title: Pro-inflammatory cytokine stimulation of human cortical spheroids containing neuroectoderm-derived and mesoderm-derived cell types

status: Public on May 02 2022

city: Nijmegen

first: Kim

middle: de

last: Kleijn

address: Geert Grooteplein Zuid 26-28

country: Netherlands

institute: Radboud University

summary: Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)functioning. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated exploration of CNS (disease) mechanisms. In this study, we developed a five-months culture protocol that reproducibly generates H9 embryonic stem cell-derived human cortical spheroids (hCSs) comprising not only neuroectoderm-derived neural progenitor populations, mature excitatory and inhibitory neurons, astrocytes and oligodendrocyte (precursor) cells, but also mesoderm-derived microglia and endothelial cell populations. We then set out to explore the effects of stimulating our hCSs for three time periods with the cytokines TNFα and IL-1β. We use transcriptome-wide RNA-sequencing (RNA-seq) analysis to show that the major process induced by TNFα as well as by IL-1β is neuroinflammation. Central in this process are endothelial cells, microglia and astrocytes, and activation of the NFκB and STAT pathways. In addition to this equiva-lent impact of TNFα and IL-1β, we find that each of the two cytokines has specific and stimulation-time-dependent effects on hCS gene expression, and that IL-1β exhibits a faster self-inhibitory feedback response to dampen neuroinflammation than TNFα. Thus, our protocol provides an inducible 3D human brain cell model containing a wide variety of innately developing neuroectoderm- as well as mesoderm-derived cell types, furnishing a versatile platform for comprehensive examination of intercellular CNS communication and neurological disease mechanisms.

overall_design: We analyzed the pooled total RNA of 4 spheroids (0h, control condition for the TNFα- or IL-1β-stimulation conditions), pooled total RNA of 5 spheroids (4h TNFα stimulation), pooled total RNA of 5 spheroids (12h TNFα stimulation), pooled total RNA of 5 spheroids (36h TNFα stimulation), pooled total RNA of 5 spheroids (4h IL-1β stimulation), pooled total RNA of 5 spheroids (12h IL-1β), pooled total RNA of 5 spheroids (36h IL-1β stimulation). Furthermore, we analyzed pooled total RNA of 4 spheroids (0h_2, control condition for the LPS+TNFα+IL-1β stimulation conditions) and pooled total RNA of 5 spheroids (24h LPS- + 24h TNFα+IL-1β stimulation).

last: De Kleijn

first: Gerard

last: Martens

first: Kirsten

last: Straasheijm

first: Wieteke

last: Zuure


title: Machine learning accelerates the dissection of mitostasis as a cross-species central biological hub for leaf senescence

status: Public on May 03 2022

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: Leaf senescence is a tightly controlled and complex developmental process that shares many similarities across species, yet our understanding of the underlying conserved molecular mechanisms is still lacking. Here, we observed functional conservation of leaf senescence underlying pathways in A. thaliana, O. sativa, and S. lycopersicum. From machine learning-based integration of data from nearly 10 000 samples to obtain a universal regulatory network of leaf senescence, it was found that mitostasis is the cross-species central biological hub. We measure and compare changes in the transcriptome and metabolome of A. thaliana, O. sativa, and S. lycopersicum leaves under mitostress/natural senescence. In data from different species, mitostasis-related transcription factors binding site enrichment and amino acids expression changes converge on putative senescence modulators. Our study provides a cross-species, multi-omics perspective for understanding the leaf senescence conserved mechanisms.

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum
Oryza sativa Japonica Group

overall_design: Comparative gene expression profiling analysis of RNA-seq data of A. thaliana, O. sativa, and S. lycopersicum leaves when 10 μ g / mg doxycycline was applied to cultivated soil.

first: Xu

last: Wang


title: Effect of mutated dhgd-1(tm6671) on C. elegans metabolism

status: Public on Apr 29 2022

city: Worcester

first: Olga

last: Ponomarova

state: MA

address: 386 Plantation Street

country: USA

institute: UMass Chan Medical School

summary: To identify metabolic processes that are affected by dhgd-1 mutation and interact with vitamin B12

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans day 1 adults. Two strains were cultured (wild type and dhgd-1(tm6671)) on a diet of E. coli OP50 with and without supplementation of 64 nM vitamin B12 in five biological replicates.

first: Xuhang

last: Li

first: Hefei

last: Zhang

first: Marian

middle: A

last: Walhout


title: The landscape of melanoma progression and immune surveillance at single cell resolution

status: Public on May 01 2022

city: Boston,

first: Ajit Johnson

last: Nirmal

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

summary: To build a pre-cancer atlas for melanoma that reveals early events in disease initiation and immune response, we performed RNA sequencing of 222 histologically distinct micro-regions (~5-20 cells per region) extracted from 3 formalin-fixed paraffin-embedded tissue sections collected from a melanoma patient. These sections capture multiple phases of disease progression from melanoma in situ to metastatic invasive melanoma and areas of effective immune surveillance. Micro-region transcript data is complemented by sub-cellular resolution imaging using tissue-based cyclic immunofluorescence and will be released via the Human Tumor Atlas data portal.

overall_design: mRNA from 40μm regions of interest were extracted from 3 FFPE melanoma tissue sections (F8, F9, F12) containing multiple histological sites (melanoma in situ, invasive melanoma, invasive melanoma boundary, exophytic melanoma, inflammatory regression and brisk TIL region). The micro-regions were sequenced and their gene expression profiles were analyzed.

first: Ajit

middle: J

first: Zoltan

last: Maliga

first: Peter

middle: K

last: Sorger


title: Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells

status: Public on Apr 26 2022

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (scRNA-Seq)

summary: T cell exhaustion is a major impediment to anti-tumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here we show that the biology of tumor-associated macrophages (TAM) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAM reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique long-lasting antigen-specific synaptic interactions that fail to activate T cells, but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor.

overall_design: Spatial transcriptomics of immune cells in the TME of a B78ChOVA melanoma using ZipSeq

first: Kelly

last: Kersten

first: Kenneth

middle: H

last: Hu

first: Alexis

last: Combes

first: Bushra

last: Samad

first: Tory

last: Harwin

first: Arja

last: Ray

first: En

last: Cai

first: Kyle

last: Marchuk

first: Jordan

last: Artichoker

first: Tristan

last: Courau

first: Quanming

last: Shi

first: Julia

last: Belk

first: Asuman

middle: T

last: Satpathy

first: Matthew

middle: F

last: Krummel


title: Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (RNA-Seq)

overall_design: Bulk RNAseq on naïve, effector and exhausted (after day 4 and day 14) OT-I T cells isolated from mouse B78ChOVA melanomas.


title: CTCF deficiency in CD8 homeostatic proliferation [RNA-seq]

status: Public on Apr 25 2022

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

summary: An intricate interplay among Tcf1/Lef1 and CTCF that orchestrates genomic architecture to coordinately promote CD8+ T cell homeostatic proliferation

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP,  wild-type, Tcf1/Lef1-double floxed, or Ctcf-floxed mice, and enriched for naive CD8+ T cells by depleting non-T lineage cells, CD4+ and CD44 high cells. The enirched cells were labeled with CTV and transferred into Rag1 KO recipients. 72 hrs later, CTV+TCRbeta+GFP+CD8+ T cells were sorted from the recipient spleens and total RNA extracted.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng


title: Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (ATAC-Seq)

first: Arjun

last: Rao

overall_design: ATAC RNAseq on naïve and exhausted (at day 14) OT-I T cells isolated from mouse B78ChOVA melanomas.

first: Kelly

last: Kersten


title: Tcf1 and Lef1 cooperate with CTCF and Stat5 to sustain CD8+ T cell homeostasis [ChIP-Seq]

summary: An intricate interplay among Tcf1/Lef1, CTCF and Stat5 that orchestrates genomic architecture to coordinately promote CD8+ T cell homeostatic proliferation

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells. The live cells wer used for CTCF ChIP-seq.


title: Tcf1-CTCF cooperativity shapes genomic architecture  to promote CD8+ T cell homeostasis [Hi-C]

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells. The sorted cells were stimulated with IL-7 and IL-15 for 72 hrs, followed by crosslinking, enzyme digestion, proximity ligation, and then HiC sequencing.


title: Tcf1-CTCF cooperativity shapes genomic architecture  to promote CD8+ T cell homeostasis [CTCF Cut&Run]

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells. The sorted cells were stimulated with IL-7 and IL-15 for 0 or 72 hrs, and the live cells wer used for CTCF Cut&Run.


title: Tcf1-CTCF cooperativity shapes genomic architecture  to promote CD8+ T cell homeostasis [DNase-Seq]

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells. The sorted cells were stimulated with IL-7 and IL-15 for 72 hrs, followed by treatment with DNase I and DNase-sequencing.


title: Gene expression profiling upon treatment with NTX-301

status: Public on Apr 20 2022

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

country: South Korea

institute: KRICT

summary: A novel hypomethylating agent NTX-301 is a promising therapeutic agent for AML patients. To examine its mechanisms of action, we produced gene expression data upon treatment with NTX-301 or decitabine (DAC) in AML cell lines.

overall_design: HL-60 and MOLM-13 leukimia cells were cultured using the RPMI1640 medium. Cells were plated on 6-well plates at the day before drug treatment, and DMSO, NTX-301, and DAC were treated during 48h. After extracting Total RNA and assessing RNA purity and integrity, sequencing library was created using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and were applied to the Illumina RNA-seq platform according to the manufacturer's protocol.


title: Tcf1-CTCF cooperativity shapes genomic architecture  to promote CD8+ T cell homeostasis


title: Tcf1-CTCF cooperativity shapes genomic architecture  to promote CD8+ T cell homeostasis [RNA-Seq]

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells. The sorted cells were stimulated with IL-7 and IL-15 for 72 hrs, and total RNA extracted.


title: Gene expression profiling and DNA methylation profiling

type: Methylation profiling by genome tiling array


title: Gene expression profiling upon treatment with NTX-301 in MV4-11

summary:
A novel hypomethylating agent NTX-301 is a promising therapeutic agent for AML patients.
To examine its mechanisms of action, we produced gene expression data upon treatment with NTX-301 or decitabine (DAC) in MV4-11 cell line.

