title: Oligodendrocyte and microglia transcriptome analysis in a mouse model of encephalopathy of prematurity induced by systemic inflammation

city: Paris

first: Anne-Laure

last: Schang

state: Select Option

address: 4, Avenue de l'Observatoire

department: Faculté de Pharmacie

institute: Université Paris Cité

summary: Premature birth is frequently associated with abnormal brain development, leading to brain damage, the most common being diffuse white matter injury. Perinatal neuroinflammation, which relies primarily on microglial activation, contributes to the myelination failure by affecting oligodendrocytes. To better understand the pathophysiological mechanisms involved in encephalopathy of prematurity, we took advantage of a mouse model in which systemic injections of proinflammatory interleukin-1β (IL1B) disrupt oligodendrocyte differentiation, leading to hypomyelination and cognitive deficits. Newborn mice received intraperitoneal injections of IL1B from postnatal day (P) 1 to P5. At P5 and P10, brains were collected from six control (PBS) and six exposed (IL1B) mice; oligodendrocytes and microglial cells were sequentially isolated using antibodies coupled to magnetic beads targeting O4 and CD11b, respectively. Gene expression analysis performed on Agilent microarray revealed that perinatal inflammation induced major changes in gene expression in both cell types. By improving our understanding of the cellular mechanisms involved in encephalopathy of prematurity, this study could ultimately help design neuroprotective strategies.

overall_design: Male swiss mice received intra-peritoneal injections of PBS or IL1B (10ng/g) from post-natal (P) 1 to P4 and once at P5. At P5 (2h after the last injection) or at P10, mice were sacrificed, brain were collected and O4+ oligodendrocytes were first isolated by Magnetic Activated Cell Sorting (MACS technology, Miltenyi), followed by isolation of CD11B+ microglial cells from the negative fraction collected after O4 sorting. Six control (PBS) and six IL1B-treated replicates were collected at P5 and P10 to perform gene expression analysis on Agilent whole genome 8x60K microarrays.

first: A

last: SCHANG

first: J

last: VAN STEENWINCKEL

first: B

last: FLEISS

first: P

last: GRESSENS


title: Senataxin and RNase H2 act redundantly to suppress genome instability during class switch recombination

status: Public on Dec 14 2022

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

country: USA

institute: UC Davis

summary: Class switch recombination generates antibody distinct isotypes critical to a robust adaptive immune system and defects are associated with auto-immune disorders and lymphomagenesis. Transcription is required during class switch to recruit the cytidine deaminase AID—an essential step for the formation of DNA doublestrand breaks—and strongly induces the formation of R loops within the immunoglobulin heavy chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here we report that cells lacking two enzymes involved in R loop removal— Senataxin and RNase H2—exhibit increased R loop formation and genome instability at the immunoglobulin heavy chain locus without impacting class switch recombination efficiency, transcriptional activity, or AID recruitment. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking Senataxin or RNase H2B alone. We propose that Senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.

overall_design: Using LAMS-HTGTS and DRIP-seq to characterize translocation/mutation profile and R-loop formation at IgH region during class switch recombination in mouse B-cells which lack R-loop removal enzymes (setx-/-, rnaseh2b-/-, and setx-/- rnaseh2b-/-).

first: Hongchang

last: Zhao

first: Stella

last: Hartono

first: Kirtney

last: De Vera

first: Zheyuan

last: Yu

first: Krishni

last: Satchi

first: Tracy

first: Roger

last: Sciammas

first: Lionel

last: Sanz

first: Jacqueline

last: Barlow


title: The difference of right and left ventricular remodeling caused by volume overload  in neonatal SD rats

status: Public on Dec 15 2022

city: Shanghai

first: Qing

last: Cui

state: Shanghai

address: Dongfang Lu No.1678

country: China

institute: Shanghai Children′s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We reported the RNAseq analyses of right ventricle (RV) and left ventricle (LV) in neonatal volume overload (VO) and sham-operated SD rat. VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) within 24 hours postnatally (P1). RNAseq analyses of RV and LV free wall of P7 from VO and sham-operated rat. It demonstrated that the 1806 differentially expressed genes (DEGs) between RV and LV at the neonatal stage were primarily enriched in GTPase mediating signal transduction, insulin signaling pathway and thyroid hormone signaling pathway. VO produced 3 more times DEGs in LV than RV . GO analysis of these DEGs demonstrated that in the top 150 enriched terms, the LV comparison and RV comparison shared 34 terms (22.7%) in common. These commonly enriched terms were primarily associated with GTPase mediating signal transduction. KEGG analysis of these DEGs demonstrated that in the top 30 enriched terms, the LV comparison and RV comparison shared 14 terms (46.7%) in common. And insulin signaling pathway and thyroid hormone signaling pathway are the top two enriched terms in common. Regarding the differently enriched GO terms, they were primarily associated with lipid metabolism and ion channel in RV and primarily associated nucleic acid metabolism in LV. The top two differently enriched KEGG terms were arrhythmogenic right ventricular cardiomyopathy (ARVC) and adipocytokine signaling pathway in RV while microRNAs in cancer and longevity regulating pathway in LV. These results were further confirmed by the determination of metabolites.

overall_design: RNAseq analyses of right ventricle (RV) and left ventricle (LV) in neonatal volume overload and sham-operated SD rat

first: Sijuan

last: Sun

first: Lincai

last: Ye

first: Jie

last: Shen


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1 [CUT&RUN]

status: Public on Dec 13 2022

city: Houston

first: Stephanie

middle: Lynn

last: Coffin

state: TX

address: 1250 Moursund St

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome wide binding profiles of CIC and H3K27ac in CIC KO (Engrailed1-Cre;Cicfl/fl), wildtype, Atxn1_154Q/2Q (SCA1),  and Atxn1_154Q[V5591A;S602D]/2Q (154Q AXH) in the cerebellum

overall_design: CIC and H3K27ac binding profiles in the cerebellum of CIC KO (Engrailed1-Cre;Cicfl/fl), wildtype, Atxn1_154Q/2Q (SCA1),  and Atxn1_154Q[V5591A;S602D]/2Q (154Q AXH) mice.

middle: L

first: Huda

middle: Y

last: Zoghbi

first: Mark

middle: A

last: Durham


title: Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters [ChIP-seq H3K4me1,me3]

city: Aachen

first: Mirna

last: Barsoum

state: North Rhine Westphalia

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Biology

country: Germany

institute: Uniklinik RWTH Aachen

summary: Cell fate decisions are closely associated with changes in gene expression programs. A large number of post-translational modifications of core histones contribute to controlling the expression of genes. A modification that is closely correlated with open chromatin and gene transcription is methylation of lysine 4 of histone H3 (H3K4). It is catalyzed by methyltransferases of the KMT2 family, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is required for organismal development and for tissue homeostasis in the mouse. In mouse embryo fibroblasts (MEFs), the loss of Ash2l results in downregulated gene expression, which provokes a senescence phenotype. We now find that both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) are deregulated. H3K4me3 is lost while H3K4me1 is increased at promoters upon knockout of Ash2l. In particular, loss of H3K4me3 at promoters correlates with downregulation of gene expression, which is particularly obvious at CpG island promoters. Ash2l loss results in an increase of histone H3 loading at promoters, paralleled by enhanced chromatin compaction. This is accompanied by an increase of repressing and a decrease of activating histone marks. One of the sequence-specific transcription factors with altered binding upon depletion of Ash2l is CTCF. It is lost from some promoter-associated sites, but gained binding in other regions of the genome. This suggests that in addition to the well-known effects on H3K4 methylation upon depleting KMT2 complex components, Ash2l loss affects chromatin compaction. Whether the decrease of H3K4me3 promotes chromatin compaction at promoters or whether these are independent consequences of Ash2l loss remains to be determined. We suggest that both contribute mechanistically to gene repression and thus to the observed cellular effects.

overall_design: Two independently generated mouse embryo fibroblast lines (from two different litters) with floxed exon 4 of Ash2l (KO1 and KO2). Two additional lines  with wt Ash2l (WT1 and WT2). All express Cre-ER and were immortalized using shArf. Cells were treated  -/+ 4-hydroxytamoxifen for 5 days.ChIP was performed with antibodies for H3K4me1 and H3K4me3.

first: Alexander

middle: T

last: Stenzel

first: Agnieszka

last: Bochyńska

first: Chao-Chung

last: Kuo

last: Tsompanidis

first: Roksaneh

last: Sayadi Boroujeni

first: Philip

last: Bussmann

first: Juliane

last: Lüscher-Firzlaff

first: Ivan

middle: G

last: Costa

first: Bernhard

last: Lüscher


title: Cell-line-specific gene expression changes following inactivation of the CTNNB1 gene in human colorectal cancer cell lines

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

institute: Albert-Ludwigs-Universität Freiburg

summary: Unrestrained transcriptional activity of β-CATENIN and its binding partner TCF7L2 frequently underlies colorectal tumor initiation and is considered an obligatory oncogenic driver throughout intestinal carcinogenesis. Yet, the TCF7L2 gene carries inactivating mutations in about 10 % of colorectal tumors and is non-essential in colorectal cancer (CRC) cell lines. To determine whether CRC cells acquire TCF7L2-independence through cancer-specific compensation by other T-cell factor (TCF)/lymphoid enhancer‑binding factor (LEF) family members, or rather lose addiction to β-CATENIN/TCF7L2-driven gene expression altogether, we generated multiple CRC cell lines entirely negative for TCF/LEF or β-CATENIN expression. Viability of these cells demonstrates complete β‑CATENIN- and TCF/LEF-independence, albeit one β-CATENIN-deficient cell line eventually became senescent. Absence of TCF/LEF proteins and β-CATENIN consistently impaired CRC cell proliferation, reminiscent of mitogenic effects of WNT/β-CATENIN signaling in the healthy intestine. Despite this common phenotype, β-CATENIN-deficient cells exhibited highly cell-line-specific gene expression changes with little overlap between β-CATENIN- and TCF7L2-dependent transcriptomes. Apparently, β‑CATENIN and TCF7L2 control sizeable fractions of their target genes independently from each other. The observed divergence of β-CATENIN and TCF7L2 transcriptional programs, and the finding that neither β-CATENIN nor TCF/LEF activity is strictly required for CRC cell survival has important implications when evaluating these factors as potential drug targets.

