title: Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids

status: Public on Aug 25 2022

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

institute: MCRI

summary: Improved specification of metanephric nephron progenitors in conditions that prolong differentiation while simultaneously preventing spontaneous nephron induction resulted in proximal tubule (PT)-enhanced kidney organoids. PT-enhanced organoids exhibited improved PT maturation, with elongated and aligned nephron segments as well as distinct loops of Henle. The striking proximo-distal orientation of nephrons was shown to result from localised WNT antagonism originating from the centre of the organoid.

overall_design: Single cell RNA-seq generated on a 10x Chromium genomics platform from human iPSC-derived kidney differentiations and organoids. D13+14 sample represents 4 barcoded replicates of 4 pooled organoids, each replicate derived from seperate monolayer differentiations of CRL1502.2 iPSCs (D13 sample; also containing 4 barcoded replicates). D13+12 represents a single organoid derived from a D13 monolayer differentiation of CRL-2429/SIX2Cre/Cre:GAPDHdual iPSCs.

first: Jessica

last: Vanslambrouck

first: Melissa

last: Little


title: Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

status: Public on Aug 29 2022

city: Perth

first: Alistair

middle: R. R.

last: Forrest

state: WA

address: 6 Verdun Street, Nedlands

country: Australia

institute: Harry Perkins Institute of Medical Research, The University of Western Australia

type: Expression profiling by high throughput sequencing

summary: 8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples obtained from the ovaries during the interval debulking surgery

first: Elena

last: Denisenko

first: Leanne

last: de Kock

first: Adeline

last: Tan

first: Aaron

last: Beasley

first: Maria

last: Beilin

first: Matthew

middle: E

last: Jones

first: Rui

last: Hou

first: Simon

last: Fox

first: Khaing

last: Hmon

first: Yen

last: Yeow

first: Elin

last: Gray

first: Paul

middle: A

last: Cohen

first: Yu

last: Yu

middle: R

first: Daithi

last: O Muiri

first: Sanela

last: Bilic

first: Ganendra

last: Mohan

first: Stuart

last: Salfinger


title: Transcriptomic comparison of a second-generation AKT degrader to the catalytic AKT inhibitor GDC0068 in breast cancer cells

status: Public on Oct 15 2022

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

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

overall_design: Refer to individual Series


title: Strand-Specific Nuclear Transcriptome Analysis of Osteoclast Precursor Cells

status: Public on Nov 01 2022

city: Seoul

first: Kibyeong

last: Kim

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

country: South Korea

institute: Yonsei University

summary: To understand the pathogenic mechanisms of bone erosion in rheumatoid arthritis (RA), we investigated osteoclast-specific epigenetic programs, RANKL-responsive super-enhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) in human osteoclasts. In this dataset, we validated the presence of the predicted SE-eRNAs.

overall_design: Strand-Specific Nuclear RNA, Control and RANKL

first: Seyeon

last: Bae

first: Kyung-Hyun

last: Park-Min

first: SungHo

last: Park


title: Base-Level Resolution Run-On Sequencing in Osteoclast Precursor Cells

summary: To understand the pathogenic mechanisms of bone erosion in rheumatoid arthritis (RA), we investigated osteoclast-specific epigenetic programs, RANKL-responsive super-enhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) in human osteoclasts. This dataset contains precision run-on sequencing (PRO-seq) data performed to detect SE-eRNA transcription activity.

overall_design: PROseq, RANKL and Control


title: Single neonatal perturbations long-lastingly shape the transcriptome and TCR repertoire of the first wave of regulatory T cells

status: Public on Aug 23 2022

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

country: China

institute: Legend Biotech

summary: The first wave of Foxp3+ regulatory T cells (Tregs) generated in neonates has been reported to be indispensable for the life-long prevention of autoimmunity. Although it is widely accepted that neonates are highly susceptible to infections, the impact of neonatal infections on the first wave of Tregs is completely unknown. Here, we challenged newborn Treg fate-mapping mice (Foxp3eGFPCreERT2xRosa26-YFP) with the Toll-like receptor agonists LPS and poly I:C to mimic neonatal bacterial or viral infections, respectively, and subsequently administrated tamoxifen during the first eight days of life to selectively label the first wave of Tregs. Neonatally-tagged Tregs preferentially accumulated in non-lymphoid tissues when compared to lymphoid organs irrespective of the treatment. One week post perturbation, unexpectedly no differences in the frequency and phenotypes of neonatally-tagged Tregs were observed between challenged mice and untreated controls. However, upon aging, a decreased frequency of neonatally-tagged Tregs in both non-lymphoid tissues and lymphoid organs was detected in challenged mice when compared to untreated controls, and became significant twelve weeks post perturbation, with no signs of altered Foxp3 stability. Remarkably, this late decrease in the frequency of neonatally-tagged Tregs only occurred upon perturbations in newborns as challenging of eight-day-old mice did not result in long-lasting alterations of the first wave of Tregs. Combined single-cell T cell receptor (TCR)-seq and RNA-seq revealed that neonatal perturbations drastically diminished TCR diversity and long-lastingly altered the transcriptome of neonatally tagged Tregs, exemplified by lower expression of Tigit, Foxp3, and Il2ra. Together, our data demonstrate that a single, transient encounter with a pathogen in neonates can have long-lasting consequences for the first wave of Tregs, which might affect immunological tolerance, prevention of autoimmunity, and other non-canonical functions of tissue-resident Tregs.

overall_design: Newborn Foxp3EGFPCreERT2Rosa26YFP mice were intraperitoneally injected with LPS, poly I:C, or PBS, followed by three times intragastrical administrations of tamoxifen on days 2, 5, and 8 after birth. Single lymphocyte suspensions were prepared from the spleen, colon, and skin of twelve-week-old PBS-, LPS- or poly I:C neonatally treated mice, and were further stained with TotalSeq-C hashtag antibody (BioLegend) according to the manufacturer's protocol. The same type of organs was labeled by the same TotalSeq Hashtag antibodies, afterward spleen, colon, and skin samples from the same mouse were pooled together for sorting CD8-CD45R-CD11c-CD11b-NK1.1-CD4+YFP+ cells. Sorted cells were then uploaded onto a 10x Chromium Next GEM Chip G using reagents from the Chromium Single Cell 5' Library and Gel Bead Kit (10x Genomics) according to the manufacturer's protocol. Amplified cDNA was used for both 5' RNA-seq library generation and TCR V(D)J targeted enrichment using the Chromium Single-Cell V(D)J Enrichment Kit for Mouse T Cells (10x Genomics). 5' RNA-seq and TCR V(D)J libraries were prepared following the manufacturer's user guide (10x Genomics). Libraries were quantified by QubitTM 3.0 Fluorometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA Kit (Agilent Technologies). scRNA-seq libraries were sequenced on an Illumina NextSeq500 sequencer to attain approximately 141,381 ± 63,000 reads per single cell and scTCR V(D)J libraries were sequenced on an Illumina NextSeq500 sequencer to obtain approximately 63,987 ± 6,131 reads per cell. The sequencing specifications for both single-cell RNA-seq and TCR V(D)J libraries were according to the manufacturer's specification (10x Genomics).

first: Juhao

last: Yang

first: Xiaojing

last: Chu

first: Stefan

last: Floess

first: Yang

last: Li

first: Michael

last: Delacher

first: Jochen

last: Huehn


title: Assessment of genomic location of acetylation of lysine 27 of histone H3 in Osteoclast Precursor Cells [ChIP_seq_H3K27ac]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand the pathogenic mechanisms of bone erosion in rheumatoid arthritis (RA), we investigated osteoclast-specific epigenetic programs, RANKL-responsive super-enhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) in human osteoclasts. This dataset represent histone modification encoding active enhancers genome-wide.

overall_design: Seyeon, Bae


title: Brain transcriptomic analysis in Parkinson's disease patients stratified by Braak Lewy body stage / Sex differences in Parkinson's disease brain transcriptome

status: Public on Oct 28 2022

city: Oslo

first: Chiara

last: Cappelletti

address: Gaustadalléen 34

country: Norway

institute: Oslo University Hospital

summary:
To investigate transcriptomic changes associated with Parkinson's disease development we compared frontal cortex gene expression across four Braak Lewy body stage groups. Additionally we investigated sex-specific gene expression differences in neuropathologically healthy donors and Parkinson's disease patients at Braak Lewy body stage 5.
We investigated sex-specific gene expression differences in neuropathologically healthy donors and Parkinson's disease patients at Braak Lewy body stage 5.

overall_design:
Comparison of frontal cortex gene expression across Braak Lewy body stage groups (Braak Lewy body stage 0, 1-4, 5 and 6)
Comparison of frontal cortex gene expression between males and females in neuropatholocially healthy donors (Braak Lewy body stage 0) and Parkinson's disease patients (Braak Lewy body stage 5)

first: Lasse

last: Pihlstrøm

first: Hanneke

last: Geut

first: Annemieke

middle: J

last: Rozemüller

first: Wilma

middle: D

last: van de Berg

first: Sandra

last: Pilar Henriksen

first: Kaja

last: Nordengen

first: Mathias

last: Toft


title: Transcriptomic comparison of a second-generation AKT degrader to the catalytic AKT inhibitor GDC0068 in breast cancer cells [RNA-seq]

first: Ralitsa

last: Madsen

summary: We report the development of a second-generation AKT degrader INY-05-040, which outperformed catalytic AKT inhibition both with respect to biochemical and cellular suppression of AKT/mTORC1-driven phenotypes in diverse breast cancer cell lines. Using multi-omic profiling and causal network integration, we demonstrate that the enhanced efficacy of INY-05-040 relies in part on potent downstream activation of stress mitogen activated protein kinase (MAPK) signaling. Systematic measurements of growth inhibition across 288 cancer cell lines confirmed the substantial improvement in potency for INY-05-040 compared to the first-generation AKT degrader (INY-03-041) and catalytic AKT inhibition with GDC-0068. Subsequent integration of breast cancer cell line-specific data with publicly available transcriptomic, proteomic and reverse phase protein array (RPPA) measurements revealed that decreased sensitivity to INY-05-040 correlates with a high baseline activation of inflammatory/stress signaling pathways. Collectively, our data uncover a unique mechanism of breast cancer cell line sensitivity to AKT degradation, further suggesting that the efficacy of catalytic AKT inhibition may be enhanced by activation of stress MAPKs in breast cancer cells with low baseline activity of these components.

