzalutamide-resistant RES-A and RES-B cells.


title: Transcriptome analysis of tendon derived from Piezo1 mutant mice

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Institute of Science Tokyo

summary: Tendon tissue growth is promoted by mechanical stimulation, but the mechanism  is not well understood. Piezo1, a mechanical stress-responsive channel receptor, is expressed in tendon cells, and the fact that tendon tissue growth was accelerated in Piezo1 gain of function mice suggests that Piezo1 plays an important role in tendon tissue growth. RNA-seq of tendon tissues from these mice showed increased expression of tendon-related genes and decreased expression of muscle-related genes, suggesting that Piezo1 may play a role in maintaining and enhancing the properties of tendon cells.

overall_design: Tendon mRNA profiles of 18-weeks old WT or Piezo1 mutant mice

first: Tomoki

last: Chiba

first: Ryo

last: Nakamichi


title: 2-hydroxyglutarate drives whole-genome hypermethylation in kidney cancer cells with inactivated VHL

status: Public on Jun 01 2021

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

type: Methylation profiling by high throughput sequencing

summary: Hypermethylation of tumor suppressors and other aberrations of DNA methylation in tumors play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions including hypoxia. The response to hypoxia is mainly achieved through activation of the transcription program associated with HIF1a transcription factor. VHL inactivation by genetic or epigenetic events, which also induces aberrant activation of HIF1a, is the most common driver event for renal cancer. With whole-genome bisulfite sequencing and LC-MS, we demonstrated that VHL inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type VHL. We show that global genome hypermethylation in VHL mutants can be explained by the accumulation of 2-hydroxyglutarate -- a metabolite that inhibits DNA demethylation by Tet enzymes.

overall_design: We profiled genome-wide DNA methylation with whole-genome bisulfite sequencing (wgBS) in three clones with independent VHL inactivation and observed global genome hypermethylation. Reexpression of exogenous wild-type VHL has partially rescued DNA methylation phenotype to wild-type state.Hypermethylawe profiled genome-wide DNA methylation with bisulfite sequencing (wgBS) in three clones with independent VHL inactivation and observed global genome hypermethylation. Reexpression of exogenous wild-type VHL has partially rescued DNA methylation phenotype to wild-type state. tion of tumor suppressors and other aberrations of DNA methylation in tumors play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions including hypoxia. The response to hypoxia is mainly achieved through activation of the transcription program associated with HIF1a transcription factor. VHL inactivation by genetic or epigenetic events, which also induces aberrant activation of HIF1a, is the most common driver event for renal cancer. With whole-genome bisulfite sequencing and LC-MS, we demonstrated that VHL inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type VHL. We show that global genome hypermethylation in VHL mutants can be explained by the accumulation of 2-hydroxyglutarate -- a metabolite that inhibits DNA demethylation by Tet enzymes.

first: Svetlana

last: Zhenilo

first: Daria

last: Kaplun

first: Alexey

last: Starshin

first: Alexander

last: Mazur

first: Egor

middle: B

last: Prokhortchouk


title: Single-cell profiling and functional characterization bridge molecular and functional features of NAc neuron subtype

status: Public on Aug 24 2021

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: The functional complexity of nucleus accumbens (NAc) has been extensively characterized in recent years. However, the molecular and cellular heterogeneity beyond the established D1 and D2 medium spiny neuron (MSN) subtypes, which likely underlie its diverse functions, are not well understand. Here, we present the cell taxonomy of mouse NAc generated from single-cell transcriptomic profiling, which not only reveals a rich cellular heterogeneity within both NAc MSN and interneuron populations, but also identified tight correlation between the transcriptional feature and spatial distribution of NAc neuron subtypes, supporting the notion that functional heterogeneity of NAc sub-regions can arises from differential distribution of molecularly distinct neuronal populations. To further test this idea, we focused on a D1 MSN subtype identified from our analysis and demonstrated that these cells possess distinct anatomic location, neural connection and more importantly, behavioral function. Collectively, our work not only created comprehensive cell taxonomy of NAc, but also provided insights into how functional heterogeneity is embedded in this brain region.

overall_design: To generate a comprehensive cell map of mouse NAc, we dissect this brain region from acute coronal sections of adult mouse brains (8-10 weeks) . After cell dissociation, single cells are captured with the 10X Chromium platform (10X Genomics), followed by cDNA synthesis, library preparation and high-throughput sequencing. A total of 11 Samples were sequenced and merged together

first: Renchao

last: Chen

first: Mohamed

middle: N

first: Wenqiang

first: Aritra

last: Bhattacherjee

first: Luis

middle: M

last: Tuesta

first: Yi

last: Zhang


title: Midkine-a regulates the formation of a fibrotic scar during zebrafish heart regeneration

status: Public on May 26 2021

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

summary: Midkine-a is a cytokine that is highly expressed in the heart upon injury that its role in regeneration has not been identified. We generated a KO zebrafish lines, mdkacn105, and studied the effect of mdka deletion in zebrafish adult heart regeneration. By combining histology and high-throughput genomics, we found that loss of mdka leads to arrest of heart regeneration. Mdka mutant hearts display increased collagen deposition in the site of the injury and decreased proliferation of the coronary endothelial cells due to increased expression of ECM including collagen and periostin as well as decreased expression of Hif1a. Our results demonstrate the importance of a balanced fibrotic respond is necessary for heart regeneration and indicates mdka importance in this process.

overall_design: Total RNA was extracted from ventricular adult tissue collected from adult hearts by removing the atrioventricular and aortic valves. KOs and control came from crosses of the same fish and a total number of 3 KOs and WT were used. For RNA extraction, QIAzol Lysis Reagent (Qiagen; CA; USA) and the miRNeasy Mini Kit (Qiagen; CA; USA) were used. RNA was quantified and its purity checked with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific; MA; USA). RNA integrity was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA).

first: Dimitrios

last: Grivas

first: Jose


title: Signaling Response to Early Oncogenesis by a Novel Panel of Murine Mutant Kras Alleles in the Mouse Lung Transcriptome

status: Public on Aug 09 2021

first: Ozgun

last: Erdogan

state: NC

address: 308 Research Dr.

department: Pharmacology and Cancer Biology


title: Sex differences in transcriptome profiles in hypothalamic and extrahypothalamic nuclei of rats impacted by adolescent stress

status: Public on Jun 06 2021

city: oxford

first: Haifei

last: Shi

state: OH

address: 700 E High Street

department: Biology

institute: Miami University

summary: In order to generate data worthy of translatability to known sex differences in human stress-induced maladies, adolescent male and female rats underwent chronic restraint stress (stress) or not (nonstress, control) from postnatal day (PD)32-PD44. Specific brain nuclei (PVN, VMH, ARC, BLA, CEA, CA1, CA3, DG, and OFC) were analyzed for genome-wide transcriptome using RNA sequencing (RNA-Seq). Global transcriptome profiles were generated, and genes differentially expressed (DE) due to stress were identified for each nuclear subregion listed. Canonical pathway analyses identified DE genes that are likely crucial for causing well-known stress-induced sex differences.

overall_design: adolescent male and female rats underwent stress or nonstress for 1 hour each day from  PD32-PD44. Specific brain nuclei (PVN, VMH, ARC, BLA, CEA, CA1, CA3, DG, and OFC) were analyzed for genome-wide transcriptome using RNA sequencing (RNA-Seq). Differential Expression transcriptional analyses between stress and nonstress for each sex and brain region were performed.

first: Kristen

last: Krolick

first: Jingyi

last: Cao

first: Andor

last: Kiss


title: Expression data of A172 cell line treated with DMSO or Ch-M'

status: Public on May 19 2021

city: Kyoto

first: Etsuko

middle: Yamamoto

last: Hattori

state: Kyoto

address: 54 Kawahara-Cho, Shogoin, Sakyo-Ku

institute: Kyoto University

summary: Glioblastoma is the most common adult brain tumour, representing a high degree of malignancy. It is reported that transcription factors are involved in the malignancy of glioblastoma , and RUNX1 is one of them. A novel gene switch-off agent, Chb-M', which is alkylating agent-conjugated pyrrole-imidazole polyamides, designed to fit the RUNX1 DNA groove, inhibits transcription of RUNX1. We We examined changes in the expression of downstream genes due to transcriptional inhibition of this agent.