overall_design: MV4-11 leukimia cells were cultured using the RPMI1640 medium. Cells were plated on 6-well plates at the day before drug treatment, and DMSO, NTX-301 (60nM), and DAC (60nM) were treated during 48, 96h. After extracting Total RNA and assessing RNA purity and integrity by ND-1000 Spectrophotometer, the RNA samples were applied to the Affymetrix Whole transcript Expression microarray according to the manufacturer's protocol (Affymetrix GeneChip Human 2.0 ST Array).


title: Vitamin D cytoprotection function in human liver cell lipotoxicity and its transcriptomic fingerprint: a comparison of natural and synthetic formulations.

status: Public on Apr 14 2022

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

country: Italy

institute: Bios-Therapy, Physiological Systems For Health S.p.A

summary:
Vitamin D, in addition to calcium/phosphate metabolism and bone homeostasis regulation, has antiproliferative, anti-inflammatory and antifibrotic properties. These protective actions may have an impact in the progression of chronic liver disease including NAFLD (Non-alcoholic fatty liver disease).
Vitamin D deficiency is associated with metabolic syndrome components, such as insulin resistance and dyslipidemia. NAFLD is often considered as the hepatic manifestation of metabolic syndrome, and a growing body of research suggests a relationship between vitamin D deficiency and NAFLD, with low levels of 25(OH)D associated with hepatic inflammation, and the severity and progression of NAFLD.

overall_design: We compared transcriptional response of OA/PA (oleic acid/palmitic acid)-treated HepaRG for 48 hours with transcriptional response of HepaRG pre-treated with different form of Vitamin D for 24 hrs and subsequent 48 hours of treatment with OA/PA.

first: Angela

last: Guerrini

first: Tiziana

last: Frammartino


title: Efferocytosis drives myeloid NLRP3 dependent inflammasome signaling and gasdermin D independent secretion of IL-1β to promote tumor growth

status: Public on Apr 13 2022

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

institute: Vanderbilt University Medical Center

summary: Caspase-1 signaling in myeloid suppressor cells can promote T-cell independent cancer progression, but the regulation of inflammasome signaling within the highly heterogeneous myeloid cells in the tumor milieu remains elusive. To resolve this complexity, scRNA-seq of human head & neck carcinoma identified distinct inflammasome complex genes within specific clusters of tumor-infiltrating myeloid cells. Among these myeloid cells, NLRP3 sensor and downstream effector IL-1β transcripts were enriched in multiple monocytic and macrophage subtypes in the TME. In vivo, we showed that NLRP3, and not AIM2, phenocopied the caspase-1/IL-1β dependent tumor progression. Paradoxically, we found that myeloid-intrinsic caspase-1 signaling within the TME increased myeloid survival without significant intratumoral trafficking as would be predicted from their canonical pyroptotic function. Mechanistically, this myeloid NLRP3/IL-1β signaling axis promotion of tumor growth was found to be gasdermin D independent. When we probed for the tumor intrinsic factors that regulated NLRP3/IL-1β signaling, we found that mononuclear phagocyte-mediated efferocytosis of dying tumor cells in the TME directly activated NLRP3 dependent inflammasome signaling to drive IL-1β secretion and to promote tumor growth. Dynamic RNA velocity analysis of the single cell transcriptomic dataset showed a strong directional flow from efferocytosis gene-sethigh macrophages to an inflammasome gene-sethigh macrophage population.  Cumulatively, we provide a novel inflammasome signaling axis between tumor apoptosis and myeloid cells that characterizes chronic inflammation induced malignancy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse bone marrow-derived macrophages (BMDM) incubated with Annexin V+/PI- Cal27 cells and BMDM that had engulfed AC (PKH26+).

first: Lang

last: Cara

first: Roy

last: Sohini

first: Wang

last: Yu

first: Graves

last: Diana

first: Xu

last: Yaomin

first: Serazani

last: Henrique

first: Korrer

last: Michael

first: Kim

last: Young


title: Orthogonal Gene Engineering Enables Novel Synthetic States of Powerful Tumor-rejecting CD8+ T Cells Escaping Canonical Exhaustion

status: Public on Apr 12 2022

city: Lausanne

first: Jesus

last: Corria-Osorio

state: Vaud

address: Chemin des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: Ludwig Institute for Cancer Research. Lausanne Branch. UNIL

summary: To date, no immunotherapy approaches have managed to fully overcome T-cell exhaustion, which remains a mandatory fate for chronically activated effector cells and a major therapeutic challenge.  Understanding how to reprogram CD8+ TILs away from exhausted effector states remains an elusive goal. Our work provides for the first-time evidence that orthogonal gene-engineering of T cells to secrete an IL-2-variant binding the IL-2R and the alarmin IL-33 reprogrammed adoptively transferred T cells to acquire a novel, synthetic state, which deviated from canonical exhaustion and displayed superior effector functions. These cells successfully overcame homeostatic barriers in the host, and led – in the absence of lymphodepletion or exogenous cytokine support – to high levels of engraftment and tumor regression. Our work unlocks the novel opportunity of rationally engineering synthetic CD8+ T-cell states endowed with the ability to avoid exhaustion and control advanced solid tumors.

overall_design:
CD45+ bulk TILs were independently sorted at  at days 5 (T1), 12 (T2) and 26 (T3) post cell transfer
Groups: Non-Treated tumor-bearing mice (G5); Mice received ACT using Untransduced OT1 T cells (G1);Mice received ACT using PD1d/IL2V-secreting OT1 (G2); Mice received ACT using PD1d/33-secreting OT1 (G3); Mice received ACT using PD1d/2V/33-secreting OT1 (G4)

first: Santiago

last: Carmona

first: Massimo

last: Andreatta

first: George

last: Coukos


title: The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells

status: Public on Apr 06 2022

city: Cambridge

first: Paul

middle: D

last: Smith

address: AstraZeneca CRUK Cambridge Institute, Robinson Way

country: United Kingdom

institute: AstraZeneca


title: Molecular characterization of cell types in the squid Loligo vulgaris

status: Public on Apr 07 2022

city: Fribourg

first: Jules

last: Duruz

address: Chemin du musée 10

department: Biology

institute: University of Fribourg

summary: Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.

overall_design: Whole heads of Loligo vulgaris pre-hatchlings were dissociated and sequenced.


title: The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells [RNA-seq]

summary: Third-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs), including osimertinib, an irreversible EGFR-TKI, are important treatments for non-small cell lung cancer with EGFR-TKI sensitizing or EGFR T790M resistance mutations. Whilst patients treated with osimertinib show clinical benefit, disease progression and drug resistance are common.  Emergence of de novo acquired resistance from a drug tolerant persister (DTP) cell population is one mechanism proposed to explain progression on osimertinib and other targeted cancer therapies. Here we profiled osimertinib DTPs using RNA-seq, ChIP-seq, and ATAC-seq to characterize the features of these cells and performed drug screens to identify therapeutic opportunities.

overall_design: The NSCLC EGFR mutant cell lines (PC9, NCI-H1975, HCC827, and HCC2935) were treated with 500 nM osimertinib for 21 days (osimertinib DTPs). Cells were either harvested immediately or washed 2x with PBS and then replaced with drug-free media for a further 24 hrs. (short washout), or for a longer time-point (long washout) until exponential cell proliferation resumed (PC9: 7 days; NCI-H1975: 3 days; HCC827: 4 days; HCC2935: 10 days) and then harvested. In parallel, parental cell lines were grown in drug-free media for 21 days then treated with 500 nM osimertinib for 24 hrs. (osimertinib acute) or vehicle DMSO control for 24 hrs. (DMSO control).   Experiment was done using biological triplicates. There are 60 total RNA-seq samples.

first: Steven

middle: W

last: Criscione

first: Matthew

last: Martin

first: Derek

middle: B

last: Oien

first: Ricardo

last: Miragaia

first: Aparna

last: Gorthi

first: Jingwen

last: Zhang

first: Huawei

last: Chen

first: Daniel

last: Karl

first: Kerrin

last: Mendler

first: Aleksandra

last: Markovets

first: Sladjana

last: Gagrica

first: Oona

last: Delpuech

first: Jonathan

middle: R

last: Dry

first: Lisa

last: Drew

first: Yi

last: Yao


title: The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells [ATAC-seq]

first: Paul

last: Smith

overall_design: The NSCLC EGFR mutant cell lines (PC9, NCI-H1975, HCC827, and HCC2935) were treated with 500 nM of osimertinib for 24 days (osimertinib DTPs) or treated with 500 nM of osimertinib for 21 days followed by 150 nM of AZD5153 for 3 days (osimertinib DTP AZD5153 sequential combination). In parallel, parental cell lines were grown in drug-free media for 21 days then treated with vehicle DMSO control for 3 days (DMSO control). As an additional control, PC9 and H1975 cell lines were grown in drug-free media for 21 days then treated with 150 nM of AZD5153 for 3 days (AZD5153 monotherapy). Experiment was done using biological triplicates.  There are 42 total ATAC-seq samples.


title: The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells [ChIP-seq]

overall_design: H1975 EGFR mutant NSCLC cells were treated with 500 nM of osimertinib for 24 days (osimertinib DTPs) or treated with 500 nM of osimertinib for 21 days followed by 150 nM of AZD5153 for 3 days (osimertinib DTP AZD5153 sequential combination). In parallel, H1975 cells were grown in drug-free media for 21 days then treated with DMSO control for 3 days (DMSO control). The experiment was done using biological triplicates.  Including the Input control there were 10 ChIP-seq samples.


title: Coordinated control of neuronal differentiation and wiring by sustained transcription factors

status: Public on Apr 01 2022

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

summary: The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.

overall_design: 2 scRNA-Seq libraries of FACSed neurons expressing R71F05-Gal4 were generated from P50 pupal Drosophila optic lobes using 10X Genomics Chromium™ Single Cell 3’ v3.1 protocol.