overall_design: We performed comparative mRNA sequencing (RNAseq) in ER+ T47D breast cancer cells, exposed to the catalytic AKT inhibitor GDC0068 or the second-generation AKT degrader INY-05-040 for 5 or 10 h. To limit the confounding effect of differential potency, we determined the doses of INY-05-040 (100 nM) and GDC-0068 (500 nM) that would result in comparable suppression of downstream signaling at these time points. Controls included treatment of cells with DMSO or the inactive stereoisomer, INY-05-040-Neg (100 nM). The data are from three independent experiments, performed in growth factor-complete medium.

first: Alex

last: Toker

first: Emily

last: Erickson


title: STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma

status: Public on Aug 26 2022

city: Memphis

first: Brian

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital


title: STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma [RNA-seq]

summary: Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T-cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here we show that dysregulated STAT3, together with a core transcriptional regulatory circuit consisting of BATF3–IRF4–IKZF1, co-occupies gene enhancers to establish an oncogenic transcription program and maintain the malignant state of ALCL. Critical downstream targets of this network in ALCL cells include the proto-oncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The activity of this auto-regulatory transcription loop is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. These findings provide new insights for understanding how dysregulated signaling pathways hijack cell-type-specific transcriptional machinery to drive tumorigenesis and create therapeutic vulnerabilities in genetically defined tumors.

overall_design: RNA-seq of ALCL cell lines treated with DMSO or crizotinib/ruxolitinib (1uM) for 24h.

first: Nicole

last: Prutsch

first: Shuning

last: He

first: Alla

last: Berezovskaya

first: Adam

last: Durbin

first: Neekesh

last: Dharia

first: Kelsey

last: Maher

first: Jamie

last: Matthews

first: Lucy

last: Hare

first: Suzanne

last: Tumer

first: Kimberly

last: Stegmaier

first: Lukas

last: Kenner

first: Olaf

last: Merkel

first: Richard

last: Young

first: A

middle: T

last: Look

first: Mark

middle: W

last: Zimmerman


title: scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing

status: Public on Sep 07 2022

city: Beijing

first: Fuchou

last: Tang

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Biomedical Pioneering Innovation Center, Peking University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Ar101 Oral Desensitization Therapy for Peanut Allergy Induces Dynamic Changes in Peanut-Specific Immune Responses

status: Public on Aug 10 2022

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Peanut allergy is increasingly prevalent among children in the United States and other industrialized countries and is now estimated to affect approximately 2% of children. While there are currently no approved treatment options, peanut allergy usually persists into adulthood, can be life-threatening, and accounts for most deaths related to food allergy.  Here, we track peanut-reactive CD4+ T effector (pTeff) cells using the CD154 up-regulation assay. We found that CRTH2+ pTeff cells and CCR6+ pTeff cells represent two mutually exclusive, non-overlapping cellular and molecular entities involved in food allergic diseases.

overall_design: 25 T-cell samples were profiled using RNA-seq. Cells were stimulated with peanut peptides overnight and ~100 peanut-reactive cells were sorted for RNA-sequencing. Cells were sorted from the total CD154+ compartment (6 samples), the CD154+/CRTH2+ compartment (5 samples), or the CD154+/CCR6+ compartment (14 samples).

first: Veronique

last: Bajzik

first: Hannah

last: DeBerg

first: Nahir

last: Garabatos

first: Blake

last: Rust

middle: K

last: O'Brien

first: Quynh-Anh

last: Nguyen

first: Colin

last: O’Rourke

first: Alex

middle: H

last: Walker

first: Charlie

last: Quinn

first: Vivian

last: Gersuk

first: Mary

last: Farrington

first: David

last: Jeong

first: Brian

middle: P

last: Vickery

first: Daniel

middle: C

last: Adelman

first: Erik

last: Wambre


title: Effect of Combinatorial Extracellular Matrix and Substrate Stiffness on Chromatin Accessibility of Activated Hepatic Stellate Cells

status: Public on Aug 13 2022

city: Urbana

first: Dr. Gregory

last: Underhill

address: 1406 West Green Street

institute: University of Illinois at Urbana Champaign

summary: Understand mechanisms of NAFLD related liver fibrosis

overall_design: Chromatin accessibility of Human Hepatic Stellate Cells  as a function underlying Extracellular Matrix Composition and Substarte Stiffness

first: Ishita

last: Jain

first: Gregory


title: scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DataSet1: scNanoATAC-seq]

first: Fuchou

last: Tang

summary: We present scNanoATAC-seq (Single-cell Assay for Transposase Accessible Chromatin by Oxford Nanopore Technologies Sequencing), an effective method for simultaneous detection of chromatin accessibility and genetic variation. Long fragments (about 4-5Kb) of single-cell ATAC-seq library were enriched and sequenced by Oxford Nanopore Technologies platform. Ends of long ATAC-seq fragments are regarded as chromatin accessibility signal in downstream analysis.

overall_design: Single-cell NanoATAC-seq was performed on following cell lines: eHAP1, GM12878, HEK293T, HFF1, K562, MEF and mESC.

first: Yuqiong

last: Hu

first: Zhenhuan

last: Jiang

first: Kexuan

last: Chen


title: Microglia regulate Zika virus infection in human developing brain and glioma

status: Public on Sep 08 2022

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: This paper shows that, whereas SOX2+ cells in HDB are highly susceptible to ZKV, SOX2+ primary GBM samples exhibit moderate to high resistance to infection. These datasets address the reasons for this difference, based on infection of primary patient GBM and human developing brain samples with mCherry Zika reporter virus, then FACS sorting the Zika-mCherry positive and negative fractions from each sample for bulk RNA-Sequencing. The primary finding of importance is that Zika resistant GBMs exhibit an immune signature reflecting high levels of infiltration by microglia which are present only in small numbers or absent altogether in human developing brain.

overall_design: These bulk RNA-Sequencing libraries were generated from primary patient glioblastoma tumour cells and human developing brain cells, infected with Zika-mCherry reporter virus and then FACS sorted for mCherry positive and negative fractions.

first: Harry

last: Bulstrode

first: Ilias

last: Moutsopoulos

last: Rowitch


title: Differentiation of malaria male gametocytes is initiated by recruitment of a chromatin remodeler to male-specific cis-acting elements (RNA-Seq)

status: Public on Aug 05 2022

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

summary: By targeting disruption of SNF2, male gametocytes lost capacity for exflagellation completely, and transcripts of male-specific genes decreased significantly, whereas female gametocytes display normal phenotype. ChIP-seq analysis showed that gSNF2 molecules were divided into two groups according to motif sequences on the genome they were recruited: those recruited to female-specific cis-acting element, TGTRNNYACA, and those recruited to a five base motif, YGTCT, that exists on the upstream of male-specific genes. Studies using a male-specific dynein promoter demonstrated that the five-base motif is a male-specific cis-acting element. ATAC-seq analysis demonstrated that the disruption of gSNF prohibits creation of a nucleosome-free region (NFR) on the promoter of male-specific target genes, and the reduction rates of NFR correlated well with those of target gene expression. These results suggests that global changes of chromatin structure by gSNF2 occur in initial step of male development. The present study also suggested that male-specific gene expression is under the control of a single kind of male-specific cis-acting element thus a single sequence-specific TF. This is a first report genome-wide changes of nucleosome positioning by a remodeling complex play a role in stage conversion of this parasite.

overall_design: Plasmodium berghei transcriptomes were analyzed in gametocytes.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tsubasa

last: Nishi

first: Yuho

last: Murata


title: Peripheral nerve derived fibroblasts promote neurite outgrowth in adult dorsal root ganglion neurons more effectively than skin-derived fibroblasts

status: Public on Aug 20 2022

city: Sapporo

first: Masato

last: Hara

state: Hokkaido

address: Kita-15 Nishi-7

department: Orthopaedic Surgery

institute: Hokkaido University

summary: Although fibroblasts (Fb) partially consist of peripheral nerves and are involved in the regenerative process associated with a peripheral nerve injury (PNI), detailed information regarding their characteristics is largely lacking. The objective of the current study was to investigate the capacity of Fb derived from peripheral nerves to stimulate the outgrowth of neurites from adult dorsal root ganglion (DRG) neurons and to clarify their molecular characteristics. Fb were primally prepared from the epineurium (Epn) and parenchyma (Par) of rat sciatic nerves and skin (Skn). The Fb  derived from Epn (Fb-Epn) showed the greatest neurite outgrowth effect, followed by the Fb derived from parenchyma (Fb-Par), indicating that Fb derived from nerves promote neurite outgrowth more effectively than Skn-derived Fb (Fb-Skn). Although both secreted and cell-surface factors contributed evenly to the neurite promoting effect of nerve derived Fb, in crush and transection injury models, Fb were not closely associated with regenerating axons, indicating that only factors that are secreted from Fb are available to regenerating axons. A transcriptome analysis revealed that the molecular profiles of these Fb were distinctly different and that the gene expression profiles of secreted factors that promote axonal growth are unique to each Fb. These findings indicate that Fb are molecularly and functionally different depending on their localization in nerve tissue and that Fb-Epn might be involved more than was previously thought in axon regeneration after PNI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three types of fibroblasts from epineurium, parenchyma and skin (Fb-Epn, Fb-Par, Fb-Skn)

first: Ken

last: Kadoya

first: Takeshi

last: Endo


title: Differentiation of malaria male gametocytes is initiated by recruitment of a chromatin remodeler to male-specific cis-acting elements (ChIP-Seq)


title: Differentiation of malaria male gametocytes is initiated by recruitment of a chromatin remodeler to male-specific cis-acting elements


title: Differentiation of malaria male gametocytes is initiated by recruitment of a chromatin remodeler to male-specific cis-acting elements (ATAC-Seq)