overall_design: A172, a glioblastoma cell line, was treated with DMSO in the control group and Chb-M' (1µM), a transcriptional inhibitor of RUNX1, for 48 hours each, and the downstream gene changes were compared.

middle: Y

first: Yoshiki

last: Arakawa


title: Murine fetal bone marrow does not support functional hematopoietic stem and progenitor cells until birth

status: Public on Jun 26 2021

city: Memphis

first: Shannon

last: McKinney-Freeman

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

summary: Fetal hematopoietic stem and progenitor cells (HSPCs) migrate from fetal liver (FL) to bone marrow (BM) around birth. While adult BM HSPCs and their extrinsic regulation is well studied, little is known about the composition, function, and extrinsic regulation of the first HSPCs to enter the BM. Here, we show that HSPCs colonize multiple fetal bones by E15.5, shift from an MPP2 to an MPP3/4-dominant phenotype by birth, and display little function until E18.5, relative to their FL counterparts. We establish a transcriptional atlas of single perinatal HSPCs, and their putative BM niches, from E15.5 through P0 and show that early fetal BM (FBM) lacks HSPCs with intrinsic stem cell programs and niche cells supportive of HSPCs. In contrast, stem cell programs are preserved in neonatal BM HSPCs, which engage with a niche expressing HSC supportive factors distinct from those seen in adult BM (i.e., IGF).

overall_design: Examination of the hematopoietic progenitor and stromal compartments of E16.5, E18.5, P0, and adult bone marrow.

first: Trent

middle: D

last: Hall

first: Hyunjn

last: Kim


title: High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

status: Public on Aug 02 2021

city: La Jolla

first: Juliana

middle: S

last: Capitanio

state: California

address: 10010 N Torrey Pines Rd

department: molecular and call biology laboratory

institute: The Salk Institute for Biological Studies

summary: The role of nuclear pore complexes (NPCs) in genome organization remains poorly characterized due to technical limitations in probing genome-wide protein-DNA interactions that are specific to the nuclear envelope. Here, we developed a sensitive method, NPC-DamID, which combines in vitro reconstitution of nuclear import and DamID technology. This fixation-free method specifically identifies genomic DNA interactions at the NPCs in intact nuclei. We found that NPCs are preferentially associated with common and hierarchically arranged super-enhancers (SEs) across multiple cells and tissue types. We also uncovered phase-separated condensates at NPCs that compartmentalize and concentrate transcriptional coactivators and structural proteins at SE-regulated genes. Our results support the idea that NPCs are sites of anchoring SE regulatory hubs through their interaction with CTCF and also maintains the conformation of SEs through interaction with structural proteins of SEs like Med1 and PolII.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The sequencing experiemnts were done using a new method called NPC-DamID. Breifly, Dam fused to Importin beta was provided to semi-permeabilized cells along with other reagents for methylation of DNA in the vicinity of nuclear pore complexes (NPCs). The genomic DNA was isolated after the assay and digested with DpnI followed by adapter ligation and PCR amplification of the DpnI digested fragements. This is very similar to convention DamID pipeline. The amplified product was purified using PCR purification kit and then sonicated and digested with alwI for removing the adapters. After this the fragemnts were purified using PCR purification kit and sequencing libraries were prepared using Hyper-Kapa kit.

first: Swati

last: Tyagi

first: Martin

last: Hetzer


title: CircVAMP3 is a circRNA with a role in alveolar rhabdomyosarcoma cell cycle progression

status: Public on Aug 03 2021

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: Circular RNAs (circRNAs), a class of covalently closed RNA formed by a back-splicing reaction, have been involved in the regulation of diverse oncogenic processes. In this article we describe circVAMP3, a novel circular RNA overexpressed in alveolar rhabdomyosarcoma. We demonstrate that circVAMP3 has a differential m6A pattern opposed to its linear counterpart, suggesting that the two isoforms can be differently regulated by such RNA modification although their sequence similarity. Moreover, we show how circVAMP3 depletion in alveolar rhabdomyosarcoma cells can impair cell cycle progression, e.g. through the downregulation of the AKT pathway, pointing to this non-coding RNA as a novel regulator of the alveolar rhabdomyosarcoma progression and a putative future therapeutic target.

overall_design: High-throughput sequencing of Poly-A+ RNA from alveolar rhabdomyosarcoma cells transfected either with a control siRNA (si-SCR) or with a siRNA targeting circVAMP3 back-splicing junction (si-circVAMP3).

first: Irene

last: Bozzoni

first: Manuel

last: Beltran

first: Dario

last: Dattilo

first: Gaia

last: Di Timoteo

first: Alvaro

last: Centron-Bróco

first: Marco

last: Guarnacci

first: Alessio

last: Colantoni


title: Pleural fluid and Human Serum albumin modulate the behavior of a hypervirulent and Multidrug-resistant (MDR) Acinetobacter baumannii representative strain

status: Public on Apr 28 2021

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

summary: Analysis of the effect of human pleural fluid (HPF) or human serum albumin (HSA) on the transcriptome of Acinetobacter baumanii AB5075

overall_design: Total mRNA of Acinetobacter baumanii AB5075 was isolated from bacteria incubated in LB with or without 4 % HPF or 0.2% HSA

first: Maria

last: Soledad Ramirez

first: Rodrigo

last: Sieira


title: Modeling SARS-CoV-2 infection and its individual differences with ACE2-expressing human iPS cells

status: Public on Apr 18 2021

first: Kazuo

last: Takayama

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

summary: Genetic differences are a primary reason for differences in the susceptibility and severity of COVID-19. As induced pluripotent stem (iPS) cells maintain the genetic information of the donor, they can be used to model individual differences in SARS-CoV-2 infection in vitro. We found that human iPS cells expressing the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) (ACE2-iPS cells) can be infected w SARS-CoV-2. In infected ACE2-iPS cells, the expression of SARS-CoV-2 nucleocapsid protein, budding of viral particles, and production of progeny virus, double membrane spherules, and double-membrane vesicles were confirmed. We performed SARS-CoV-2 infection experiments on ACE2-iPS/ embryonic stem (ES) cells from eight individuals. Male iPS/ES cells were more capable of producing the virus compared with female iPS/ES cells. These findings suggest that ACE2-iPS cells can not only reproduce individual differences in SARS-CoV-2 infection in vitro but also are a useful resource to clarify the causes of individual differences in COVID-19 due to genetic differences.

overall_design: Total RNA was isolated from uninfected or infected ACE2-iPS cells, and then RNA-seq was performed. At day 3 after the infection, total RNA was collected and RNA-seq was performed.


title: Single Cell Analyses of Renal Cell Cancers Reveal Insights into Tumor Microenvironment, Cell of Origin, and Therapy Response

status: Public on May 22 2021

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Diverse subtypes of renal cell carcinomas (RCC) display a wide spectrum of histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical behavior. Delineating the ontogeny of these malignancies with the identification of cells of origin for different RCC subtypes will provide mechanistic insights into their diverse pathobiology. With this aim, we performed single cell RNA sequencing (scRNA-seq) analysis of ~30,000 cells dissociated from benign human kidney and renal tumor specimens. The benign renal tissue cell atlas comprised 26 distinct cell clusters representing all known major and minor cell types, as well as two rare proximal tubule cell types (PT-B and PT-C) and one novel entity containing both intercalated and principal cell (IC-PC) phenotypes. In comparison, the tumor cell atlas was comprised of 13 different cell clusters encompassing neoplastic cells and components of the tumor microenvironment. Using a random forest model trained on the scRNA-seq data from benign tubular epithelial cell types, we predicted the putative cell of origin for more than 10 different RCC subtypes.

overall_design:
Single-cell suspensions from 8 renal tumor specimens and  6  benign human kidney specimens from clear cell cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) patients were obtained by enzymatic dissociation.  The cell suspension was used to prepare single cell RNA-seq libraries using the 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).

*** This GEO submission contains only processed data (raw counts tables in HDF5 format), raw data (FASTQ files) will be submitted  to dbGaP/SRA due to to patient privacy concerns.