overall_design: We used RNA-seq to compare gene expression profiles of human colorectal cancer cell lines HCT116, HT29, and SW480 with CTNNB1 wild-type or knockout genes. For each cell line, two wild-type and two CTNNB1 knock-out cell clones were examined. Two independent biological replicates were performed.

first: Janna

last: Fröhlich

first: Katja

last: Rose


title: Inhibition of coronavirus HCoV-OC43 by targeting the eIF4F complex [Vero E6]

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: This study reports a screen to identify putative inhibitors of the eIF4F complex for potential effects on blocking coronavirus replication, using HCoV-OC43 (OC43) infection of Vero E6 cells and the lung epithelial cancer line A549 as models.

overall_design: Gene expression comparison of uninfected control, HCoV-OC43 infected, and HCoV-OC43 infected treated with compounds on Vero E6 cells using RNA-seq.

first: Yongmei

last: Feng


title: Inhibition of coronavirus HCoV-OC43 by targeting the eIF4F complex [A549]

overall_design: Gene expression comparison of uninfected control, HCoV-OC43 infected, and HCoV-OC43 infected treated with compounds on lung epithelial cancer line A549 using RNA-seq.


title: Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

summary:
Drug repurposing is a fast and effective way to develop drugs for an emerging disease such as COVID-19. The main challenges of effective drug repurposing are the discoveries of the right therapeutic targets and the right drugs for combating the disease.
Here, we present a systematic repurposing approach, combining Homopharma and hierarchal systems biology networks (HiSBiN), to predict 327 therapeutic targets and 21,233 drug-target interactions of 1,592 FDA drugs for COVID-19. Among these multi-target drugs, eight candidates (along with pimozide and valsartan) were tested and methotrexate was identified to affect 14 therapeutic targets suppressing SARS-CoV-2 entry, viral replication, and COVID-19 pathologies. Through the use of in vitro (EC50 = 0.4 uM) and in vivo models, we show that methotrexate is able to inhibit COVID-19 via multiple mechanisms.
Our in vitro studies illustrate that methotrexate can suppress SARS-CoV-2 entry and replication by targeting furin and DHFR of the host, respectively. Additionally, methotrexate inhibits all four SARS-CoV-2 variants of concern. In a Syrian hamster model for COVID-19, methotrexate reduced virus replication, inflammation in the infected lungs. By analysis of transcriptomic analysis of collected samples from hamster lung, we uncovered that neutrophil infiltration and the pathways of innate immune response, adaptive immune response and thrombosis are modulated in the treated animals.
We demonstrate that this systematic repurposing approach is potentially useful to identify pharmaceutical targets, multi-target drugs and regulated pathways for a complex disease. Our findings indicate that methotrexate is established as a promising drug against SARS-CoV-2 variants and can be used to treat lung damage and inflammation in COVID-19, warranting future evaluation in clinical trials.

overall_design: Male Syrian golden hamsters, aged 7-9 weeks old were obtained from Taiwan National Laboratory Animal Center. Hamsters were randomly allocated to study groups for antiviral evalution. 100 μL of PBS containing 1x104 pfu of SARS-CoV-2 was intranasal instilled under intraperitoneal anesthesia with Zoletil 50 (4mg/kg)/ Xylazine (0.5mg/kg) at day 0, and the mock-infected hamsters were challenged with 100 μL of PBS. Treatment groups were intraperitoneally given either MTX (2 mg/kg/day) or PBS (vehicle controls) for five consecutive days. At day-4 postinfection, all the hamsters were euthanized, and the lung tissues were for RNA extraction.

first: Yun

last: Chen

first: Yu

middle: H

last: Chang

first: Nikhil

last: Pathak

first: Shey

middle: C

last: Tzou

first: Yong

last: Luo

first: Yen

last: Hsu

first: Tian

middle: N

last: Li

first: Jung

last: Lee

first: Yi

middle: W

last: Huang

first: Hsin

middle: J

first: Nung

first: Hui

middle: P

last: Tsai

first: Tien

first: Shu

first: Ping

last: Liu

first: Yuan

middle: F

last: Chin

first: Wen

last: Lin

first: Chuen

middle: M

first: Hsueh

last: Wu

first: Chia

last: Wang

first: Jann

first: Chih

first: Chi

first: Po

middle: S

last: Hsieh

first: Yan

last: Wu Lee

last: Hung

first: Jinn


title: RNA-sequencing of three murine memory CD8 T cell subsets: IL-7Rα+KLRG1- , IL-7Rα+KLRG1+, and IL-7Rα-KLRG1+

status: Public on Dec 12 2022

first: William

last: Hudson

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

summary: The goal of this study is to characterize the transcriptional profile of three memory CD8 T cell subsets: IL-7Rα+KLRG1- (memory precursors, MP),  IL-7Rα+KLRG1+ (KLRG1+ MP) and IL-7Rα-KLRG1+ (terminal effectors, TE).

overall_design: Splenocytes were isolated from mice that had been infected with LCMV Armstrong 50 days prior (2×105 pfu, intraperitoneally). Cells were stained with extracellular antibodies (CD4, CD8, CD19, IL-7Rα, and KLRG1 from Biolegend and SouthernBiotech) and an LCMV-GP33 tetramer for 30 minutes. Cell viability was determined with the Live/Dead fixable aqua dead cell stain kit (Invitrogen). Cells were washed with PBS + 2% FBS and sorted on a FACSAria II (BD Biosciences). Three populations of GP33+ CD8 T cells were sorted in triplicate: IL-7Rα+KLRG1- (MP), IL-7Rα+KLRG1+ (KLRG1+ MP), and IL-7Rα-KLRG1+ (TE). RNA was isolated from each sample using the All-Prep DNA/RNA Micro Kit (Qiagen) and then submitted for sequencing.


title: Single cell gene expression profiling of cell lines and murine peripheral blood mononuclear cells (PBMCs)

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

summary: To demonstrate the efficacy of our developed Automated Live-imaging and cell Picking System for downstream RNA sequencing  (ALPS&RNA-seq), we isolated single cells of three cell lines (murine T cell, murine leukemia cell, and murine hematopoietic progenitor cell) and of murine peripheral blood mononuclear cells (PBMCs). The detemined profiles of the three cell lines were different, and the profiles of the PBMSc showed three subpopulations which were determined as CD4+ T cells, CD8+ T cells, and B cells based on the marker genes.

overall_design: Four 96-well plates containing single cells were isolated from a cell line mixture of murine leukemia cells, T cells, and hematopoietic progenitor cells by ALPS with random selection mode (3mix-random). Four plates of 36 leukemia cells, 36 T cells, 24 hematopoietic progenitor cells in order were isolated by ALPS with target selection mode (3mix-target). Two plates of 36 leukemia cells, 36 T cells, 24 hematopoietic progenitor cells in order were sorted by FACS (3mix-FACS). Sixteen plates of leukemia cells, T cells, and hematopoietic progenitor cells were isolated by ALPS after time-lapse imaging (3mix-timelapse).  Eight plates of PBMCs of C57BL/6J mice were isolated by ALPS after time-lapse imaging (PBMC-timelapse).

first: Jianshi

last: Jin

first: Taisaku

last: Ogawa


title: Inter-layer and inter-subject variability of circadian gene expression in human skin

city: Berlin

first: Bharath

last: Ananthasubramaniam

address: Philippstr. 13, House 20, R. 209

institute: Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin

summary: This work reports 24 h gene expression rhythms in two skin layers, epidermis and dermis, in a cohort of young, healthy adults, who maintained natural, regular sleep-wake schedules. 10% of the expressed genes showed such diurnal rhythms at the population level, of which only a third differed between the two layers. Amplitude and phases of diurnal gene expression varied more across subjects than layers, with amplitude being more variable than phases. Expression amplitudes in the epidermis were larger and more subject-variable, while they were smaller and more consistent in the dermis. Core clock gene expression was similar across layers at the population-level, but were heterogeneous in their variability across subjects. This work provides a valuable resource to advance our understanding of human skin and presents a novel methodology to quantify sources of variability in human circadian rhythms.

overall_design: To analyze diurnal gene expression in human dermis and epidermis, eleven different young and healthy adults who maintained their natural, regular sleep schedules were biopsied from the upper back every 4 h for 1 full day and whole genome microarray analysis was performed. We used this data to quantify variability in rhythm parameters across skin layers and individuals, and to identify small sets of biomarker genes for internal clock phase in each layer.

first: Marta

last: del Olmo

first: Achim

last: Kramer


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [LLC RNA-seq]

first: Yong-Dong

summary: Cachexia is a systemic wasting syndrome that develops in many cancers and increases mortality. Despite its importance, it is largely unknown how cachexia progressively and differentially induces tissue wasting. Although cachexia occurs also in pediatric patients, little is known on the underlying mechanisms. Here, we have used pediatric melanoma xenografts to determine the progression and tissue-specific impact of juvenile cachexia on skeletal muscles, heart, white and brown adipose, liver, and brain. We find that the heart and muscles undergo wasting at early stages and are the tissues most strongly impacted transcriptionally. Beyond wasting, we identify general and organ-specific transcriptional changes that likely indicate derangement of organ/tissue function by cachexia.  Moreover, also the transcriptome of tissues that do not undergo wasting, such as the brain, is profoundly remodeled by cachexia. Altogether, this study provides insight into the progression of melanoma-induced pediatric cachexia and its differential impact on distinct organ systems.

overall_design: RNA-sequencing data from neocortex (NEO), cerebellum (CER), and hippocampus (HIP) obtained from male C57BL/6J at 4 months of age that were injected with LLC cells, which were allowed to grow up to ~3 weeks, compared to control (CON) mock-injected mice.