title: Impact of shRNA-mediated MXD4/MAD4 down-modulation on the transcriptome profile of human keratinocyte precursor cells

status: Public on Aug 02 2022

city: Evry

first: Nicolas

last: FORTUNEL

address: 2 Rue Gaston Cremieux

country: France

institute: CEA

summary: Characterization at the global transcriptome level of the gene networks ensuring the regulation of the immature status of cutaneous stem- and precursor-cells is a necessary step to further understand the concept of ‘stemness’ in this tissue. Moreover, considering possible clinical applications, the search for molecular targets to control stem cell characteristics and regenerative capacity is a necessary step to improve therapeutic approaches. Cutaneous cell therapy is concerned by this objective, as skin graft bioengineering requires a phase of ex vivo expansion of keratinocytes from donors, during which the preservation of a sufficient stem cell pool is critical for graft take and long-term skin regeneration. We have investigated the role of transcription factor MXD4/MAD4 in native keratinocyte precursors from adult human skin. A stable lentiviral-based shRNA-mediated MXD4 knock‑down (KD) approach was developed and used to study the properties of MXD4-deficient [MXD4KD] versus control [MXD4WT] native keratinocyte precursors. Using long-term cultures and clonal assays, we found that decreased MXD4 expression increased keratinocyte precursor immaturity and clonogenic potential, thus promoting self-renewal. Importantly, [MXD4KD] keratinocyte precursors exhibited an improved capacity for three-dimensional epidermis reconstruction, which was preserved at a late ex vivo expansion stage where this potential was lost in [MXD4WT] keratinocytes. To analyze the biological impact of MXD4 knock‑down at the molecular level, comparative transcriptome profiling of [MXD4WT] and [MXD4KD] cells was performed using next-generation RNA sequencing (RNA-seq). This set of data provides a material that permits the dissection of genetic networks modulated by MXD4 in human keratinocyte precursor cells, and controlling their immature status and epidermis regeneration capacity.

overall_design: The study is based on the comparative RNA-seq analysis of human keratinocyte precursor cells corresponding to 2 cellular contexts: 1) cells transduced with a control lentiviral vector driving the expression of the reporter gene GFP, [MXD4WT]; 2) cells transduced with a lentiviral vector driving the expression of GFP and an anti-MXD4 shRNA, [MXD4KD]. For each cellular context 3 biological replicates were conducted (Bio rep).

middle: O

first: Julien

last: COUTIER

first: Jean-François

last: DELEUZE

first: Michèle

last: MARTIN


title: Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma (Digital Spatial Profiling)

status: Public on Aug 06 2022

city: Lausanne

first: François

last: Kuonen

address: Av. de Beaumont 29

country: Switzerland

institute: CHUV

summary: To progress, tumors need to invade the surrounding tissues. However, the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insights for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas (BCCs), we define the cellular contributors of the invasive front. In the invasive niche, tumor cells harbor a collective migration phenotype, supported by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts (CAFs) with extracellular matrix-remodeling features, as required to support collective migration. Moreover, while tumor cells specifically express Activin A, we find Activin A-induced gene signature enrichment in adjacent CAFs subpopulations, further supporting their biological crosstalk. Altogether, our data identify the subpopulations and their transcriptional reprogramming contributing to the spatial organization of the BCC invasive niche. They also bring the proof-of-concept for integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop therapeutic targeting.

overall_design:
Total 95 areas of interest from 12 basal cell carcinomas were sequenced using Digital Spatial Profiling (DSP) using GeoMX Nanostring, with the Cancer Transcriptome Altas (1812 genes)

*** FASTQ raw data files have been requested. ***

first: Laura

last: Yerly

first: Stéphanie

last: Tissot


title: Pten and p53 loss in the mouse lung causes adenocarcinoma and sarcomatoid carcinoma

status: Public on Aug 17 2022

city: Madrid

first: Corina

last: Lorz

state: Madrid

address: Avda. Complutense 40

country: Spain

institute: Ciemat (Centro de Investigaciones Energeticas Mediambientales y Tecnologicas)

summary:
Here we describe novel murine models of pulmonary adenocarcinoma (ADC) and sarcomatoid carcinoma (PSC) driven by the loss of two tumor suppressors: deletion of Trp53 and Pten. Combined deletion of Pten and Trp53 in the lungs of adult conditional mice leads to the development of both ADC and PSC irrespective of the lung targeted cell type or naphthalene induced airway epithelial regeneration. Although this model shows long latency periods and incomplete penetrance for tumor development, it is the first PSC mouse model reported so far, and sheds light on the relationships between ADC and PSC and their cells of origin. Moreover, human ADC show strong transcriptomic similarities to mouse PSC, providing a link  between these  tumor types and human ADC.
Ablation of Trp53 and Pten in pulmonary cells was achieved by intratracheal administration of purified Ad5-CMVcre or Ad5-K5cre (Du Page et al, 2009) to Trp53F/F; PtenF/F  8–10 week old mice. Mice were sacrificed at different time points after the Ad5-cre infection and tumors processed for whole transcriptome analysis. As control animals, Trp53F/F; PtenF/F littermates were used.

overall_design: Gene expression was studied in normal mouse lung and in lung tumours from Trp53F/F; PtenF/F mice treated by intratracheal administration of Ad5-CMVcre or Ad5-K5cre to ablate Trp53 and Pten in pulmonary cells. Some mice were pretreated with a single dose of naphthalene delivered by intraperitoneal injection (200mg naphthalene per kg body weight) three days before intratracheal administration of adenovirus.

first: Sara

last: Lázaro

first: Jesús

middle: M

last: Paramio

first: Mirentxu

last: Santos


title: Aberrant paracrine signalling underlies oncohistone-driven giant cell tumour of bone [RNA-seq]

city: London

first: Adrienne

last: Flanagan

state: Middlesex

address: Huntley Street

institute: University College London

summary: The identification of oncohistones underscores the neoplasm-driving role of chromatin dysfunction. However, we have limited understanding of how these perturbations alter communication in the tumour microenvironment (TME) and the functional implications of this crosstalk. In this respect, clinical evidence shows that the maturation block of the H3F3A (H3.3G34W)-mutated osteoblastic stromal population in benign giant cell tumours (GCTs), a neoplasm characterised by a prominent mutation-free osteoclast component, is reversed on osteoclast depletion, suggesting aberrant interactions between these two cell populations. Here, we reveal a bidirectional paracrine mechanism at the root of oncohistone-driven neoplasia in this bone tumour. H3.3G34W fails to induce stromal cell proliferation but inhibits their maturation. Altered chromatin landscape of these cells leads to enhancer remodelling, including at SCUBE3, a Tgfbeta family member. Reduced SCUBE3 expression contributes to increased osteoclasts that secrete high levels of SEMA4D, which disproportionately blocks maturation of H3.3G34W-expressing cells. Together, our findings suggest that non-cell autonomous provision of a growth advantage to a cancer driver-bearing cell  represents a paradigm for a benign neoplasm.

overall_design: hFOB 1.19 osteoblastic cell line engineered to express H3.3-WT-HA, H3.3-G34W-HA or empty vector, profiled for RNA-seq.

first: Lucia

last: Cottone


title: RNA-sequencing (RNA-seq) of iPSC-derived astrocytes from control and Parkinson's disease patients carrying LRRK2 G2019S point mutation.

status: Public on Jul 11 2022

city: L'Hospitalet de Llobregat

first: Meritxell

last: Pons

state: Barcelona

address: Avinguda de la Gran Via, 199-203

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

summary: Purpose: The goal of this study is to compare the NGS-derived from transcriptome profiling (RNA-seq) of human iPSC-derived astrocytes from control and Parkinson’s disease LRRK2 G2019S to gain insight into the mechanisms driving astrocyte's alterations in PD.

overall_design: Total RNA was assayed for quantity and quality using Qubit® RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100.  The RNASeq libraries were prepared from total RNA using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013). Briefly, 500ng of total RNA was used as the input material and was enriched for the mRNA fraction using oligo-dT magnetic beads. The mRNA was fragmented in the presence of divalent metal cations and at high temperature (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.  The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4. We generated over 30 million paired-end reads for each sample in a fraction of a sequencing v4 flow cell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files by CASAVA.


title: Dissecting the process of human neutrophil lineage determination by using alpha-lipoic acid inducing neutrophil deficiency model

status: Public on Jul 20 2022

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

summary: Neutrophil deficiency or differentiation disorder might cause serious diseases, such as neutropenia and neutrophilia. To reveal the molecular mechanism of human neutrophil lineage commitment, single cell RNAseq and bulk cells RNAseq were performed to reveal the characteristics and essential genes of neutrophil lineage determination.

overall_design: To explore the molecular mechanism of early commitment of neutrophil progenitors derived from GMPs, we performed single cell RNAseq for GMPs derived early progenitors, early neutrophil bias progenitors (CD34+CD15- NbP1, CD34mid CD15mid NbP2, CD34int/-CD15+NbP3) gated from CD115-CD73-CD1C-CD116- cells and CD34midCD115+MoPs. In addition, we also performed bulk cell RNAseq for ALA treated NbP1/NbP2, ELK1 and S-ELK1 overexpressed NbP1. The single cell RNAseq and bulk cell RNAseq were performed as we described in previous published paper (PMID:29434353, 31443434). 10X single cell RNAseq was performed for human bone marrow derived Lin- CD371+ progenitors.

first: Yimeng

last: Zhang

first: Feng

last: Ma


title: Transcriptomic analysis of pathways associated with alpha(v) integrin-dependent autophagy in human B cells

status: Public on Jul 29 2022

first: Stephanie

last: Osmond

summary: Autophagy proteins have been linked with development of immune-mediated diseases including lupus, but the mechanisms for this are unclear due to complex roles of these proteins in multiple immune cell types. We have previously shown that a form of non-canonical autophagy induced by av-integrins regulates B cell activation by viral and self-antigens, in mice. Here we investigated the involvement of this pathway in B cells from human tissue. Our data revealed that autophagy is specifically induced in germinal-center and memory B cell sub-populations from human tonsil and spleen. Transcriptomic analysis showed that induction of autophagy is related to unique aspects of activated B cells such as mitochondrial metabolism. To understand the function of ITGAV/av integrin-dependent autophagy in human B cells, we used CRISPR-mediated knockdown of autophagy genes. Integrating data from primary B cells and knockout cells we found that -dependent autophagy limits activation of specific pathways related to B cell responses, while promoting others. These data provide new mechanistic links for autophagy and B cell-mediated immune dysregulation in diseases such as lupus.