The cell annotation file *csv files were added on Sep 23, 2022.

first: Yuping

last: Zhang

first: Sathiya

middle: P

last: Narayanan

first: Saravana

last: Dhanasekaran

first: Gregory

last: Raskind

first: Xiaoming

last: Wang

first: Pankaj

last: Vats

first: Rahul

last: Mannan

first: Fengyun

last: Su

first: Lisha

first: Xuhong

last: Cao

first: Chandan

last: Kumar-Sinha

first: Thomas

last: Giordono

first: Todd

last: Morgan

first: Sethu

last: Pitchaya

first: Ajjai

last: Alva

first: Rohit

last: Mehra

first: Marcin

last: Cieslik


title: Loss of Ten-Eleven Translocation 2 Exacerbates allergic inflammation by 5-Hydroxymethylcytosine Remodeling in Immunologic Pathways

status: Public on Mar 29 2021

city: Hanzhou

first: Lei

last: Gu

address: 79 Qingchun Rd

institute: First Affiliated Hospital, Zhejiang University School of Medicine

summary: Here we show that loss of ten-eleven translocation protein (Tet2) could impact the severity of allergic rhinitis (AR) in ovalbumin-induced mouse model. Genome-wide 5hmC profiling of wildtype, Tet2+/- and Tet2-/- mice in response to AR revealed that the loss of Tet2 could lead to the 5hmC alteration at specific immune response genes on RNA-seq.

overall_design: Nasal mucosa mRNA profiles and 5hmC captured ChiP-seq profiles of adult wild type (WT), Tet2 +/- and Tet2-/- mice in allergic rhinitis or control conditions.

first: Cuida

last: Meng

first: Yujing

last: Li

first: Ronghua

first: Peng

last: Jin


title: Expression profiling of human foetal and calcified adult aortic valves links inflammation to aging and identifies early disease gene markers

status: Public on Apr 01 2021

first: Jose Luis

last: de la Pompa

summary: Aims  Calcific aortic valve disease (CAVD) is a significant cause of illness and death worldwide. The disease mechanism involves age-associated immuno-osteogenic processes but developmental origins and early disease mechanisms are not fully characterized. Identification of early predictive markers could help optimize therapy decisions and patient follow-up.   Methods and Results  RNA-sequencing was carried out on human fetal aortic valves at weeks 9, 13, and 22, and adult control, calcified bicuspid (BAV) and tricuspid aortic valves (TAV). K-means clustering was implemented to identify co-expressed gene patterns simultaneously up- and down-regulated over the different conditions. Canonical pathway analysis revealed a predominant immune-metabolic gene signature indicative of ongoing innate and adaptive immune responses, including lymphocyte T-cell metabolic adaptation. Specifically, cytokine and chemokine signalling, cellular migration and proliferation, were all increased in CAVD, while oxidative phosphorylation and protein translation were decreased. Discrete immune-metabolic gene signatures were present at foetal stages and adult controls, indicating that inflammation initiates as soon as the valves are formed and is maintained and amplified during post-natal life. Multiple pathways involved in cellular stress response and neurodegenerative disease were also aberrantly expressed, suggesting that chronic inflammation drives metabolic stress- and age-associated valve pathology in CAVD. Comparing the valve RNA-sequencing dataset with whole blood transcriptomes from asymptomatic individuals with early aortic valve calcification identified a gene signature including the CD28 pathway, highly predictive of patients with CAVD and healthy individuals with moderate levels of aortic valve calcification.  Conclusion  These data deepen and broaden our understanding of the molecular basis of CAVD, and identify a gene signature for the early detection of aortic valve calcification.    Keywords  Human foetal valve, CAVD, BAV, inflammation, biomarker, gene signature,PESA

first: Donal

last: MacGrogan

first: Jose

first: Fátima

last: Sánchez-Cabo


title: RNA- and ATAC-seq data from hESCs differentiated with Wnt and Activin with or without CPI-203

city: New York

first: Anna

last: Yoney

state: NY

address: 701 W 168th Street

department: Genetics and Development

institute: Columbia University

summary: We report genome-wide changes in chromatin state and transcriptional output following Wnt-priming and subsequent Activin induced differentiation of human embryonic stem cell and the effects of BET bromodomain inhibition during Wnt-priming. The two signals, Wnt and Activin, although provided sequentially, result in stable mesendoderm differentiation (Yoney et al., 2018).

overall_design: We performed RNA-seq and ATAC-seq of human embryonic stem cells differentiated with Wnt and Activin and treated with BET inhibitor, CPI-203 (Selleckchem, Cat. No. S7304). Two replicates per condition for both RNA- and ATAC-seq were performed and samples were collected after 24 or 48 h.

first: Lu

last: Bai

first: Ali

last: Brivanlou

first: Eric

last: Siggia


title: Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes

status: Public on Apr 14 2021

city: Shanghai

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

summary: Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDH alpha genes. Thus, REST/NRSF represses PCDH alpha gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.

overall_design: We performed ChIP-nexus experiments in HEC-1-B and  SK-N-SH cells to pinpoint the NRSEs, and uncover the DNA-recognition code of NRSF. We performed ChIP-Seq experiments for REST, H3K4me3, H3K27ac after REST knockdown by shRNA or HS5-1 NRSE deletion in HEC-1-B cells and HEK293T cells by CRISPR/Cas9, and for REST, H3K4me3, CTCF after  HS5-1 NRSE deletion in mice by CRISPR/Cas9. RNA-seq results revealed the influence on the expression of clustered Pcdh alpha by knockdown of NRSF or deletion of HS 5-1 NRSE in HEC-1-B and HEK293T cells, or in mouse cortex, and kidney, taking wild-type (WT) as control.  QHR-4C experiments were used to supervise the DNA interactions between PCDH apha promoters and HS5-1 in the HEC-1-B cells after  REST knockdown or HS5-1 NRSE deletion, and in the kidney of HS5-1 NRSE-deleted mice.

first: Qiang

last: Wu


title: Lentiviral-driven discovery of cancer drug resistance mutations

status: Public on Jul 28 2021

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Identifying resistance mutations in a drug target provides crucial information. Lentiviral transduction creates multiple types of mutations due to the error-prone nature of the HIV-1 reverse transcriptase (RT). We optimized and leveraged this property to identify drug resistance mutations, a technique we term LentiMutate. After validating this technique by identifying clinically relevant EGFR resistance mutations, we applied this technique to two additional anti-cancer drugs, imatinib and AMG 510. We find novel deletions in BCR-ABL1 that confer resistance to BCR-ABL1 inhibitors and point mutations in the AMG 510 binding pocket or oncogenic non-G12C mutations, in KRAS-G12C or wild-type KRAS, respectively, that confer resistance to AMG 510. LentiMutate may prove highly valuable to clinical and preclinical cancer drug development.

overall_design: RNAseq on 120 CML patient samples, either at relapase or upon diagnosis, was performed. This GEO submission is only the reads that mapped to ABL.

first: Paul

last: Yenerall

first: Rahul

middle: K

last: Kollipara

first: Kimberly

last: Avila

first: Michael

last: Peyton

first: Christopher

middle: A

last: Eide

first: Daniel

last: Bottomly

first: Shannon

last: McWeeney

first: Yan

last: Liu

first: Kenneth

last: Westover

first: Brian

last: Druker

first: John

last: Minna


title: Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning [a]

status: Public on Jun 05 2021

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

summary: N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing, such as RNA stability and translation. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites in the transcriptome with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present several experimental and computational innovations that significantly improve transcriptome-wide detection of m6A sites. Based on the recently developed iCLIP2 protocol, the optimised miCLIP2 results in high-complexity libraries using less input material, leading to a more comprehensive representation of m6A sites. Next, we established a robust computational pipeline to identify true m6A sites from our miCLIP2 data. The analyses are calibrated with data from Mettl3 knockout cells to learn the characteristics of m6A deposition, including a significant number of m6A sites outside of DRACH motifs. In order to make these results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.

overall_design: miCLIP2 experiments were performed on polyA+ RNA from human and mouse cells, with 3 biological replicates per condition. Mettl3 KO cells served to calibrate the m6A detection.

first: Nadine

last: Körtel

first: Cornelina

last: Rücklé

first: You

last: Zhou

first: Anke

last: Busch

first: FX

middle: R

last: Sutandy

first: Dan

last: Dominissine

first: Christoph

last: Dieterich

first: Julian

last: König


title: Candida glabrata haploid and diploid

status: Public on Apr 30 2021

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: The different expression of Candida glabrata haploid and diploid.

overall_design: Total RNA profiles of Candida glabrata haploid and diploid cells.