first: Flavia

last: Graca

first: Anna

last: Stephan

first: Abbas

last: Shirinifard

first: Jianqin

last: Jiao

first: Peter

last: Vogel

first: Myriam

last: Labelle

first: Fabio

last: Demontis


title: IkBNS-deficiency protects mice from Listeria monocytogenes infection by blunting pro-inflammatory signature in Ly6Chigh monocytes and preventing exaggerated innate immune responses

status: Public on Dec 11 2022

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research


title: IkBNS-deficiency protects mice from Listeria monocytogenes infection by blunting pro-inflammatory signature in Ly6Chigh monocytes and preventing exaggerated innate immune responses [Liver monocytes]

summary: IkB proteins regulate the inhibition and activation of NF-kB transcription factor complexes. While classical IkB proteins keep NF-kB complexes inactive in the cytoplasm, atypical IkB proteins act on activated NF-kB complexes located in the nucleus. Most of the knowledge regarding the function of IkB proteins has been collected in vitro, while far less is known regarding their impact on activation and regulation of immune responses during in vivo infections. Combining in vivo Listeria monocytogenes (Lm) infection with comparative ex vivo transcriptional profiling of the hepatic response to the pathogen we observed that in contrast to wild type mice that mounted a robust inflammatory response, IkBNS-deficiency was generally associated with a transcriptional repression of innate immune responses. Whole tissue transcriptomics revealed a pronounced IkBNS-dependent (Nfkbid gene) reduction of myeloid cell-associated transcripts in the liver together with an exceptionally high Nfkbid promoter activity uncovered in Ly6C-high inflammatory monocytes prompted us to further characterized the specific contribution of IkBNS in the inflammatory response of monocytes to the infectious agent. Indeed, Ly6C-high monocytes primed during Lm infection in the absence of IkBNS displayed a blunted response compared to wild type-derived Ly6C-high monocytes as evidenced by the reduced early expression of hallmark transcripts of monocyte-driven inflammation such as Il-6, Nos2 and Il1-β. Strikingly, altered monocyte activation in IkBNS-deficient mice was associated with an exceptional resistance against Lm infection and protection was associated with a strong reduction in immunopathology in Lm target organs. Of note, mice lacking IkBNS exclusively in myeloid cells failed to resist Lm infection, indicating that the observed effect was not monocyte intrinsic but monocyte extrinsic. While serum cytokine-profiling did not discover obvious differences between wild type and IkBNS -/- mice for most of the analyzed mediators, IL-10 was virtually undetectable in IkBNS-deficient mice, both in the steady state and following Lm infection. Together, we show here a crucial role for IkBNS during Lm infection with IkBNS-deficient mice showing an overall blunted pro-inflammatory immune response attributed to a reduced pro-inflammatory signature in Ly6C-high monocytes. Reduced immunopathology and complete protection of mice against an otherwise lethal Lm infection identified IkBNS as molecular driver of inflammation in listeriosis.

overall_design: WT and IκBNS-/- mice (n = 3 - 5 per group, from two independent experiments) were infected with 3×10^4 CFU Lm i.v., sacrificed on day 3 post infection, liver tissue was enzymatically digested, total leukocytes were isolated using Percoll density gradient centrifugation, Ly6C-high inflammatory monocytes were FACS sorted and pooled per genotype and total RNA was isolated. Transcriptome was analyzed using Affymetrix Mouse Clariom S microarrays.

first: Sarah

last: Frentzel

first: Alexander

last: Pausder

first: Olivia

last: Kershaw

first: Julia

last: Volckmar

first: Ingo

last: Schmitz

first: Dunja

last: Bruder


title: Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1

first: Stephanie

last: Coffin


title: Unbiased screening identifies TGF-β signaling and Creb5 cooperatively regulate FGF18 to control pharyngeal muscle development

city: Alhambra

first: Eva

last: Janeckova

address: 2250 Alcazar street

institute: USC, CCMB

summary: In the present work, we investigated the mechanism that regulates perimysial-to-myogenic communication using the development of the pharyngeal muscle LVP as a model. Using unbiased single-cell RNAseq (scRNAseq) data analysis combined with mouse genetic approaches, we identified TGF-β signaling as the predominant signaling activity that enables the perimysial cells to interact with the adjacent myogenic cells during late pharyngeal muscle development. Furthermore, we identified that perimysial-specific regulator Creb5 interacts specifically with TGF-β signaling to co-activate the expression of specific perimysial-to-myogenic signals such as Fgf18 to regulate pharyngeal myogenesis. Taken together, our findings reveal that TGF-b signaling and perimysial-specific regulators may cooperatively define perimysial-to-myogenic signals in regulating pharyngeal myogenesis.

overall_design: Single-cell transcriptomes were obtained from E14.5 control and Osr2-Cre;Alk5fl/fl soft palate tissue

first: Jifan

last: Feng


title: Deletion of the Alzheimer’s disease risk associated Abi3 gene locus in mice results in obesity and systemic metabolic disruption

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

summary: A rare coding variant was identified within the human ABI3 gene that is associated with increased risk of Alzheimer’s disease (AD). Following this discovery, we recently demonstrated that deletion of Abi3 gene locus notably   exacerbates AD neuropathology in the 5xFAD transgenic mouse model of amyloidosis. In the course of a related investigation into the functional impact of Abi3 deletion in mice, we made an unexpected discovery regarding the impact of Abi3 deletion on the non-transgenic littermates of those 5xFAD mice. In those mice, we found that deletion of Abi3 gene locus resulted in an obese phenotype. Therefore, we investigated this serendipitous discovery. In this report, we demonstrate that mice lacking Abi3   have dramatically increased body weight and body fat. Further, we determined that these mice without Abi3 have reduced energy expenditure. Additionally, we found that deletion of the Abi3 gene locus altered gene expression, particularly within immune pathways, within the hypothalamus. Subsequent immunohistological analysis of the central nervous system (CNS) revealed that microglia number and area were decreased specifically within the mediobasal hypothalamus of mice without Abi3. Altogether, this investigation establishes the functional importance of the Abi3 gene locus, particularly within the CNS, in the regulation of systemic metabolism and maintenance of healthy weight.

overall_design: Quant-seq (3' mRNA-seq) analysis of hypothalami & brown adipose of male mice with Abi3 WT or Abi3 KO genotypes at 15 months of age

first: Daniel

last: Smith

first: Hande

last: Karahan

first: H.R. Sagara

last: Wijeratne

first: Md Mamun

last: Al-Amin

first: Brianne

last: McCord

first: Younghye

last: Moon


title: Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters [ChIP-seq CTCF]

first: Mirna

last: Barsoum

overall_design: One mouse embryo fibroblast line with floxed exon 4 of Ash2l (congruent to KO2 in ChIPseq experiments for H3K4me1/3 from the same study) were used. The cell line express Cre-ER and were immortalized using shArf. Cells were treated  -/+ 4-hydroxytamoxifen for 7 days .ChIP was performed with antibodies for CTCF.

last: Stenzel

first: Agnieszka

last: Bochyńska

first: Chao-Chung

last: Kuo

last: Tsompanidis

first: Roksaneh

last: Sayadi Boroujeni

first: Philip

last: Bussmann

first: Juliane

last: Lüscher-Firzlaff

first: Ivan

last: Costa

first: Bernhard

last: Lüscher


title: Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters.


title: Change in gene expression following CSF1 stimulation of mouse cancer prostate cell lines overexpressing the c-fms receptor.

status: Public on Dec 09 2022

city: Lille

first: Roland

last: Bourette

address: 1, rue du Professeur Calmette

country: France

institute: CNRS

summary: To study the role of the c-fms tyrosine kinase receptor expression in prostate cancer cells, we generated a cell line model from the C2H mouse prostate cancer cell line overexpressing the c-fms receptor (N18-CFMS clone) and treated it or not with the c-fms ligand CSF1.

overall_design: Gene expression in N18-CFMS cells was measured after 24H or 48H of CSF1 treatment as well as in untreated cells.

first: Boris

last: Guyot


title: Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters [ATAC-seq]

overall_design: One mouse embryo fibroblast line with floxed exon 4 of Ash2l (congruent to KO2 in ChIPseq experiments for H3K4me1/3 from the same study) were used. The cell line express Cre-ER and were immortalized using shArf. Cells were treated  -/+ 4-hydroxytamoxifen for 7 days. ATAC-seq was performed with engineered hyperactive Tn5-Transposase for accessibility analysis. For both treating conditions, two technical replicates were prepared.

first: Alexander


title: Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1 [RNA-seq]

first: Stephanie

last: Coffin

summary: mRNA profiles of 10-week mice in wild-type (WT), Atxn1_154Q/2Q (SCA1),  Atxn1_154Q[V5591A;S602D]/2Q (154Q AXH) genotypes across 5 different brain regions (cerebellum, brainstem, hippocampus, striatum and cortex)

overall_design: Examination of differential gene expression in WT compared to Atxn1_154Q/2Q (SCA1),  Atxn1_154Q[V5591A;S602D]/2Q (154Q AXH).

first: Huda

last: Zoghbi


title: Extracellular vesicle characteristics and microRNA content in cerebral palsy and typically developed individuals at rest and in response to aerobic exercise [EV]

status: Public on Dec 10 2022

city: Lincoln

last: Vechetti

state: NE

address: 1700 N. 35th Street

institute: University of Nebraska-Lincoln

summary: In this study, the properties of circulating EVs were examined in cerebral palsy (CP) and typically developed (TD) individuals at rest and after aerobic exercise. We performed smallRNA-seq anf focused on the microRNA cargo of EVs

overall_design: We compared microRNA profile within EVs isolated from blood of CP and TD before and after aerobic exercise. We pooled samples (for TD two groups n=3 and one n=4; for CP n=3 per group) to have a final n=3 pooled samples/per group.

first: Ferdinand

last: von Walden

first: Rodrigo

last: Fernandez-Gonzalo


title: Evidence of shared transcriptomic dysregulation of HNRNPU-related disorder between human organoids and embryonic mice

city: New York

first: Andrew

middle: K

last: Ressler

state: NY

institute: Columbia University

summary: Generating effective therapies for neurodevelopmental disorders has remained elusive. An emerging drug discovery approach for neurodevelopmental disorders is to characterize transcriptome wide dysregulation in an appropriate model system and screen therapeutics based on their capacity to restore functionally relevant expression patterns. We characterized transcriptomic dysregulation in a human model of HNRNPU-related disorder to explore the potential of such a paradigm. We identified widespread dysregulation in functionally relevant pathways and then compared dysregulation in a human model to transcriptomic differences in embryonic and perinatal mice to determine whether dysregulation in an in vitro human model is partially replicated in an in vivo model of HNRNPU-related disorder. Strikingly, we find enrichment of co-dysregulation between 45-day-old human organoids and embryonic, but not perinatal, mice from distinct models of HNRNPU-related disorder. Thus, hnRNPU deficient human organoids may only be suitable to model transcriptional dysregulation in certain cell types within a specific developmental time window.