title: The CpG Island-Binding Protein SAMD1 Contributes to an Unfavorable Gene Signature in HepG2 Hepatocellular Carcinoma Cells

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

summary: The unmethylated CpG island-binding protein SAMD1 is upregulated in many human cancer types, but its cancer-related role has not yet been investigated. Here, we used the hepatocellular carcinoma cell line HepG2 as a cancer model and investigated the cellular and transcriptional roles of SAMD1 using ChIP-Seq and RNA-Seq. SAMD1 targets several thousand gene promoters, where it acts predominantly as a transcriptional repressor. HepG2 cells with SAMD1 deletion showed slightly reduced proliferation, but strongly impaired clonogenicity. This phenotype was accompanied by the decreased expression of pro-proliferative genes, including MYC target genes. Consistently, we observed a decrease in the active H3K4me2 histone mark at most promoters, irrespective of SAMD1 binding. Conversely, we noticed an increase in interferon response pathways and a gain of H3K4me2 at a subset of enhancers that were enriched for IFN-stimulated response elements (ISREs). We identified key transcription factor genes, such as IRF1, STAT2, and FOSL2, that were directly repressed by SAMD1. Moreover, SAMD1 deletion also led to the derepression of the PI3K-inhibitor PIK3IP1, contributing to diminished mTOR signaling and ribosome biogenesis pathways. Our work suggests that SAMD1 is involved in establishing a pro-proliferative setting in hepatocellular carcinoma cells. Inhibiting SAMD1’s function in liver cancer cells may therefore lead to a more favorable gene signature.

overall_design: ChIP-Seq of SAMD1  in HepG2 Control and SAMD1 knockout cells. RNA-Seq of Control and SAMD1 knockout HepG2 cells (3 replicates).

first: Clara

last: Simon

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: Effective Menin inhibitor-based combinations against AML with MLL rearrangement or NPM1 mutation (NPM1c)

status: Public on Mar 12 2022

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Treatment with Menin inhibitor (MI) disrupts interaction between Menin and MLL1 or MLL1-fusion protein (FP), inhibits HOXA9/MEIS1, induces differentiation and loss of survival of AML harboring MLL1 re-arrangement (r) and FP, or expressing mutant (mt)-NPM1. Following MI treatment, although clinical responses are common, majority of patients with AML with MLLr or mt-NPM1 succumb to their disease. Pre-clinical studies presented here demonstrate that genetic knockout or degradation of Menin, or treatment with the MI SNDX-50469 reduces MLL1/MLL1-FP targets, associated with MI-induced differentiation and loss of viability. MI treatment also attenuates BCL2 and CDK6 levels. Co-treatment with SNDX-50469 and BCL2 inhibitor (venetoclax), or CDK6 inhibitor (abemaciclib) induces synergistic lethality in cell lines and patient-derived AML cells harboring MLL1r or mtNPM1. Combined therapy with SNDX-5613 and venetoclax exerts superior in vivo efficacy in cell line or PD AML cell xenografts harboring MLL1r or mt-NPM1. Synergy with the MI-based combinations is preserved against MLLr AML cells expressing FLT3 mutation, also CRISPR edited to introduce mtTP53. These findings highlight the promise of clinically testing these MI-based combinations against AML harboring MLL1r or mtNPM1.

overall_design: 4 samples; Input controls are provided for each condition.

first: Warren

last: Fiskus

first: Kapil

middle: N

last: Bhalla


title: Nuclear m6 A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3' processing machinery

status: Public on Mar 11 2022

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

summary: N6-methyladenosine (m6 A) and alternative polyadenylation (APA) are important regulators of gene expression in eukaryotes. Recently, it was found that m6 A is closely related to APA. However, the molecular mechanism of this new APA regulation remains elusive. Here, we show that YTHDC1, a nuclear m6 A reader, can suppress proximal APA sites and produce longer 3' UTR transcripts by binding to their upstream m6 A sites. YTHDC1 can directly interact with the 3' end processing factor FIP1L1 and interfere with its ability to recruit CPSF4. Binding to the m6 A sites can promote liquid-liquid phase separation of YTHDC1 and FIP1L1, which may play an important role in their interaction and APA regulation. Collectively, YTHDC1 as an m6 A "reader" links m6 A modification with pre-mRNA 3' end processing, providing a new mechanism for APA regulation.

overall_design: We knockdowned YTHDC1 in HEK293T and MCF-7cell with siRNA and applied a alternative polyadenylation high sequencing (IVT-SAPAS) method to detect dynamic change of 3‘UTR length.

first: Liutao

first: Yonggui

last: Fu


title: Transcriptional response to single amino acid starvation in HeLa cells

status: Public on Mar 26 2022

city: Epalinges

first: Manuele

last: Rebsamen

address: Chemin des Boveresses 155 - CP 51

department: Department of Biochemistry

institute: University of Lausanne

summary: We analyzed gene expression profiles in response to starvation of single amino acids in HeLa cells.

overall_design: 34 samples; 2 biological replicates for 17 amino acid starvation conditions.

first: Stefania

last: Scorzoni

first: Vitaly

last: Sedlyarov

first: Giulio

last: Superti-Furga


title: Genome wide association study between segregate wild-type and homozygous mutant

status: Public on Mar 06 2022

city: Jena

first: Yu-Heng

last: Tseng

state: Thuringia

address: Dornburgerstr. 159

department: Plant Physiology

institute: Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller University Jena

summary: Purpose: We want to identify the perception components of cellooligomer based on cytoplasmic calcium elevation in Arabidopsis root.

overall_design: Aequorin-expressing wild-type Arabidopsis seedlings in pMAQ background were mutagenized with EMS. Seedlings from the F2 generation was screened based on cytoplasmic calcium elevation in root tissue upon cellobiose treatment. The non-responsive EMS mutant was back-crossed to the Aequorin wild-type. The subsquent F2 generation was separated into two groups: 1. segregated wild-type and heterogygotes (responsive) 2. homozygoutes (non-responsive). DNA from 50 seedlings per group was extracted and sequenced on Illumina sequencer by Novogene Co. UK (PE150). SIMPLE (v. 1.8.1) was used to compare SNPs found in the two groups. Candidate genes were selected for further confirmation.


title: Single-cell sequencing quantitative analysis of skin tissues of wild-type and Chrna5-/- mice treated with imiquimod

status: Public on Feb 28 2022

city: Jinan

first: Dianhao

last: Guo

address: 6699 Qingdao Road

department: Institute of Basic Medicine

institute: shandong first medical university

summary:
Purpose: To understand the molecular processes and cell subsets involved in an increase in the psoriatic inflammatory response in Chrna5 signaling compared with WT mice, we performed single-cell sequencing with dorsal skin tissues after IMQ and vaseline treatment.
Methods: Skin mRNA profiles of wile-type (WT) and cholinergic receptor nicotinic alpha 5 subunit knockout (Chrna5-/-)mice were generated by deep sequencing. The samples of KO and WT mice after IMQ and vaseline treatment were processed in terms of alignment, barcode assignment, and UMI counting with Cell Ranger, version 3.0.2 (https://github.com/10XGenomics/cellranger) count pipeline.
Results: The cell clustering analysis , the heat map analysis , the cell subpopulations of keratinocytes analysis, the gene enrichment analysis and signal pathway analysis were all carried out . The results of these studies indicated that Chrna5 knockout has a significant effect on the proliferation of keratinocytes after IMQ treatment. Further gene analysis and signal pathway analysis showed that Chrna5 knockout down-regulated the JAK/STAT signal pathway, which is a key signal pathway for the occurrence and development of psoriasis.
Conclusions: These results revealed the potential role of Chrna5 in the occurrence and development of psoriasis, and provided a basis for it as a potential drug target.

overall_design: Skin mRNA profiles of WT and Chrna5-/- mice treated with imiquimod

first: Jing

last: Wang

first: Xiangying

last: Li

first: Ping

last: Zhang

first: Tao

last: Yang

last: Liu

first: Li

last: Qin

first: Guanghui

last: Ma

first: Xiaobing

first: Huiping

last: Fan

first: Shuhong

last: Huang

first: Ningning

last: Dang


title: Single-cell transcriptome characteristics of the recurred psoriasis

status: Public on Mar 19 2022

city: Seodaemun-gu, Seoul

first: Won Seok

last: Roh

address: 50-1, Yonsei-ro

institute: severance hospital

summary: To understand immunological differences between recurred and non-recurred psoriatic lesion after cease of treatment with ixekizumab

overall_design: We obtained 5-mm biopsied skin samples from recurred site and non-recurred site. Skin tissue was processed for single cell RNA sequencing.

first: Tae-Gyun

last: KIm

first: Min-Geol

last: Lee

first: Jongwook

last: Oh

first: Won

middle: S


title: Next Generation Sequencing Facilitates Quantitative Analysis of the transcriptome of different developmental stages and tissues in Ostrinia furnacalis

status: Public on Mar 04 2022

city: Hangzhou

first: Lei

address: Shiqiao Road

institute: Zhejiang Academy of Agricultural Science

summary:
The goals of this study are to obtain  the transcriptome profiling (RNA-seq) of different developmental stages and tissues in Ostrinia furnacalis.
Methods: O. furnacalis embryos were collected less than 12 h post oviposition. 1st, 3rd and 5th instar of the Asian corn borer, which represents the newly hatched larvae, the middle stage of larvae and the mature larvae, was harvested for subsequent experiments. Pupae and adults were grouped into females and males, then female and male samples were mixed at the ratio of 1:1. The 3rd instar larvae were anesthetized on an ice plate for tissue extraction. The midgut, fat body and silk gland were isolated. All these samples were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: We obtained the transcriptome profiling (RNA-seq) of different developmental stages and tissues in Ostrinia furnacalis
Conclusions: Our study representsa detailed analysis of different developmental stages and tissues in Ostrinia furnacalis

overall_design: mRNA profiles of  different developmental stages and tissues of Ostrinia furnacalis were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000

first: Junfeng

last: Xu


title: Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty

status: Public on Jan 12 2022

first: Oscar Junhong

last: Luo

state: Guangdong Province

address: 601 Huangpu Ave West

institute: Jinan University

summary: Frailty is an intermediate status of human ageing process, associated with decompensated homeostasis and death. The immune phenotype of frailty and its underlying cellular and molecular processes remain poorly understood. Here we profiled 114,467 immune cells from cord blood, young adults, healthy and frail elderly using single-cell RNA and TCR V(D)J sequencing. An age-dependent accumulation of cell heterogeneity and transcriptome variability in defined immune cell types was observed. With the specific expression of gene sets, characteristic transcription factors were identified in given immune cell types of certain age group. Trajectory analysis revealed cells from non-frail and frail elderly often fall into distinct trajectories, despite similar chronological age. Numerous TCR clonotypes were shared among T cell subtypes in aged and frail samples, indicating differential pluripotency and resilience capability of aged T cells. Finally, a frailty-specific monocyte subset was identified with exclusively high expression of lncRNAs NEAT1 and MALAT1. Our results discover human frailty-specific immune cell characteristics based on the comprehensive dimensions in immune landscape of ageing and frailty.