first: Guanghua

last: Huang

first: Qiushi

last: Zheng


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and JAK2-V617F expressing hematopoietic stem and progenitor subsets

status: Public on Mar 03 2021

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Transcriptomics analysis was performed on FACS purified HSPC subsets from SclCre;V617F mice and WT mice bone marrow. The goal of this study is to identify the molecular signatures that are specific to the mutant JAK2 expressing HSPC subsets. We found that mutant JAK2 activation caused dysregulated expression of large numbers of genes in primitive HSPC subsets. Furthermore, this analysis revealed molecular identity and developmental proximity of HSC CD41+/- cells within the HSPC hierarchy.

overall_design: To activate JAK2-V617F mutation, SclCre;V617F (SF1) transgenic mice and Wildtype (WT) were treated with tamoxifen for 5 consequetive days. 12 weeks post-tamoxifen injections, titbia and femur from both legs were havested and curshed in a mortor and pistle to extract total bone marrow cells. Total bone marrow cells were subjected to ACK lysis to remove erythrocytes. Cells were then surface stained with the antibodies to identify hematopoietic stem and progenitor subsets. Following subsets were isolated using FACS Aria3:  Long-term Hematopoietic Stem Cells (LT-HSC; Lineage negative/cKit+/Sca-1+/CD48-/CD150+); CD41+ HSCs Lineage negative/cKit+/Sca-1+/CD48-/CD150+CD41+); CD41-HSCs (Lineage negative/cKit+/Sca-1+/CD48-/CD150+ CD41-); Megakaryocyte progenitors (MkPs: Lineage negative/cKit+/Sca-1-/CD150+CD41+). Cells were sorted directly into eppendorf tubes containing RNA lysis buffer. Total RNA was prepared using Acturus PicoPure RNA preparation kit (Applied Biosystems). RNA samples with RIN value >8 were used for library preparation using Illumina RNA Seq library preparation kit.

first: Tata

last: Nageswara Rao

first: Radek

middle: C

last: Skoda


title: RNA-seq of hematopoietic stem and progenitor cells from 40 hours post fertilization ddx41 mutant and sibling zebrafish

status: Public on Mar 01 2021

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead-box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development.

overall_design: mRNA profiling of cd41-positive hematopoietic stem and progenitor cells isolated from 40 hours post fertilization ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.


status: Public on Feb 05 2021

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary:
Transcriptional landscape of MyceliopTranscriptional profiling of Myceliophthora thermophila on galactose and metabolic engineering for improved galactose utilization thora thermophila responding to soluble starch and the role of regulator AmyR on polysaccharide degradation
Efficient biological conversion of all sugars from lignocellulosic biomass is necessary for cost-effective production of biofuels and commodity chemicals. Galactose is the next most abundant sugar in many hemicelluloses and it will be important to capture this carbon for an efficient bioconversion process of plant biomass. Thermophilic fugus Myceliophthora thermophila has been used as cell factory to produce biochemicals directly from renewable polysaccharides. This study determined the transcriptomic profiles of M. thermophila responding to galactose and identified the gene involved in the oxido-reductive pathway for galactose degradation, of which hexokinase might be the rate-limiting enzyme in this thermophilic fungus. Galactokinase was necessary for high induction of galactose transporter and disruption of galK resulted in decreased galactose utilization. Both of galactokinase deletion and sugar transporter overexpression could further activate the oxido-reductive pathway and led to improved galactose utilization. In addition, disruption of the Leloir pathway brought about reduced tolerance to cell wall perturbation, oxidative stress and high osmolality. In order to accelerate galactose consumption, the third galactose-degradation pathway- De Ley-Doudoroff pathway was successfully integrated into M. thermophila and the consumption rate of galactose was increased by 57%. This study will be benefit for the rational design of fungal strains to produce biofuels and biochemical from plant biomass, especially, marine plant biomass with the abundant of galactose, such as red seaweed and molasses.

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to carbon starvation, glucose and galactose.

first: Chaoguang

last: Tian


title: In Vitro Model for a Drug Assessment of Cytochrome P450 Family 3 Subfamily A Member 4 Substrates Using Human Induced Pluripotent Stem Cells and Genome Editing Technology

status: Public on May 06 2021

first: Kazuo

last: Takayama

summary: In drug development, a system for predicting drug metabolism and drug-induced toxicity is necessary to ensure drug safety. Cytochrome P450 family 3 subfamily A member 4 (CYP3A4) is an important drug-metabolizing enzyme expressed in the liver and small intestine, and predicting CYP3A4-mediated drug metabolism and drug-induced toxicity is essential. We previously developed procedures to differentiate human induced pluripotent stem (iPS) cells into hepatocyte-like cells (HLCs) or intestinal epithelial-like cells (IECs) with a fetal phenotype as well as a highly efficient genome editing technology that could enhance the homologous recombination efficiency at any locus, including CYP3A4. By using human iPS cells and our genome editing technology, we generated CYP3A4-knockout (KO) iPS cell-derived HLCs and IECs for the evaluation of CYP3A4-mediated drug metabolism and drug-induced toxicity. CYP3A4 deficiency did not affect pluripotency and hepatic and intestinal differentiation capacities, and CYP3A4 activity was entirely eradicated by CYP3A4 KO. Off-target effects (e.g., inhibition of bile acid excretion) were hardly observed in CYP3A4-KO cells but were observed in CYP3A4 inhibitor-treated (e.g., ketoconazole) cells. To evaluate whether drug-induced hepatotoxicity and enterotoxicity could be predicted using our model, we exposed CYP3A4-KO HLCs and IECs to acetaminophen, amiodarone, desipramine, leflunomide, tacrine, and tolcapone and confirmed that these cells could predict CYP3A4-mediated toxicity. Finally, we examined whether the therapeutic effects of an anti-hepatitis C virus (HCV) drug metabolized by CYP3A4 would be predicted using our model. CYP3A4-KO HLCs were treated with asunaprevir (antiviral drug metabolized by CYP3A4) after HCV infection, and the anti-viral effect was indeed strengthened by CYP3A4 KO. Conclusion: We succeeded in generating a novel evaluation system for prediction of CYP3A4-mediated drug metabolism and drug-induced toxicity.

overall_design: Gene expression profiles were compared between wild type iPS cell-derived hepatocyte-like cells and CYP3A4-knockout iPS cell-derived hepatocyte-like cells

first: Sayaka

last: Deguchi

first: Shintani

last: Tomoki

last: Harada

first: Toru

last: Okamoto

first: Akinori

last: Takemura

first: Kazumasa

last: Hirata

first: Kousei

last: Ito

first: Hiroyuki

last: Mizuguchi


title: Development of Specific Therapy Against Right Ventricular Failure

status: Public on Sep 07 2021

city: Tokyo

first: Shogo

address: 35 Shinanomachi Shinjuku-ku

department: Cardiology

institute: Keio University School of Medicine

summary: Right ventricular (RV) failure plays a critical role in any type of heart failure. However, there is no specific therapy developed for RV failure. To understand RV failure, we focused on the RV specific genes. Global gene expression analysis showed that alternative complement pathway-related genes including C3 and Cfd were significantly upregulated in right ventricle in murine heart. We generated the RV failure by right ventricle-specific pressure overload model mice, pulmonary artery constriction (PAC), which induces RV failure around 14 days. In C3 knockout (C3KO) mice, PAC-induced RV dysfunction and fibrosis were significantly attenuated. C3a is produced from C3 by C3 convertase complex including Cfd. Cfd knockout mice also attenuated PAC-induced RV failure. Moreover, C3a receptor (C3aR) antagonist dramatically improved PAC-induced RV dysfunction in wild type mice. Here we revealed the crucial role of C3-Cfd-C3a-C3aR axis in RV failure and highlight the potential therapeutic target for RV failure with no pharmacologic option.

overall_design: Murine hearts were separated into RV, LV and ventricular septum using different individuals for each experiment.