overall_design: Sorted tonsil B cell subsets with and without stimulation subjected to RNAseq, cell lines with CRISPR of autophagy genes or ITGAV gene subjected to RNA seq

first: Mridu

last: Acharya

last: Sagediev

first: Virginia

last: Muir


title: Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development

status: Public on Jul 07 2022

city: Bethesda

first: Joshua

last: Stone

state: Maryland

address: 37 Convent Drive Room 3050

institute: NIH

summary: Dysbiosis, or changes within the microbiome, is a common feature of solid tumors, however whether this dysbiosis directly contributes to tumor development is largely unknown. We previously characterized the lung cancer microbiome and identified the Gram-negative Acidovorax temperans as enriched in tumors and associated with smoking status and TP53 mutations. To determine if A. temperans exposure could contribute to the development of lung cancer, we investigated its effect in an animal model of lung adenocarcinoma driven by mutant Kras and Tp53 alleles. This revealed A. temperans exposure accelerates tumor development and burden through infiltration of proinflammatory cells in the lungs. Neutrophils exposed to A. temperans displayed a mature, pro-tumorigenic phenotype with increased cytokine signaling, with a global shift away from IL-1β signaling. Neutrophil to monocyte and macrophage signaling promoted maturation of the latter cell types which upregulated MHC II to activate CD4+ T cells. Activated T cells were then polarized to an IL-17A+ phenotype detectable in CD4+ and γδ populations. Furthermore, T17 cells shared a common gene expression profile predictive of poor survival in human LUAD cases. These data indicate a clear role for microbiota-induced inflammation as a key mechanism in the development of lung cancer, demonstrating that dysbiosis contributes to tumor growth.

overall_design: CD45+ cells were sorted by FACS from tumor tissue within the mutant K-ras/p53 (KP) mouse model of lung adenocarcinoma and sent for scRNA-seq

first: Mohammed

last: Khan

first: Chenran

first: Natalia

last: von Muhlinen

first: Curtis

last: Harris


title: Endothelial-specific c-Myc depletion enhances diet-induced liver inflammation and fibrosis

status: Public on Jun 30 2022

city: Boca Raton

first: Claudia

last: Rodrigues

state: Florida

address: 777 Glades Road, BC-71, Room 224

department: Biomedical Science

institute: Florida Atlantic University

summary: Endothelial cells play an essential role in inflammation through synthesis and secretion of chemoattractant cytokines and expression of adhesion molecules required for inflammatory cell attachment and infiltration. The mechanisms by which endothelial cells control its pro-inflammatory response depends on the type of inflammatory stimuli, endothelial cell origin and tissue involved. In the present study, we investigate the role of the transcription factor c-Myc in inflammation using a conditional knockout mouse model in which Myc is specifically deleted in the endothelium (EC-Myc KO). Using an experimental model of nonalcoholic steatohepatitis, we investigated the involvement of endothelial c-Myc in diet-induced inflammation. EC-Myc KO animals displayed enhanced pro-inflammatory response relative to control, which was characterized by increased expression of pro-inflammatory cytokines and leukocyte infiltration as well as worsened liver fibrosis. Transcriptome analysis suggested that different pro-inflammatory pathways are activated in control and endothelial Myc knockout after exposure to high-fat diet. Analysis of published single cell RNA-sequencing data available on human cirrhotic livers indicated that MYC was downregulated in endothelial cells relative to healthy individuals. Our results suggest a protective role for endothelial c-Myc in diet-induced liver inflammation and fibrosis. Targeting c-Myc and its downstream pathways in the endothelium may be a promising strategy for treatment of diet-induced inflammatory disease.

overall_design: Floxed control (CT) and endothelial c-Myc knockout (EC-Myc KO) mice received tamoxifen injection at 5 weeks of age to induce Cre activity. 2 weeks after injection, animals were fed with low fat control diet (CTD) or high-fat/cholesterol diet (HFC) for 5 weeks. Livers were haversted for transcriptome analysis.

first: Yue

last: Qi

first: Mirza

last: Fahd Qadir


title: IL-6 driven pSTAT1 response is linked to T cell features implicated in early immune dysregulation

status: Public on Jun 27 2022

summary: Here, we performed an in-depth characterization of the effect of classic IL-6 signaling in primary human T cells from healthy individuals. We generated a detailed map of IL-6 signaling in CD4+ and CD8+ naïve and memory T cell subsets, linking mbIL-6R expression levels to the magnitude and balance of phosphorylation of STAT1 and STAT3 and the transcriptomics response to IL-6 in these subsets.

overall_design: Primary human CD3+ T cells derived from healthy donors with the rs2228145 AA genotype were cultured with or without IL-6 (20 ng/mL) for 4 hours and the transcriptomic response to IL-6 signaling was determined in flow sorted T cell subsets including CD4+ naïve (CD4+CD45RA+), CD4+ memory (CD4+CD45RO+) and CD8+ naive (CD8+CD45RA+) T cells.

first: Katharina

last: Lambert

first: Kirsten

last: Diggins

first: Britta

last: Jones

first: Christian

last: Hundhausen

first: Megan

last: Maerz

first: Anne

last: Hocking

first: Srinath

last: Sanda

first: Carla

last: Greenbaum

first: Peter

middle: S

last: Linsley

first: Karen

last: Cerosaletti

first: Jane

last: Buckner


title: Tissue-wide Mechanisms Overrule Cell-intrinsic Gene Function in Radial Neuronal Migration

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

summary: The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation is based on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps that are regulated by a large array of signaling pathways. However, based on genetic loss-offunction experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not well understood. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to either sparsely or globally delete gene function followed by quantitative single cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominates cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically impacts the overall migration phenotype of individual cortical projection neurons. In a broader context our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development (FMCD) in particular, and neurological diseases in general.

overall_design: RNA-Seq of sorted neurons

first: Andi

last: Hansen

first: Simon

last: Hippenmeyer


title: Resistin Forms a Network with Cytokines Associated with Endothelial Damage and Worse Outcome in COVID-19

status: Public on Jun 09 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To obtain a detailed view of genes and pathways regulated in whole blood obtained from COVID-19 patients in the Osaka cohort, we carried out global RNA sequencing.

overall_design: We performed RNA-sequencing analysis using samples of leukocyte samples from 10 COVID-19 patients and 5 healthy controls.

first: Takeshi

last: Ebihara

first: Hisatake

last: Matsumoto


title: Effect of Combinatorial Extracellular Matrix and Substrate Stiffness Gene Expression and Chromatin Accessibility of Activated Hepatic Stellate Cells

first: Dr. Gregory

last: Underhill

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of gene expression in mouse macrophages treated with bacterial endotoxin lipopolysaccharide

status: Public on Jun 03 2022

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

summary: Relative mRNA levels of 27 genes were evaluated with the SYBR Green qPCR assays after LPS treatment for 2-24 h.

overall_design: Mouse macrophages (RAW264.7 cells, TIB-71) were established from a tumor in a male mouse induced with the Abelson murine leukemia virus (ATCC). The  cells in triplicate were treated with various concentrations of LPS for 2, 8 and 24 h. RNA isolation and cDNA synthesis were performed as described previously. Relative mRNA levels were evaluated with the SYBR Green qPCR assays using Bio-Rad reagents. Rpl32 mRNA was selected as the internal reference for qPCR analysis for this cell type. 1% DMSO treatment was the sample control. The 2-ΔCT and 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

first: Cao

last: Heping


title: Polyploid Giant Cancer Cells are dependent on cholesterol for progeny formation through amitotic division

status: Public on Jun 01 2022

city: Charleston

first: Christina

last: Voelkel-Johnson

state: SC

address: 173 Ashley Ave

department: Micro/Immuno

institute: Medical University of South Carolina

summary: Polyploid Giant Cancer Cells (PGCC) are increasingly being studied for their role in cancer recurrence and mortality.  These cells are induced in bulk cancer cell populations when under stress such as hypoxia or treatment stress (i.e. chemotherapy or radiation).  PGCC utilize temporary senescence achieved via a dedifferentiation pathway to survive transient stresses, providing a seed population for later regrowth. Our previous work demonstrated a dependence on the lysosomal enzyme acid ceramidase (ASAH1) in these cells, such that they are unable to perform division without ASAH1.  The pro-drug LCL521 is lysosomally targeted, fully inhibits ASAH1 activity within 5 hours, and ablates the ability of PGCC to generate progeny while permitting mitotic cancer cells to proliferate normally.  We used an RNASeq approach to compare the responses of parental PPC1 prostate cancer cells and their radiation-induced PGCC counterparts to 5 hours of LCL-521 treatment.  RNASeq confirmed that no major changes were triggered in parental PPC1 cells while PGCC appeared to respond as if they had undergone cholesterol depletion.

overall_design: The experiment included four conditions.  For each, 8 X 10^5 PPC1 cells were plated on day 1 in 100 mm plates.  Condition 1 (UT) were simply harvested on day 5 with trypsinization, processed using a Qiagen RNAEasy kit, purity assessed with a Nanodrop, and packaged for delivery to Novogene for analysis.  Condition 2 (UT_LCL) were exposed to 5 µM LCL-521 for five hours on day 5 prior to harvest.  Condition 3 (PGCC) were irradiated with 8 Gy on day 2 and on day 5 trypsinized, passed through a 20 micron PluriSelect cell filter, and the captured cells eluted.  Condition 4 (PGCC_LCL) were irradiated with 8 Gy on day 2 and on day 5 exposed to 5 µM LCL-521 prior to harvest with the same 20 micron filtration step as condition 3.  All harvests were performed in parallel for all 4 conditions each time the experiment was done.  The experiment was done 6 independent times, for a total of 24 samples.