overall_design: Single-cell RNA-sequencing experiments (Experiment 1 - three human cortical organoid lines (PGP1 control, D11 HNRNPU KO, M20 HNRNPU het KO different mutation) with three samples per line. Experiment 2 - Same three lines with organoids same age, two samples per line from differentiations beginning at a later date). Bulk RNA-sequencing experiments - three experiments deposited. Hnrnpu constitutive het KO at E13 (3 HET, 4 WT mice) and at P0 (4 litters, 2 experiments, 7 HET, 4 WT mice). Hnrnpu conditional truncating mutation in Emx1+ cells at P1 (3 litters, 3 HOM, 4 HET, 5 WT mice).


title: RNA-Sequencing analysis of white adipose tissue from wild type mice and Ccdc92 knockout mice

city: Columbus

first: Wa

last: Du

state: OH

address: 460 West 12th Avenue, Biomedical Research Tower, Rm 360A

department: Department of Surgery, Division of Vascular Diseases and Surgery

institute: The Ohio State University

summary: Multiple independent genome-wide association studies (GWAS) have uncovered specific genetic variants in the Coiled-Coil Domain Containing 92 (CCDC92) locus that are associated with obesity and insulin resistance in humans. However, the biological function of CCDC92 in metabolism remains unclear. We explored the effects of CCDC92 on obesity and insulin resistance by utilizing wild-type (WT) and Ccdc92 knockout (KO) mice. RNA-seq was used to analyze the gene expression profile regulated by CCDC92 in white adipose tissue.

overall_design: Wild-type (WT) control mice and Ccdc92 knockout (KO) mice were fed a high-fat diet for 14 weeks. RNA sequencing analysis was performed in epididymal white adipose tissue (eWAT; WT, n=4; KO, n=4).

first: Lu

last: Ren

first: Yanbo

last: Fan


title: IkBNS-deficiency protects mice from Listeria monocytogenes infection by blunting pro-inflammatory signature in Ly6Chigh monocytes and preventing exaggerated innate immune responses [Liver]

first: Andreas

last: Jeron

summary: IkB proteins regulate the inhibition and activation of NF-kB transcription factor complexes. While classical IkB proteins keep NF-kB complexes inactive in the cytoplasm, atypical IkB proteins act on activated NF-kB complexes located in the nucleus. Most of the knowledge regarding the function of IkB proteins has been collected in vitro, while far less is known regarding their impact on activation and regulation of immune responses during in vivo infections. Combining in vivo Listeria monocytogenes (Lm) infection with comparative ex vivo transcriptional profiling of the hepatic response to the pathogen we observed that in contrast to wild type mice that mounted a robust inflammatory response, IkBNS-deficiency (Nfkbid gene) was generally associated with a transcriptional repression of innate immune responses. Whole tissue transcriptomics revealed a pronounced IkBNS-dependent reduction of myeloid cell-associated transcripts in the liver together with an exceptionally high Nfkbid promoter activity uncovered in Ly6C-high inflammatory monocytes prompted us to further characterized the specific contribution of IkBNS in the inflammatory response of monocytes to the infectious agent. Indeed, Ly6C-high monocytes primed during Lm infection in the absence of IkBNS displayed a blunted response compared to wild type-derived Ly6C-high monocytes as evidenced by the reduced early expression of hallmark transcripts of monocyte-driven inflammation such as Il-6, Nos2 and Il1-β. Strikingly, altered monocyte activation in IkBNS-deficient mice was associated with an exceptional resistance against Lm infection and protection was associated with a strong reduction in immunopathology in Lm target organs. Of note, mice lacking IkBNS exclusively in myeloid cells failed to resist Lm infection, indicating that the observed effect was not monocyte intrinsic but monocyte extrinsic. While serum cytokine-profiling did not discover obvious differences between wild type and IkBNS -/- mice for most of the analyzed mediators, IL-10 was virtually undetectable in IkBNS-deficient mice, both in the steady state and following Lm infection. Together, we show here a crucial role for IkBNS during Lm infection with IkBNS-deficient mice showing an overall blunted pro-inflammatory immune response attributed to a reduced pro-inflammatory signature in Ly6C-high monocytes. Reduced immunopathology and complete protection of mice against an otherwise lethal Lm infection identified IkBNS as molecular driver of inflammation in listeriosis.

overall_design: WT and IkBNS -/- mice were infected with 10^5 CFU LM i.v. or left untreated (d0). Mice were sacrificed on day 2, 3 and 4 post infection, liver homogenates were prepared and sampled for total RNA isolation. Equal amounts of RNA from n = 3-5 mice per genotype and sampling time were pooled per experimental group and applied to Affymetrix Gene 2.0 ST microarray analysis.

first: Sarah

last: Frentzel

last: Pausder

first: Olivia

last: Kershaw

first: Julia

last: Volckmar

first: Ingo

last: Schmitz

first: Dunja

last: Bruder


title: miRNA expression in plasma samples from Non-functional adenoma (NFA), Cortisol-producing adneoma (CPA)and primary bilateral macronodular adrenal hyperplasia (PBMAH)

status: Public on Dec 08 2022

city: Bunkyo-ku

first: Masanori

last: Murakami

state: Tokyo

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate circulating miRNA expression sinatures of PBMAH, we collected plasma samples of patients with PBMAH and other phenotypes of adrenal diseases including NFA and CPA. MiRNAs were extracted from plasma samples and its expression signatures were examined.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for plasma samples from patients with NFA, CPA and PBMAH

first: Kazunari

last: Hara

first: Mitsuhide

last: Naruse


title: TNFα secreted from macrophages increases expression of prometastatic integrin αV in gastric cancer

city: Daejeon

first: Bo-Kyung

last: Kim

address: Kwahag-ro

country: South Korea

institute: KRIBB

summary: We performed RNA-Seq to confirm the changes in expression of genes in the relevant pathway in human gastric cancer cells (AGS cells) and AGS cells cocultured with macrophages (RAW264.7 cells). In the gene ontology enrichment analysis of the 160 genes that were increased in AGS cells cocultured with RAW264.7 cells, pathways related to immune response, cell adhesion, and cytokine response were enriched.

overall_design:
AGS cells cocultured with RAW264.7 cells for 24 hours.

>>>Submitter states that raw data are not available because they were not provided nor retained by the sequencing company<<<


title: Inhibition of coronavirus HCoV-OC43 by targeting the eIF4F complex

first: Ze'ev

last: Ronai

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

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: Refer to individual Series


title: An in-cluster Sfp-type phosphopantetheinyl transferase instead of the holo-ACP synthase activates the granaticin biosynthesis under natural physiological conditions

city: Guangzhou

first: Ming-Rong

last: Deng

state: Guangdong

address: No.100 Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary: When cultivated on ISP2 plates for sporulation, the gra-orf32 deletion mutant of Streptomyces vietnamensis produced much more granaticins than in liquid or on solid YEME. The transcriptome analysis showed that the transcription levels of more than 1,600 genes were significantly changed (p < 0.05, log2 fold change >1). Amongst them, 872 genes were upregulated and 762 genes were downregulated on ISP2 plates, compared to those on YEME plates. KEGG pathway enrichment analysis showed that four pathways were enriched significantly, including two type II PKS biosynthesis pathways, namely, the granaticin biosynthetic pathway and the kinamycin-like biosynthetic pathway. These results suggested that the kinamycin-like biosynthetic pathway was activated on ISP2 plates and might associate with the elevated production of granaticins. Most of the PPTase genes kept in low-levels of expression or inactivated, even the expression level of the FAS ACPS gene (SVTN_RS23020) was not as high as expected. Two PPTase genes, SVTN_RS03505 and SVTN_RS28640 were slightly upregulated on ISP2 plate, while the FAS ACPS gene (SVTN_RS23020) was downregulated, compared to those on YEME plates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the gra-orf32 deletion mutant of Streptomyces vietnamensis cultivated on ISP2 and YEME plates for 24 h.

first: Sin

last: Chik

first: Yan

last: Li

first: Honghui

last: Zhu


title: Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS81 and LVFX-treated P. aeruginosa PAS81 Transcriptomes

first: Wenru

address: No.100, Xianliezhong Road

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAS81 (RNA-seq) to transcriptome profiling of LVFX-treated P. aeruginosa PAS81 and to evaluate protocols for optimal high-throughput data analysis.
Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS81 at a concentration of 1.0E8 CFU/mL. Levofloxacin  was then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three LVFX treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.
Results: The transcriptome sequencing data of control and LVFX-treated groups were compared and analyzed in the form of the following: control vs LVFX. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and LVFX-treated group was high (total 5581, up-regulated 241, down-regulated 16).

overall_design: The mRNA profiles of P. aeruginosa PAS81 (control) and LVFX-treated P. aeruginosa PAS81  were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.

first: Wen-Ru

first: Zhi-Qing

last: Zhang


title: Injured Sciatic Nerve Atlas (iSNAT)

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: Description of cellular and molecular changes in the mouse sciatic nerve following crush injury

overall_design: The goal was to carry out a longitudinal scRNAseq study aimed at a detailed description of the cellular and molecular changes in the mouse sciatic nerve following a mid-thigh crush injury.  For comparison, we carried out scRNAseq of naïve nerve immune and peripheral blood mononuclear cells (PBMC). During cell isolation, transcription was blocked with actinomycin D.  From naive nerve, immune cells were captured with an anti-CD45 magnetic bead column and processed for scRNAseq.  From the same nerves, non-immune cells (CD45 negative cells) were collected and processed for scRNAseq. The resulting datasets were combined and used as baseline to describe the cellular composition and gene expression profiles at single cell resolution in the naïve sciatic nerve.  Next, cohorts of mice were subjected to sciatic nerve crush injury and nerve trunks were collected at different time points during the first week following injury.  Specifically, nerves were harvested at 1-day post-crush (Day1), Day3, and Day7.  For a comparative analysis of the nerve micro-environment at the injury site, versus the distal nerve, 3 mm nerve segments with the injury site at the center were collected, and in addition, 3 mm nerve segments spanning from 1.5-4.5 mm distal to injury site were collected. In separate reactions, nerves were digested, cells purified over a percoll gradient, depleted of myelin and processed for scRNAseq.