first: Tomohisa

last: Seki

first: Shinsuke

last: Yuasa


title: Engineering the Cellulolytic Fungus Myceliophthora thermophila into a Platform for Producing Commodity Chemicals Directly from Lignocellulose

status: Public on May 04 2021

summary: Producing the fuels and chemicals from renewable plant biomass has been thought as a feasible way for global sustainable development. However, the economical efficiency of biorefinery remains challenges. Here a cellulolytic thermophilic fungus, Myceliophthora thermophila, was constructed into a platform through metabolic engineering, which can efficiently convert lignocellulose to important bulk chemicals for polymers, four carbon 1, 4-diacids (malic and succinic acid), directly from lignocellulose without any extra enzymes addition or complicated pretreatment, with titer of over 200 g/L on cellulose and 110 g/L on plant biomass (corncob) during fed-batch fermentation. Our study represents a milestone of consolidated bioprocessing technology (CBP) and offers a new promising system for cost-effectively production of biomass-based chemicals and potentially fuels.

overall_design: mRNA profiles of Myceliophthora thermophila ATCC42464 wild-type strain and it derivatives exposed to glucose or cellulose (Avicel). The derivates (JG141,JG207, JG207Ncclr2, and JG336 strains) were obtained by genetic manipulation in M. thermophila wild-type strain.


title: 6mer Seed toxicity and platinum resistance in ovarian cancer [DISE-43]

status: Public on Feb 02 2021

city: Chicago

first: Marcus

last: Peter

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: We demonstrate that 6mer seed toxicity plays a role in platinum resistance of ovarian cancer

overall_design: Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Monal

last: Patel

first: Elizabeth

last: Bartom


title: Age-dependent replacement of neural-crest derived enteric neurons by a novel mesodermal lineage and its functional consequences

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: During fetal development, neural crest precursors give rise to neurons of the enteric nervoussystem (ENS). However, given our evolving understanding of the dynamic nature of the ENS, itis not clear whether this developmental paradigm holds true at different post-natal stages. Here,we show that due to loss of GDNF-RET signaling with age, neural crest-derived neurons un-dergo a progressive decline in numbers. They are replaced by neurons derived from the embry-onic mesoderm which, with increasing age, become the dominant form of neurons in the ENS,and this is associated with functional deficits in intestinal motility. Using single cell transcrip-tomics and immunochemical approaches, we characterize these mesoderm-derived neuronsand show that this novel lineage of neurons expresses MET and is dependent on HGF for itsexpansion. Normal intestinal function in the adult gastrointestinal tract therefore appears to re-quire an optimal balance between these two distinct lineages within the ENS.

overall_design: Two replicate samples of dissociated, postnatal day P180, mouse small intestinal longitudinal muscle-myenteric plexus were prepared and run through the 10x Chromium 3' Single Cell Gene Expression platform (V2.0).

first: Subhash

last: Kulkarni

first: Monalee

last: Saha

first: Laren

last: Becker

first: Zhuolun

last: Wang

first: Jenna

last: Leser

first: Mithra

last: Kumar

first: Shriya

last: Bakhshi

first: Matthew

last: Anderson

first: Mark

last: Lewandoski

first: Jared

last: Slosberg

first: Sushma

last: Nagaraj

last: Vincent

first: Pankaj

last: Pasricha


title: Understanding downstream signaling pathways regulated by miR-34a-5p in articular cartilage by RNA sequencing using miR-34a knock-out mice

status: Public on Mar 08 2021

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

summary: The goal of this study was to determine the role of miR-34a in regulating chondrocyte transcript profiles. Next Generation Sequencing of total RNA extracted from mouse KO and WT chondrocytes revealed 175 significantly differentially expressed genes (84 up, 91 down) in miR-34a KO chondrocytes compared to WT cells. We are currently validating potential direct targets of miR-34a from our NGS data and performing computational pathway analysis to identify novel pathways regulated by miR-34a.

overall_design: Heterozygous miR-34a KO mice were bred to generate global homozygous KOs. Articular cartilage was harvested and pooled from hips and knees, and enzymatically digested to isolate chondrocytes from 5 week-old homozygous miR-34a KO and WT mice. Chondrocytes were cultured in complete medium for approximately ten days. Total RNA was extracted from miR-34a KO or WT mouse chondrocytes followed by RNA quality assessment, sample library preparation, and library quality assessment. The prepared libraries were sequenced on the Illumina NextSeq 550 sequencer for 75 paired end read-cycles.

first: Helal

last: Endisha

first: Poulami

last: Datta

first: Anirudh

last: Sharma

first: Sayaka

last: Nakamura

first: Evgeny

last: Rossomacha

first: Carolen

last: Younan

first: Shabana Amanda

last: Ali

first: Ghazaleh

last: Tavallaee

first: Starlee

last: Lively

first: Pratibha

last: Potla

first: Jason

last: Rockel

first: Roman

last: Krawetz

first: Nizar

last: Mahomed

first: Igor

last: Jurisica

first: Rajiv

last: Gandhi


title: The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

summary: We compared the change of transcriptome induced by the over expression of the lncRNA APOLO, the downregulation of the methylcytosine-binding protein VIM1 and the increased temperature of growth. A correlation of up- and down-regulated genes in WT in response to 29°C is observed for OE APOLO-1 and vim1-3 at 23°C.

overall_design: 4-day-old Col, 35S:APOLO or vim1-3 seedlings growing at 23°C or 29°C were analyzed for RNA-Seq in triplicates

first: Camille

last: Fonouni-Farde

first: Aurélie

last: Christ

first: Federico

last: Ariel


title: Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse [RNA-seq]

status: Public on Aug 17 2021

city: Tampere

first: Sinja

last: Taavitsainen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.

overall_design: RNA sequencing of testosterone-dependent VCaP, androgen-independent VCaP, enzalutamide-resistant VCaP, bicalutamide-resistant VCaP, and enzalutamide- + bicalutamide-resistant VCaP.

first: Teemu

last: Murtola

first: Merja

last: Bläuer

first: Heimo

last: Syvälä

first: Reetta

last: Nätkin

first: Tapio

last: Visakorpi


title: Transcriptional landscape of Myceliophthora thermophila responding to soluble starch and the role of regulator AmyR on polysaccharide degradation

first: Jingen

last: Li

summary: Thermophilic fungus Myceliophthora thermophila with great capacity for polysaccharides degradation is attractive to be engineered into a cell factory to produce chemicals and biofuels directly from renewable polysaccharides such as starch. Understanding the molecular mechanism of starch degradation of the fungi would be helpful. To date, there has been no transcriptome analysis on starch in thermophilic fungi. In this study, we performed the transcriptomic profile of M. thermophila responding to soluble starch, and a 342-gene set was identified as “starch regulon”, including the major amylolytic enzyme (Mycth_72393), which was verified thereafter as the most important such hydrolase for starch degradation in this fungus. Moreover, the function of key amylolytic enzyme regulator AmyR in M. thermophila was evaluated by analyzing the performance of its deletion mutant using our CRISPR/Cas9 system, which showed significantly decreased amylase activity and poor growth on starch. Additionally, deletion of amyR led to resistance to carbon catabolite repression (CCR) and enhanced cellulases production. Our study provides an insight into understanding the molecular basis of starch degradation in this thermophilic fungus, and will accelerate the fungal strain rational engineering for starch-based biochemical production.

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to carbon starvation, glucose and starch.

first: Chaoguang

last: Tian


title: 6mer Seed toxicity and platinum resistance in ovarian cancer [DISE-18]

first: Marcus

last: Peter

type: Non-coding RNA profiling by high throughput sequencing

first: Monal

last: Patel


title: 6mer Seed toxicity and platinum resistance in ovarian cancer [DISE-41]

overall_design: Small RNA was isolated from A2780 and Pt resistant A2780R ovarian cancer cells 24 hrs after transfection with 1nM of three different siRNAs

first: Elizabeth

last: Bartom


title: Biphasic effects of pleiotropic cytokine IL-27 during Staphylococcus aureus implant-associated osteomyelitis

status: Public on Mar 16 2021

city: rochester

first: Yugo

last: Morita

state: New York

address: 601 Elmwood Avenue, Box 665, Center for Musculoskeletal Research

institute: University of Rochester Medical Center

summary: We aimed to elucidate the mechanism of IL-27/ IL-27 receptor signaling effects on S. aureus osteomyelitis via gene expression studies.

overall_design: C57BL/6 mice were intramuscularly injected with recombinant adeno-associated virus expressing murine IL-27 (rAAV-IL-27) or recombinant adeno-associatd virus expressing GFP (rAAV-GFP, control) and then challenged with a S. aureus contaminated trans-tibial implant. Subsequently, infected tibia were collected on days 1, 3, 7 and 14 post-septic surgery for RNA sequencing.