first: Shai

last: White-Gilbertson

first: Ping

last: Lu


title: A single-cell atlas of human brain middle temporal gyrus reveals sex-specific and cell-type-specific gene expression regulation in Alzheimer’s disease

city: New Haven

first: Le

last: Zhang

state: CT

address: 300 George Street

department: Neurology

institute: Yale University

summary: Alzheimer’s disease (AD), the most common age-related neurodegenerative disease, is closely associated with and manifested by neuroinflammation, yet the alteration of immune landscape in AD is largely unknown, preventing a deeper mechanistic understanding of neuroinflammation in AD. Two thirds of AD patients are females, and women have a higher risk of developing AD. Women with AD have more extensive brain histological changes than men with AD, more severe cognitive symptoms, and more severe neurodegeneration, suggesting that the disease affects female and male brains differentially. Despite evident AD sex variance, mechanisms and pathways are still poorly understood. Thus, a focus on sex differences in AD is essential to move the field towards effective interventions and to develop sex-specific therapies. To understand the cellular heterogeneity and disease-associated cellular changes in human AD brain, we performed unbiased massively parallel single nucleus RNA sequencing with postmortem frozen human brain tissues of middle temporal gyrus, a brain cortical region strongly affected by AD. From 12 individuals with and without AD, we isolated brain nuclei by sucrose gradient ultracentrifugation, generated single nucleus libraries with 10x Chromium platform (10x Genomics), and sequenced on NovaSeq6000 S4 sequencer (Illumina). We integrated snRNA-seq data of human brains from these 12 individuals of both Alzheimer’s Disease (AD, Braak Stage V/VI, n = 6) and age-matched healthy controls (HC, Braak Stage I/II, n = 6) by single nucleus analysis using Seurat. After quality control filtering, we profiled and analyzed 64,845 single nucleus transcriptomes, clustered all the cells jointly across the 12 donors that include 6 females and 6 males, and identified and annotated the major cell types of the human brain by interrogating the expression patterns of known gene markers, including neurons, excitatory neurons, inhibitory neurons, astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells, endothelial cells, and pericytes.

first: Stephen

last: Strittmatter


title: Spatial transcriptome data of Longissimus dorsi muscle from 3 pigs

status: Public on May 17 2022

city: Chengdu

first: Bo

last: Zeng

state: Sichuan

address: 211 Huimin road, Wenjiang district

institute: Sichuan Agricultural University

summary: This study takes pig longissimus dorsi muscle as the object. Through spatial transcriptome research, we clarified the gene expression distribution of different types of muscle fibers in the tissue, and their corresponding marker genes were identified.

overall_design: Spatial transcriptomic study of the longissimus dorsi of Tibetan pigs and Berkshire pigs, including one sample of Tibetan and two replicates of Berkshire. Compare the gene expression of different muscle fibers types and between the two breeds.

first: Qianzi

last: Tang

first: Yu

last: Lin


title: C57BL/6J tMCAO brain scRNAseq data

status: Public on May 25 2022

city: Ulju-gun

first: Wonhyo

last: Lee

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

institute: UNIST

summary: Single Cell RNA sequencing data from C57BL/6J mouse brain hemisphere after 24hours and 48hours after tMCAO surgery.

overall_design: examination of Prdx1 effects on ischemia-reperfusion stroke in mus musculus with transient middle cerebral artery occlusion model

first: Sinai

last: Kim

first: Sung

last: Park

first: Goo

last: Oh


title: Gene expression profiling of filaggrin-insufficient keratinocytes exposed to inflammatory mediators and allergens

status: Public on May 20 2022

city: Gdańsk

first: Anna

last: Supernat

address: Dębinki 1

department: Division of Translational Oncology

country: Poland

institute: Medical University of Gdansk

summary: Loss-of-function mutations in the filaggrin gene are heavily associated with the incidence and severity of atopic dermatitis. Moreover, filaggrin insufficiency in epidermal keratinocytes can lead to persistent allergic inflammation and an associated immune response suggesting a role for this protein in regulation of immunity. Here, we investigate how filaggrin insufficiency affects the gene expression pattern in a filaggrin-insufficient (shFLG) keratinocyte cell line HaCaT in response to stimulation with various inflammatory mediators and allergens.

overall_design: Untreated shC and shFLG cells were used as controls for their corresponding conditions. Treatment with the following compounds was performed: histamine, amphiregulin, IFNy, IL-4/IL-13, cysteine, derp1/cysteine, derp2; concentrations for every compound were provided below in sample description. Biological triplicates of every condition were generated. A total of 48 samples were analyzed. The filaggrin gene (FLG) in the HaCaT cell line was silenced by shRNA delivered to the cells using lentiviral particles. Scrambled RNA was used for generation of control (shC) cells.

first: Eleni

last: Giannoulatou

first: Xinwen

last: Wang

first: Danuta

last: Gutowska-Owsiak

first: Graham

last: Ogg


title: Aberrant paracrine signalling underlies oncohistone-driven giant cell tumour of bone.

status: Public on Aug 05 2022

first: Adrienne

last: Flanagan


title: Dissecting the role of CBLB in human T cell activation and suppression

status: Public on Jul 19 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Cbl-b is a negative regulator of T cell activation and in murine models a lack of CBLB results in resistance of T effectors to Tregs, a feature of T cells in many autoimmune diseases. Here, we used trackable gene-editing approaches to knock out CBLB in primary human CD4+ T cells. We found that CBLB-KO CD4+ T cells were hyper-proliferative and produced excess amounts of IL-2 at baseline and upon TCR stimulation. CBLB-KO CD4+ T cells were resistant to Treg suppression in vitro, which was partially reversed by blockade of IL-2. RNAseq and puromycin incorporation assays demonstrate that CBLB-KO CD4+ T cells can overcome Treg suppression on the transcriptional and translational level resulting in the overproduction of cytokines to drive the proliferation and activation of Teffs. These findings also highlight a potential mechanism of Teff resistance in human autoimmune disease and the power of gene editing of primary T cells to explore disease mechanisms.

overall_design: 24 samples total. 4 donors, 2 treatments (CBLB-KO or AAVS1-KO), 3 stimulations (none, CD3CD28 beads, CD3CD28 beads + Treg exposure)

first: Jing

last: Song

first: Warren

last: Anderson

first: Kazushige

last: Obata-Ninomiya

first: Steven

last: Ziegler

first: Alex

last: Hu

first: David

last: Rawlings

first: Jane

last: Buckner


title: Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics [RNA-Seq]

status: Public on May 15 2022

city: Chapel Hill

first: Gang Greg

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

summary: WD repeat domain 5 (WDR5), a chromatin regulator associated with MLL complex and MYC oncoproteins, was shown to be critical for oncogenesis in human cancers and represents an attractive drug target. Inhibitors for targeting protein-protein interaction interfaces (PPIs) within WDR5 were developed; however, they inhibited only a part of WDR5-mediated functional interactions, exerting rather limited antitumor effects. We report a cereblon (CRBN)-based proteolysis targeting chimera (PROTAC) of WDR5, MS40, which is capable of selectively degrading cellular WDR5 and well-established imide:CRBN targets such as Ikaros (IKZF1).  MS40-induced WDR5 degradation caused disassociation of MLL complex off chromatin, resulting in a decrease of global H3K4me2. Transcriptomic profiling also revealed targets of both WDR5 and imide:CRBN to be repressed by MS40. In MLL-rearranged acute leukemias, which exhibit high IKZF1 expression and IKZF1 dependency, co-suppression of WDR5 and IKZF1/3 by MS40 is superior at suppressing tumor growth not only to WDR5 PPI inhibitors but also to a VHL-based WDR5 PROTAC, MS169, which selectively targets WDR5 only. Furthermore, MS40 suppressed growth of primary leukemia patient cells in vitro and patient-derived xenografts (PDX) in vivo. Collectively, we report the discovery of a dual WDR5 and Ikaros degrader as anti-cancer therapeutic.

overall_design: Examination of transcriptome profiles using the MV4;11 cells treated with either DMSO, MS40 (a WDR5 and Ikaros degrader), MS40N1 (an E3-“dead” analog of MS40) or pomalidomide, or cells transduced with a WDR5-targeting hairpin (sh#47) or vector (shEV).

first: Dongxu

last: Li

first: Greg


title: Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

status: Public on May 13 2022

city: Tampa

first: Suman

last: Gurung

state: FL

address: 560 Channelside Dr

department: Pathology and Cell Biology

institute: University of South Florida

summary: We applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hours post fertilization (hpf) stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes

overall_design: We crossed previously established Tg(kdrl:mCherry) and etv2ci32Gt; UAS:GFP lines. GFP and mCherry positive embryos were collected at 24 hpf. GFP+mCherry+ and GFP+mCherry- cell populations were isolated by FACS (fluorescent activated cell sorting) and subjected to single-cell RNA-seq analysis using Chromium Controller (10x Genomics) followed by the next-generation sequencing.

first: Saulius

last: Sumanas


title: Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types

status: Public on May 10 2022

city: Philadelphia

first: Matthew

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia


title: Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types [ATAC-seq]

summary: To investigate the potential role of COVID-19 severity associated GWAS signals affecting the cis-regulatory architecure of human immune cell types. We used high-resolution chromatin conformation capture and accessibility to identify potential effector genes

overall_design: We performed ATAC-seq, RNA-seq, and Promoter Focused Capture C on primary Monocytes, Naïve B and GCB cells

first: Kathleen

last: Sullivan

first: Neil

last: Romberg

first: Struan

middle: F

last: Grant

first: Andrew

last: Wells


title: The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis

status: Public on Apr 07 2022

city: Wuhan

first: Yuexia

last: Lv

state: Hubei

address: Hubei, Wuhan, Hongshan district, Luoyu Road, Huazhong University of Science and Technology

department: College of Life Science and Technology

summary: Pre-mRNA splicing is a precise regulated process, and is crucial for system development and homeostasis maintenance. Mutations in spliceosomal components have been found in various hematopoietic malignancies (HMs), and have been considered as oncogenic derivers of HMs. However, the role of spliceosomal components in normal and malignant hematopoiesis remain largely unknown. Pre-mRNA processing factor 31 (PRPF31) is a constitutive spliceosomal component, which mutations are associated with autosomal dominant retinitis pigmentosa. PRPF31 was found to be mutated in several HMs, but the function of PRPF31 in normal hematopoiesis has not been explored. In this study, we generated a prpf31 knockout zebrafish line, and discovered that prpf31 mutants exhibited severe defects in hematopoietic stem and progenitor cell (HSPC) expansion and its sequentially differentiated lineages. Immunofluorescence results showed that Prpf31 deficient HSPCs underwent malformed mitosis and M phase arrest during HSPC expansion. Transcriptome analysis and experimental validations revealed that Prpf31 deficiency extensively perturbed the alternative splicing of mitosis-related genes. Collectively, our findings elucidate a previously undescribed role for Prpf31 in HSPC expansion, through regulating the alternative splicing of mitosis-related genes.