overall_design: Three cord blood samples, PBMC samples from 3 healthy young, 6 healthy old and 5 frail donors were used for single-cell RNA, TCR and cell surface protein (CCR7, CD45RA, CD4 and CD8) antibody barcoded sequencing to create a single-cell transcriptome and TCR atlas from newborns to frailty.

first: Oscar


title: Candida auris infection of human whole blood

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: To mimic the initial phases of systemic Candida infections with dissemination via the bloodstream, we used an ex vivo whole blood infection model. Dual TP of C. auris in blood gave insights into fungal adaptations and survival mechanisms as well as the host response to the infection.

sample_organism:
Homo sapiens
Candidozyma auris

platform_organism:
Homo sapiens
Candidozyma auris

overall_design: The design was in acccordance with a previous study of C. albicans, C. glabrata, C. tropicalis and C. parapsilosis in the ex vivo whole blood model by Kämmer et al. 2020.

first: Stefanie

last: Allert

first: Thomas

last: Wolf

first: Peter

last: Großmann


title: RNA seq of eWAT from tumor induced cachectic mice and normal mice

status: Public on Jan 18 2022

city: hefei

first: dong

last: wang

address: shushan district

summary: Cancer cachexia is a deadly wasting syndrome that accompanies various diseases, including approximately 50% of cancers. To assess the pathological transformations that occur in the local wasting tissue microenvironment during lung cancer cachexia, we assessed changes in wasting tissues at the transcriptomic level. KEGG analysis of the up-regulated DEGs enrichment for pathways including fatty acid degradation, inflammation, and ferroptosis.

overall_design: eWAT mRNA profiles of LLC induced cachectic mice and control mice

first: Dong

last: Wang

first: Xiaohu

last: Zheng


title: Drosophila photoreceptor nuclear RNA-seq timecourse [AgingATACseq]

status: Public on Dec 31 2021

city: West Lafayette

first: Vikki

middle: M

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

summary: We report the chromatin accessibility landscape of Drosophila photoreceptor neurons obtained using a tissue-specific approach at different time points after eclosion

overall_design: Photoreceptor neuron-specific chromatin accessibility profiling at day 20, 30, 40, 50 and 60 after eclosion

first: Juan

middle: P

last: Jauregui-Lozano


title: Transcriptomic clustering of critically-ill COVID-19 patients

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Drosophila photoreceptor nuclear RNA-seq timecourse

summary: We report the nuclear transcriptome of Drosophila photoreceptor neurons obtained using a tissue-specific approach at different time points after eclosion

overall_design: Photoreceptor neuron-specific nuclear transcriptome profiling at day 20, 30, day 40, day 50 and day 60 post eclosion


title: RNA-seq of Acinetobacter baumannii ATCC 17978: deleted effects of dna adenine methylase

status: Public on Jan 31 2022

city: Seongbuk-gu

first: Mingyeong

last: Kang

state: Seoul

address: Anam-ro 145

institute: Korea university

summary: Comparison for gene expression of Acinetobacter  baumannii ATCC 17978 by deleted effects of dna adenine methylase

overall_design: 1 control (WT) and 1 sample (dam KO strain)


title: Fertilization triggers a transcription program mouse & human one-cell embryos

status: Public on Dec 22 2021

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Following fertilization, the new embryo reprograms parental genomes to begin transcription (embryonic genome activation, EGA). EGA is indispensable for development, but its dynamics, profile or when it initiates in vertebrates are unknown. We here characterize the onset of transcription in mouse one-cell embryos. Precise embryo staging eliminated noise to reveal a cascading program of de novo transcription initiating within six hours of fertilization. This immediate EGA (iEGA) utilized canonical promoters, produced spliced transcripts, was distinctive and predominantly driven by the maternal genome. Expression represented pathways not only associated with embryo development but with cancer. In human one-cell embryos, hundreds of genes were up-regulated, days earlier than thought, with conservation to mouse iEGA. These findings provide a functional basis for epigenetic analysis in early-stage embryos and illuminate networks governing totipotency and other cell-fate transitions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA-Seq of MII oocytes and early mouse single-cell embryos
RNA-Seq of early human single-cell embryos

middle: Y

first: Maki

last: Asami

first: Matthew

last: VerMilyea

last: Braun

first: Marcella

last: Ma

first: Kara

last: Rainbow

first: Giles

last: Yeo

first: Anthony

middle: C

last: Perry


title: Landscape of human spinal cord cell type diversity at midgestation

status: Public on Dec 30 2021

city: Palo Alto

first: Jimena

last: Andersen

address: 318 Campus Drive, Clark Center, 2nd floor/W200

institute: Stanford University

summary: In this study we performed single cell and single nucleus RNA sequencing of PCW17 and PCW18 human spinal cord

overall_design:
We profiled a total of 4 samples. Two PCW17 samples and two PCW18 samples were collected, with one sample per timepoint processed as single cells and one sample processed as single nuclei. In addition, some cells were immunopanned for Th1y and some nuclei were sorted for NeuN.
*** Raw data not provided due to patient privacy concerns ***

first: Sergiu

last: Pasca

first: Nicholas

last: Thom


title: Nuclear RNA-seq of Drosophila Top3beta-deficient photoreceptor neurons

first: Hana

last: Hall

address: 175 S University St, Biochemistry Builiding, room 320

summary: We report the nuclear transcriptome of Drosophila Top3beta-deficient photoreceptor neurons obtained using a tissue-specific approach to purify nuclei and express an siRNA against Top3beta or mCherry for negative control

overall_design: Photoreceptor neuron-specific nuclar transcriptome profiling at day 30


title: Transcriptomes of B cells in the context of adenoviral TGF-β1- or bleomycin-induced lung fibrosis in mice

status: Public on Dec 29 2021

city: Hannover

first: David

middle: S.

last: DeLuca

address: Carl-Neuberg-Str 1

department: Biomedical Research in End-stage and Obstructive Lung Disease Hannover

institute: Hannover Medical School

summary: Idiopathic pulmonary fibrosis (IPF) is an irreversible diffuse parenchymal lung disease of poorly defined etiology. Patients with IPF frequently demonstrate distinctive lymphoplasmacellular infiltrations within remodeled lung tissue, the relevance of which in lung fibrogenesis is still understudied. Histopathological examination of explant lung tissue of patients with IPF revealed accentuated lymphoplasmacellular accumulates in close vicinity to or even infiltrating remodeled lung tissue. Similarly, we found significant accumulations of B cells interfused with T cells within remodeled lung tissue in two murine models of adenoviral TGF-β1 or bleomycin (BLM)-induced lung fibrosis. Such B cell accumulates coincided with significantly increased lung collagen deposition, lung histopathology and worsened lung function in WT mice. Importantly however, B cell deficient µMT KO mice responded similarly with lung tissue remodeling and worsened lung function upon either AdTGF-β1 or BLM treatment as did WT mice. Comparative transcriptomic profiling of sorted B cells collected from lungs of AdTGF-β1 and BLM exposed WT mice identified a large set of commonly regulated genes, however with significant enrichment observed for gene ontology terms (GO terms) apparently not related to lung fibrogenesis. Collectively, although we observed B cell accumulates in lungs of IPF patients as well as two experimental models of lung fibrosis, comparative profiling of characteristic features of lung fibrosis between WT and B cell-deficient mice did not support a major involvement of B cells in lung fibrogenesis in mice.

overall_design: RNA samples of mice exposed to AdTGF-β1/AdCL or Bleomycin/saline for 14 or 21 days.

first: Marie

last: Moog

first: Christopher

last: Hinze

first: Franziska

last: Aschenbrenner

first: Lars

last: Knudsen

first: Danny

last: Jonigk

first: Lavinia

last: Neubert

first: Tobias

last: Welte

first: Jack

last: Gauldie

first: Martin

last: Kolb

first: Ulrich

middle: A

last: Maus


title: RNA-seq analysis comparing primary NKTL sample over tonsil control

status: Public on Dec 17 2021

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: RNA-seq analysis was performed in primary NKTL (Natural killer T-cell lymphoma) samples and healthy tonsil samples to analyze gene expression changes in lymphoma sample.

overall_design: Total RNA was extracted from frozen NKTL primary tumor samples and matched normal tonsils by using miRNeasy Mini Kit (Qiagen) as as per the manufacturer recommendation.

first: Jianbiao

last: Zhou

first: Tze

middle: K

first: Jing

middle: Q

last: Lim

first: Choon

last: Ong

first: Chng

last: Joo


title: Natural killer/T-cell lymphoma (NKTL) enhancer and expression analysis for their pathogenicity


title: Deciphering the spatial-temporal molecular features of human developing hypothalamus at single-cell level

status: Public on Dec 07 2021

city: Beijing

first: Xin

address: 15 Datun Road

department: State key laboratory of Brain and Cognitive Science

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: We revealed the molecular and cellular composition along spatial-temporal development of human hypothalamus by single-cell transcriptomic sequencing. The hypothalamus was manually micro-dissected from serial coronal 600-800μm thick slice using a vibratome. We excluded poor quality cells after the gene expression matrix was generated by Cell Ranger with Scanpy (V1.4.4) package. We identified 11 major transcriptomic types including neuroepithelium (NE), neural progenitors (NP), neurons, astrocytes, oligodendrocyte precursor cells (OPC), oligodendrocyte (OL), ependymocytes (Ependy), microglial cells, endothelial cells (Endoth), mural cells as well as vascular and leptomeningeal cells (VLMCs) that were characterzied with their respective classic markers. We uncovered molecular diversity of NP subtypes and constructed their developmental trajectory. We also identified various neuronal subpopulations mapped into distinct spatial location. Overall, our data provided cellular and molecular landscape of human hypothalamic development.