first: Gowrishankar

last: Muthukrishnan

first: Edward

last: Schwarz

first: Anthony

last: Franchini


title: Influence of Liver Fibrosis on Pien Tze Huang by RNA-Seq Analysis of Circular RNAs

first: Jinhang

last: Zhu

address: Huashan Road 1954

summary:
Purpose: We investigate the regulation circRNAs in the damaged fibrotic liver treated with Pien Tze Huang (PZH) by RNA-seq.
Methods: Liver tissue circRNAs expression profiles from 8-week carbon tetrachloride (CCl4)-induced, and PZH-treated and CCl4-induced liver fibrosis control mice were investigated by RNA-seq and dysregulated circRNAs in PZH-treated were identified. Various bioinformatics analyses established competing endogenous RNA (ceNRA) in circRNAs-miRNAs-mRNAs axis. Moreover, GO annotation and Kegg pathway were analyzed to identify the relational biological processes and pathway. qRT–PCR validation was performed using LX-2 cell sample pairs and SYBR Green assays.
Results: We identified 91 differentially expressed circRNAs in the PZH-treated compared with control mice, of which 58 up-regulated circRNAs and 43 down-regulated circRNAs. The ceRNA network were constructed suggesting the potential role of circRNAs is the regulation of target gene expression as a miRNAs sponge. Moreover, GO and Kegg pathway analysis showed that these predicted mRNAs were related to liver fibrosis-related pathways such as TNF, PI3K-Akt, and MAPK signaling pathway. Meanwhile, the results of validation qRT-PCR of target genes in LX-2 cells were in accordance with RNA-seq with high confidence.
Conclusions: We identified the dysregulated circRNAs and established functional network of circRNA-miRNA-mRNA to further reveal the potential interactions and biological processes in PZH-treated liver fibrosis mice. These findings indicate that mmu_circ_Slc25a25 may modulate the transcription of certain genes, such as Slc7a11 and Slc39a14, which may provide a more precise and comprehensive perspective for clarifying the role of PZH therapy as a potential agent for treatment of liver fibrosis.

overall_design: Investigation of dysregulated circRNA in liver tissue of 8-week PZH-treated or without mice by RNA-seq, using Illumina Hiseq 4000.

first: Shengyin

last: Qin

first: Ting

last: Wang


title: A novel conserved transcription factor CLR-4 regulates cellulase genes expression through controlling the intracellular cAMP level in ascomycete fungi

status: Public on Mar 18 2021

summary: Fungal degradation of lignocellulosic biomass requires various (hemi-)cellulases and plays key roles in biological carbon cycle. Although cellulases induction recently described in some saprobic filamentous fungi, regulation of cellulase transcription has not been studied thoroughly. Here, we identified and characterized the novel cellulase regulation factors clr-4 in Neurospora crassa and its ortholog Mtclr-4 in Myceliophthora thermophila. Deletion of clr-4 and Mtclr-4 displayed similarly defective phenotypes in cellulolytic enzymes production and activities. Transcriptomics analysis of Δclr-4/ΔMtclr-4 revealed down-regulation of not only encoding genes of (hemi-)cellulases and pivotal regulators (clr-1, clr-2 and xyr-1), but also the key genes of cAMP signaling pathway such as adenylate cyclase cr-1. Consistently, the significant decreased levels of intracellular cAMP were observed in Δclr-4/ΔMtclr-4 compared to wild-type during cellulose utilization. Electrophoretic mobility shift assays (EMSA) verified that CLR-4 could directly bind to the promoter regions of adenylyl cyclase (Nccr-1) and cellulose regulator clr-1, while MtCLR-4 bind to upstream regions of adenylyl cyclase Mtcr-1 and biomass deconstruction regulators Mtclr-2 and Mtxyr-1. Concluded, the novel cellulase expression regulators (CLR-4/MtCLR-4) findings here significantly enrich our understanding of the regulatory network of cellulose degradation and provide new targets for industrial fungi strain engineering for plant biomass deconstruction in biorefinery.

sample_organism:
Neurospora crassa
Thermothelomyces thermophilus

overall_design: mRNA profiles of Neurospra crassa and Myceliophthora thermophila cells exposed to 4h Avicel, respectively.

first: Qian

last: Liu


title: Transcriptome profiling of Cd resistance by exogenous treatment of melatonin in Italian Lettuce

status: Public on Jan 13 2021

city: Chengdu

first: Jiyun

last: Peng

state: Sichuan

address: Huimin Road 211,Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: This study is the first transcriptome study for Cd and melatonin treatment in lettuce, both transcriptomes and the expression profile would provide the foundation for further exploring the molecular mechanism of Cd accumulation, and develop breeding strategies aimed at decreasing Cd in crop plants.

overall_design: Italian Lettuce (Lactuca sativa L. var. ramose Hort.) seeds were sterilized with 10 % hydrogen peroxide for 10 min and rinsed thoroughly with distilled water for three times, then germinated on moist filter paper in the dark at 20 °C. After the initiation for 0.5 cm, the seeds were transferred to a salver (40 x 30 cm) filled with perlite and covered by vermiculite for moisture holding. Then, they were transferred into the incubator under 23℃/18℃ for 14h/10h in day and night time, respectively. The relative humidity set as 70% and the light intensity was 15,000 lx. After the formation of seedlings, they were watered with 200ml half-strength Hoagland’s nutrient solution per day for 20 days, subsequently cultivated in a growth chamber. 20 days later, the seedlings were divided into two groups: 1) seedlings cultivated with the nutrient solution with 1μmol/L (Sigma-Aldrich, USA) melatonin. 2) seedlings cultivated with the nutrient solution without melatonin. Then, these two groups were treated by 50 μmol/L CdCl2 for simulation a Cd stress environment, and the nutrient solution was replenished regenerated once for three days to maintain constant concentrations. The leaves and root of 0d, 1d, and 5d seedlings in two groups have been sampled, and three biological repeats were included for each treatment . All samples were stored in Ultra-low Temperature Freeze under -80° before conducting.

first: Yi

last: Tang


title: 6mer Seed toxicity and platinum resistance in ovarian cancer

state: IL

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

overall_design: Refer to individual Series


title: Dynamic IFNβ signalling underlies treatment response to immune checkpoint therapy in cancer

status: Public on Dec 07 2020

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

country: Australia

institute: National Centre For Asbestos Related Diseases


title: 6mer Seed toxicity and platinum resistance in ovarian cancer  [DISE-29]


title: ZFP36L1 Regulates Fgf21 mRNA Turnover and Modulates Alcoholic Hepatic Steatosis and Inflammation in Mice

status: Public on Jan 01 2021

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

summary: The objective of this project is to identify the differential gene expression changes between WT and Zfp36l1 liver-specific knockout mice fed with control diet versus fed with Ethanol containing diet.


title: 6mer Seed toxicity and platinum resistance in ovarian cancer  [DISE-39]


title: RNA-sequencing of Early vs Late Mouse Pancreas Reentrainment

status: Public on Jan 21 2021

city: Madison

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

summary: The objectives of this study was to understand the implication of early (day 1:ZT8) vs late (day 8 [for female]/day 9 [for males]:ZT176/200) reentrainment in mouse pancreas following a chronic (1-month) phase shift protocol. 4-6 week old mice underwent 4 weeks of either a normal circadian light-dark cycle or a circadian disrupted light-dark cycle whereby mice were phase shifted forward 8 hours every 2-3 days. At 4 weeks all mice were normalized to normal circadian conditions 12 hours prior to the 4 week mark. Mice were then sacraficed at 14:00 each day. Of the mice evaluated, those from ZT8 and ZT176/200 were selected for further evaluation with RNA-sequencing.

overall_design: A total of 24 samples were included from two timepoints. At each timepoint, 6 mice were evaluated from each condition, including normal circadian and circadian disrupted conditions. A total of 3 males/females were included per condition per timepoint.