first: Roman

last: Giger

first: Craig

last: Johnson

first: Xiao-Feng

last: Zhao


title: Transcriptomic analysis of engineered cardiac tissue in an oxygen gradient

city: Los Angeles

first: Megan

last: McCain

state: California

address: 1042 Downey Way

institute: University of Southern California

summary: We report the use of RNA-seq for transcriptional analysis of engineered cardiac tissues cultured in microphysiological systems developed for tight control of oxygen levels, comparing normoxia, hypoxia, and a gradient divided into the normoxic side and hypoxic side.

overall_design: mRNA profiles of engineered cardiac tissues from neonatal rat veintricular myocytes (NRVMs) exposed to normoxia, hypoxia, and a linear oxygen gradient (20-0%)

middle: L

last: Rexius-Hall


title: scRNA-seq of e14.5 MGE - WT vs. St18(-/-)

first: Edmund

last: Au

address: 630 West 168th Street, room P&S14-401

institute: Columbia University Irving Medical Center

summary: Medial ganglionic eminence was dissected from e14.5 mouse embryonic brain, dissociated and processed using 10X Genomics chemistry for single cell library creation. 2 experimental groups were analyzed: St18 null and wildtype littermate controls (2 biological replicates of each group)

overall_design: An analysis of single cell gene expression in progenitors and neurons obtained from medial gangionic eminence of e14.5 wildtype and St18(-/-) mice.

first: Luke

last: Nunnelly


title: ES-derived Dlx6a-Cre fate-mapped neuron bulk RNA-seq

summary: Parental ES reporter line Dlx6a-Cre; Ai9 was differentiated using 2 different transcriptional specifiation strategies: 1) Nkx2-1/Dlx2 or 2) Nkx2-1/Dlx2/St18. Neurons were directeed towards neural, telencephalic and then ventral telencephalic identity prior to neuronal differentiation and reporter gene activation. Cells were differentiated for 12 days. tdTomato+ neurons were isolated by flow cytometry prior to RNA isolationa and library construction.

overall_design: Comparison of DIFF12 N/D and N/D/S tdTomato+ neurons by bulk RNA-seq


title: Extracellular vesicle characteristics and microRNA content in cerebral palsy and typically developed individuals at rest and in response to aerobic exercise [miR-486]

first: Ivan

last: Vechetti

summary: In this study, the properties of circulating EVs were examined in cerebral palsy (CP) and typically developed (TD) individuals at rest and after aerobic exercise. We performed small RNA-seq and focused on the microRNA cargo of EVs. The role of miR-486 was further explored using cell culture experiments.

overall_design: We investigated the effects of miR-486 on C2C12 myoblasts to a control scramble miRNA. N=3 per condition.

first: Ferdinand

last: von Walden

first: Rodrigo

last: Fernandez-Gonzalo


title: Extracellular vesicle characteristics and microRNA content in cerebral palsy and typically developed individuals at rest and in response to aerobic exercise


title: Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers [Proj_07182_W]

status: Public on Dec 07 2022

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Inflammation has long been recognized to contribute to cancer development, particularly across the gastrointestinal tract. Patients with inflammatory bowel disease have an increased risk for bowel cancers, and it has been posited that a field of genetic changes may underlie this risk. Wnt pathway alterations are infrequent, and our data suggest transcriptional rewiring away from Wnt. These findings suggest neoplastic bowel lesions developing in a background of inflammation experience lineage plasticity away from Wnt activation early during tumorigenesis and largely occur as genetically independent events.

overall_design: We are comparing expression profiles between 6 sporadic colorectal cancers and 5 colitis-associated cancers.

first: Yaeger

last: Rona


title: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [SLAM-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary:
Background: CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations to investigate the function of CTCF.
Results: We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcripts changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF.
Conclusions: By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.

overall_design: SLAM-seq was performed on cells depleted for CTCF by either the AID1 or AID2 auxin degradation systems and showed early transcriptional changes after auxin treatment in the AID1 system more likely represented cytotoxic effects from combined high auxin treatment with CTCF degradation versus CTCF degradation alone, making the AID2 system preferred for studying acute CTCF degradation effects on transcription. AID1 and AID2 auxin degradation was combined with endogenous AID tagged CTCF in the human B-ALL cell line SEM. SLAM-seq was performed to identify early transcript changes in response to CTCF loss.

first: Justin

last: Williams

first: Judith

last: Hyle

first: Mohamed

last: Nadhir Djekidel

first: Shaela

last: Wright

first: Ying

last: Shao

first: Chunliang


title: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [HiChIP]

overall_design: In order to characterize CTCF-dependent and independent chromatin loops, we conducted HiChIP using CTCF antibody to pull down proximity ligation DNA fragments in DMSO and 5-Ph-IAA treatment condition. CTCF-AID knockin cells were treated for DMSO or 5-Ph-IAA to remove genome-wide CTCF proteins.

last: Li


title: Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers [Proj_07182_Z]

overall_design: We want to compare the genes expressed in WNt Wt vs WNT Mut cases and will evaluate changes in Wnt output genes.


title: Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers [Proj_07182_Q]

overall_design: Three PDX models were treated with control (vehicle) or WNT inhibitors (G-007-LK, LGK-974).  We want to compare the genes expressed after vehicle treatment versus each WNT inhibitor and will evaluate changes in Wnt output genes.  Each treatment (G-007-LK and LGK-974) should be analyzed separately against control.


title: Expression data from heart expressing cofilin-1(Th25) variants

city: Paris

first: Antoine

last: MUCHIR

address: 105 bld de l'Hopital

institute: INSERM

summary: We used microarrays to detail the global programme of gene expression underlying cardiac dysfunction and identified distinct classes of up-regulated genes during this process.

overall_design: We transduced wild type mice with AAV expressing cofilin-1 (GROUP 3) and cofilin-1 T25A (inactive) variant (GROUP 2). We will compare transcriptome of these mice with those of wild type mice (GROUP 1) and Lmna mutated mice (GROUP 4).

last: Muchir


title: Mechanistic target of rapamycin complex 1 orchestrates the interplay between hepatocytes and Kupffer cells to determine the outcome of immune-mediated hepatitis

city: Nanjing

first: Xiaoli

last: Sun

address: 262 North Zhongshan Road, Nanjing, Jiangsu

institute: 2nd Affiliated Hospital, Nanjing Medical University

summary: The cell-cell interaction between hepatocytes and Kupffer cells (KCs) is crucial for maintaining liver homeostasis, and the loss of KCs and hepatocytes is known to represent a common pathogenic phenomenon in autoimmune hepatitis. Until now, the mechanisms of cell-cell interaction between hepatocytes and KCs involved in immune-mediated hepatitis remains unclear. Here we dissected the impact of activated mTORC1 on the cell-cell interaction of KCs and hepatocyte in immune-mediated hepatitis. In the liver from patients with AIH and mice administrated with Con-A, mTORC1 was activated in both KCs and hepatocytes. The activated mTORC1 signal in hepatocytes with Con-A challenge caused a markedly production of miR-329-3p. Upregulated miR-329-3p inhibited SGMS1 expression in KCs through paracrine, resulting in the death of KCs. Most of maintained KCs were p-S6 positive and distributed in hepatocyte mTORC1 negative area. The activation of mTORC1 enabled KCs expressed complement factor B (CFB) to enhance the complement alternative system, which produced more complement factors to aggravate liver injury. Our findings remonstrate a heterogeneous role of mTORC1 in specific cell type for maintaining tolerogenic liver environment, and will form the basis for the development of new interventions against immune-mediated hepatitis.

overall_design: Total RNA samples were extracted from BMMs of MΦ-Tsc1+/+ or MΦ-Tsc1-/- mice.

first: Chunsun

last: Dai


title: Heightened Cocaine-Seeking in Male Rats Associates with a Distinct   Transcriptomic Profile in the Medial Prefrontal Cortex

city: Galveston

first: Kamil

last: Khanipov

address: 301 University Blvd

institute: University of Texas Medical Branch

summary: Drug overdose deaths involving cocaine have skyrocketed, an outcome attributable in part to the lack of FDA-approved medications for the treatment of cocaine use disorder (CUD), highlighting the need to identify new pharmacotherapeutic targets. Vulnerability to cocaine-associated environmental contexts and stimuli serves as a risk factor for relapse in CUD recovery, with individual differences evident in the motivational aspects of these cues. The medial prefrontal cortex (mPFC) provides top-down control of striatal circuitry to regulate the incentive-motivational properties of cocaine-associated stimuli. Clinical and preclinical studies have identified genetic variations that impact the degree of executive restraint over drug-motivated behaviors, and we designed the present study to employ next-generation sequencing to identify specific genes associated with heightened cue-evoked cocaine-seeking in the mPFC of male, outbred rats. Rats were trained to stably self-administer cocaine, and baseline cue-reinforced cocaine-seeking was established. Rats were phenotyped as either high cue (HC) or low cue (LC) responders based upon lever pressing for previously associated cocaine cues and allowed 10 days of abstinence in their home cages prior to mPFC collection for RNA-sequencing. The expression of 309 genes in the mPFC was significantly different in HC vs. LC rats. Functional gene enrichment analyses identified ten biological processes that were overrepresented in the mPFC of HC vs. LC rats. The present study identifies distinctions in mPFC mRNA transcripts that characterizes individual differences in relapse-like behavior and provides prioritized candidates (i.e., Htr2c, Adora2a, Drd2) for future pharmacotherapeutics aimed to help maintain abstinence in CUD.

overall_design: We designed the present study to employ next-generation sequencing to identify specific genes associated with heightened cue-evoked cocaine-seeking in the mPFC of male, outbred rats.

first: Christina

middle: R

last: Merritt

first: Ashley

middle: E

last: Smith

first: George

last: Golovko

first: Noelle

last: Anastasio

first: Kathryn

last: Cunningham


title: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation [RNA-Seq]

last: Xu

overall_design: AID2 auxin degradation was combined with endogenous AID tagged CTCF in the human B-ALL cell line SEM. RNAseq was performed to identify transcript changes in response to CTCF loss.


title: Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS71 and LVX-treated P. aeruginosa PAS71 Transcriptomes

first: Wenru

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAS71 (RNA-seq) to transcriptome profiling of LVX-treated P. aeruginosa PAS71 and to evaluate protocols for optimal high-throughput data analysis.
Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS71 at a concentration of 1.0E8 CFU/mL. Levofloxacin  was then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three LVX treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.
Results: The transcriptome sequencing data of control and LVX-treated groups were compared and analyzed in the form of the following: control vs LVX. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and LVX-treated group was high (total 5581, up-regulated 241, down-regulated 16).