overall_design: RNA-seq profiles of wild-type sibling and  prpf31-/- zebrafish embryos at 36 hours post fertilization for triplicates

first: Jingzhen

first: Mugen

last: Liu


title: Aberrant paracrine signalling underlies oncohistone-driven giant cell tumour of bone [ChIP-seq]

city: London

first: Adrienne

last: Flanagan

address: Huntley Street

institute: University College London

summary: The identification of oncohistones underscores the neoplasm-driving role of chromatin dysfunction. However, we have limited understanding of how these perturbations alter communication in the tumour microenvironment (TME) and the functional implications of this crosstalk. In this respect, clinical evidence shows that the maturation block of the H3F3A (H3.3G34W)-mutated osteoblastic stromal population in benign giant cell tumours (GCTs), a neoplasm characterised by a prominent mutation-free osteoclast component, is reversed on osteoclast depletion, suggesting aberrant interactions between these two cell populations. Here, we reveal a bidirectional paracrine mechanism at the root of oncohistone-driven neoplasia in this bone tumour. H3.3G34W fails to induce stromal cell proliferation but inhibits their maturation. Altered chromatin landscape of these cells leads to enhancer remodelling, including at SCUBE3, a Tgfbeta family member. Reduced SCUBE3 expression contributes to increased osteoclasts that secrete high levels of SEMA4D, which disproportionately blocks maturation of H3.3G34W-expressing cells. Together, our findings suggest that non-cell autonomous provision of a growth advantage to a cancer driver-bearing cell  represents a paradigm for a benign neoplasm.

overall_design: hFOB 1.19 osteoblastic cell line engineered to express H3.3WT, H3.3G34W or empty vector, profiled for H3K27ac and H3K36me3 binding using spike-in calibrated cross-linked ChIP-seq.

first: Lucia

last: Cottone


title: Real-time quantitative PCR analysis of gene expression in human colon cancer cells treated with LPS

status: Public on Apr 18 2022

first: Heping

last: Cao

summary: Relative mRNA levels of 55 genes were evaluated with the SYBR Green qPCR assays after LPS treatment for 8 h.

overall_design: Human colon cancer cells (COLO 225) were purchased from ATCC. The  cells in triplicate were treated with various concentrations of LPS for 8 h. RNA isolation and cDNA synthesis were performed as described previously. Relative mRNA levels were evaluated with the SYBR Green qPCR assays using Bio-Rad reagents. BCL2 mRNA was selected as the internal reference for qPCR analysis for this cell type. 1% DMSO treatment was the sample control. The 2-ΔCT and 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.


title: RNA sequencing data of germ cell tumor cell lines co-cultured with microenvironmental cells in 3D

status: Public on Apr 01 2022

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary: Single end 3' RNA sequencing of GFP-transduced germ cell tumor cell lines (TCam-2, 2102EP, JAR, GCT72) co-cultured in 3D with mCherry-transduced or deepred-stained microenvironmental cells (HUVEC, JURKAT, THP-1-M2, HVHF2)  for 72 h before cell sorting both populations using flow cytometry.


title: Regulation of human trophoblast gene expression by endogenous retroviruses

status: Public on Apr 15 2022

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute


title: Regulation of human trophoblast gene expression by endogenous retroviruses [CUT&RUN]

summary: The placenta is a fast-evolving organ that displays large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here were assessed the contribution of transposable elements to human trophoblast gene expression by acting as enhancers or promoters. Using epigenomic data from primary trophoblast and human stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential trophoblast expression. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as expression enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting trophoblast migration and secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.

overall_design: CUT&RUN for histone modifications and transcription factors in human trophoblast stem cells.

first: Jennifer

last: Frost

first: Samuele

last: Amante

first: Hiroaki

last: Okae

first: Eleri

last: Jones

first: Brogan

last: Ashley

first: Rohan

last: Lewis

first: Jane

last: Cleal

last: Caley

first: Takahiro

last: Arima

first: Tania

last: Maffucci


title: Functional heterogeneity of cancer-associated fibroblasts in pancreatic cancer

status: Public on Mar 19 2022

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Single-cell RNA-sequencing analyses were performed on unfractionated live cell mixtures or sorted fibroblasts from pancreatic tumors of KPC;YFP mice, so as to investigate the functional heterogeneity of cancer-associated fibroblasts in early-stage and late-stage tumors.

overall_design: Unfractionated live cell mixtures or sorted fibroblasts from pancreatic tumors of KPC;YFP mice were analyzed by 10x single-cell RNA-sequencing. Cancer-associated fibroblasts were extracted using the reverse sorting selection of CD45/CD31/YFP triple-negative cells. As an alternative route, aSMA-expressing cancer-associated fibroblasts were sorted by RFP expression from KPC;YFP;aSMA-RFP mice.

first: Raghu

last: Kalluri

first: Yang

last: Chen


title: Single-cell and spatial mapping identify cell types and signaling networks in the human ureter

status: Public on Mar 31 2022

first: Angela

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

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


title: Silver nitrate has a measurebale but minor impact on gene expression in Arabidopsis thaliana

status: Public on Mar 15 2022

city: Springfield

first: Laszlo

middle: G

last: Kovacs

state: Missouri

address: 901 S  National Avenue

department: Biology

institute: Missouri State University

summary:
Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to chronic exposure to silver nitrate at 4 μg/mL concentration.
Methods: mRNA was extracted from non-treated and silver nitrate-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were paired-end sequenced (100-nt read length) on an Illumina Nova Seq6000 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 20.0.4, Qiagen).
Results: Chronic exposure of A. thaliana plants to silver nitrate caused a change in the abundance of transcripts: AT2G01520 and AT4G12550, but no measureable impact on the rest of the transcriptome.
Conclusions: Exposure of A. thaliana to silver nitrate at 4 μg/mL has minor impact on the transcriptome.

overall_design: mRNA profile comparison between non-treated and silver nitrate-treated 14-day old Arabidopsis thaliana (Col-0) seedlings.

first: Margaret

last: White

first: Cody

middle: N

last: Pham


title: Me-RIP- Sequencing  Analysis of normal and senescent nucleus pulposus cells Transcriptomes

status: Public on Mar 23 2022

first: gaocai

last: li

state: HuBei

address: JIefang Avenve 1277, Jianghan District

department: Department of Orthopeadics

institute: wuhan union hospital

summary: N6-methyladenosine (m6A) is the most prevalent modification of eukaryotic cells st post-transcriptional level. The goals of this study are to compare the N6-methyladenosine modification of transcripts in normal and senescent nucleus pulposus cells using Me-RIP-seq

overall_design: nucleus pulposus cells N6-methyladenosine  profiles of three groups of normal human nucleus pulposus cells and three groups of senescent  human nucleus pulposus cells isolated and cultured from human nucleus pulpopsus tissues.

first: Gaocai

last: Li

first: Cao

last: Yang

first: Kun

last: Wang


title: scRNA sequencing analysis for human ureters and patient derived ureter oragnoid

summary: Tissue engineering offers a promising treatment strategy for ureteral strictures. Successful ureter engineering is necessitated by detailed understanding of the tissue architecture, cellular heterogeneity, and signaling pathways underlying regeneration. We define and spatially map cell populations within the human ureter by using a combinatorial approach: single-cell RNA sequencing, 10X Visium spatial transciptomics, and immunofluorescence. The stromal and urothelial cell populations are analyzed in detail, and we infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Specifically, we analyze and experimentally validate the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells support organoid generation in vitro, and accurately predict the differentiation trajectory of basal stem cells, to terminally differentiated umbrella cells, in vivo. Our results highlight essential processes involved in adult ureter tissue homeostasis, and provide a toolkit for guiding ureter tissue engineering.

overall_design: 10 normal human ureters each were subjected to RNA sequencing at single cell resolution on Novaseq using 10X Gemonics library preparation platform. Data was processed using Cellranger 4.0.0 and anayzed using Seurat v3.2.1 to characterize various cell types and understand finer details of the regenrative pathways in the ureter urothelium. This was further explored by analyzing single cell RNA sequencing data from human ureter derived organoid (generated in the same manner as the 10 ureter samples). Freshly processed and thawed tissue sample from the same human subject was used as control to further understand the urothelial regenerative pathways.

first: Byron

last: Lee

first: Emily

middle: E

last: Fink

first: Surbhi

last: Sona


title: single cell RNA-sequencing of matched lesional and nonlesional skin from vitiligo patients

city: Baltimore

first: Jessica

last: Shiu

state: MD

address: 655 W Baltimore St

department: Pediatrics

institute: University of Maryland School of Medicine

summary: We performed scRNA-seq analyses on patient matched lesional and nonlesional skin from viitiligo patients using the 10x genomics platform to examine different cell populations and keratinocyte states that may contribute to vitiligo disease persistence.