first: Patrick

last: Schwartz

first: Mark

last: Berres


title: Effect of ASCL1 phosphorylation status on chromatin binding and target regulation in neuroblastoma

status: Public on Mar 15 2021

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: ASCL1, a basic helix-loop-helix family transcription factor, is a master regulator of developmental neurogenesis and a crucial component of transcription factor cocktails that can convert heterologous cell types such as fibroblasts into neurons. The ability of ASCL1 to drive neuronal differentiation is controlled by multi-site phosphorylation but how this modification controls the genome-wide transcriptional activity of ASCL1 is unknown.  Using human neuroblastoma cells that maintain a rapidly dividing neuroblastic phenotype yet retain the ability to undergo differentiation as a model system, we find that phosphorylation of ASCL1 has limited effect on target gene promoter association, but predominantly regulates  its binding to a subset of distal enhancer regions, resulting in extensive differences in target control by activation, as well as direct and indirect gene repression.  These genome-wide analyses reveal how post-translational modification of ASCL1 can change its structure and function, driving it to differential regulatory elements to change cell fate, and controlling ASCL1’s activity as a master transcription regulator of neurogenesis. Using functional mutational and pharmacological approaches, we find that preventing CDK-dependent phosphorylation of ASCL1 in neuroblastoma cells results in co-ordinated suppression of the MYC-driven core circuit supporting neuroblast identity and proliferation, while simultaneously activating a gene programme driving neuronal differentiation. Thus, we show targeting the post-translational modification of a key developmental regulator can re-engage  a latent genome-wide programme forcing mitotic exit and differentiation in cancer cells.

overall_design:
RNA-seq analysis of SH-SY5Y ASCL1-doxycycline-inducible cells. 5 replicates each of 2 unique clones were used, for uninduced, WT-induced, and S-A induced cells. ASCL1 ChIP-seq analysis of SH-SY5Y ASCL1-doxycycline-inducible cells. 3 replicates each of 2 unique clones were used , for WT-induced, and S-A induced cells, plus input for each sample.

Generation of lentivirally transduced cell lines:
Viral constructs were generated by site directed mutagenesis using the QuikChange II XL Site- Directed Mutagenesis Kit (Agilent Technologies) and cloned into a 3rd Generation Lenti-X vector (pLVX-TREG) (Clontech) using In-Fusion® HD Cloning Kit (ClonTech). Viral constructs were made by transfecting Lenti-X™ 293T cell line (Clontech) with 250mM calcium phosphate and the vector of interest, and packaging mix: PMD2G, PMLg, REV/PRSV in a ratio of 6:3:4:2 respectively. Viruses were concentrated using LenitiX concentrator (Clontech) and titered using the Lenti-XTM qRT-PCR Titration Kit (ClonTech). Neuroblastoma cells were transduced with a Tet-On transactivator (pLVX-CMV-Tet3G) (Clontech) at an MOI of 10. After 48 hours, cells were selected with 500 μg/ml G418 for 72 hours based on a previously determined optimal antibiotic kill curve. These cells were then transduced with pLVX-TREG - encoding either human WT or S-A ASCL1 at a multiplicity of infection of 10 and then selected after 48 hours with 1 μg/ml puromycin for 72 hours based on previously determined kill curves.

ChIP-seq:
ChIPseq was performed as described previously (Jozwik et al., 2016; Schmidt et al., 2009) using anti-ASCL1 (Abcam, cat# ab74065).  ChIPseq experiments were performed in two separate clones of each of WT and S-A SH-SY5Y tetracycline-inducible stable cell lines induced with 1 µg/ml doxycycline for 24 hours, before cross-linking with 1% formaldehyde. ChIPseq experiments were performed in at least four biological replicates. ChIP-seq and the input libraries were prepared using the ThruPLEX® DNA-seq Kit (Rubicon Genomics). Reads were mapped to hg19 genome using Bowtie2 2.2.6. Aligned reads with the mapping quality less than five were filtered out. The read alignments from four replicates were combined into a single library, and peaks were called with model based analysis for ChIP-seq 2 (MACS2) version 2.0.10.20131216 using sequences from SH-SY5Y chromatin extracts as a background input control. Meme version 4.9.1 was used to detect known and discover binding motifs among tag-enriched sequences. For visualising tag density and signal distribution heatmap, the normalized read coverage in a window of a ±2.5- or 5-kb region flanking the tag midpoint was generated using a bin size of 1/100 of the window length. Differential binding analysis (Diffbind) was performed as described previously (Jozwik et al., 2016).

RNA-seq:
RNA-sequencing experiments were performed in SH-SY5Y, WT and S-A SH-SY5Y tetracycline-inducible stable cell lines, using two clones of each. For the inducible cell lines, cells were induced with 1 µg/ml doxycycline for 24 hours and RNA extracted. Experiment was performed in at least five biological replicates for each cell line. Single-end 40-bp reads generated on the Illumina HiSeq sequencer were aligned to the human genome version GRCh37 and read counts were generated using STAR 2.5.1a (Anders and Huber, 2010).

first: Fahad

last: Ali

first: Laura

last: Woods

first: Daniel

last: Corchado

first: Igor

last: Chernukhin

first: Luke

last: Wylie

first: Lydia

last: Parkinson

first: Lewis

last: Chaytor

first: Thomas

last: Hiscock

first: Tatiana

last: Papkovskaia

first: Roshna

last: Gomez

first: Liam

last: Lee

first: Christopher

last: Weekes

first: John

last: Davies

first: Suzanne

last: Turner

first: Revathy

last: Ramachandran

first: Jason

last: Carroll

first: Anna

last: Philpott


title: 6mer Seed toxicity and platinum resistance in ovarian cancer [DISE-26]

first: Marcus

last: Peter

overall_design: Small RNA was isolated from A2780 and Pt resistant A2780R ovarian cancer cells

first: Monal

last: Patel


title: Analysis of cytoplasmic, nucleoplasmic, nucleolar transcriptome in Raw264.7 macrophages during LPS stimulation

status: Public on Oct 13 2020

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

institute: Yonsei University

summary: To understand a novel function of nucleolus during infectious conditions, we purified cytoplasmic, nucleoplasmic, and nucleolar fractions from macrophages for a time course of LPS stimulation and performed RNA-seq.

overall_design: RNA-seq using RNAs extracted from cytoplasmic, nucleoplasmic or nucleolar fractions in Raw264.7 macrophages during LPS stimulation (0, 2, 6, 12, or 15 h) in triplicate

first: Taeyun

first: Heunjong

last: Han


title: Non-human primate blood-brain barrier and in vitro brain endothelium: from transcriptome to the establishment of a new model

status: Public on Jul 23 2020

city: Chilly-Mazarin

first: Dominique

last: Lesuisse

address: 1, avenue Pierre Brossolette

department: Rare and neurologic diseases therapeutic area

institute: Sanofi

summary: The blood-brain barrier (BBB) represents a major challenge when developing central nervous system (CNS)-active therapeutics. The non-human primate (NHP)-brain endothelium constitutes an essential alternative to human in the prediction of molecule trafficking across the BBB and in the search of new brain-specific transport mechanisms. This study presents a comparison between the NHP transcriptome of freshly isolated brain microcapillaries and in vitro-selected brain endothelial cells (BECs), focusing on important BBB features – tight junctions, receptors mediating transcytosis (RMT), ABC and SLC transporters. In vitro BECs conserved most of the BBB key elements for barrier integrity and control of molecular trafficking. We also assessed the function of RMT via the Transferrin Receptor (TFRC) in the characterized NHP-BBB model, where both human transferrin and anti-hTFRC antibody showed increased apical-to-basolateral passage in comparison to control molecules. In parallel, we investigated eventual BBB-related regional differences in 7-day in vitro-selected BECs from 5 brain structures: brainstem, cerebellum, cortex, hippocampus and striatum. Our analysis retrieved very few differences in the brain endothelium from these 5 brain regions, suggesting a rather homogeneous BBB role and function across the brain parenchyma. In conclusion, the presently established NHP-derived BBB model closely mimics the physiological BBB, therefore representing a ready-to-use tool for assessment of the penetration of biotherapeutics into the human CNS.