overall_design: The mRNA profiles of P. aeruginosa PAS71 (control) and LVX-treated P. aeruginosa PAS71  were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.

first: Wen-Ru

first: Zhi-Qing

last: Zhang


title: Distinct non-coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary:
Purpose: Macrophages are often classified into M1 ‘classical’ and M2 ‘alternatively-activated’ macrophages. Extracellular vesicles (EVs) are biomolecule carriers involved in cell-cell communication. Here, we provide a first insight into the complete small RNA cargo of human macrophage M1/M2 EVs.
Methods: Monocyte-derived macrophages were polarised into M1 (GM-CSF+LPS+IFNγ) or M2 (M-CSF+IL-4+IL-13) and EVs isolated by size exclusion chromatography. EVs were characterised by nanoparticle tracking analysis, electron microscopy and ELISA. EV RNA samples were prepared for small RNA sequencing using Qiagen’s GIAseq small RNA Library Prep kit and sequenced on an Illumina NextSeq500, single end 75 bp. Functional enrichment analysis was performed using MIENTURNET, based on validated miR-target interactions from miRTarBase.
Results: Many types of small non-coding RNAs were found in EVs from M1/M2 macrophages including miRNAs, isomiRs, tRNA fragments, piRNA, snRNA, snoRNA and yRNA fragments. Distinct differences were observed between M1 and M2 EVs, with higher relative abundance of miRNAs, and lower abundance of tRNA fragments in M1 EVs compared to M2 EVs. MicroRNA-target enrichment analysis identified several gene targets involved in gene expression and metabolic processes.
Conclusions: M1 and M2 cells release EVs with distinct tRNA and miRNA cargo, which have the potential to contribute to the unique effect of these cell subsets on their microenvironment.

overall_design: Small RNA sequencing of the RNA cargo of EVs from M1 and M2 primary monocyte derived macrophages

first: Beth

last: Holder

first: Paschalia

last: Pantazi

first: Toby

last: Clements

first: Vikki

last: Abrahams


title: Nonclassical beta catenin signaling regulate skeletal cell fate determination

city: Cambridge

first: Wei

last: Hsu

state: MA

address: 245 First St

department: Mineralized TIssue Biology

institute: Forsyth Institute

summary: To rigorously examine the role of b-catenin dependent transcription, we created mice deficient for the transcriptional output of beta-catenin in skeletal mesenchyme (bcat-dTF-Dermo1-cKO) and compare the transcriptional profiles to that of the beta-catenin conditional KO mice in skeletal mesenchyme (bcat-Dermo1-cKO).

overall_design: Total RNAs were isolated from calvarial mesenchyme at E15.5 and followed by comparative gene expression profiling analysis of RNA-seq data for control, bcat-dTF-Dermo1-cKO, and bcat-Dermo1-cKO.

first: Takamitsu

last: Maruyama


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia [scRNA-seq and scVDJ-seq]

first: Janek

last: Walker

state: Ohio

address: 410 W 12th Ave

department: Division of Hematology, Department of Internal Medicine

summary: Purpose: Richter’s Transformation (RT) is a poorly understood and often fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. PRMT5 is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 developed a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice uniformly developed a highly aggressive disease that histologically resembles RT; where large-scale transcriptional profiling identified unique oncogenic pathways that mediate PRMT5-driven disease progression. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases

overall_design: Single cell RNA-sequencing and single cell V(D)J-sequencing of patient matched Richter's Lymph node, Richter's PBMC, and CLL PBMC samples

first: Zachary

middle: A

last: Hing

first: Ethan

last: Whipp

first: Lindsey

last: Brinton

first: Katie

last: Williams

first: Jami

last: Shaffer

first: Jordan

last: Skinner

first: Casey

middle: B

last: Cempre

first: Charles

last: Gregory

first: Alexander

last: Pan

first: Pearly

last: Yan

first: James

last: Blachly

first: Lapo

last: Alinari

first: John

last: Byrd

first: Bradley

last: Blaser

first: Robert

last: Baiocchi

first: Rosa

last: Lapalombella


title: Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers

first: Bic

last: MSKCC

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

overall_design: Refer to individual Series


title: Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers

city: Warszawa

first: Anna

middle: Maria

last: Stroynowska-Czerwińska

address: Trojdena 4

department: Laboratory of Structural Biology

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: Histone lysine-specfic methyltransferase 2 (KMT2A-D) proteins, alternatively called mixed lineage leukaemia (MLL1-4) proteins, mediate positive transcriptional memory. As the catalytic subunits of human COMPASS-like complexes, they methylate H3K4 at promoters and enhancers. KMT2A-D contain understudied highly conserved triplets and a quartet of plant homeodomains (PHDs). Here, we show that all clustered PHDs localise to the well-defined loci of H3K4me3 and H3 acetylation-rich active promoters and enhancers. Surprisingly, we observe little difference in binding pattern between PHDs from promoter-specific KMT2A-B and enhancer-specific KMT2C-D. Fusion of the KMT2A CXXC domain to the PHDs drastically enhances their preference for promoters over enhancers. Hence, the presence of CXXC domains in KMT2A-B, but not KMT2C-D, may explain the promoter/enhancer preferences of the full-length proteins. Importantly, targets of PHDs overlap with KMT2A targets and are enriched in genes involved in the cancer pathways. We also observe that PHDs of KMT2A-D are mutated in cancer, especially within conserved folding motifs (Cys4HisCys2Cys/His), which cause a domain loss-of-function. Taken together, our data suggests that PHDs of KMT2A-D guide the full-length proteins to active promoters and enhancers, and thus play a role in positive transcriptional memory.

overall_design:
GreenCUT&RUN experiment in 2 replicates of six different stable HeLa cell lines, expresing NLS-EYFP-tagged clustered PHD domains. Control sample for MACS2 peak calling was HeLa cells from correspoding experiment. In addition, 2 replicates of CUT&RUN in HeLa S3 cells with antibodies against three COMPASS complex subunits and eleven various histone marks. Control sample for MACS2 peak calling was IgG from corresponding experiment.

Please note that each merged processed data was generated from both replicates and is linked to the corresponding rep1 sample records -or- as Series supplementary files

first: Matthias

last: Bochtler


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia

first: Janek

last: Walker


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia [ATAC-Seq]

overall_design: - RNA-sequencing from B cells isolated from the spleen of Eµ-PRMT5, Eµ-PRMT5/TCL1, and Eµ-TCL1 mice at ERC.  - RNA-sequencing and ATAC-sequencing from B cells isolated from the spleen of Eµ-PRMT5/TCL1 and Eµ-TCL1 mice at 3 and 6 months of age.   - Single cell RNA-sequencing in Eµ-PRMT5, Eµ-PRMT5/TCL1, and Eµ-TCL1 mice at ERC.

first: Zachary

last: Hing

first: Lindsey

last: Brinton

first: Katie

last: Williams

middle: C


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia [bulk low-input RNA-Seq]

first: Jami

last: Shaffer

first: Jordan

middle: N

last: Skinner

first: Casey

last: Cempre


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia [scRNA-Seq]

first: Charles

last: Gregory

first: Alexander

last: Pan

first: Pearly

last: Yan

middle: W


title: Effect of Zika virus noncoding RNA (sfRNA) on gene expression in human placental cells

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University Of Queensland

summary: Transcriptome-wide gene expression profiling of cells infected with WT and sfRNA-deficient ZIKV was performed to fully map the effects of sfRNA on the entire spectrum of host antiviral responses. The human placental cell line BeWo was used for this experiment as it is known to support ZIKV replication, is capable of  responding to all three types of IFNs, and has a placental origin. BeWo cells were infected with WT ZIKV or xrRNA2’-mutant viruses and at 72 hpi and total RNA was isolated and used for RNA-Seq. RNA Seq data was subjected to the differential gene expression analysis, which demonstrated that production of sfrNA inhibits expression of antiviral genes.

overall_design: Comparison of gene expression in cells human placental cells infecetd with WT and sfRNA-deficient Zika virus agains mock-infected cells.


title: Neural precursor cells contribute to decision-making by tuning striatal connectivity via secretion of IGFBPL-1

city: Milan

first: Giulia

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary: We identified the Igfbpl1 gene by RNAseq of the neural precursor cells (NPCs) of the mice subventricular zone (SVZ), as an important gene released by SVZ-NPCs that play an important role in control of the striatal homeostasis and in particular involved in the cognitive processes and decision-making.

overall_design: Undestanding the role of SVZ-NPCs on the striatal homeostasis control in physiological conditions using a transgenic mice (NestinTK) in which we can selectively killed the NPCs of the SVZ.

first: Erica

last: Butti


title: Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32oN

status: Public on Dec 06 2022

city: wenzhou

first: Xing

last: Liu

address: xueshan street

institute: Zhejiang Institute of Subtropical Crops

summary: Mangrove Kandelia obovata, an important coastal shelterbelt and landscape tree, is distributed in tropical and subtropical shores and likely delimited in the latitudinal range by varying sensitivity to cold. Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~32oN, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance.

overall_design: Five different concentrations of ABA (0, 5, 25, 50, and 100 mg L-1) were set to treat K. obovata with a hand-held sprayer until run off. Each treatment was set up with three subplots for a total of 9 replicate seedlings.

first: Xiang

last: Lu

first: Sheng

last: Yang

first: Yu


title: Effect of SASP factors on mouse intestinal organoids [bulk RNA-seq]

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

summary: We report bulk RNAseq data from the mouse intestinal organoids cultured in different conditions.  Differential gene expression analysis revealed a large overlap in induced genes between Wnt5a and SCM, consistent with a major contribution of non-canonical Wnt signaling to the SCM-induced cystic organoid phenotype. Of genes differentially regulated by Wnt5a and SCM, about half were Ptk7 dependent, which displayed strong enrichment for TEAD binding motifs.