overall_design: Identification of temporospatial molecular and cellular features of human developing hypothalamus ranging from 7-20 gestational weeks (GW)

first: X

last: Wang


title: Disentangling glial diversity in peripheral nerves at single-nuclei resolution

status: Public on Dec 06 2021

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

department: Genetics

institute: Washington University School of Medicine


title: H3K27ac ChIP-seq for multiple primary samples, normal tonsil samples and cell lines

summary: ChIP-seq analysis was performed in primary NKTL (Natural killer T-cell lymphoma) samples, normal tonsil samples and 2 cell lines to analyze acetylation of histone H3K27ac.

overall_design: Three primary NKTL tumor samples and their matched normal tonsils (controls) and NKYS and HANK1 cell lines were crosslinked with formaldehyde for 10 min. DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against histone H3 lysine 27 acetylation (H3K27Ac: Abcam, ab4729).


title: Disentangling glial diversity in peripheral nerves at single-nuclei resolution [bulk and RiboTag RNA-seq]

summary: The peripheral nerve contains diverse cell types that support its proper function and maintenance. We analyzed multiple peripheral nerves using single-nuclei RNA-sequencing (snRNA-seq), which allowed us to circumvent difficulties encountered in analyzing cells with complex morphologies via conventional single cell methods. The resultant mouse peripheral nerve cell atlas highlights a diversity of cell types, including multiple subtypes of SCs, immune cells, and stromal cells. We identified a distinct myelinating-SC subtype that expresses Cldn14, Adamtsl1, and Pmp2 and preferentially ensheathes motor axons. The number of these motor-associated, Pmp2+ SCs is reduced in both ALS SOD1G93A mouse model and human ALS nerve samples. Our findings reveal the diversity of SCs and other cell types in peripheral nerve and serve as a reference for future studies of nerve biology and disease.

overall_design: Comparison between Mpz-RiboTag enriched RNA-seq and bulk RNA-seq data for both sciatic and vagus nerves

first: Aldrin

last: Yim

first: Amy

last: Strickland

first: John

last: Bermingham


title: Disentangling glial diversity in peripheral nerves at single-nuclei resolution [single-cell and single-nuclei RNA-seq]

overall_design: Profiling the transcriptional signatures of individual cells in four peripheral nerve types through single-nuclei RNA-seq.


title: Pre-neoplastic stromal cells drive BRCA1-mediated breast tumorigenesis

status: Public on Nov 17 2021

city: IRVINE

first: Kevin

last: Nee

address: 839 Health Science Road, Sprague Hall 114

department: Biological Chemistry

institute: University of California, Irvine

summary: Women with germline mtuation in BRCA1 have increased risk for developing hereditary breast cancer. The role of the epitheilum-assocaited niche during BRCA1-driven tumor intiation remains unclear. Here, we show that the pre-malignant stromal niche promotes epithelial prolifeation and BRCA1-driven cancer intiation in trans. Using single-cell RNA seq analysis of human pre-neoplastic BRCA1 and control breast tissue, we show that stromal cells provide numerous pro-proliferative paracrine signals inducing epithelial proliferation.

overall_design: Library generation for four 10x genomics v1 chemistry, and twenty-four 10x genomics v2 chemistry was performed following the Chromim Singel Cell 3' Reagents Kits v2 User Guide: CFG00052 Rev B. Libraries were sequenced on the Illumina NovaSeq6000 platform targeting approximately 50,000 reads per cell.

first: Quy

last: Nguyen

first: Kai

last: Kessenbrock


title: STAT5 regulation of tumor associated macrophage function in murine models of breast cancer

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: In breast cancer, interactions between tumor cells and surrounding stromal cells, such as macrophages, are critical for tumor growth, progression, and therapeutic response. Recent studies have highlighted the complex nature and heterogeneous populations of macrophages associated with both tumor promoting and tumor inhibiting phenotypes. Identifying the specific signaling pathways that regulate macrophage function within the tumor microenvironment will lead to new approaches that suppress tumor promoting functions while enhancing their anti-tumor functions. We demonstrated STAT5 (signal transducer and activator of transcription 5) is robustly activated in tumor-associated macrophages and that granulocyte-macrophage colony stimulating factor (GM-CSF) is a major cytokine stimulating this pathway. To define impacts of GM-CSF/STAT5 on macrophage function, we used in vitro and in vivo models to demonstrate that STAT5 has a significant role in stimulating expression profiles in macrophages consistent with an anti-tumor, adaptive immune response. Our results also indicate that loss of STAT5 in the myeloid lineage leads to enhanced metastatic disease. These findings reveal that disrupted STAT5 signaling in tumor-associated macrophages supports tumor progression, which suggests STAT5 may regulate anti-tumor macrophage function. Understanding how to enhance the anti-tumor capacity of macrophages will be vital in developing effective treatment strategies for patients with aggressive breast cancer.

overall_design: Bone marrow mRNA profiles of 6-week old STAT5 wild type and STAT5 knock-out mice treated with with DMEM, 20 ng/mL rmGM-CSF (Fisher Scientific), or 4T1 tumor cell conditioned media

first: Kathryn

middle: L

first: Christine

middle: H

last: O'Connor

first: Emily

last: Jesser


title: Spec-seq sequencing data for CTCF [2021 series]

status: Public on Nov 06 2021

first: Zheng

last: Zuo

address: Stanford

institute: Stanford university

summary: This series is an updated dataset consisting of the Spec-seq and Methyl-Spec-seq samples for human CTCF with a bigger sequencing libraries and different epigenetic modifications. Each sample has replicate to gurantee the reproducibility for each measurement.

overall_design: Spec-seq is an intemediate throughput method to quantify the relative binding energy of some TF to thousands of DNA sequences with resolution down to 0.2kT. In this work, we utilized Spec-seq to study the recognition property ot CTCF, the genomic insulator, to its underlying core and upstream sequences, with different epigienetic modifications. Each sample has replicate to check for reproducibility. The state of epigenetic modification within CTCF's core binding site can be infered from the upstream barcoding positions. The EMSA separation work is performed in cold room, 12% Tris-glycine gel, 200V, 50mins.


title: Gene expression profiling of peripheral blood from uncontrolled and controlled asthma

status: Public on Nov 09 2021

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: We analyzed the transcriptomes of children with controlled and uncontrolled asthma in Taiwanese Consortium of Childhood Asthma Study (TCCAS). Hierarchical clustering, differentially expressed gene (DEG), weighted gene co-expression network analysis (WGCNA) and pathway enrichment methods were performed, to investigate important genes between two groups.

overall_design: Analysis of gene expression obtained from human whole blood comparing uncontrolled and controlled asthma.

first: C

last: Tsai

first: Y


title: The SEQC2 epigenomics quality control (EpiQC) study

status: Public on Oct 26 2021

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

type: Methylation profiling by high throughput sequencing

summary: We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications.

overall_design:
Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC). All libraries were aligned to the human reference genome (build GRCh38) using bwa-meth followed by MethylDackel for DNA methylation estimation.

Please note that the methylation array data is available in the GSE230132 records.

first: Foox

last: Jonathan

first: Nordlund

last: Jessica

first: Lalancette

last: Claudia

first: Gong

last: Ting

first: Lacey

last: Michelle

first: Mason

last: Christopher

first: Deng

last: Youping


title: Engineering Extracellular Vesicles by Three-dimensional Dynamic Culture of Human Mesenchymal Stem Cells

status: Public on Oct 15 2021

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

summary: In current study, hMSCs were grown as 3D aggregates under wave motion to promote EV secretion (3D EVs). mRNA sequencing reveals global transcriptome alterations (e.g., upregulated Wnt, TNF, and Hippo signaling and downregulated cellular senescence) for 3D aggregates.

overall_design: MSC cell were cultured under either 2D, 3D or hypoxia conditions, and harvested for mRNA-seq.

first: Li

last: Sun

first: Xuegang

last: Yuan


title: Whole transcriptome profiling of H37Rv- and H37Rv△1759c-infected macrophages.

status: Public on Sep 30 2021

city: ChangSha

first: Yongwei

last: Zhu

state: Hunan

address: No.87,  Xiangya Street

institute: CSU Xiangya hospital

summary: To explore the regulatory network of noncoding RNAs after M.tb infection and the role of Rv1759c in the infection process, we collected samples of H37Rv- and H37Rv△1759c-infected macrophages and explored the full transcriptome expression profile. We constructed DE-lncRNA/DE-circRNA-DE-miRNA-DE-mRNA regulatory networks during H37Rv and H37Rv△1759c infection. In addition, we first discovered the close relationship between Rv1759c and chemokines during M.tb infection by comparing the transcription profiles of H37Rv and H37Rv△1759c and bioinformatics analysis. Here, our study comprehensively characterizes the ncRNA and mRNA profiles in macrophages infected with H37Rv and H37Rv△1759c, which provides support and new directions for in-depth exploration of ncRNA and PE/PPE family functions during the infection process.

overall_design: Explore the Whole transcriptome profiling of H37Rv- and H37Rv△1759c infected macrophages.

first: Chen

last: Tan

first: Wenqi

last: Dong

first: Gaoyan

last: Wang


title: BAF45D Cooperates with SMAD Signaling and Promotes Early Neural Differentiation in P19 Cells

city: Hefei

first: Chao

last: Liu

state: Anhui

address: 81 Meishan Road

department: Histology and Embryology

institute: Anhui Medical University

summary: We sought to explore whether BAF45D regulates PAX6 expression through cooperating with TGF-beta/SMAD signaling in RA treated P19 cells. Here we identified BAF45D is required for expression of phosphorylated SMAD3 and PAX6 induced by RA. Genome-wide analysis revealed that during RA-induced early neural differentiation, BAF45D knockdown failed to activate TGF-beta/SMAD signaling and induce expression of Stat3 and Smad7, two negative regulators of TGF-beta/SMAD signaling. Moreover, BAF45D was immunoprecipited with BRG1and phosphorylated SMAD3. In addition, Smad3 siRNA abolished RA-indueced expression of phosphorylated SMAD3, PAX6, STAT3 and SMAD7. Finally, overexpression of BAF45D directly induced expression of PAX6 and phosphorylated SMAD3.These results suggest that a novel effect of BAF45D cooperating with TGF-beta/SMAD signaling pathway on PAX6 level control, which may shed new light on neural differentiation of P19 cells.

overall_design: P19 cells from the NC siRNA and BAF45D siRNA groups (three biological replicates per group) were subjected to RA-induced differentiation for 5 days and treated with TRIzol (Invitrogen).

first: Hu

last: Xiujuan

first: Liu

last: Chao


title: Mycoplasma genitalium and M. pneumoniae induce a distinct set of protein-coding genes in epithelial cells.

status: Public on Oct 07 2021

city: El Paso

first: Shrikanth

last: Gadad

address: 5001 El Paso Drive

department: Department of Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

summary: Mycoplasma genitalium and M. pneumoniae are two significant mycoplasmas that infect the urogenital and respiratory tracts of humans. Despite distinct tissue tropisms, they both have similar pathogenic mechanisms and infect/invade epithelial cells in the respective regions and persist within these cells. However, the pathogenic mechanisms of these species in terms of bacterium-host interactions are poorly understood. To gain insights on this, we infected HeLa cells independently with M. genitalium and M. pneumoniae and assessed gene expression by whole transcriptome sequencing (RNA-seq) approach. The results revealed that HeLa cells respond to M. genitalium and M. pneumoniae differently by regulating various protein-coding genes. Though there is a significant overlap between the genes regulated by these species, many of the differentially expressed genes were specific to each species. KEGG pathway and signaling network analyses revealed that the genes specific to M. genitalium are more related to cellular processes. In contrast, the genes specific to M. pneumoniae infection are correlated with immune response and inflammation, possibly suggesting that M. pneumoniae has some inherent ability to modulate host immune pathways.

overall_design: We infected HeLa cells independently with M. genitalium and M. pneumoniae and assessed gene expression by whole transcriptome sequencing approach.

first: Subramanian

last: Dhandayuthapani

first: Kishore

last: Das

first: Enrique

middle: I

last: Ramos

first: Alana

last: Harrison

first: Anissa

last: Garcia


title: Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma

status: Public on Sep 29 2021

city: Washington

first: Rency

last: Varghese

address: 4000 Reservoir Rd NW, Building D

department: Oncology

institute: Georgetown University

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

overall_design: Refer to individual Series


title: Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma [miRNA-Seq]

summary:
We evaluate the epigenetic mechanisms of racial disparity in HCC through an integrated analysis of DNA methylation, miRNA, and combined regulation of gene expression. Specifically, we acquired DNA methylation, mRNA-seq, and miRNA-seq data through the analysis of tumor and adjacent normal liver tissues from African Americans (AA) and European Americans (EA) with HCC.
Results: Using mixed ANOVA, we identified cytosine-phosphate-guanine (CpG) sites, mRNAs, and miRNAs that are statistically significantly altered in HCC vs. adjacent normal in a race-specific manner. Through integrative analysis, we identified significantly differentially expressed genes in HCC with disparate epigenetic regulation, associated with changes in miRNA expression for AA and DNA methylation for EA.

overall_design: miRNA profiles of 16 HCC and 16 adjacent normal liver tissue

first: Habtom

middle: W

last: Resssom


title: Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma [DNA-Methylation]

overall_design: Genome wide DNA methylation profiling of 16 HCC and 16 adjacent normal samples from 8 African American and 8 Europen American patients.


title: Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma [RNA-Seq]

overall_design: mRNA profiles of 16 HCC and 16 adjacent normal liver tissue


status: Public on Oct 20 2021

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Transcriptional profiling of in vitro cultured mouse hepatocytes and hepatocyte-derived biliary cells demonstrated that in vitro cultured cells recapitulates the major transcriptional features of in vivo biliary cells and hepatocytes.

overall_design: Mouse hepatocytes were isolated from mouse liver samples and then cultured in vitro. Transcripts from in vitro cultured hepatocytes and hepatocyte-derived biliary cells were then sequenced for transcriptional profiling.

first: Jinyang

last: Li

first: Ben

last: Stanger


title: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases [breast cancer validation cohort]

status: Public on Nov 23 2021

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

institute: Linköping University

summary: Breast cancer validation study of CD4+ T cells in an independent group of 24 patients (median age [range], 61.5 [35–88] years) was recruited, based on the same inclusion criteria. All recruited patients were women. Additionally, 14 independent healthy controls were profiled.

overall_design: Total RNA was extracted using the AllPrep DNA/RNA Micro kit (Qiagen, Hilden, Germany; cat. no. 80284) according to the manufacturer’s instructions. RNA concentration and integrity were evaluated using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, California, USA; cat. no. 5067-1511) on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). Microarrays were then further computationally processed as described in One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (Agilent Technologies, Santa Clara, California, USA).

middle: R

first: Jordi

last: Serra-Musach

first: Jesper

last: Aagesen

first: Alex

last: Arenas

first: Bengt

last: Asking

first: Malin

last: Bengnér

first: Janne

last: Björkander

first: Sophie

last: Biggs

first: Jan

last: Ernerudh

first: Henrik

last: Hjortswang

middle: E

last: Karlsson

first: Mattias

last: Köpsen

first: Eun

middle: J

last: Lee

first: Antonio

last: Lentini

first: Xinxiu

first: Sandra

last: Lilja

last: Magnusson

first: Andreas

last: Matussek

first: Colm

last: Nestor

first: Samuel

last: Schäfer

first: Oliver

last: Seifert

first: Ceylan

last: Sonmez

last: Stjernman

last: Tjärnberg

first: Simon

last: Wu

first: Karin

last: Åkesson

last: Shalek

first: Margaretha

last: Stenmarker

first: Huan

last: Zhang

first: Mika

last: Gustafsson

first: Mikael

last: Benson


title: Top2a promotes the development of social behavior via PRC2 and H3K27me3

status: Public on Sep 20 2021

city: Salt Lake City

first: Yijie

last: Geng

state: UT

institute: University of Utah

summary: Human infants exhibit innate social behaviors at birth, yet little is understood about the embryonic development of sociality. We screened 1120 known drugs and found that embryonic inhibition of topoisomerase IIα (Top2a) resulted in lasting social deficits in zebrafish. In mice, prenatal Top2 inhibition caused behavioral defects related to core symptoms of autism, including impairments in social interaction and communication. Mutation of Top2a in zebrafish caused downregulation of a set of genes highly enriched for genes associated with autism in humans. Both the Top2a-regulated and autism-associated gene sets possess binding sites for polycomb repressive complex 2 (PRC2), a regulatory complex responsible for H3K27 trimethylation. Moreover, both gene sets are highly enriched for H3K27me3. Inhibition of PRC2 component Ezh2 rescued social deficits caused by Top2 inhibition. Therefore, Top2a is a key component of an evolutionarily conserved pathway that promotes the development of social behavior through PRC2 and H3K27me3.

overall_design: RNAseq data for 3 days post fertilization (dpf) wild type (WT) and Top2a mutant (can4-/-) zebrafish. 5 replicas were analyzed for each condition; each replica contains tissues collected from 9 larvae.

first: Randall

last: Peterson


title: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

first: Danuta

last: Gawel


title: Telomerase RNA subunit of Ustilago maydis

status: Public on Sep 17 2021

city: Puebla

first: Patricia

last: Sanchez-Alonso

state: Puebla

address: Av. San Claudio y 24 Sur, Col. San Manuel

department: Centro de Investigaciones en Ciencias Microbiologicas

country: Mexico

institute: Instituto de Ciencias, Benemerita Universidad Autonoma de Puebla

summary: The RNA subunit of telomerase is an essential component whose primary sequence and length are poorly conserved among eukaryotic organisms. The phytopathogen Ustilago maydis is a dimorphic fungus of the Ustilaginaceae family. We analyzed several members of the Ustilaginaceae family to computationally identify the TElomere RNA (TER) gene ter114. To confirm the identity of the TER gene, we disrupted the gene and characterized telomerase-negative mutants. Similar to catalytic TERT mutants, ter114Δ mutants exhibit phenotypes of telomere shortening and low replicative potential. However, ter114Δ mutants had very prolonged replication times, and survivors arose more rapidly in ter114Δ (252 replication rounds) than in their counterpart trt1Δ mutant strains (300 replication rounds). ter114-disrupted mutants were unable to infect maize seedlings in heterozygous crosses and showed defects such as cell cycle arrest and segregation failure. We concluded that ter114, which encodes the TER subunit of the telomerase of U. maydis, could have distinct or more extensive functions than trt1. To further characterize the ter114 gene, we analyze the transcriptomes of both, mRNA nuclear transcripts and nuclear RNA ribo-depleted transcripts of the wild-type strain 521, from the reads of both nuclear fractions, we find four reconstructed transcripts of the ter114 locus, which constitute four isoforms containing the structural domains of TER. The results showed that the transcription start site for the four isoforms is located upstream the start codon of the uncharacterized gene UMAG_03168, while the differential expression analysis showed that the ter114-i4 isoform is up-regulated with respect to the polyadenylated fraction, suggesting that this transcript could correspond to the precursor of the mature form of TER.

overall_design: Examination of the expression profiles of the polyA nuclear fraction and the total nuclear fraction in wild-type haploid cells

first: Juan

last: Sanpedro-Luna

first: José

last: Jacinto-Vázquez

first: Estela

last: Anastacio-Marcelino

first: Carmen

middle: M

last: Posadas-Gutiérrez

last: González-Bernal

first: Ivan

last: Olmos-Pineda

first: Moises

last: Carcaño-Montiel

first: Leticia

last: Vega-Alvarado

first: Candelario

last: Vázquez-Cruz

first: Maria

last: Sánchez-Alonso


title: Multiomics of reprogramming fibroblasts enhanced by siAJSZ

status: Public on Sep 01 2021

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University


title: scATAC-seq of human dermal fibroblasts reprogrammed with MGT

summary: scATAC-seq experiments were performed with control (untreated) HDFs, MGT_siControl HDFs, and MGT_siAJSZ HDFs.

overall_design: We determined how siRNAs targeting Atf7ip, JunB, Sp7, and Znf207 would change chromatin accessibility in cell fate reprogramming of fibroblasts to cardiomyocytes

first: Sean

last: Murphy

first: Alexandre

last: Colas


title: CTCF Spec-seq

status: Public on Nov 04 2021

city: Palo Alto

first: Zheng

last: Zuo

state: CA


title: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases [study of 13 diseases]

summary:
We conducted prospective clinical studies to validate the importance of CD4+ T cells in 13 diseases from the following ICD-10-CM chapters: Neoplasms (breast cancer, chronic lymphocytic leukemia); endocrine, nutritional and metabolic diseases (type I diabetes, obesity); diseases of the circulatory system (atherosclerosis); diseases of the respiratory system (acute tonsillitis, influenza, seasonal allergic rhinitis, asthma); diseases of the digestive system (Crohn’s disease [CD], ulcerative colitis [UC]); and diseases of the skin and subcutaneous tissue (atopic eczema, psoriatic diseases).
Study participants were recruited by clinical specialists based on diagnostic criteria defined by organizations representing each specialist’s discipline. Age and gender matched healthy controls (n = 127 and 39, respectively) were recruited in the Southeast region of Sweden from outpatient clinics at the University Hospital, Linköping; Ryhov County Hospital, Jönköping, a primary health care center in Jönköping; and a medical specialist unit for children in Värnamo. Study participants represented both urban and rural populations with an age range of 8–94 years. Patients with type I diabetes and obesity had an age range of 8–18 years. 12 patients had more than one diagnosis.

first: Jordi

last: Serra-Musach

first: Jesper

last: Aagesen

first: Alex

last: Arenas

first: Bengt

last: Asking

first: Malin

last: Bengnér

first: Janne

last: Björkander

first: Sophie

last: Biggs

first: Jan

last: Ernerudh

first: Henrik

last: Hjortswang

last: Karlsson

first: Mattias

last: Köpsen

first: Eun

last: Lee

first: Antonio

last: Lentini

first: Xinxiu

last: Li

first: Sandra

last: Lilja

last: Magnusson

first: Andreas

last: Matussek

first: Colm

last: Nestor

first: Samuel

last: Schäfer

first: Oliver

last: Seifert

first: Ceylan

last: Sonmez

last: Stjernman

last: Tjärnberg

first: Simon

last: Wu

first: Karin

last: Åkesson

last: Shalek

first: Margaretha

last: Stenmarker

first: Huan

last: Zhang

first: Mika

last: Gustafsson

first: Mikael

last: Benson


title: MSX2 safeguards syncytiotrophoblast fate of human TSCs

status: Public on Aug 28 2021

city: Vienna

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: The majority of placental pathologies arise from failures in trophoblast differentiation, yet the underlying transcriptional regulation is poorly understood. Here, we use human trophoblast stem cells to elucidate the function of the transcription factor MSX2 in trophoblast specification. We show that depletion of MSX2 de-represses the syncytiotrophoblast program, while forced expression of MSX2 blocks it. We demonstrate that a large proportion of the affected genes are directly bound and regulated by MSX2 and identify components of the SWI/SNF complex as its strong interactors. Our findings uncover the pivotal role of MSX2 in cell fate decisions that govern human placental development and function.

overall_design: RNAseq of MSX2 KD and control hTSCs in self-renewing conditions and MSX2 inducible overexpression in syncytiotrophoblast differentiated from hTSCs. ChIPseq data of MSX2 in hTSC.

first: Ruth

last: Hornbachner

first: Paulina

last: Latos


title: RNA-seq of NIK Kockdown and control cells in lung metastatic human breast cancer cells established from MDA-MB-231 by orthotopic xenograft model

status: Public on Aug 18 2021

city: Shinjuku-ku

first: Yusuke

last: Hayashi

state: Tokyo

address: 2-2 Wakamatsu-cho

department: Dept. of Life Sci. & Med.Biosci.

country: Japan

institute: Waseda Univ.

summary: Orthotopic xenograft (OX) model can mimics early process of spontaneous metastasis comparing than intra-cardiac injection (ICI) or tail vein injection (TVI) model. However, many gene signatures in orthotopic breast cancer metastasis have not yet been studied in detail. Here we have established new highly lung metastatic breast cancer cells from MDA-MB231 by OX model.Comparative analysis between Parent cells (MDA-MB231) and the highly lung metastatic breast cancer cells (LM05) revealed that Non-canonical NF-κB pathway was constitutively activated by NIK up-regulation in protein level.  In addition, the NIK up-regulation was ascribed to a decrease in translation of cIAP1 which degrade NIK by ubiquitination. Next, we investigated the NIK function in LM05 and found the NIK up-regulation contributed to tumorigenicity. To further analyze NIK funcion of tumorigenicity, we conducted RNA-seq and immunohistochemistry staining of  NIK Knockdown cells and control cells. As these results,the suppression tumorigenicity caused by NIK knockdown is attributed to the down-regulation of attraction of CAFs by decreased in some cytokines and chemokines expressions. Finally, we investigated the relationship between NIK protein levels and breast cancer malignancy. From this analysis,  NIK expression in breast cancer revealed that normal breast tissue was hardly detectable NIK protein. On the other hand, the expression of NIK protein was increased in malignancy tumors. In conclusion, our results demonstrated that a new role and up-regulation mechanism for NIK in breast cancer progression.

overall_design: NIK knockdown cell lines were established by retroviral infection of pSUPER- target shRNA knockdown vectors and selected with 3 µg/ml puromycin for 3 days. Total RNA was extracted from control cell line  (shGFP) and NIK knockdown cell lines (shNIK no.1, no.2). RNA-seq was performed to characterize these cells in detail.

first: Jun

last: Nakayama

last: Yamamoto

first: Kentaro

last: Semba


title: Time-course single-cell and spatial transcriptomics of reovirus-induced myocarditis in neonatal mice

status: Public on Dec 03 2021

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: A significant fraction of sudden death in young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used single-cell and spatially resolved RNA sequencing (RNA-seq) to study the cellular and spatial  heterogeneity of myocarditic processes in the hearts of reovirus-infected neonatal mice at multiple predetermined time points after initial infection at the primary site of infection. We further applied these technologies to study the innate response to reovirus infection in the intestine. In addition, we performed time-dependent single-cell RNA-seq (scRNA-seq) of cardiac tissues of mice infected with a reovirus point mutant that does not cause myocarditis. To establish viral tropism, we implemented molecular enrichment of non-polyadenylated viral transcripts that were otherwise poorly represented in the transcriptomes. Our measurements give insight into the cardiac cell-type specificity of innate immune responses, into the tropism of the virus in the intestine and the heart, into the transcriptional states of cell types involved in the production of inflammatory cytokines and the recruitment of circulating immune cells, and into the cell type specific gene expression in a spatial context. Overall, our data identify cellular interactions and cell-type specific host responses during reovirus-induced myocarditis.

overall_design: Time-course single-cell and spatial transcriptomics of ileum and heart tissues from reovirus-infected neonatal mice

first: Madhav

last: Mantri

first: Meleana

last: Hinchman

first: John

last: Parker


title: ChIP-seq of AJSZ in human dermal fibroblasts

first: Chulan

last: Kwon

summary: We ran ChIP-sequencing using antibodies targeting Atf7ip, JunB, Sp7, and Znf207 on HDFs

overall_design: To determine where AJSZ bound in the human fibroblast genome, we used ChIP-seq.

first: Sean

last: Murphy

first: Alexandre

last: Colas


title: Development of a two-circular RNA panel as potential prognostic biomarker for gastric cancer

status: Public on Aug 12 2021

city: Tianjin

first: Jing

last: Liu

address: Huanhu West Road

institute: Tianjin Medical University Cancer Institute and Hospital

summary: Background: Circular RNAs (circRNAs) have attracted increasing attention in recent years for their potential application as disease biomarkers due to their high abundance and stability. In this study, we attempted to screen circRNAs that can be used to predict postoperative recurrence and survival in patients with gastric cancer (GC).  Methods: High-throughput RNA sequencing was used to identify differentially expressed circRNAs in GC patients with different prognoses. The expression level of circRNAs in the training set (n=136) and validation set (n=167) was detected by quantitative real-time PCR (qRT-PCR). Kaplan–Meier estimator, receiver operating characteristic (ROC) curve and cox regression analysis were used to evaluate the prognostic value of circRNAs on recurrence-free survival (RFS) and overall survival (OS) in GC patients. CeRNA network prediction, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for the circRNAs with prognostic significance.  Results: A total of 259 differentially expressed circRNAs were identified in GC patients with different RFS. We found two circRNAs (hsa_circ_0005092 and hsa_circ_0002647) that highly expressed in GC patients with good prognoses, and subsequently established a predictive model for postoperative recurrence and prognosis evaluation, named circPanel. Patients with circPanellow might have shorter recurrence-free survival (RFS) and overall survival (OS). We also performed circRNA-miRNA-mRNA network prediction and functional analysis for hsa_circ_0005092 and hsa_circ_0002647.  Conclusions: CircPanel has the potential to be a prognostic biomarker in GC patients with greater accuracy than a single circRNA and certain traditional tumor markers (e.g., CEA, CA19-9 and CA724).

overall_design: CircRNA expression profile of gastric cancer patients with different prognosis

first: Meinan

last: Yan

first: Hui

last: Li


title: Cardiovascular disease perturbs the vascular hematopoietic stem cell niche

status: Public on Sep 27 2021

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: Hematopoiesis advances cardiovascular disease by generating inflammatory leukocytes that attack the arteries, heart and brain. While it is well documented that the bone marrow niche regulates hematopoietic stem cell proliferation and hence the systemic leukocyte pool, it is less clear how cardiovascular disease affects the vasculature forming this niche. Here we show that arterial hypertension, atherosclerosis and myocardial infarction alter the anatomy and function of bone marrow vasculature. Hypertension and atherosclerosis instigated vascular fibrosis, leakage and endothelial dysfunction in the bone marrow. Myocardial infarction induced vascular leakage and bone marrow angiogenesis via Vegf signaling. Endothelial cell-specific deletion of the Vegf receptor 2 limited emergency hematopoiesis after myocardial infarction, indicating that new vasculature supports higher blood cell production. RNA-sequencing of bone marrow endothelial cells revealed inflammatory gene expression in mice with cardiovascular disease. Endothelial cell-specific deletion of interleukin 6 or versican, which were highly expressed in mice with atherosclerosis or myocardial infarction, respectively, reduced hematopoiesis and systemic myeloid cells. Taken together, cardiovascular disease affects the vascular bone marrow niche, thus influencing hematopoietic stem cell behavior and expanding innate immune cell supply to atherosclerotic plaque and ischemic myocardium. Interrupting this feed back loop may constrain cardiovascular inflammation.

overall_design: We performed transcriptional profiling using RNA-seq in flow sorted bone marrow endothelial cells isolated from i) naïve control mice (Ctr), ii) mice 2 days after acute myocardial infarction (MI), iii) hypertensive mice with chronic angiotensin II treatment (HTN), and iv) atherosclerotic Apoe knockout mice (ApoE). n=3 animals per group.

first: Matthias

last: Nahrendorf


title: Developmental regulation of neuronal gene expression by Elongator complex protein 1 dosage

status: Public on Oct 25 2021

first: Susan

last: Slaugenhaupt

state: MA

address: 185 Cambridge St

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Elongator is a highly conserved protein complex required for transcriptional elongation, intracellular transport and translation. Elongator complex protein 1 (ELP1) is the scaffolding protein of Elongator and is essential for its assembly and stability. Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by a mutation in ELP1 that lead to a tissue-specific reduction of ELP1 protein. Our work to generate a phenotypic mouse model for FD led to the discovery that homozygous deletion of the mouse Elp1 gene leads to embryonic lethality prior to mid-gestation. Given that FD is caused by a reduction, not loss, of ELP1, we generated two new mouse models by introducing different copy numbers of the human FD ELP1 transgene into the Elp1 knockout mouse (Elp1-/-) and observed that human ELP1 expression rescues embryonic development in a dose dependent manner. We then conducted a comprehensive transcriptome analysis in mouse embryos to identify genes and pathways whose expression correlates with the amount of ELP1.  We found that ELP1 is essential for the expression of genes responsible for the formation and development of the nervous system. Further, gene length analysis of the differentially expressed genes showed that the loss of Elp1 mainly impacts the expression of long genes and that by gradually restoring Elongator their expression is progressively rescued. Finally, through evaluation of co-expression modules, we identified gene sets with unique expression patterns that depended on ELP1 expression.  Overall, this study highlights the crucial role of ELP1 during early embryonic neuronal development and reveals gene networks and biological pathways that are regulated by Elongator.

overall_design: Paired-end RNASeq in Elp1 KO mouse embryos with different dosage of human ELP1 gene with FD mutation. Total 29 RNASeq libraries. This includes 8 WT mouse embryos, 8 embryos KO Elp1 embryos, 7 FD1/KO embryos  (KO for Elp1 endogenous gene with one copy of human FD ELP1 transgene), and 6 FD9/KO embryos (KO for Elp1 endogenous gene with nine copies of human FD ELP1 transgene ).

first: Dadi

last: Gao

first: Elisabetta

last: Morini


title: Global gene expression profile of GC-Tfh cells derived from Peyer's patches at steady state, as well as dLNs from KLH-immunized, influenza-infected, SEA-immunized, ESS-induced mice and of FNg+ Tfh and IFNg-Tfh cells derived from influenza infection

status: Public on Jul 28 2021

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Tfh cells are critical in providing help for B cells in the germinal center reaction. However, with regards to the isotypes of antibodies produced by B cells in responses to distinct pathogens, it is unclear whether and how Tfh cells determine differential antibody isotype responses. Through transcriptional profiling of GC-Tfh cells derived from various types of immune responses, we identified culsters of differentially expressed genes corresponding to Th1, Th2 or Th17 cells. Of special interest, a subset of Tfh cells producing IFNg were generated in an influenza virus infection. In order to understand the transcriptional and functional differences, we performed RNA-sequencing to compare the transcriptional profiles of IFNg+ and IFNg- Tfh cells.

overall_design: Global gene expression profile of 1) GC-Tfh cells derived from Peyer's patches at steady state, as well as dLNs from KLH-immunized, influenza-infected, SEA-immunized, ESS-induced mice. 2)IFNg+ Tfh and IFNg-Tfh cells derived from influenza infection. IFNg+ Tfh cells and IFNg-Tfh cells were sorted from IfngYFPxBcl6RFP reporter mice at day 9 post H1N1 PR8 infection. The total RNA were extracted and sequenced

first: Han

last: Feng

first: Xiaohong

last: Zhao

first: Jenny

last: Xie

first: Xue

last: Bai


title: Zfp318 controls the recallability of memory B cells

status: Public on Jul 25 2021

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

summary: Memory B cells (MBCs) are important for efficacious antibody-based vaccines and develop via germinal center (GC)-dependent and -independent routes. We find all MBCs are not equally recallable by antigen. Zfp318, a transcription regulator of spermatogenesis and IgD expression, is not expressed in GC B cells but upregulated in MBCs. GC-derived MBCs are far more recallable than GC-independent MBCs in a Zfp318-dependent manner. Zfp318 expression is inhibited by BCR but promoted by CD40 signaling, while its levels are positively correlated with B-cell receptor affinities. Enforced Zfp318 expression markedly increases the recallability of GC-independent MBCs. Zfp318-deficient MBCs show reduced expression of mitochondrion-related genes, exhibit lower mitochondrial membrane potentials, contain more structurally compromised mitochondria, and are susceptible to activation-induced cell death. The abundance of Zfp318-expressing MBCs positively correlates with the quality of vaccine-induced antibody immunity. Therefore, Zfp318 defines the recallability of the MBC compartment and represents a key regulator of humoral immune memory.

overall_design: Differential gene expression analyses between Zfp318-sufficient MBCs and Zfp318-deficient MBCs

first: Yifeng

last: Wang

first: Wen

last: Shao


title: Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [ATAC-seq]

first: Yingtian

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: We analyzed chromatin accessibility, ChIP-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.

overall_design: ATAC-seq analysis of PDXs and clinical tissues.

first: Henry

last: Long


title: Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [ChIP-seq]

overall_design: ChIP-seq analysis of ASCL1 and NEUROD1 transcription factors of PDXs tissues.


title: Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [RNA-seq]

overall_design: RNA-seq analysis of PDXs and clinical tissues.


title: Tcf1/Lef1 transcription factors and CD8 T cell identity [Hi-C]

status: Public on Jul 11 2021

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Comparison of global genome organization between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells, followed by crosslinking, enzyme digestion, proximity ligation, and then HiC sequencing.

first: Hai-Hui

last: Xue

first: Xiang


title: Tcf1/Lef1 transcription factors and CD8 T cell identity [DNAase-seq]

summary: Comparison of chromatin accessibility profiles between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells, followed by treatment with DNase I and DNase-sequencing

last: Li


title: Tcf1/Lef1 transcription factors and CD8 T cell identity [RNA-seq]

summary: Comparison of transcriptomes between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells, followed by RNA extraction and RNA sequencing


title: Tcf1/Lef1 transcription factors and CD8 T cell identity [ChIP-seq]

summary: Determine genome-wide binding locations by Tcf1 in naive CD8+ T cells

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells, followed by crosslinking and ChIPseq with Tcf1 antiserum


title: Tcf1/Lef1 transcription factors and CD8 T cell identity [H3K27ac ChIP-seq]

summary: Comparison of H3K27ac profiles ibetween WT and Tcf1/Lef1-deficient naïve CD8+ T cells

overall_design: Splenocytes were harvested from hCD2-Cre, Rosa26-lsl-GFP, Tcf1/Lef1 wild-type or double floxed mice, and sorted for GFP+TCRbeta+ naïve CD8+ T cells, followed by crosslinking and ChIPseq with H3K27ac antibody.


title: Tcf1/Lef1 transcription factors and CD8 T cell identity

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

overall_design: Refer to individual Series


title: Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis (RNA-seq)

status: Public on Jul 10 2021

city: Bristol

first: Johannes

last: Reul

address: Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School

institute: University of Bristol

summary: We conducted Ribo-Zero RNA-Seq studies on rat hippocampus to elucidate changes in RNA expression in the hippocampus under physiological conditions such as acute stress and circadian variation. Rats were subjected to 15-min forced swim (FS) session and hippocampus tissue was collected at 30, 60, 120, 180 or 360 minutes after the onset of swimming. Tissues were also collected under early morning baseline (BL AM) or late afternoon baseline (BL PM) conditions. Based on this analysis, we have identified many genes that are differentially expressed as a result of acute stress exposure and circadian variation.

overall_design: 37 Ribo-Zero RNASeq samples across 7 conditions:  5 biological replicates per condition for BLAM, BLPM, FS120, FS180, FS360; and 6 biological replicates for FS30 and FS60

first: K

last: Mifsud

first: C

last: Kennedy

first: J

first: Eshita

last: Sharma


title: Effect of epigenotoxic chemicals on transcriptomic profiles of human induced pluripotent stem cells

status: Public on Jul 23 2021

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences


title: Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis

status: Public on Jul 09 2021