overall_design:
7 sample groups:
Isolated brain microvessels_Cortex_P0D0
Brain Endothetlail Cells (BECs)_Cortex_P0D7
Brain Endothetlail Cells (BECs)_Cortex-P1D7
Brain Endothetlail Cells (BECs)_Brainstem_P0D7
Brain Endothetlail Cells (BECs)_Hippocampus_P0D7
Brain Endothetlail Cells (BECs)_Striatum _P0D7
Brain Endothetlail Cells (BECs)_Cerebellum _P0D7

first: Catarina

last: Chaves

first: Tuan-Minh

last: Do

first: Céline

last: Cegarra

first: Valérie

last: Roudières

first: Sandrine

last: Tolou

first: Gilbert

last: Thill

first: Corinne

last: Rocher

first: Michel

last: Didier


title: Sequencing identifies a distinct signature of circulating microRNAs in early radiographic knee osteoarthritis

status: Public on Oct 07 2020

first: Mohit

last: Kapoor

summary:
OBJECTIVE: MicroRNAs act locally and systemically to impact osteoarthritis pathophysiology, but comprehensive profiling of the circulating miRNome in early versus late stages of osteoarthritis has yet to be conducted. Our objective was to sequence the plasma miRNome from 91 patients with early [Kellgren-Lawrence grade 0 or 1 (n=41)] or late [Kellgren-Lawrence grade 3 or 4 (n=50)] symptomatic radiographic knee osteoarthritis to identify unique microRNA signatures in each disease state.
MicroRNA libraries were prepared using the QIAseq miRNA Library Kit and sequenced on the Illumina NextSeq550. Counts were produced for microRNAs captured in miRBase and for novel microRNAs.

overall_design: miRNA sequencing and analysis was performed using 91 plasma samples from patients with early and late radiographic knee OA.

first: Shabana

last: Ali

first: Rajiv

last: Gandhi

first: Pratibha

last: Potla

first: Sareh

last: Keshavarzi

first: Osvaldo

last: Espin-Garcia

first: Konstantin

last: Stestopaloff

first: Chiara

last: Pastrello

first: Dylan

last: Bethune-Waddell

first: Starlee

last: Lively

first: Anthony

last: Perruccio

first: Y

last: Rampersaud

first: Christian

last: Veillette

last: Rockel

first: Jurisica

last: Igor

first: Tom

last: Appleton

first: Kapoor

last: Mohit


title: Tumor hypoxia represses γδ T cell-mediated antitumor immunity against brain tumors

status: Public on Dec 04 2020

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

institute: Korea Advanced Institute of Science and Technology

summary: The anatomic location and immunologic characteristics of brain tumors result in strong lymphocyte suppression. Consequently, conventional immunotherapies targeting CD8 T-cells are ineffective against brain tumors. Tumor cells escape immunosurveillance by various mechanisms, and tumor cell metabolism can affect the metabolic states and functions of tumor-infiltrating lymphocytes. Oxygen tension is one important factor influencing immune responses. Here, we discovered that brain tumor cells had a particularly high demand for oxygen, which affected γδ T-cell-mediated antitumor immune responses but not those of conventional T-cells. Specifically, tumor hypoxia activated the γδ T-cell protein kinase A (PKA) pathway at a transcriptional level, resulting in repression of NKG2D expression. Alleviating tumor hypoxia reinvigorated NKG2D expression and the antitumor function of γδ T-cells. These results reveal a hypoxia-mediated mechanism by which brain tumors and γδ T-cells interact and emphasize the importance of γδ T-cells for antitumor immunity against brain tumors.

overall_design: 10X genomics was used to measure single-cell RNA sequencing (scRNA-seq) to characterize brain tumor-infiltrated immune cells.   C57BL/6 mice were intracranially injected with GL261 cells. After 20 days of injection, brain cells were isolated. CD45hi TILs were isolated by FACS Aria.

first: Jang Hyun

last: Park


title: Prenatal exposure to environmental toxins induces sexually dimorphic transcriptome changes in neonatal offspring

status: Public on Oct 29 2020

city: Durham

first: Wei

last: Chen

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Purpose: Gestational exposure to environmental toxins and socioeconomic stressors are epidemiologically linked to neurodevelopmental disorders with strong male-bias, such as autism. We modeled these prenatal risk factors in mice, by co-exposing pregnant dams to an environmental pollutant and limited-resource stress, which robustly activated the maternal immune system. Only male offspring displayed long-lasting behavioral abnormalities and alterations in the activity of brain networks encoding social interactions. Cellularly, prenatal stressors diminished microglial function within the anterior cingulate cortex, a central node of the social coding network, in males during early postnatal development. Genetic ablation of microglia during the same critical period mimicked the impact of prenatal stressors on a male-specific behavior, indicating that environmental stressors alter neural circuit formation in males via impairing microglia function during development.

overall_design: Methods: Pregnant dams were exposed with either CON or DEP+MS, at P8 prefrontal cortices of male and female offspring born to exposed mothers were collected and RNA was extracted. . RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit. Sequencing was performed  on an  Illumina NovaSeq 6000 using S-Prime flow cell at 50bp paired-end

first: Staci

last: Bilbo

first: Cagla

last: Eroglu

first: Carina

last: Block


title: Epigenome analysis of normal and recent onset psychosis samples

status: Public on Sep 02 2020

city: Jeonju-si

first: Young-Chul

last: Chung

address: 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

department: Psychiatry

institute: Medical School; Research Institute

summary: Genome wide DNA methylation profiling of normal and recent onset psychosis samples . The Infinium Human Methylation 850 K BeadChips was used to obtain DNA methylation profiles across approximately 853 307  CpGs in samples. Samples included 50 normal , 84 recent onset psychosis.

overall_design: Bisulphite converted DNA from the 134 samples were hybridised to the Infinium Human Methylation 850 K BeadChips

first: YanHong

last: Piao


title: RNAseq of mRNA from splenic and hepatic CD8 T cells in ND and CD-HFD mice

status: Public on Dec 18 2020

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

summary: In this study we want to compare the gene expression profile of CD44+CXCR6+ CD8+ T cells from the liver of ND and CD-HFD mice with hepatic CD44+CXCR6neg and splenic CD44+ CX3CR1neg CD8 T cells of ND and CD-HFD mice.  This comparison will reveal transcriptional signatures of hepatic CD44+CXCR6+ CD8+ T cells in CD-HFD responsible for causing liver pathology in NASH.

overall_design: splenic and hepatic CD8 T cell populations in different diets (ND and CD-HFD)

first: Michael

last: Dudek

first: Sainitin

last: Donakonda

first: Rupert

last: Oellinger

first: Thomas

last: Engleitner

first: Percy

last: Knolle


title: 6mer Seed toxicity and platinum resistance in ovarian cancer [DISE-37]

status: Public on Feb 02 2021

city: Chicago

first: Marcus

last: Peter

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: We demonstrate that 6mer seed toxicity plays a role in platinum resistance of ovarian cancer

overall_design: Ago protein associated short RNAs were pulled down using a GW182 pepotide and subjected to smRNA Seq

first: Monal

last: Patel


title: RNA-seq of patient-derived melanoma cells depleted for GLI1 and SOX2

status: Public on Oct 06 2020

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We report the RNA-seq of melanoma cells depleted for SOX2 and GLI1. Three pairs of total RNAs from each condition were generated for library preparations and subsequent RNA-seq. All samples had over 50 million reads with over 93% of the reads mapping to the human genome (obtained from the UCSC Genome Browser assembly ID:hg19). Using differential expression analysis (fold change (FC)>1.5, false discovery rate (FDR)<0.1 as standard cut-offs), we identified 1104 entities commonly altered in both SOX2- and GLI1-knocked down cells. We grouped genes into enrichment clusters revealed by DAVID functional annotation tool (https://david.ncifcrf.gov/).

overall_design: Examination of the top pathways significantly downregulated in both SOX2-and GLI1-depleted melanoma cells and identification of SOX2/GLI1 commonly regulated genes

first: Silvia

last: Pietrobono

first: Barbara

last: Stecca

first: Luciana

middle: L

last: Almada

first: Martin

middle: E

last: Fernandez-Zapico


title: CD95 suppresses immune infiltration in a model of triple negative breast cancer

status: Public on Jul 20 2020

summary: CD95 acts as an immune suppressor for TNBC tumors when grown in syngeneic mice. 4T1 cells were grown in two mouse strains. Comparisons included parental, a pool stably expressing vCas9 and two clones in which CD95/Fas was deleted using CRISPR-Cas9 gene editing, clone #54 and clone #69.

overall_design: Examination of differential gene mRNA expression in tumor with and without CD95 expression in NSG or Balb/c mice.

first: Syed

last: Qadir

first: Matthew

last: Schipma


title: Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

status: Public on Nov 01 2020

city: Seattle

first: Jason

middle: W

last: Reeves

state: WA

address: 530 Fairview Blvd

department: R&D

institute: Nanostring

sample_organism: Severe acute respiratory syndrome coronavirus 2