overall_design: Suction blisters were generated from patient matched lesional and nonlesional skin from 7 vitiligo patients, unfortunately 1 set (Patient B) did not have sufficient cells and was excluded from analysis

last: Flesher

first: Anand

last: Ganesan

first: Lihua

last: Zhang


title: Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells [MPRA]

status: Public on Mar 02 2022

first: Stephanie

last: Osmond

summary: Determining causal variants for autoimmune disease is an enormous challenge - 90% of autoimmune disease-associated variants are non-coding and there are often 10s-100s are in tight linkage disequilibrium with the causal variant(s), making identification of the true causal variants difficult. Using massively parallel reporter assays in a T cell line, we prioritized variants that enriched highly for likely causal variants according to statistical fine-mapping. We followed up on one of the prioritized variants, rs72928038 in the BACH2 locus, which had a high effect size, finding that it regulates Bach2 expression in a human T cell line. We created mice containing a small deletion over this non-coding variant, and have tested mutant vs. WT antigen-specific T cells for their responses during acute viral infection. In the context of rs72928038-deleted mice (termed Bach218del), we found an increase in effector T cell differentiation, which highlights a potential role for rs72928038 in modulating effector T cell differentiation in the context of autoimmune disease.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: This project contains MPRA data of 18,312 variants identified from 578 GWAS index variants (representing 531 distinct GWAS loci) associated with autoimmune disease in which T-cells are known to play a role. Additonally, it includes and 91 positive enhancer controls and 506 negative controls. The dataset includes 5 samples of plasmid DNA barcode sequencing and 3 samples of mRNA barcode sequencing read replicates.

first: Kousuke

last: Mouri

first: Michael

last: Guo

first: Carl

last: de Boer

first: Michelle

last: Lissner

first: Ingrid

middle: A

last: Harten

first: Gregory

last: Newby

first: Hannah

last: DeBerg

first: Winona

last: Platt

first: Matteo

last: Gentili

first: David

middle: R

last: Liu

first: Dan

last: Campbell

first: Nir

last: Hacohen

first: Ryan

last: Tewhey

first: John

last: Ray


title: Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells [BaseEditing]

overall_design: Jurkat T cells were base edited with a guide RNA targeting rs72928038 or a safe harbor site and PrimeFlow RNA Label Probe was used to track BACH2 transcript expression. Base edited BACH2 PrimeFlowed cells were either not sorted (denoted by NS for sort bin) or sorted into bins according to BACH2 RNA expression.

middle: J


title: Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics [ChIP-Seq]

first: Gang Greg

last: Wang

overall_design: Examination of the genome-wide binding of H3K4me2 and MLL1 in MV4;11 cells. By using the spike-in fly chromatin as a normalization control, we accessed the changes of H3K4me2 and MLL1 binding in cells treated with MS40, compared to DMSO.

first: Dongxu

last: Li

first: Greg


title: Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types [Capture-C]

first: Matthew

last: Pahl

summary: To investigate the potential role of COVID-19 severity associated GWAS hits affecting the cis-regulatory architecure of human immune cell types. We used high-resolution chromatin conformation capture and accessibility to identify potential effector genes

first: Kathleen

last: Sullivan

first: Neil

last: Romberg

first: Struan

last: Grant

first: Andrew

middle: D

last: Wells


title: Implicating effector genes at COVID-19 GWAS loci using promoter-focused Capture-C in disease-relevant immune cell types [RNA-seq]

overall_design: We performed ATAC-seq, RNA-seq, and Promoter Focused Capture C on Naïve B and GCB cells


title: Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells [scRNA-seq]

first: Stephanie

last: Osmond

overall_design: This project contains 10X single cell RNA-seq and feature barcode data from WT and Bach2-18del CD8 T-cells from five mice pooled across two samples. Pool 1 contains WT cells from mouse 1 (M1), M2, and M3 and Bach2-18del cells from M4 and M5. Pool2 contains Bach2-18del cells from M1, M2, and M3 and WT cells from M4 and M5.

first: Kousuke

last: Mouri

first: Michael

last: Guo

first: Carl

last: de Boer

first: Michelle

last: Lissner

first: Ingrid

last: Harten

first: Gregory


title: Diversification of multipotential postmitotic mouse retinal  Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

status: Public on Feb 01 2022

city: Berkeley

first: Karthik

last: Shekhar

state: CA

address: 101D Gilman Hall

institute: University of California, Berkeley

summary: The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly-born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC type identity is not specified at mitotic exit, but acquired by gradual, asynchronous fate restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity has been determined. Optimal transport inference identifies groups of RGC precursors with largely non-overlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.

overall_design: We profiled and analyzed RGCs at 5 developing stages: E13 and E14 (during the period of peak RGC genesis), E16 (by which time RGCs axons are reaching target retinorecipient areas), P0 (as dendrite elaboration begins), and P5 (shortly after RGCs begin to receive synapses).

first: Irene

last: Whitney

first: Salwan

last: Butrus

first: Yi-Rong

last: Peng

first: Joshua

last: Sanes


title: BRBseq of Naïve T cells from Bach2_18del and WT controls

summary: Genome-wide association studies have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variant(s) within each locus are mostly unknown. Here, we perform high-throughput allele-specific reporter assays to prioritize disease-associated variants for five autoimmune diseases. By examining variants that both promote allele-specific reporter expression and are located in accessible chromatin, we identify 60 putatively causal variants that enrich for statistically fine-mapped variants by up to 57.8-fold. We introduced the risk allele of a prioritized variant (rs72928038) into a human T cell line and deleted the orthologous sequence in mice, both resulting in reduced BACH2 expression. Naïve CD8 T cells from mice containing the deletion had reduced expression of genes that suppress activation and maintain stemness, and, upon acute viral infection, displayed greater propensity to become effector T cells. Our results represent an example of an effective approach for prioritizing variants and studying their physiologically relevant effects.

overall_design: Naïve CD4 and CD8 T cells were sorted from spleens by using 150 days old three homozygous of Bach2<18del> (The Jackson Laboratory #35028) and three wild type littermates.

first: Ryan

last: Tewhey

first: John

last: Ray


title: MAdCAM-1 Costimulates T Cells Through Integrin Alpha4/Beta7 to Cause Gene Expression Events Resembling Costimulation Through CD28

status: Public on Feb 11 2022

summary: After revealing no effect of vedolizumab upon T cell density in colon biopsies, we demonstrate that MAdCAM-1 delivers a costimulatory signal comparable to that of CD28 in T cells both functionally and at the gene expression level, with only subtle differences identified in the latter concerning cytokines involved in pyogenic inflammation.

overall_design: 102 T-cell samples were profiled using RNA-seq. PBMC from three donors were stimulated with each of four conditions ((1) OKT3 (anti-CD3) + human IgG (2) OKT3 + MAdCAM-1 (3) OKT3 + MAdCAM-1+ vedolizumab (4) OKT3 + anti-CD28) and samples were collected at five timepoints( 0, 0.5, 2, 6, and 24) following stimulation. From each donor, condition, and timepoint, 1000 CD4 and 1000 CD8 T-cells were sorted and sequenced.

first: Hannah

last: DeBerg

last: Konecny

first: Donna

last: Shows

first: James

last: Lord


title: Single-cell RNA-Sequencing data of microfluidic neural tube-like structures

status: Public on Jan 28 2022

city: Ann Arbor

first: Xufeng

last: Xue

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering

institute: University of Michigan

summary: We analyzed scRNA-seq data in human pluripotent stem cells derived neural tube models. This in vitro system recapitulates some key aspects of neural patterning in the entire neural tube, including both brain and SC regions, along both rostral-caudal and dorsal-ventral axes

overall_design: scRNA-seq was performed on dissociated cells from microfluidic neural tube-like structures at three timepoints (day 4, day 9, day 21)

first: Jianping

last: Fu


title: Regulation of human trophoblast gene expression by endogenous retroviruses [CUT&TAG]

first: Miguel

last: Branco

overall_design: CUT&Tag for histone modifications and transcription factors in mouse and human trophoblast stem cells, and in vitro differentiated extravilous trophoblast.

first: Jennifer

last: Frost

first: Samuele

last: Amante

first: Hiroaki

last: Okae

first: Eleri

last: Jones

first: Brogan

last: Ashley

first: Rohan

last: Lewis

first: Jane

last: Cleal

first: Matthew

last: Caley

first: Takahiro

last: Arima

first: Tania

last: Maffucci


title: Stimulating microglial glucose metabolism and phagocytosis for post-stroke remyelination and cognitive function recovery

city: Pittsburgh

first: Shanshan

last: Song

address: 3501 Fifth Ave

institute: University of Pittsburgh

summary: New research shows that disease-associated microglia (DAM) in neurodegenerative brains present features of elevated phagocytosis, lysosomal functions, and lipid metabolism, which benefit brain repair. The underlying mechanisms remain poorly understood. Intracellular pHi is important for regulating aerobic glycolysis in microglia, where Na/H exchanger (NHE1) is a key pH regulator by extruding H+ in exchange of Na+ influx. We report here that post-stroke Cx3cr1-CreER+/-;Nhe1flox/flox (Nhe1 cKO) brains displayed stimulation of microglial transcriptomes of rate-limiting enzyme genes for glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation (OXPHOS). The other upregulated genes included the DAM hallmark genes (Apoe, Trem2, Spp1) as well as genes for phagocytosis and LXR/RXR pathway activation. The cKO microglia exhibited increased OXPHOS capacity and higher phagocytic activity, which led to enhanced synaptic pruning, oligodendrogenesis, and remyelination. This study reveals that genetic blockade of microglial NHE1 stimulated glucose immunometabolism to support phagocytosis function for tissue remodeling and post-stroke cognitive function recovery.

overall_design: Examination of effect of deletion of Nhe1 in microglia on post-stroke recovery

first: Dandan

last: Sun


title: Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells

status: Public on Feb 28 2022

first: Stephanie

last: Osmond

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1 [RNA-Seq]