overall_design: Crypts isolated from 6 different mice (animal origin ID 1-6) were used to establish the intestinal organoid culture. Freshly passaged crypts from these organoids were cultured in complete media, QCM or SCM (with or without anti-Ptk7), and complete media with Wnt5a (with or without anti-Ptk7)

first: Jina

last: Yun

first: Otto

last: Morris

first: Yuxin

last: Liang

first: Zora

last: Modrusan

first: Heinrich

last: Jasper


title: Modeling of Alpha-1 Antitrypsin Deficiency with Syngeneic Human iPSC-Hepatocytes Reveals Metabolic Dysfunction and Cellular Heterogeneity in PiMZ and PiZZ Hepatic Cells

city: Boston

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University


title: Modeling of Alpha-1 Antitrypsin Deficiency with Syngeneic Human iPSC-Hepatocytes Reveals Metabolic Dysfunction and Cellular Heterogeneity in PiMZ and PiZZ Hepatic Cells (scRNA-Seq)

summary: Individuals homozygous for the "Z" mutation in alpha-1 antitrypsin deficiency are known to be at increased risk for liver disease. It has also become clear that some degree of risk is similarly conferred by the heterozygous state. A lack of model systems that recapitulate heterozygosity in human hepatocytes has limited the ability to study the impact of a single Z alpha-1 antitrypsin (ZAAT) allele on hepatocyte biology. Here, we describe the derivation of syngeneic induced pluripotent stem cells (iPSCs) engineered to determine the effects of ZAAT heterozygosity in iPSC-hepatocytes (iHeps). We find that heterozygous MZ iHeps exhibit an intermediate disease phenotype and share with ZZ iHeps alterations in AAT protein processing and downstream perturbations including altered endoplasmic reticulum (ER) and mitochondrial morphology, reduced mitochondrial respiration, and branch-specific activation of the unfolded protein response in cell subpopulations. Our model of MZ heterozygosity thus provides evidence that a single Z allele is sufficient to disrupt hepatocyte homeostatic function.

overall_design:
10X:  We profiled the transcriptome of 11,284 individual iHeps derived from PiZZ1 syngeneic (ZZ, MZ, MM) and PiZZ6 ZZ iPSCs that underwent directed differentiation to the hepatic lineage using 10x Chromium controller.
For scRNA-seq iHeps were disassociated using 0.25% Trypsin and sorted for live cells using Calcein Blue (ThermoFisher Scientific) on a MoFlo Astrios EQ (Beckman Coulter). Single live cells were then captured, and library preparation performed using the Chromium Single Cell 3’ v3 user protocol and Chromium Controller instrument per manufacturer instructions (10X Genomics). Each library was then sequenced using the Illumina NextSeq 500 to obtain sequencing depths of between 25-50K reads/cell. Fastq and count matrix files were generated using Cell Ranger v 3.0.2 and the transcriptome mapped again to the ENSEMBL human reference genome GRCh38. We then used Seurat v3 to further process and analyze the data. Data was normalized using the regularized negative binomial regression method with cell degradation regressed out.

Fluidigm_C1:  We profiled the transcriptome of 475 individual iHeps derived from PiZZ100 syngeneic ZZ and MM iPSCs that underwent directed differentiation to the hepatic lineage using Fluidigm C1 platform. Additionally day 12 progenitor cells from PiZZ100 ZZ were also sequenced but not used in this manuscript
For scRNA-seq iHeps were disassociated using 0.25% Trypsin and sorted for live cells using Calcein Blue (ThermoFisher Scientific) on a MoFlo Astrios EQ (Beckman Coulter). Single live cells were then captured using a large (15-25mm cell diameter) 800 cell capacity microfluidic chip for mRNA-seq (Fluidigm) was utilized for single cell capture. After a live-dead sort cells were loaded onto the chip per manufactures instructions using the Fluidigm C1 HT workflow to capture, lyse, reverse transcribe RNA and for library preparation.

first: Joseph

last: Kaserman

first: Jonathan

last: Lindstrom-Vautrin

first: Carlos

last: Villacorta-Martin

first: Taylor

last: Matte

first: Ignacio

last: Caballero

first: Andrew

last: Wilson


title: Effect of SASP factors at single nucleus level of mouse intestinal organoids [snRNA-seq]

summary: We report single nucleus RNAseq data from the mouse intestinal organoids cultured in quiescent or senescent conditioned media.  Analysis revealed changes in cell composition and gene expression caused by SASP factors in senescent conditioned media.

overall_design: Freshly passaged crypts from mouse intestinal organoids were cultured in quiescent or senescent conditioned media.

first: Michelle

last: Chen

first: Christopher

last: Overall


title: Defining Cellular Population Dynamics in Advanced Prostate Cancer using Single-cell RNA Sequencing

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Advanced prostate cancer is a leading cause of cancer-related deaths in men, in large part due to our poor understanding of advanced castration-resistant prostate cancer (CRPC). This form of prostate cancer is uniformly lethal. Currently, the main treatments against this disease are anti-androgenic therapies; however, CRPC always develops resistance to these therapeutic modalities. Of particular interest is CRPC lacking androgen receptor (AR) activity, or AR-low CRPC. This subtype has dramatically increased in incidence in the past decade. While many studies have identified a complex architecture in the prostate, we still lack a unified view of the cellular interactions and phenotypes that facilitate advanced prostate cancer maintenance and survival, particularly without AR signaling.To better understand the cellular changes that drive CRPC, we harvested prostates from a mouse model of prostate cancer under multiple conditions and performed single-cell RNA sequencing (scRNASeq). Our findings reveal a subset of the epithelial compartment that is primed for AR-low survival during tumorigenesis, as well as a complex basal-driven mechanism to facilitate expansion of this subtype. Androgen deprivation via castration of the mouse modulates this process by increasing proliferation rates in epithelia. In addition, we observe a dramatic increase in immune cell population upon tumorigenesis. We identify this immune influx as pro-tumor and pinpoint unique signaling phenotypes from individual epithelial subtypes, demonstrating a multifaceted process of recruitment and remodeling by the tumor to build a favorable environment. Androgen signaling is also crucial for maintaining these immune populations, and castration dramatically remodels the tumor environment. Finally, we uncover the importance of protein synthesis regulation in maintaining these complex dynamics; inhibiting the eIF4F translation initiation complex leads to decreased epithelial proliferation and immune recruitment. These findings shed new light on the cellular dynamics of advanced prostate cancer and highlight the importance of employing high-throughput technologies to provide a complete picture of the tumor and its microenvironment. Better understanding of the epithelial subtypes involved in tumor growth, as well as their influence on immune populations in the prostate, can lead to new avenues of treatment.

overall_design: We harvested prostates from a mouse model of prostate cancer under multiple conditions and performed single-cell RNA sequencing for 13 samples ( 3 wt castrate, 3 WT intact, 2 PTEN intact, 3 PTEN castrate, 2 PTEN castrate 4EBP1) using 10x genomics v2 kit.

first: Alexandre

last: Germanos

last: Hsieh


title: Expression of human CD8+ T cells 21 d after BCL11B KO or control treatment

city: Greifswald

first: Maren

last: Depke

department: Klinik fuer Innere Medizin C

institute: Universitaetsmedizin Greifswald KoeR

summary: BCL11B, an essential transcription factor for thymopoiesis, regulates also vital processes in post-thymic lymphocytes. Increased expression of BCL11B was recently correlated with the maturation of NK cells, whereas reduced BCL11B levels were observed in native and induced T cell subsets displaying NK cell features. We show that BCL11B-depleted CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics. These induced innate CD8+ (iiT8) cells expressed multiple innate receptors like NKp30, CD161, and CD16 as well as factors regulating migration and tissue homing while maintaining their T cell phenotype. The iiT8 cells effectively killed leukemic cells spontaneously and neuroblastoma spheroids in the presence of a tumor-specific monoclonal antibody mediated by CD16 receptor activation. These iiT8 cells integrate the innate natural killer cell activity with adaptive T cell longevity, promising an interesting therapeutic potential. Our study demonstrates that innate T cells, albeit of limited clinical applicability given their low frequency, can be efficiently generated from peripheral blood and applied for adoptive transfer, CAR therapy, or combined with therapeutic antibodies.

overall_design:
The setting included three experimental groups: non-treated control, mock electroporated control, and BCL11B knock-out. All cells were cultivated in supplemented medium. CD8+ T cells were prepared from three donors as biological replicates. Thus, nine samples were analyzed in total.
Affymetrix Human Clariom S GeneChip was used for recording the global transcriptome pattern.

first: Hannes

last: Forkel

first: Piotr

last: Grabarczyk

first: Christian

last: Schmidt


title: Modeling of Alpha-1 Antitrypsin Deficiency with Syngeneic Human iPSC-Hepatocytes Reveals Metabolic Dysfunction and Cellular Heterogeneity in PiMZ and PiZZ Hepatic Cells (bulk RNA-Seq)

summary: We profiled the global transcriptomes of PiZZ6 syngenenic ZZ, MZ, and MM iPSCs that underwent directed differentiation to the hepatic lineage using RNA sequencing.

overall_design: Total RNA was extracted and then mRNA isolated using magnetic bead based poly(A) selection followed by synthesis of cDNA fragments. These were then end paired, and PCR amplified to create each cDNA library and sequenced on the NextSeq 500. Reads were then eliagned to ENSEMBL human reference genome GRCh38.91 using STAR. The Bioconductor package edgeR was used to normalize count matrix, followed by the limma and voom packages for linear model fitting and differential expression testing.


title: Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter in Multiple Sclerosis (MS)

status: Public on Dec 05 2022

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: The human brain is populated by perivascular CD8+ and CD4+ T cells with a tissue-resident memory T (TRM)-cell phenotype. In multiple sclerosis (MS), these cells associate with white matter (WM) and, to a lesser extent, grey matter (GM) lesions. We here investigated the transcriptional and functional profile of brain-resident T cells. Of n=11 subsequent post-mortem brain donors, we isolated CD8+ and CD4+ effector memory and effector memory re-expressing CD45RA T cells from blood and CD8+ and CD4+ CD69+ T cells from corpus callosum WM and cortical GM. Additionally, brain CD69+ T cells were sorted from subcortical WM, corpus callosum WM, and medulla WM/GM of n=3–5 brain donors as well as from paired normal-appearing WM and GM and from WM and GM lesions of n=6 MS brain donors. In all donors, WM and GM T cells were overwhelmingly CD69+CD103+/-. Bulk RNA sequencing of CD8+ and CD4+ CD69+ T cells revealed TRM-cell signatures, as marked by differential expression of, among others, SELL (CD62L), ITGA1 (CD49a), and S1PR1. Notably, gene expression hardly differed between lesional and normal-appearing WM CD8+ and CD4+ CD69+ T cells in MS brains. Genes up-regulated in brain TRM cells were MS4A1 (CD20) and SPP1 (osteopontin, OPN). OPN is also abundantly expressed by microglia and has been shown to inhibit T-cell activity. In line with the increased presence of OPN in active MS lesions, we noticed a reduced production of the inflammatory cytokines IL-2, TNF, and IFNγ by MS lesion-derived CD8+ and CD4+ T cells ex vivo. This study discloses essential characteristics of human brain CD8+ and CD4+ TRM cells in non-MS and MS post-mortem WM and GM, reports OPN as a generic product of brain-resident immune cells, and shows a tight control of the activation state of TRM cells in MS lesions.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of brain CD8+ and CD4+ CD69+ T cells from paired normal-appearing WM and GM and from WM and GM lesions of n=6 MS brain donors. Third dataset of 3.