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: About 70% of human genes carry multiple polyadenylation signals, and mRNA 3’end formation is dynamically regulated under different physiological conditions. Global 3’end shortening through alternative polyadenylation (APA) correlates with enhanced cellular proliferation, and 3’ untranslated region (UTR) shortening is a widespread phenomenon in tumour cells, where it appears to enhance tumorigenic properties. However, the mechanisms responsible for this dynamic APA regulation remain incompletely understood. Here we show that transcription factor Sp1 binds directly to RNA in vivo and is a common repressor of distal poly (A) site usage. RNA-sequencing (RNA-seq) analysis identified 2344 genes (36% of total mapped mRNA transcripts) with lengthened 3’UTRs upon Sp1 depletion. Sp1 preferentially binds in vivo within the 3’UTRs of many of these lengthened transcripts and inhibits cleavage at distal sites by interacting physically with subunits of the core cleavage and polyadenylation (CPA) machinery. The 3’UTR lengths of Sp1 target genes in breast cancer patient RNA-seq data correlate with Sp1 expression levels, implicating Sp1-mediated APA regulation in modulating tumorigenic properties. Taken together, our findings reveal an important mechanism for dynamic APA regulation by unraveling a novel function of Sp1.

overall_design: RNA-Seq of HEK293 cells upon RNAi-mediated knockdown of SP1, or control non-targeting knockdown, in two replicates.

first: Jingwen

first: Syed

last: Nabeel-Shah

first: Shuye

last: Pu

first: Hyunmin

last: Lee

first: Zuyao

last: Ni

first: Edyta

last: Marcon

first: Guoqing

last: Zhong

first: Debashish

last: Ray

first: Kevin

last: Ha

first: Xinghua

last: Guo

first: Zhaolei

last: Zhang

first: Timothy

last: Hughes

first: Benjamin

last: Blencowe

first: Jack

last: Greenblatt


title: RNA-seq analysis of Arabidopsis root with MBZ treatment

status: Public on Apr 29 2022

city: La Jolla

first: Ling

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: we reported the identification of a small molecule, Mebendazole (MBZ) that modulates GSA in Arabidopsis thaliana roots. To identify pathways immediately response to MBZ, we performed an mRNA-seq using roots of 14-days-old Arabidopsis grown on DMSO plates treated with DMSO or 10 µM MBZ for 4 hours. Differenetial expressed genes between DMSO and MBZ_4h treatments were analyzed. It has 8 samples in total, with 4 replicates for each treatment.

overall_design: 14 d old seedlings of Col-0 on DMSO plates were transferred to DMSO plates with 10 µM mebendazole or DMSO. After treatment for 4 h, root tissues were collected for RNA extraction and sequencing. Every treatment have 4 replicates.

first: Wolfgang

last: Busch

first: Wenrong

last: He


title: Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1

first: Ulrich


title: Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1 [CLIP-seq]

overall_design: iCLIP-seq of GFP-tagged and endogenous proteins in HEK293 cells

first: Jingwen

last: Song

first: Syed


title: Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1 [ChIP-Seq]

last: Braunschweig

overall_design: CHIP-seq of SP1 endogenous protein in HEK293 cells, in two replicates

first: Shuye

first: Hyunmin


title: Translation Control in CD4 T Cell Activation enforced by T-regulatory cells

status: Public on Jan 20 2022

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Increased protein synthesis is a hallmark of CD4 effector T cell (Teff) activation. Regulatory T cells (Tregs) suppress the activation, proliferation, and subsequent effector functions of Teff cells.  Several mechanisms have been proposed for Treg-mediated suppression, including release of suppressive cytokines and expression of inhibitory receptors.  However, molecular mechanisms that enforce suppression on Teff cell function are unclear.  Control of CD4 effector T cell activation has largely been defined at the transcriptional level, which does not reflect changes in post-transcriptional control. We Tregs suppress CD4 Teff activation through regulation of global protein synthesis prior to cell division. Using polysome profiling, we analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teff cells. We found that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated Teff cells, and that Tregs their translation without affecting their transcription.  This translational inhibition is controlled by Treg-mediated regulation of Torc1 signaling.  These data show that peripheral tolerance is enforced by Tregs through mRNA translational control in Teff cells.

overall_design: 75 samples total. 9 mice; 5 RiboTag mice (per mouse: Ribo IP and Input, 3 stimulations), 4 C57/B6 mice (per mouse: Polysomal, Subpolysomal, Input. 4 stimulations with some missing)

first: Lomon

last: So

first: Ram

last: Savan

first: Kazushige

last: Ninomiya

first: Steven

last: Ziegler

first: Alex

last: Hu


title: Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)

status: Public on Jan 11 2022

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Analysis of CITE-seq data , Nuclei RNA-seq data and single cell RNA-seq data on CD45+ and CD45- cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar), from healthy and steatotic human livers, from hamster liver, pig liver, chicken liver, monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers, NAFLD mouse livers, healthy human livers and steatotic human livers.

overall_design:
Single cell RNA Seq = Liver CD45+ and CD45- cells derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar). Liver CD45+ and CD45- cells derived from healthy and obese humans.
10 Visium Spatial Seq = mouse StSt liver, mouse StSt capsule, mouse NAFLD liver,  human non-steatotic liver, human steatotic liver.

first: Martin

last: Guilliams

first: Johnny

last: Bonnardel

first: Birthe

last: Haest

first: Bart

last: Vanderborght

first: Camille

last: Wagner

first: Anneleen

last: Remmerie

first: Anna

last: Bujko

first: Tinne

last: Thoné

first: Robin

last: Browaeys

first: Federico

last: De Ponti

first: Bavo

last: Vanneste

first: Christian

last: Zwicker

first: Freya

last: Svedberg

first: Tineke

last: Vanhalewyn

first: Amanda

last: Gonçalves

first: Saskia

last: Lippens

first: Bert

last: Devriendt

first: Eric

last: Cox

first: Giuliano

last: Ferrero

first: Valerie

last: Wittamer

first: Andy

last: Willaert

first: Suzanne

last: Kaptein

first: Johan

last: Neyts

first: Kai

last: Dallmeier

first: Peter

last: Geldhof

first: Stijn

last: Casaert

last: Deplancke

last: ten Dijke

first: Anne

last: Hoorens

first: Aude

last: Vanlander

first: Frederik

last: Berrevoet

first: Yves

last: Van Nieuwenhove

first: Yvan

last: Saeys

first: Wouter

last: Saelens

first: Hans

last: Van Vlierberghe

first: Lindsey

last: Devisscher

first: Charlotte

middle: L

last: Scott


title: Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (single cells)

first: Liesbet

last: Martens

sample_organism:
Danio rerio
Gallus gallus
Macaca mulatta
Homo sapiens
Sus scrofa
Mesocricetus auratus
Mus musculus

overall_design:
Single cell RNA Seq = Liver CD45+ and CD45- cells derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar). Liver CD45+ and CD45- cells derived from healthy and obese humans.
10,Visium,Spatial,Seq,=,mouse,StSt,liver,,mouse,StSt,capsule,,mouse,NAFLD,liver,,,human,non-steatotic,liver,,human,steatotic,liver

first: Martin

last: Guilliams

first: Johnny

last: Bonnardel

first: Birthe

last: Haest

first: Bart

last: Vanderborght

first: Camille

last: Wagner

first: Anneleen

last: Remmerie

first: Anna

last: Bujko

first: Tinne

last: Thoné

first: Robin

last: Browaeys

first: Federico

last: De Ponti

first: Bavo

last: Vanneste

first: Christian

last: Zwicker

first: Freya

last: Svedberg

first: Tineke

last: Vanhalewyn

first: Amanda

last: Gonçalves

first: Saskia

last: Lippens

first: Bert

last: Devriendt

first: Eric

last: Cox

first: Giuliano

last: Ferrero

last: Wittamer

last: Willaert


title: Single-cell RNA sequencing reveals the temporal diversity and dynamics of cardiac immunity after myocardial infarction

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

summary:
Background: The onset, progression, and outcomes of myocardial infarction (MI), a serious issue worldwide, are regulated by inflammatory responses. Numerous studies have demonstrated the complexity and importance of post-infarction immunity. Nonetheless, little is known about dynamic changes in cell type and function during disease progression.
Methods: Single-cell RNA sequencing (scRNA-seq) was used to map the Cd45+ immune cell composition at different time points (0, 3, 7 and 14 days) after MI within a mouse left anterior descending coronary artery (LAD) ligation model. A time course-analysis was performed to characterize dynamic changes in cell populations. Multiparameter flow cytometry, immunohistochemistry, and immunofluorescence were performed using the same mouse model.
Results: Major immune cell populations, distinct subsets, and dynamic changes were identified. Macrophages (Mø)/monocytes were most abundant, peaking at 3 days after infarction. Mø-5 and Mø-6 were the predominant infiltrated subsets at this time point, with strong expression of inflammatory factors. Further analysis demonstrated that suppressing these sets attenuated pathological MI progression by preventing subsequent leukocyte extravasation and adverse remodeling. We also detected abundant apoptotic neutrophils and a profibrotic macrophage subset on days 7 and 14 respectively.
Conclusions: Our results provide  a basis for developing cell type- and time-specific interventions in MI.

overall_design: 3 experimental condtions, 3 time points

first: Kaiyu

last: Jin

first: Shan

last: Gao

first: Penghui


title: The transcriptomic signature of physiological trade-offs caused by larval overcrowding in Drosophila melanogaster

status: Public on Jan 08 2022

city: Rennes

first: Herve

last: Colinet

address: UMR CNRS 6553 EcoBio

institute: University of Rennes

summary: This study examined the transcriptomic response of Drosophila melanogaster larvae to crowding conditions. The phenotypic and transcriptomic changes from low larval density (5 eggs/ml) to medium density (60 eggs/ml) were minor, yielding somewhat reduced adult fitness and only 24 differentially expressed genes (DEGs). In contrast, high density (300 eggs/ml) caused extensive detrimental effects on adult fitness and yielded 2107 DEGs. Among these, upregulated gene sets were enriched in sugar, steroid and amino acid metabolism as well as DNA replication pathways, whereas downregulated gene sets were enriched in ABC transporters, Taurine, Toll/Imd signalling and P450 xenobiotics metabolism pathways.

overall_design: mRNA from larval pools (10 larvae per pool); three larval densities (low: 5 eggs/ml; medium: 60 eggs/ml; high: 300 eggs/ml); three replicates per density

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