first: Cheng-Chih

last: Hsiao

first: Hendrik

middle: J

first: Aldo

last: Jongejan

first: Jing

last: Zhu

first: Baohong

last: Zhang

first: Michael

last: Mingueneau

first: Perry

middle: D

last: Moerland

first: Inge

last: Huitinga

first: Joost

last: Smolders

first: Jörg

last: Hamann


title: Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter in Multiple Sclerosis (Location)

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of brain CD8+ CD69+ T cells from subcortical WM, corpus callosum, and medulla oblongata of n=3–5 brain donors. Second dataset of 3.


title: Prostaglandin F2α promotes human retinal microvascular endothelial cell proliferation and migration

city: Shanghai

first: Yan

last: Zhao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: To identify the downstream signaling pathways that contribute to proliferation and migration of human retinal microvascular endothelial cells by PGF2α

overall_design: Human retinal microvascular endothelial cells (HRMECs) were purchased from Cell Biologics. Cells were treated in culture for 6 hours with DMSO or prostaglandin F2α in biological triplicates.

first: Ying

last: Yu


title: DNase-seq from suppressor macrophage (ENCSR564XXO)

status: Public on Dec 04 2022

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from suppressor macrophage (ENCSR405FAK)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR566XSD)


title: Pulmonary EV miRNA profiles identify disease and distinct inflammatory endotypes in COPD

city: Southampton

first: Hannah

last: Burke

state: Hampshire

address: Tremona Road

country: United Kingdom

institute: University Hospital Southampton

summary: COPD is a heterogeneous condition without effective disease modifying therapies. Identification of novel inflammatory endotype markers such as extracellular vesicles (EVs), which are important intercellular messengers carrying microRNA (miRNA), may enable earlier diagnosis and disease stratification for a targeted treatment approach.  Our aim was to identify differentially expressed EV miRNA in the lungs of COPD patients compared with healthy ex-smokers and determine whether they can help define inflammatory COPD endotypes.  EV miRNA were isolated and sequenced from ex-smoking COPD patients and healthy ex-smoker bronchoalveolar lavage fluid. Results were validated with RT-qPCR and compared to differential inflammatory cell counts.  Differential expression analysis identified five upregulated miRNA in COPD (miR-223-3p, miR-2110, miR-182-5p, miR-200b-5p and miR-625-3p) and three downregulated miRNA (miR-138-5p, miR-338-3p and miR-204-5p), all with a log2 fold change of >1/-1, FDR<0.05. These miRNAs correlated with disease defining characteristics such as FEF 25-75% (a small airways disease measure) and DLCO % (a surrogate measure of emphysema). Receiver operator curve analysis demonstrated miR-2110, miR-223-3p and miR-182-5p showed excellent combinatory predictive ability (AUC 0.91, p<0.0001) in differentiating between health and mild COPD. Furthermore, miR-223-3p and miR-338-3p correlated with airway eosinophilia and were able to distinguish “pure eosinophilic” COPD from other airway inflammatory subtypes (AUC 0.94 and 0.85 respectively).   This is the first study to identify differentially expressed miRNA in COPD bronchoalveolar lavage fluid EVs. These findings suggest specific lung derived EV miRNA are a strong predictor of disease presence even in mild COPD. Furthermore, specific miRNA correlated with inflammatory cell numbers in COPD, and may have a role in defining inflammatory endotypes for future treatment stratification.

overall_design: Twenty-four subjects with stable mild or moderate COPD and Twenty healthy, age-matched ex-smokers (>10-pack year history) were recruited as a control group

first: Doriana

last: Cellura

first: Anna

last: Freeman

first: Alex

last: Hicks

first: Kris

last: Ostridge

first: Alastair

last: Watson

first: Nicholas

middle: P

last: Williams

first: Mirella

last: Spalluto

first: Karl

last: Staples

first: Tom

last: Wilkinson


title: Neuroendocrinology of the lung revealed by single cell RNA sequencing

first: Christin

last: Kuo

address: 240 Pasteur Dr.

institute: Stanford University

summary: Single cell RNAseq has revolutionized study of rare cell types. Here we use single cell RNA sequencing to determine the expression profiles of hundreds of the rare pulmonary neuroendocrine cells (PNECs) in mouse and human lungs.

overall_design: Normal mouse PNECs were permanently labeled with ZsGreen by intaperitoneal injection of mice with 3 mg tamoxifen to induce Cre-ERT2, and 3-7 days later (PN21, PN90, and PN120) euthanized. Lungs were micro-dissected en bloc at room temperature, and the trachea and peripheral regions of each lobe removed with a razor blade. The remaining bronchiolar regions (where PNECs reside) of individual lobes were prepared as described in Kuo, et al for dissociation to single cell suspension.

first: Spyros

last: Darmanis

first: Stephen

last: Quake

first: Mark

last: Krasnow


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR941MHZ)


title: DNase-seq from T-helper 17 cell (ENCSR139KYP)


title: DNase-seq from suppressor macrophage (ENCSR367FKP)


title: DNase-seq from suppressor macrophage (ENCSR325GNM)


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCSR483PGP)


title: Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter (Circulation)

first: Jeen

last: Engelenburg

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of CD8+ and CD4+ effector memory and effector memory re-expressing CD45RA T cells from blood and CD8+ and CD4+ CD69+ T cells from corpus callosum WM and cortical GM of n=11 subsequent post-mortem brain donors. First dataset of 3.

first: Cheng-Chih

last: Hsiao

first: Hendrik

first: Aldo

last: Jongejan

first: Jing

last: Zhu

first: Baohong

last: Zhang

first: Michael

last: Mingueneau

first: Perry

last: Moerland

first: Inge

last: Huitinga

first: Joost

last: Smolders

first: Jörg

last: Hamann


title: PRMT5 Promotes Progression of Chronic Lymphocytic Leukemia [3_vs_6_mo_RNA-Seq]

city: Columbus

first: Janek

last: Walker

institute: The Ohio State University

summary: Purpose: Richter’s Transformation (RT) is a poorly understood and often fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. PRMT5 is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 developed a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice uniformly developed a highly aggressive disease that histologically resembles RT; where large-scale transcriptional profiling identified unique oncogenic pathways that mediate PRMT5-driven disease progression. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases

first: Zachary

last: Hing

first: Lindsey

last: Brinton

first: Katie

last: Williams

first: Jami

last: Shaffer

first: Jordan

last: Skinner

first: Casey

last: Cempre

first: Charles

last: Gregory

first: Alexander

last: Pan

first: Pearly

last: Yan

first: James

last: Blachly

first: Lapo

last: Alinari

first: John

last: Byrd

first: Bradley

last: Blaser

first: Robert

last: Baiocchi

first: Rosa

last: Lapalombella


title: Effect of SASP factors on mouse intestinal organoids

first: David

last: Garfield

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

overall_design: Refer to individual Series


title: Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter in Multiple Sclerosis

first: Jeen

last: Engelenburg


title: total RNA-seq from K562 (ENCSR303IRE)

first: ENCODE

last: DCC

summary:
Homo sapiens K562 treated with Panobinostat for 48 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Exon junction complex shapes m6A epitranscriptome during splicing

first: Xin

last: Yang

address: Karp Building, 6th floor, 06007E, 1 Blackfan Circle

institute: Boston childrens' hospital

summary: N6-methyladenosine (m6A) is the most abundant post-transcriptional methylation of mature mRNA and plays a crucial regulatory role in various biological functions, involving development and cancer progression. m6A is deposited by methyltransferase complex composed of METTL3 and METTL14 cotranscriptionally, and removed by demethylase FTO or ALKBH5. m6A is highly enriched within the 3’ UTRs and in the vicinity of the stop codon of mature mRNA. However, the mechanism that causes this distribution pattern is still enigmatic. Here, we show that EJC packages mRNAs to shape mRNA m6A landscape. We first tested the possibility that demethylase removes m6A during spicing and found that ALKBH5 depletion had a minor effect on m6A levels. Thus, we ruled out the demethylation model. We then hypothesized that splicing factors inhibit the methylation process of internal exons, but not the 3’ UTR. Knockdown of EIF4A3, a core component of the exon junction complex, significantly increased m6A levels in mature mRNAs. The hypermethylated sites are enriched in short internal exons. Furthermore, EIF4A3 depletion upregulates METTL3 binding affinity to mRNA to deposit m6As. In conclusion, Our results demonstrate that EIF4A3 blocks METTL3 binding and methylating internal short exons of mRNA. These findings shed light on the fact that RNA packaging formed during splicing acts as a regulator that shapes mRNA modifications.

overall_design: Comparative m6A modification profiling analysis of meRIP-seq data and METTL3 binding profiling analysis of eCLIP-seq data for HeLa cells and its KD derivatives (siALKBH5 and siEIF4A3).

first: Richard

middle: I


title: total RNA-seq from left cerebral cortex (ENCSR723XFW)

summary:
5xFAD X Cast L. cortex (brain)_8-10 months female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: CRISPR RNA-seq from K562 (ENCSR300UBK)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against SKIV2L2. (SKIV2L2-BGKcLV33)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from A549 (ENCSR300FPD)


title: CRISPR RNA-seq from K562 (ENCSR300LXO)

summary:
RNA-seq on K562 cells treated with a CRISPR gRNA against DDX18. (DDX18-BGKcLV28)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf