title: The transcription factor DDIT3 is a Potential Driver of Dyserythropoiesis in Myelodysplastic Syndromes [overexpression_and_knockdown]

status: Public on Nov 10 2022

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

summary: Myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell (HSC) malignancies characterized by ineffective hematopoiesis with increased incidence in elderly individuals. Genetic alterations do not fully explain the molecular pathogenesis of the disease, indicating that other types of lesions may play a role in its development. In this work, we analyzed the transcriptional lesions of human HSCs, demonstrating how aging and MDS are characterized by a complex transcriptional rewiring that manifests as diverse linear and non-linear transcriptional dynamisms. While aging-associated lesions seemed to predispose elderly HSCs to myeloid transformation, disease-specific alterations may be involved in triggering MDS development. Among MDS-specific lesions, we detected the overexpression of the transcription factor (TF) DDIT3. Exogenous upregulation of DDIT3 in human healthy HSCs induced an MDS-like transcriptional state, and a delay in erythropoiesis, with an accumulation of cells in early stages of erythroid differentiation, as determined by single-cell RNA-sequencing. Increased DDIT3 expression was associated with downregulation of transcription factors required for normal erythropoiesis, such as KLF1, TAL1 or SOX6, and with a failure in the activation of their erythroid transcriptional programs. Finally, DDIT3 knockdown in CD34+ cells from MDS patients was able to restore erythropoiesis, as demonstrated by immunophenotypic and transcriptional profiling. These results demonstrate that DDIT3 may be a driver of MDS transformation, and a potential therapeutic target to restore the inefficient erythropoiesis characterizing these patients.

overall_design: To determine the role of DDIT3 overexpression in MDS, this factor was overexpressed in healthy CD34+ cells. Cells were either grown for 2 days or sujected to erythroid differentiation for different time points (4, 10 and 14 days). Furthermore, DDIT3 was  knocked-down in CD34+ cells from MDS patients and subjected to erythroid differentiation for 7 days. For all experiments, transduced cells (GFP+) were sorted prior to RNA-seq

first: Nerea

last: Berastegui

first: Juan

last: Romero

first: Ana

last: Alfonso-Pierola

first: Céline

last: Philippe

first: Amaia

last: Vilas

first: Patxi

last: San Martin

first: Raquel

last: Ordoñez

last: Alignani

first: Sarai

last: Sarvide

first: Laura

last: Castro

first: José

last: Lamo-Espinosa

first: Mikel

last: San-Julian

first: Tamara

last: Jimenez

first: Félix

last: López

first: Sandra

last: Muntion

first: Fermin

last: Sanchez-Guijo

first: Antonieta

last: Molero

first: Julia

last: Montoro

first: Bárbara

last: Tazón

first: Guillermo

last: Serrano

first: Aintzane

last: Diaz-Mazkiaran

last: Hernaez

first: Sofía

last: Huerga

first: Findlay

last: Copley

last: Rio-Machin

first: Matthew

last: Maurano

first: María

last: Díez-Campelo

first: David

last: Valcarcel

first: Kevin

last: Rouault-Pierre

last: Lara-Astiaso

first: Teresa

last: Ezponda

first: Felipe

last: Prosper


title: Roles of Iron in Chemoresistance of Multiple Myeloma Depends on the Interaction with Bone Marrow Stromal Cells

status: Public on Oct 07 2022

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The single-cell landscape of kidney immune cells reveals transcriptional heterogeneity in early diabetic kidney disease

status: Public on Nov 08 2022

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

country: USA

institute: Ichan School of Medicine at Mount Sinai

summary: The pathogenesis of diabetic kidney disease (DKD) involves multifactorial processes that converge to initiate and advance the disease. Although DKD is not typically classified as an inflammatory glomerular disease, mounting evidence supports the involvement of renal inflammation as a key contributor in DKD pathogenesis, particularly through macrophages. However, detailed identification and corresponding phenotypic changes in macrophages in DKD remain poorly understood. To capture the gene expression changes in specific macrophage cell subsets in early DKD, we performed a single-cell transcriptomic analysis of CD45-enriched kidney immune cells from type 1 diabetic OVE26 mice at two time points during the disease development and undertook a focused analysis of mononuclear phagocytes (i.e., macrophages and dendritic cells). Our results now show increased resident and infiltrating macrophage subsets in the diabetic kidneys over time, with heightened expression of pro-inflammatory or anti-inflammatory genes in a subset-specific manner. Further analysis of macrophage polarization states in each subset showed changes consistent with the continuum of activation and differentiation states, and their gene expression tended to shift toward undifferentiated phenotypes but with increased M1-like inflammatory phenotypes over time and in the diabetic kidneys. By deconvolution analysis of RNAseq samples of human DKD biopsies and immunostaining, we further confirmed a differential expression of select genes in specific macrophage subsets. Thus, the current study provides a comprehensive analysis of macrophage transcriptomic profiles in early DKD that underscores the dynamic macrophage phenotypes in disease progression.

overall_design: To capture the gene expression changes in specific macrophage cell subsets in early DKD, we performed a single-cell transcriptomic analysis of CD45-enriched kidney immune cells from type 1 diabetic OVE26 mice at two time points during the disease development and undertook a focused analysis of mononuclear phagocytes.

first: Jia

last: Fu

first: Xuan

last: Wang

first: Tuo

last: Zhang

first: Weijie

last: Yuan

first: Weijia

first: Kyung

last: Lee

first: John

middle: C

last: He


title: The transcription factor DDIT3 is a Potential Driver of Dyserythropoiesis in Myelodysplastic Syndromes [Young_Elderly_MDS]

first: Marina

last: Ainciburu

overall_design: Human HSCs (CD34+ CD38- CD90+ CD45RA-) from healthy young and elderly (>65 years old) individualas, as well as  from untreated MDS patients, were analyzed by MARS-seq

first: Nerea

last: Berastegui

first: Juan

middle: P

last: Romero

first: Ana

last: Alfonso-Pierola

first: Céline

last: Philippe

first: Amaia

last: Vilas

first: Patxi

last: San Martin

first: Raquel

last: Ordoñez

first: Diego

last: Alignani

first: Sarai

last: Sarvide

first: Laura

last: Castro

first: José

middle: M

last: Lamo-Espinosa

first: Mikel

last: San-Julian

first: Tamara

last: Jimenez

first: Félix

last: López

first: Sandra

last: Muntion

first: Fermin

last: Sanchez-Guijo

first: Antonieta

last: Molero

first: Julia

last: Montoro

first: Bárbara

last: Tazón

first: Guillermo

last: Serrano

first: Aintzane

last: Diaz-Mazkiaran

last: Hernaez

first: Sofía

last: Huerga

last: Copley

middle: T


title: Glucocorticoids target the CXCL9/10-CXCR3 axis and confer protection against immune-mediated kidney injury

status: Public on Nov 11 2022

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Single-cell RNA-seq of renal T cells from steroid treated or not treated crescentic glomerulonephritis mouse model and steroid treated ANCA-GN patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA-seq of kidney T cells from steroid treated or untreated cGN mice, and single-cell sequencing of kidney T cells from steroid treated ANCA-GN patients.

first: Jan

middle: H

last: Riedel

first: Lennart

last: Robben

first: Hans

middle: J

last: Paust

first: Nariaki

last: Asada

first: Ning

last: Song

first: Anett

last: Peters

first: Anna

last: Kaffke

first: Alina

last: Borchers

first: Gisa

last: Tiegs

first: Larissa

last: Seifert

first: Nicola

last: Tomas

first: Elion

last: Hoxha

first: Ulrich

middle: O

last: Wenzel

first: Tobias

middle: B

last: Huber

first: Thorsten

last: Wiech

middle: E

last: Turner

first: Christian

middle: F

last: Krebs

first: Ulf

last: Panzer


title: Improving gene set enrichment analysis (GSEA) by using regulation directionality

status: Public on Sep 30 2022

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

summary: To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.

overall_design: To illustrate the use of GINtool, we used original RNA-seq data from a B. subtilis strain overexpressing the industrial-relevant xylanase XynA and compared this with RNA-seq data from a strain that does not express XynA. Data have been collected from two independent biological replicates.

first: Frans

last: van der Kloet

first: Mariah

last: Kes

first: Joen

last: Luirink

first: Leendert

middle: W

last: Hamoen


title: The transcription factor DDIT3 is a Potential Driver of Dyserythropoiesis in Myelodysplastic Syndromes

first: Marina

last: Ainciburu


title: Single cell RNA seq analysis of cells isolated from mouse livers

status: Public on Sep 28 2022

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: We performed single cell RNA seq analysis of cells isolated from mouse livers (CD49a positive cells)

overall_design:
CD31-/CD45.2-/CD49a+ cells were isolated from normal diet-fed mouse livers and high fat diet-fed mouse livers, and the cells  were analyzed by single-cell RNA-sequencing analysis.
3 Sample types:
ND: CD49+ cells isolated from normal diet-fed mouse livers
NT: CD49+ cells isolated from non-tumor region of high fat diet-fed mouse livers
T: CD49a+ cells isolated from tumor region of high fat diet-fed mouse livers

first: Yi

last: Cheng

first: Ryota

last: Yamagishi

first: Yoshiki

last: Nonaka

first: Naoko

last: Ohtani


title: Roles of Iron in Chemoresistance of Multiple Myeloma Depends on the Interaction with Bone Marrow Stromal Cells [treatment]

first: Zhiqiang

last: Liu

summary: To investigate the role of iron(FeAc) on bortezomib-induced drug resistance of multiple myeloma cells, we administrated MM.1S with iron and bortezomib

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of four different groups,which treated with vehicle, iron(FeAc), bortezomib and iron(FeAc)  plus bortezomib respectively.

first: Hongmei

last: Jiang

first: Sheng


title: The transcription factor DDIT3 is a Potential Driver of Dyserythropoiesis in Myelodysplastic Syndromes [scRNA-Seq]

overall_design: Healthy CD34+ cells were transduced with a DDIT3-overexpression plasmid or a control one, and cells were sujected to erythroid differentiation for 14 days. Transduced and live cells were FACs-isolated prior to scRNA-seq processing..

first: Nerea

last: Berastegui

first: Juan

last: Romero

first: Ana

last: Alfonso-Pierola

first: Céline

last: Philippe

first: Amaia

last: Vilas

first: Patxi

last: San Martin

first: Raquel

last: Ordoñez

first: Diego

last: Alignani

first: Sarai

last: Sarvide

first: Laura

last: Castro

first: José

last: Lamo-Espinosa

first: Mikel

last: San-Julian

first: Tamara

last: Jimenez

first: Félix

last: López

first: Sandra

last: Muntion

first: Fermin

last: Sanchez-Guijo

first: Antonieta

last: Molero

first: Julia

last: Montoro

first: Bárbara

last: Tazón

first: Guillermo

last: Serrano

first: Aintzane

last: Diaz-Mazkiaran

last: Hernaez

first: Sofía

last: Huerga

first: Findlay

last: Copley

last: Rio-Machin

first: Matthew

last: Maurano

first: María

last: Díez-Campelo

first: David

last: Valcarcel

first: Kevin

last: Rouault-Pierre

last: Lara-Astiaso

first: Teresa

last: Ezponda

first: Felipe

last: Prosper


title: Single cell RNA seq analysis of cells isolated from mouse livers [CD31-/CD45.2-]

first: Daisuke

last: Motooka

summary: We performed single cell RNA seq analysis of cells isolated from mouse livers (CD45-negative and CD31-negative cells)

overall_design: ND_and_NT_and_T' sample represents mixed sample records of CD31-/CD45.2- cells isolated from normal diet-fed mouse livers and high fat diet-fed mouse livers, and the cells  were analyzed by single-cell RNA-sequencing analysis.

first: Yi

last: Cheng

first: Ryota

last: Yamagishi

first: Yoshiki

last: Nonaka

first: Naoko

last: Ohtani


title: Roles of Iron in Chemoresistance of Multiple Myeloma Depends on the Interaction with Bone Marrow Stromal Cells [coculture]

first: Zhiqiang

last: Liu

summary: To investigate the role of coculture treatment of multiple myeloma cells to bortezomib drug resistance, multiple myeloma cells were cocultured with bone marrow mesechymal stem cells

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of Mock group and coculture treatment group.

first: Hongmei

last: Jiang

first: Sheng

last: Wang


title: Impaired dynamic X-chromosome inactivation maintenance in T lymphocytes is a feature of spontaneous lupus in female mice that is exacerbated in female-biased disease models

status: Public on Sep 20 2022

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: Rosenthal Building - 3800 Spruce St. Room 304

department: Department of Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary: The molecular basis for the female bias of systemic lupus erythematosus remains unclear. We sought to determine the fidelity of dynamic X-chromosome inactivation maintenance in the pathogenesis of murine models of spontaneous lupus, including the heavily female-biased NZM2328 model.

overall_design: Splenic CD3+ cells were isolated from 18-24-week-old wild-type C57BL/6 female mice (n=3), NZM2328 female mice (n=5), and NZM2328 male mice (n=3). Cells were activated in vitro using anti-CD3 and anti-CD28 antibodies for 48 hours prior to RNAseq analysis.

first: Natalie

last: Toothacre

first: Nikhil

last: Jiwrajka

first: William

last: Stohl


title: Genome-scale CRISPR screen identifies nucleotide metabolism as an actionable therapeutic vulnerability in diffuse large B-cell lymphoma

status: Public on Oct 18 2022

city: Tabuk

first: Sael

last: Alatawi

address: Duba Road

country: Saudi Arabia

institute: University of Tabuk

type: Non-coding RNA profiling by high throughput sequencing


title: Complex Genomic Patterns of Abasic Sites in Mammalian DNA Revealed by High-Resolution SSiNGLe-AP Method

status: Public on Sep 15 2022

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

summary: DNA damage plays critical role in biology and disease, however, precise understanding of how different types of DNA damage affect cellular functions is far from clear. A major underlying reason for this is paucity of high-resolution methods that can map locations of different types of DNA damage in complex genomes such as those of mammals. Here, we present development and validation of SSiNGLe-AP method that can map a common type of DNA damage, abasic (AP) sites, genome-wide and with high-resolution. We applied this method to six different tissues of mice of different ages and human cancer cell lines. We found non-random distribution of AP sites in mammalian genome that exhibits dynamic enrichment at specific genomic locations, and is significantly influenced by gene expression, age and especially by tissue-type. Overall, these results suggest that we are at the very beginning of understanding the true complexities of genomic patterns of DNA damage.

overall_design: Development of high-resolution SSiNGLe-AP method to map AP sites genome-wide and its application to reveal genomic patterns of AP sites in different mouse tissues of different ages

first: Ye

last: Cai

first: Philipp

last: Kapranov


title: FIT Links c-Myc and P53 Acetylation by Recruiting RBBP7 During Carcinogenesis of Colorectal Cancer

status: Public on Aug 29 2022

city: Hefei

first: yang

last: xia

state: Anhui

address: Sanlian

institute: Anhui medical university

summary: Colorectal cancer (CRC) poses one of the most serious threat against human health worldwide, and abnormally expressed c-Myc and p53 are deemed the pivotal driving forces of CRC progression. Here we discovered a lncRNA FIT, which was down-regulated in CRC clinical samples, was transcriptionally suppressed by c-Myc and promoted CRC cells apoptosis by inducing FAS expression. FAS is a p53 target gene, and we found that FIT formed a trimer with RBBP7 and p53 which facilitated p53 acetylation and transcription. Moreover, FIT was capable of retarding CRC growth in mice xenograft model and positively relevant to FAS expression clinically. Thereby our study elucidated the role of lncRNA FIT in human colorectal cancer growth and provides a potential target for anti-CRC drugs.

overall_design: lncRNA and mRNA expression for CRC tissue ,pCDH and pCDH-lnc-FIT in HCT116 cells by high throughput sequencing

first: Lili

last: Guo

first: Yang

last: Xia

first: Hao

last: Gu

first: Wanglai

last: Hu


title: A multi-omics integrative network map of maize.

status: Public on Oct 30 2022

city: wuhan

first: qian

middle: lin

last: han

state: hubei

address: Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: These data include RNA-seq, circRNA-seq, and small RNA-seq of transcriptome, Ribo-seq of translatome and protein protein binary interactions by recombination-based library vs. library yeast-2-hybrid throughout the lifecycle of the maize inbred line B73.

overall_design: We constructed a integrative network map involving co-expression, co-translation and interactome network.

first: Linqian

last: Han

first: Wanshun

last: Zhong

first: Jia

last: Qian


title: T-cell activation and B-cell interaction signatures in rectal tissues are associated with HIV replication in ex-vivo model of infection

status: Public on Aug 26 2022

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The rectal mucosa is a critical site of HIV vulnerability. We sought to identify transcriptomic features of rectal mucosal tissue prior to exposure associated with support or restriction of HIV replication. For the first time, we identified rectal tissue transcriptomic signatures associated with increased p24 production utilizing an ex-vivo model. Our findings are highly relevant to HIV transmission and the early establishment of HIV reservoirs in humans.

overall_design: Rectal tissue from HIV-negative cisgendermen (n=57) underwent concurrent RNAseq transcriptomic analyses (two biopsies/participant) and challenge with HIV in the ex-vivo explant model of infection (three biopsies challenged/participant) as part of a larger cohort study to understand the rectal mucosal immune environment among MSM.

first: S

middle: A

last: Smith

first: Phillip

last: Murray

first: Praveen

last: Amancha

first: Cassie

middle: G

last: Ackerley

first: Steven

last: Bosinger

first: Rama

middle: R

last: Amara

first: Colleen

last: Kelley


title: The comparison of gene expression profiles in hepatic stellate cells isolated from mouse livers by perfusion method at 37 degrees or 6 degrees

first: Daisuke

last: Motooka

summary: We compared transcriptome profiling (bulk RNA-seq) of hepatic stellate cells isolated from mouse livers by perfusion method using collagenase at 37 degrees or 6 degrees and evaluated the heat-stressed gene expression at 37 degrees.

overall_design: To scrutinize the side effects of high temperature incubation on the transcriptome, we examined the  gene expression profoles in hepatic stellate cells isolated from mouse livers by perfusion method at 37 degrees or 6 degrees

first: Yi

last: Cheng

first: Ryota

last: Yamagishi

first: Yoshiki

last: Nonaka

first: Naoko

last: Ohtani


title: Analysis of wild type and Sema6d-/- lung ILC2 transcriptomes in IL-33 induced acute lung inflammation

status: Public on Aug 28 2022

summary: Semaphorin 6D (Sema6D) have various effects in immune responses. However, the involvement of Sema6D in ILC2 funcions remains unclear. We identified the genes regulated by Sema6D in lung ILC2s during IL-33 induced acute lung inflammation.

overall_design: Lung ILC2 mRNA profiles of non stimulated or IL-33 stimulated wild type and Sema6d-/- mice (n=3 each)


title: A novel Long non-coding RNA AL136131.3 inhibits hair growth through mediating glycolysis in androgen alopecia

status: Public on Sep 02 2022

city: Shanghai

first: Yulong

last: Tang

address: Songhu Road 2005

institute: Fudan University

summary: The key pathophysiological changes in androgenetic alopecia (AGA) are limited to hair follicles (HFs) in frontal and vertex regions, except for the occipital region. To identify biological differences among HF subpopulations. Paired vertex and occipital HFs from 10 male AGA donors were collected for RNA-seq assay. Furthermore, hair follicle and cell experiments were conducted on the identified key genes to reveal their roles in AGA. Our study aimed to uncover potential lncRNA indicators for AGA and reveal the potential mechanism underlying the involvement of AL136131.3 in hair growth in AGA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ten paired hair follicle (HF) samples from androgenetic alopecia patients by comparing their HF subpopulations (affected frontal HFs and unaffected occipital HFs)

first: Qingmei

last: Liu

first: Xiao

first: Yuting

last: Zhang

first: Jinran

last: Lin

first: Wenyu

last: Wu


title: Integrated transcriptome analysis of radioresistant cells revealed genes and pathways predictive of tumor response to radiotherapy and chemotherapy in breast cancer

status: Public on Aug 09 2022

city: Cuajimalpa de Moreles

first: Isidro

middle: Xavier

last: Perez-Añorve

state: CIUDAD DE MÉXICO

address: Vasco de Quiroga 4871, Contadero.

department: Departamento de Ciencias Naturales

country: Mexico

institute: Universidad Autónoma Metropolitana

summary:
Radiotherapy, in addition to surgery and chemotherapy, remains the core of the current clinical management of breast cancer. Although radiotherapy is effective in most patients, some of them will develop recurrent disease because of radioresistant tumor cell.
MCF-7RR and MDA-MB-231RR cell lines were established from their parental MCF-7 and MDA-MB-231 cells parental cells were irradiated with a linear accelerator

overall_design: Cells received 15 sequential fractions of 2 Gy week, allowing irradiated cell populations a period of recovery between exposures. Non-irradiated controls were handled identically to the irradiated cells without radiation exposure. All of the experiments were performed within 4–10 passages after the final irradiation

first: I

middle: X

first: E

last: Arechaga-Ocampo


title: Effect of SIRPA perturbation on transcriptome of B16 murine melanoma cells

status: Public on Aug 18 2022

city: Houston

first: Han

last: Liang

state: Texas

address: 7007 Bertner Avenue

department: Department of Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: To explore the effect of SIRPA perturbation on the expression changes of melanoma differentiation antigens (MDA), which directly mediates the immunogenicity of melanoma cells, we profiled the transcriptomes of B16F10 cells with SIRPA knockdown, overexpression, or control.

overall_design: Total RNA were extracted from B16F10 cells with SIRPA knockdown, overexpression or control and were subjected to mRNA paired-end sequencing by Novogene Co., LTD. Each cell line has three biological repeats.

first: Zhou

last: Zhicheng

first: Luo

last: Yikai


title: Direct transposition of native DNA for sensitive multimodal single-molecule sequencing I

status: Public on Aug 08 2022

city: San Francisco

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

institute: Gladstone Institutes / UCSF

summary: Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.

overall_design: Chromatin profiling with m6dA methyltransferase footprinting of the OS152 osteosarcoma cell line, followed by transposase-mediated PCR-free library construction in situ (SAMOSA-Tag) and single molecule sequencing.

first: Ke

first: Sivakanthan

last: Kasinathan

first: Megan

last: Ostrowski

first: Ansuman

last: Satpathy

last: Sweet-Cordero

first: Hani

last: Goodarzi

first: Vijay

last: Ramani


title: RNA transcriptome sequencing analysis of SNU-668 Erastin-resistant cells transfected with shRNA-SOX13 or control shRNA

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

summary: a RNA transcriptome sequencing analysis was performed in SNU-668 erastin-resistant cells that were transfected with  shRNA-SOX13 or control shRNA

overall_design: mRNA profiles of  SNU-668 Erastin-resistant cells transfected with shRNA-SOX13 or control shRNA

first: Mingzhe

first: Hui

last: Yang


title: Methylation studies in roe deer

status: Public on Aug 02 2022

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples of roe deer
n=94 blood samples

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Jean-Francois

last: LeMaitre


title: Super-enhancer-associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells

status: Public on Jul 28 2022

city: Dubai

first: Fahad

last: Ali

address: Bldg 14, Dubai Healthcare City

country: United Arab Emirates

institute: Mohammed Bin Rashid University of Medicine and Health Sciences

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: Super-enhancer-associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells [ChIP-Seq]

summary: Neuroblastoma is a pediatric tumor that accounts for more than 15% of cancer-related deaths in children. Survival chances for high-risk patients are less than 50%. Retinoic acid treatment is part of the maintenance therapy given to neuroblastoma patients; however, not all tumors respond to retinoic acid-mediated differentiation. Among neuroblastoma tumors, two phenotypically distinct cell types-adrenergic (ADRN) and mesenchymal (MES), have been identified based on their super-enhancer landscape and transcriptional core regulatory circuitries. We hypothesized that distinct super-enhancers in these different tumor cells could mediate differential response to retinoic acid. To this end, we treated four different neuroblastoma cell lines, comprising both ADRN (MYCN amplified and non-amplified) and MES subtypes, with retinoic acid and studied the super-enhancer landscape upon treatment and after removal of retinoic acid. Using H3K27ac ChIP-seq paired with RNA-seq, we compared the super-enhancers in cells that respond to retinoic acid-mediated differentiation versus those that fail to differentiate. We identified unique super-enhancers associated with cells differentiation; however, even among cells that respond to treatment, there was heterogeneity upon removal of retinoic acid, with MYCN amplified cells remaining differentiated whereas MYCN non-amplified cells reverted to a proliferative state. This study identifies regulatory super-enhancers as a plausible mechanism behind the differential response to retinoic acid-mediated differentiation.

overall_design: The H3K27ac landscape was determined in three neuroblastoma cell lines to investigate the effect of retinoic acid treatment and withdrawal. Three replicates were generated for each condition - control, ATRA treated, and withdrawn. Input libraries were derived from control samples.

first: Roshna

last: Gomez

first: Laura

last: Woods

first: Anna

last: Philpott


title: AGO2 silences mobile transposons in the nucleus of quiescent cells [RNA-seq]

status: Public on Jul 18 2022

city: Bethesda

first: Joana

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

summary: Argonaute 2 (AGO2) is a cytoplasmic component of the miRNA pathway with essential roles in development and disease. Yet, little is known about its regulation in vivo. Here, we show that in mouse quiescent cells, AGO2 localizes almost exclusively to the nucleus. In quiescent splenocytes, AGO2’s subcellular localization is modulated by the Pi3K-AKT-mTOR pathway, a well-established regulator of quiescence. Signaling through this pathway in proliferating cells promotes AGO2 cytoplasmic accumulation at least in part by stimulating the expression of TNRC6, an AGO2 binding partner in the miRNA pathway. In contrast, low signaling in quiescent cells enables AGO2 to accumulate in the nucleus where it binds to young mobile transposons co-transcriptionally. Loss of AGO2 in quiescent cells results in upregulation of transposon transcripts suggesting it performs functions analogous to those of PIWI in the germline. Our results point to an essential but previously unrecognized nuclear role for AGO2 during mammalian quiescence as part of a genome-defense system against transposable elements.

overall_design: Total RNA sequencing from resting splenic B cells isolated from WT B6 mice (3 biological replicates)

last: Sala


title: AGO2 silences mobile transposons in the nucleus of quiescent cells [miRNA-seq]

status: Public on Jul 22 2022

overall_design: Total RNA sequencing from resting spleenic B cells isolated from WT B6 mice (3 biological replicates)


title: AGO2 silences mobile transposons in the nucleus of quiescent cells [ChIP-seq]

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA epitope in freshly isolated splenic B cells from wild-type (control) or Ago2HA/HA mice.

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 in splenic B cells from wild-type, Ago2+/flx, and Ago2ADH/flx mice following CRE-mediated recombination.

Please note that the additional samples (GSM6351517, GSM6351518 included on July 19th, 2022) are exactly the same samples as GSM6152936, GSM6152938. However, they have been re-sequenced with Paired-end sequencing.

first: Mahendra

last: Prajapat


title: Differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) [10X]

status: Public on Jul 09 2022

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: By utilizing single-cell analysis of neurons that are produced at day 9 of mESC differentiation period (day 9) under the developmentally relevent signals- Retinoic acid and BMP4, we identified that our protocol can generate all major sensory neuron subtypes that are required for relaying sensation like pain, itch, heat and proprioception in the spinal cord. This analysis also identified functional features in each neuronal subtypes, confirming the bonafide status of the in vitro derived sensory neurons.

overall_design: Two 10X genomics chromium samples from mouse ESC differentiations under RA and RA+BMP4 conditions.

first: Sandeep

last: Gupta

first: Salena

last: Gallardo

first: Stephanie

last: Castellanos

first: Igor

last: Mandric

first: Samantha

last: Butler


title: Multiple knockout mouse models indicate a role of miR-124a in neuronal maturation

status: Public on Jul 07 2022

first: Daisuke

last: Motooka

summary: MicroRNA-124a (miR-124a) is one of the most abundantly expressed miroRNAs in the central nervous system (CNS) and encoded by three genomic loci of miR-124a-1/2/3 in mammals; however, its in vivo roles and mechanisms in neuronal development and function remain ambiguous. In the present study, we investigated the effect of loss of miR-124a on neuronal differentiation in mice and embryonic stem (ES) cells. Since primary miR-124a-3 shows a background level expression in the brain and we could not obtain miR-124a-1/2/3 triple knockout (TKO) mice by mating, we generated and analyzed miR-124a-1/2 double knockout (DKO) mice. We found that miR-124a-1/2 DKO mice exhibit perinatal lethality. RNA-sequencing analysis demonstrated that the expression levels of proneural and neuronal marker genes are almost unchanged between the control and miR-124a-1/2 DKO brains, while the genes related to neuronal synaptic formation and function were enriched in the down-regulated genes of the miR-124a-1/2 DKO brain. In addition, the transcription regulator Tardbp/TDP-43, whose loss leads to defects in neuronal maturation and function, was inactivated in the miR-124a-1/2 DKO brain. We next generated miR-124a-1/2/3 TKO ES cells by using the CRISPR-Cas9 system as an alternative to miR-124a-1/2/3 TKO mice. Phase-contrast microscopic, immunocytochemical, and gene expression analyses showed that miR-124a-1/2/3 TKO ES cell lines can differentiate into neurons. Collectively, these results suggest that miR-124a plays roles in neuronal maturation rather than neurogenesis in vivo, and may advance our understanding of functional roles of microRNAs in CNS development in vivo.

overall_design: We performed RNA-sequencing analysis using total RNAs purified from control (miR-124a-1+/−) and miR-124a-1/2 DKO mouse brains at embryonic day 17.5 (E17.5) in triplicate.

first: Taro

last: Chaya

last: Okuzaki

first: Takahisa

last: Furukawa


title: Single cell RNA-seq of E8.5 mouse embryonic craniofacial tissues

status: Public on Jul 21 2022

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: The craniofacial region encompassing rhombomere 2 and adjacent putative BA1 together with all more anterior tissues was collected from E8.5 mouse embryos, processed and analyzed by 10X Genomics Chromium scRNA-seq

overall_design: Two samples of craniofacial tissues were collected from E8.5 mouse embryos and analyzed by 10X Genomics Chromium scRNA-seq

first: Ruonan

last: Zhao

middle: M

first: Paul

last: Trainor


title: Mycobacterium tuberculosis infection drives a Type I IFN signature in lung lymphocytes

status: Public on Jun 24 2022

city: Saint Louis

first: Shabaana

middle: Abdul

last: Khader

state: Missouri

address: 660 S Euclid Avenue, Campus Box 8230

department: Department of Molecular Microbiology

institute: Washington University in St. Louis

summary: Mycobacterium tuberculosis (Mtb) infects a quarter of the world’s population and causes tuberculosis (TB), which is a leading cause of death globally. A clear understanding of the dynamics of immune response at cellular level is crucial to design better strategies to control TB. We have employed single-cell RNA-seq approach on lung lymphocytes derived from healthy and Mtb-infected mice. Our results show enrichment of type I IFN responsive phenotypes among the lymphoid cell clusters, as well as heat shock responses in natural killer (NK) cells from Mtb-infected mice lungs. We have identified Ly6A as a novel lymphoid cell activation marker and validated its upregulation in activated lymphoid cells post Mtb infection. The cross analysis of type I IFN signature in human TB infected peripheral blood samples further validates our results. These findings significantly contribute toward understanding and characterizing the transcriptional parameters at single-cell depth in a highly relevant and reproducible mouse model of TB.

overall_design: To characterize the lung lymphocyte landscape of mice infected with low dose Mtb, we performed 10x scRNA-seq on single-cells from the lungs of control (uninfected, n = 2), 50 days post-infection (dpi) (D50 Inf, n = 3), and 100 dpi (D100 Inf, n = 3) mice

first: Sadia

last: Akter

first: Kuldeep

last: Chauhan

first: Micah

middle: D

last: Dunlap

first: José

last: Choreño-Parra

first: Lan

last: Lu

first: Ekaterina

last: Esaulova

first: Joaquin

last: Zúñiga

first: Maxim

last: Artyomov

first: Deepak

last: Kaushal


title: Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2

status: Public on Jul 26 2022

city: St Lucia

first: Mohammed

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

summary: Why individuals with Down Syndrome (DS, trisomy 21) are particularly susceptible to SARS-CoV-2 induced disease remains largely unclear. The choroid plexus secrets the cerebrospinal fluid and strongly expresses the ACE2 receptor and the chromosome 21 encoded TMPRSS2 protease. To investigate the role of the choroid plexus in SARS-CoV-2 central nervous system infection in DS, we established a new type of brain organoid from DS and isogenic euploid control iPSC that consists of a core of appropriately patterned functional cortical neuronal cell types that is surrounded by a patent and functional choroid plexus (CPCOs). Remarkably, DS-CPCOs not only recapitulated abnormal features of DS cortical development but also revealed defects in ciliogenesis and epithelial cell polarity of the developing choroid plexus. We next demonstrate that the choroid plexus layer facilitates SARS-CoV-2 replication and infection of cortical neuronal cells, and that this is increased in DS-CPCOs. We further show that inhibition of TMPRSS2 activity in DS-CPCOs inhibits SARS-CoV-2 infectivity. We conclude that CPCOs are a useful model for dissecting the role of the choroid plexus in euploid and DS forebrain development and enables screening for therapeutics that can inhibit SARS-CoV-2 induced neuro-pathogenesis.

overall_design: Examination of 2 sets of human choroid plexus brain organoids at week 4 and week 8, and cortical brain organoids at week 8 of in vitro culture

first: Ernst

middle: J

last: Wolvetang


title: Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness Versus Lineage Output in Murine Dnmt3a-Mutant Clonal Hematopoiesis

status: Public on May 25 2022

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Clonal hematopoiesis resulting from enhanced fitness of mutant hematopoietic stem cells (HSCs) associates with both favorable and unfavorable health outcomes related to the types of mature mutant blood cells produced, but how this lineage output is regulated is unclear. Using a mouse model of DNMT3AR882/+ clonal hematopoiesis (Dnmt3aR878H/+), we found that aging-induced TNFα signaling promoted the selective advantage of mutant HSCs as well as stimulated mutant B lymphoid cell production. Genetic loss of TNFα receptor TNFR1 impaired mutant HSC fitness without altering lineage output, while loss of TNFR2 reduced lymphoid cell production and favored myeloid cell production from mutant HSCs without altering overall fitness. These results support a model where clone size and mature blood lineage production can be independently controlled to harness potential beneficial aspects of clonal hematopoiesis.

overall_design: 1x10^6 CD45.2+ cells were competed against 1x10^6 CD45.1+ post-ficoll whole BM cells and transplanted into aged, lethally irradiated CD45.1+ recipient animals. One month post-transplant, the recipients received one IP injection of poly(I:C) and recombination was checked via PCR on PB. One month post poly(I:C), animals were bled monthly for 16 weeks. Bone marrow was harvested and 4x10^6 post-ficoll whole BM cells were used for secondary transplantation into aged, lethally irradiated recipients. Recipients were harvested 20 weeks post-transplant.

last: SanMiguel


title: Multi-omics identifies the link between intratumor steatosis and exhausted tumor immune microenvironment in hepatocellular carcinoma

status: Public on May 22 2022

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary:
Immunotherapy becomes standard-of-care treatment of hepatocellular carcinoma (HCC) but still limited number of patients benefit from immunotherapy due to the high heterogeneity of tumor immune-microenvironment (TIME) of HCC patients. Therefore, it is important to stratify patients who benefit from immunotherapy by analyzing the molecular and immunological diversity of HCC.  Since non-viral HCC is rapidly increasing all over the world, in this study, we focused on non-viral HCC and aimed to identify immunotherapy-susceptible patients through multi-omics.
Global RNA sequencing of surgically-resected tumor tissues in 113 non-viral HCC patients  was performed.
Unsupervised hierarchical clustering classified non-viral HCCs into 3  molecular classes associated with patient prognosis and corresponding driver gene abnormality. We further identified the immune-enriched but -exhausted subclass with intratumor steatosis in non-viral HCCs, characterized by T-cell exhaustion, infiltration of M2 macrophage and cancer-associated fibroblast (CAF), high PD-L1 expression, and TGF-β signaling activation..

overall_design: Global RNA sequencing of surgically-resected tumor tissues in 113 non-viral HCC patients.

first: Hiroki

last: Murai

first: Takahiro

last: Kodama

first: Tetsuo

last: Takehara


title: Transcriptomic profile of canine mammary ductal carcinoma

status: Public on May 26 2022

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: Mammary neoplasms are the most frequent in non-neutered bitches. Here we used next generation sequencing (NGS), to determine the transcriptional profile of samples of canine mammary ductal carcinomas and to contribute to the clarification of the importance of deregulated molecules in the molecular pathways involved in the disease. For this, samples of tumor tissue from mammary ductal carcinoma (without metastases) and non-tumor breast tissue from radical mastectomy of six bitches of different breeds and ages were used.

overall_design: Samples of tumor tissue from mammary ductal carcinoma and adjacent non-tumor mammary tissue, from the radical mastectomy of 6 bitches of different breeds, not neutered, aged between 5 and 14 years, attended by the Small Animal Surgery Service of the Veterinary Hospital.RNA was extracted and was pooled with three samples each, forming four groups (two tumoral and two control samples). Each pool was used to build the four sequencing libraries. The cDNA libraries were built with the TruSeqTM Stranded Total RNA Sample Preparation Kit v2 (Illumina) and sequencing took place on the NextSeq 500 System platform (Illumina, USA) using the NextSeq 500/550 High Output v2 150 cycles (Illumina) Sequencing Kit, according to the manufacturer's instructions.

first: Fernandez

last: Geysson Javier

first: Camargo

last: Adriana


title: Super-enhancer-associated core regulatory circuits mediate susceptibility to retinoic acid in neuroblastoma cells [RNA-seq]

first: Fahad

last: Ali

overall_design: RNA-seq libraries were generated in three neuroblastoma cell lines to investigate the effect of retinoic acid treatment and withdrawal. Three replicates were generated for each condition - control, ATRA treated, and withdrawn.

first: Roshna

last: Lawrence Gomez

first: Laura

last: Woods

first: Ahmad

middle: N

last: Abou Tayoun

first: Anna

last: Philpott


title: AGO2 silences mobile transposons in the nucleus of quiescent cells

first: Joana

last: Vidigal


title: Single cell RNA-sequencing based characterization of cell compositions in human multiple primary lung cancer

status: Public on Apr 23 2022

city: Dalian

first: Hai-long

last: Piao

state: Liaoning

address: No.457 Zhongshan Road

institute: Dalian Institute of chemical physics

summary: Multiple primary lung cancers (MPLC) pose diagnostic and therapeutic challenges in the clinic. Here, we orchestrated the cellular atlasof MPLC by single cell RNA-sequencing and identified the heterogeneity between different lesions within the same MPLC patients.

overall_design: We collected 19 tissue samples from four MPLC patients (one squamous carcinoma and three adenocarcinomas); each patient had two separate lung tumor lesions.For the first two patients (P1 and P2), we collected one tissue specimen from each of the tumor lesions. For the third patient (P3), to understand the intra-lesion heterogeneity, two repetitive tissue specimens from each of the tumor lesions were collected. For the last patient (P4), two tissue specimens from one of the larger tumor lesions and one tissue specimen from the other small tumor lesion were collected.As comparisons, one normal tissue sample adjacent to each tumor lesion was collected. Single cell RNA-sequencing was performed on all the collected 19 samples.

first: Yawei

last: Wang

first: Di

last: Chen


title: Next generation sequence analysis of cells derived from mouse hair follicles after long term culture

status: Public on Jun 30 2022

state: Osaka

summary: Follicle epithelial stem cells (HFSCs) have important functions for homeostasis of skin as well as hair follicle morphogenesis. In the present study, we screened different types of commercially available culture medium for culturing HFSCs. Among those tested, one type was shown capable of supporting the expression of stem cell markers in cultured HFSCs. However, the differentiation ability of HFSCs serially passaged using that optimal medium was found to be impaired, leading to unsuccessful formation of hair follicles in vivo.

overall_design: Examination of 2 different time point in hair follicle stem cells cultured during long term

first: Y

last: Ouji


title: Fluorescent tracking identifies tumor migratory dendritic cells as critical for cross-presentation in the lymph node following radiation therapy induced maturation

status: Public on Apr 24 2022

city: Portland

first: Michael

last: Gough

state: OR

address: 4805 NW Glisan St, Suite 2N35

institute: Earle A Chiles Research Institute

summary: To understand the early effect of radiation therapy on tumor-infiltrating immune cells in two different tumor types, we established MC38 or Panc02-SIY tumors in C57BL/6 mice. scRNASeq was performed on CD45+ cells sorted by flow cytometry from single cell suspensions of tumors 1 day following 12Gy radiation therapy (RT), or control untreated (NT) tumors.

overall_design: Tumors were implanted subcutaneously into the right flank as follows; 2 x 10^5 MC38, 5 x 10^6 Panc02-SIY. When tumors were approximately 5mm in average diameter, mice were randomized to receive treatment with CT-guided radiation using the Small Animal Radiation Research Platform from XStrahl. Dosimetry was performed using Murislice software from XStrahl. The SARRP delivered a single dose of 12Gy to an isocenter within the tumor using a 10mm x 10mm collimator and a 45 degree beam angle to minimize dose delivery to normal tissues. Tumors were harvested 24 hours post treatment (n=4 animals/group), processed into a single cell suspension as described above and magnetically enriched using CD45+ TIL MicroBeads (Miltenyi Biotec). Enriched cells were labeled with viability dye and CD45-APC. Live CD45+ cells were sorted using a 100uM nozzle on a BD Biosciences Aria cell sorter and cells were processed according to the manufacturers protocol for the Chromium Single Cell 3’ Reagent kit (v3.0) from 10X Genomics. Libraries were sequenced using an Illumina NovaSeq 6000 using the NovaSeq 6000 S2 reagent kit (v1.0).

first: Tiffany

middle: C

last: Blair

first: Shelly

last: Bambina

first: Gwen

middle: F

last: Kramer

first: Alexa

last: Dowdell

first: Alejandro

last: Alice

first: Jason

last: Baird

first: Amanda

last: Lund

first: Brian

last: Piening

first: Marka

last: Crittenden


title: Spatial transcriptomics based characterization of spatial architecture in human multiple primary lung cancer

summary: Multiple primary lung cancers (MPLC) pose diagnostic and therapeutic challenges in the clinic. Here, we orchestrated the cellular atlas and spatial architecture of MPLC based on spatial transcriptomics.

overall_design: We collected three MPLC patients (one squamous carcinoma and twk adenocarcinomas); each patient had two separate lung tumor lesions. Spatial transcriptomics sequencing was applied on 12 samples, including paired tumor and tumor-adjacent normal tissues from each of the two different tumor lesions of  three MPLC patients (P1, P2, P3).


title: Step-wise differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) using developmental logic [bulk RNA-seq]

first: Riki

last: Kawaguchi

summary: We directed mESCs towards the neuromesodermal progenitor state (NMPs) that contribute to the spinal cord cells in the embryo. We then tested if ESC-derived NMPs can be directed to generate diverse sensory neuronal subtypes by testing different combinations of growth factors RA and BMP4 which are crucial for providing patterning information during spinal cord development. By bulk-RNA seq analysis of the entire timeline of the mESC differentiation under various conditions, we identified differentiation trajectories that lead to sensory neurons or completely different cardiac cell types under RA/+BMP4 conditions. We also characterized the gene expression changes that occur when cells transition from different states while differentiating into sensory neurons and identified Wnt signaling being a regulator of proliferation working directly downstream of BMP4 signaling in the mESC cultures.

overall_design: 3- replicate samples were collected at each time points between day 0 and day 9 under different conditions. Total 45 samples were collected from 3-independent differentiations.

first: Sandeep

last: Gupta

first: Salena

last: Gallardo

first: Stephanie

last: Castellanos

first: Igor

last: Mandric

first: Samantha

last: Butler


title: Differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells

status: Public on Jul 08 2022

overall_design: Refer to individual Series


title: A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants

status: Public on May 16 2022

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the cellular response to SARS-CoV-2 infections in Syrian hamsters previously immunized with mRNA, Adenovirus, and life-attenuated virus vaccines.

overall_design:
Two experiments were conducted. In the first, single vaccination were done with either an mRNA vaccine, and adenovirus vector vaccine, or the life-attenuated sCPD9 (prime only). The second experiment follows prime-boost strategies with the combination adenovirus + adenovirus, mRNA + mRNA, sCPD9 + sCPD9, and mRNA + sCPD). In both experiments, there were also mock-vaccinated animals.
Histopathology was performed from lungs and nasal mucosa, antibody levels were determined in blood and nasal washes, bulk RNA sequencing was performed from lungs, and scRNA-seq was performed from lung, blood and nasal mucosa. Note that the data quality of the blood samples from experiment 1 is very poor.

first: Geraldine

last: Nouailles

first: Julia

last: Adler

first: Peter

last: Pennitz

first: Gustavo

last: Teixeira

first: Stefan

last: Peidli

first: Morris

last: Baumgart

first: Judith

last: Bushe

first: Anne

last: Voss

first: Alina

last: Langenhagen

first: Fabian

last: Pott

last: Kazmierski

first: Cengiz

last: Gökeri

last: Praktiknjo

first: Szandor

last: Simmons

last: Xing

first: Christine

last: Langner

first: Ricardo

last: Vidal

first: Azza

last: Abdelgawad

first: Günter

last: Cichon

first: Victor

last: Corman

first: Daniela

last: Niemeyer

first: Nils

last: Blütghen

first: Haibo

last: Wu

first: Achim

last: Gruber

last: Goffinet

first: Nikolaus

last: Osterrieder

first: Markus

last: Landthaler

first: Martin

last: Witzenrath

first: Dusan

last: Kunec

first: Jakob

last: Trimpert


title: Methylation studies in yellow-bellied marmots

status: Public on Apr 13 2022

first: Steve

last: Horvath

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples from yellow-bellied marmots (Marmota flaviventris).
DNA methylation data from n=159 blood samples. All samples were collected as part of a long-term study of a free-living population of yellow-bellied marmots in the Gunnison National Forest, Colorado (USA), where marmots were captured and blood samples collected biweekly during the their active season (May to August). Genomic DNA was extracted with Qiagen DNeasy blood and tissue kit.

overall_design: N=159 Blood samples from marmots. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Daniel

last: Blumstein

first: Gabriela

last: Pinho


title: Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [unfractionated PB]

city: Rochester

first: Stephan

last: Emmrich

state: NY

address: 213 Hutchison Hall, River Campus

institute: University of Rochester

summary: Naked mole-rats are a mammalian model organism of exceptional longevity. We mapped the hematopoietic hierarchy and used functional characterizations to define a purified stem and progenitor cell (HSPC) compartment similar to mouse LIN-/Sca-1+/Kit+ HSPCs or human LIN-/CD34+/CD38lo HSPCs.

overall_design:
Naked mole-rat peripheral blood was extracted, RBC-lysed and submitted to scRNA-Seq as unfractionated BM. The mRNA libraries were aligned to either the FRAMA bone marrow transcriptome assembly from our publication.

Note: Raw data represents only gene expresion (GEX). Raw data for ADT not included.


title: Profiling H3K9me3 and H3K27ac in M07e cells upon SEKIT CRISPRi inhibition

status: Public on Mar 04 2022

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: In the recent years, massively parallel sequencing approaches identified hundreds of mutated genes in cancer providing an unprecedented amount of information about mechanisms of cancer cell maintenance and progression. However, while (it is widely accepted that) transformation processes result from oncogenic cooperation between deregulated genes and pathways, the functional characterization of candidate key players is mostly performed at the single gene level which is generally inadequate to identify these oncogene circuitries. In addition, studies aimed at depicting oncogenic cooperation involve the generation of challenging mouse models or the deployment of tedious screening pipelines. Genome wide mapping of epigenomic modifications on histone tails or binding of factors such as MED1 and BRD4 allowed identification of clusters of regulatory elements, also termed Super-Enhancers (SE). Functional annotation of these regions revealed their high relevance during normal tissue development and cancer ontogeny. An interesting paradigm of the tumorigenic function of these SE regions comes from ETO2-GLIS2-driven acute megakaryoblastic leukemia (AMKL) in which the fusion protein ETO2-GLIS2 is sufficient to promote an aberrant transcriptional network by the rewiring of SE regions4. We thus hypothesized that important regulatory regions could control simultaneously expression of genes cooperating in functional modules to promote cancer development. In an effort to identify such modules, we deployed a genome-wide CRISPRi-based screening approach and nominated SE regions that are functionally linked to leukemia maintenance. In particular, we pinpointed a novel SE region regulating the expression of both tyrosine kinases KIT and PDGFRA. Whereas the inhibition of each kinase alone affected modestly cancer cell growth, combined inhibition of both receptors synergizes to impair leukemia cell growth and survival. Our results demonstrate that genome-wide screening of regulatory DNA elements can identify co-regulated genes collaborating to promote cancer and could open new avenues to the concept of combined gene inhibition upon single hit targeting.

overall_design: ChIPseq for H3K9me3 and H3K27Ac in CRISPRi treated M07e cells


title: Fusion oncogene rewiring of Super Enhancers can promote leukemia through cooperative gene induction

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


title: Transcriptome analysis of HLA-DR(+) HSPCs and HLA-DR(-) HSPCs in aplastic anemia patients

status: Public on May 31 2022

city: Kanazawa

first: Noriaki

last: Tsuji

address: 13-1 Takaramachi

department: Hematology

institute: Kanazawa University

summary: HLA-DR-lacking HSPCs [HLA-DR(-) HSPCs] were detected in aplastic anemia (AA) patients with HLA-DR15. HLA-DR(-) HSPCs may evade the attack by CD4+ T-cells recognizing the autoantigen presented by HLA-DR15. The goal of this study is to clarify  the  immune escape mechanisms from antigen-specific T-cells by comparing the trranscriptome profile of HLA-DR(+) HSPCs and HLA-DR(-) HSPCs.

overall_design: Examination of HLA-DR(+) HSPCs and HLA-DR(-) HSPCs from 3 patients

first: Kohei

last: Hosokawa

first: Shinji

last: Nakao


title: Daily changes in light influence mood via inhibitory networks within the thalamic perihabenular nucleus

status: Public on Apr 20 2022

first: Samer

last: Hattar

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

summary: Exposure to irregular light-dark schedules leads to deficits in affective behaviors. The retino-recipient perihabenular nucleus (PHb) of the dorsal thalamus has been shown to mediate these effects in mice. However, the mechanisms of how light information is processed within the PHb remains unknown. Here, we show that the PHb contains a distinct cluster of GABAergic neurons that receive direct retinal input. These neurons are part of a larger inhibitory network composed of the thalamic reticular nucleus and zona incerta, known to modulate thalamocortical communication. Additionally, PHbGABA neurons locally modulate excitatory-relay neurons, which project to limbic centers. Chronic exposure to irregular light-dark cycles alters photo-responsiveness and synaptic output of PHbGABA neurons, disrupting daily oscillations of genes associated with inhibitory and excitatory PHb signaling. Consequently, selective and chronic PHbGABA manipulation results in mood alterations that mimic those caused by irregular light exposure. Together, light-mediated disruption of PHb inhibitory networks underlies mood deficits.

overall_design: Gene expression profiling in n=4 biological replicates of PHb tissue (4 individual PHb samples pooled per biological replicate) harvested from T24 or T7 cycle-housed mice during their active phase (circadian time 14) or inactive phase (circadian time 2).

first: Michael

middle: B

last: Thomsen

first: Diego

last: Fernandez

first: K

last: Daly

first: Tenley

last: Weil


title: Genome-wide mapping of chromatin state in RPMI-8226 control versus REIIBP stable overexpressing cells

status: Public on Mar 09 2022

city: Singapore

first: Phyllis

last: Chong

address: 14 Medical Drive #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

summary: We performed ChIP-seq analysis with 40 million reads to generate genome-wide mapping of histone 3 lysine 27 trimethyl and histone 3 lysine 4 trimethyl marks driven by REIIBP overexpression

overall_design: Examination of 2 different histone modifications in human multiple myeloma cell line


title: Cohesin and CTCF control chromosomal contact dynamics in living cells [Hi-C]

status: Public on Feb 27 2022

city: Basel

first: Luca

last: Giorgetti

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Mammalian chromosomes are partitioned into topologically associating domains (TADs) by the loop-extrusion activity of cohesin that is blocked at specific DNA sites bound by CTCF. Chromosome structure inside TADs is highly variable in single cells, yet little is known about its temporal dynamics, how it influences the rates and durations of chromosomal contacts, and how it depends on CTCF and cohesin. To address these questions we combine two quantitative live-cell imaging strategies that minimize locus-specific confounding effects. We show that loop extrusion by cohesin globally reduces the mobility of the chromatin fiber in living cells, while also increasing the rates of formation and durations of contacts between sequences inside the same TAD. Quantitative analysis of high-resolution microscopy data reveals that contacts assemble and disassemble frequently in the course of the cell cycle, and become substantially more frequent and longer in the presence of convergent CTCF sites. Comparison with polymer modeling additionally reveals that cohesin-mediated CTCF loops last around 10 minutes on average. Our data support the notion that chromosome structure within TADs is highly dynamic and provide a quantitative framework for understanding the principles that link chromosome structure to biological function.

overall_design: We performed Hi-C experiment for 3 conditions: WT, 90min af Rad21 degradation and 240min of Rad21 degradation. There are 2 aims. 1. Choose induction time : 90 or 240 min. The changes at 90 similar to 240 so we proceed with 90 min. 2. Check that after Rad21 degradation CTCF loopes on the contact map are gone, which holds true.

first: Pia

last: Mach

first: Pavel

last: Kos

first: Yinxiu

last: Zhan

first: Julie

last: Cramard

first: Simon

last: Gaudin

first: Jana

last: Tünnermann

first: Jan

last: Eglinger

first: Jessica

last: Zuin

first: Mariya

last: Kryzhanovska

first: Sebastien

last: Smallwood

first: Laurent

last: Gelman

first: Edoardo

last: Marchi

first: Elphège

middle: P

last: Nora

first: Guido

last: Tiana


title: IL11RA signaling and EZH2 activity in osteosarcoma

status: Public on Mar 01 2022

city: Houston

first: Richard

middle: Eric

last: Davis

state: TX

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

summary:
Lung metastasis is the principal cause of death by osteosarcoma (OS), and has been shown by in vivo modeling to depend on interleukin-11 receptor alpha (IL11RA). To investigate IL11RA signaling in OS, we determined the effects of IL11RA knockdown on gene expression in the OS cell line KRIB.
Increased expression of genes repressed by the methyltransferase EZH2 was observed after IL11RA knockdown. Subsequent studies confirmed that IL11RA signaling promotes EZH2 activity and lung metastasis in OS.

overall_design: Gene expression in KRIB cells with 4 different shRNA sequences targeting EZH2 was compared to that in control cells. The most compelling results were for the 3 shRNA sequences with the greatest knockdown of IL11RA: C1, H8, and H2.

first: Eswaran

last: Devarajan

first: Zhiqiang

last: Wang

first: Valerae

middle: O

last: Lewis

first: R

middle: E


title: Cohesin and CTCF control chromosomal contact dynamics in living cells [capture C]

first: Luca

last: Giorgetti

overall_design: We performed capture C experiments in cell lines to measure the perturbation of TetO/LacO cassette and the effect of ectopic CTCF to chromosome structure

first: Pia

last: Mach

first: Pavel

last: Kos

first: Yinxiu


title: Cohesin and CTCF control chromosomal contact dynamics in living cells [4C-seq]

overall_design: We performed 4C experiments in cell lines carrying random 3xCTCF-TetO insertions in the genome, to show that new interactions were formed between the 3xCTCF and endogenous CTCF sites and to show that Cre recombination and/or Rad21 depletion led to loss of these interactions.

last: Zhan

first: Julie

last: Cramard

first: Simon

last: Gaudin

first: Jana

first: Jan


title: 10x BPH sequencing

status: Public on Feb 16 2022

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Single-cell mRNA sequencing (scRNA-seq) study was conducted to to probe heterogeneity of human BPH associated leukocytes

overall_design: leukocytes were sorted using FACs

first: Renee

last: Vickman

last: Hayward

first: Greg

last: Cresswell

first: Meaghan

last: Broman

first: Omar

last: Franco

first: Timothy

middle: L

last: Ratliff


title: Monthly dynamics of microbial functional diversity and composition in a tall-grass prairie, 2012

status: Public on Feb 10 2022

city: Beijing

first: Jiesi

last: Lei

state: Beijing

address: School of Environment, Tsinghua

institute: Tsinghua University

summary: We carried out an in-depth analysis of the monthly variations of a temperate grassland ecosystem to examine a range of biotic and abiotic factors that underpin soil respiration changes in response to warming.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Warming experiments were conducted at the Kessler Atmospheric and Ecological Field Station (KAEFS) in McClain County, Oklahoma, USA. One surface soil (0 - 15 cm) sample core was collected monthly for each of the eight warmed and control plots in 2012 (the third year of experimental manipulation). In total, 96 monthly samples were collected.

first: Jizhong

last: Zhou


title: Transcriptome analysis after knockdown of target genes (either HSP27 or TGF-β1, both HSP27 and TGF-β1) via shRNAs in MDA-MB-231 cells

status: Public on Feb 08 2022

city: Seoul

first: Jae

last: Song

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

summary:
Comparing expression profiles : among comparable samples in which target genes are knocked down
Global gene expression profiling has shown that more than 1500 (3.2%) genes over 2-fold gene fluctuations are differentially expressed in shTGF-β1-treated cells compared to control shRNA-treated cells.

overall_design: Analysis of differentially expressed genes in a total of 4 samples, a total of 3 comparative combinations.

first: Soojin

last: Choi


title: Transcriptome analysis after knockdown of target genes (either HSP27 or TGF-β1, both HSP27 and TGF-β1) via shRNAs in SNU-398 cells

summary:
Comparing expression profiles : among comparable samples in which target genes are knocked down
Global gene expression profiling has shown that only 134 (0.3%) genes over 2-fold gene fluctuations are differentially expressed in shTGF-β1-treated cells compared to control shRNA-treated cells.

overall_design:
Total 4 samples and 3 comparisons were analyzed. Comparing expression profiles among comparable samples using Affymetrix Human 2.0ST data. Intensity (CEL) Data files are generated by Affymetrix® GeneChip Command Console® Software(AGCC).
SNU-398_data1-raw data.xlsx: Normalized data:53,617 probes, 4 samples
SNU-398_data2.xlsx: Processed data: 44,629 probes, 4 samples
SNU-398_data3.xlsx: Criteria for significant result: |fc|≥1.5. SNU-398_data3.xlsx contains significant 3,826 probes in at least one of total comparison pairs.


title: Transcriptome analysis after knockdown of target genes (either HSP27 or TGF-β1, both HSP27 and TGF-β1) via shRNAs in MIA PaCa-2 cells


title: Transcriptome analysis after knockdown of target genes (either HSP27 or TGF-β1, both HSP27 and TGF-β1) via shRNAs in A549 cells

overall_design:
Total 4 samples and 3 comparisons were analyzed. Comparing expression profiles among comparable samples using Affymetrix Human 2.0ST data. Intensity (CEL) Data files are generated by Affymetrix® GeneChip Command Console® Software(AGCC).
A549_data1-raw data.xlsx: Normalized data:53,617 probes, 4 samples
A549_data2.xlsx: Processed data: 44,629 probes, 4 samples
A549_data3.xlsx: Criteria for significant result: |fc|≥2. A549_data3.xlsx contains significant 3,873 probes in at least one of total comparison pairs.


title: Lariat mapping of wild type and DBR1 KO cells after knockdown of AQR

status: Public on Jan 31 2022

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

summary: Using wild type HEK293T cells and our DBR1 CRISPR knockout cell line (C22), we investigated the effect of AQR knockdown on cellular lariat levels. Samples were taken after transfection with either one of two AQR-targeting siRNAs or a non-targeting control siRNA. After sequencing the samples, lariat mapping of the reads revealed that AQR knockdown increased the lariat recovery rate by ~50% relative to the level observed in the negative control samples.

overall_design: Lariat mapping of wild type and DBR1 KO cells treated with AQR siRNAs

first: Jing

last: Wang

first: Luke

last: Buerer

first: Rachel

last: Soemedi


title: Lariat mapping of a DBR1 CRISPR KO cell line

status: Public on Feb 03 2022

summary: We used CRISPR in HEK293T cells to create two DBR1 knockout cell lines (C19 and C22). After high-throughput sequencing of total RNA extracted from these cells, we performed lariat read mapping using the method described in "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo" (Taggart et al, 2012). We found lariats in the two DBR1- cell lines to be ~20-fold enriched relative to the levels observed in the HEK293T control samples.

overall_design: Lariat mapping of wild type and DBR1- HEK293T cells

first: Allison

last: Taggart


title: Lariat mapping of DBR1 KO and DBR1 KO+DBR1 addback cells

status: Public on Jan 29 2022

summary: We constructed a DBR1 knockout cell line (C22) using CRISPR in HEK293T cells. Through mapping of lariat reads, lariat levels in the DBR1 - samples are shown to increase dramatically (~20x) relative to wild type cells. Over 60% of this increase in lariat levels is abrogated upon rescue of DBR1 - cells with a DBR1 expression vector

overall_design: Lariat mapping of wild type, DBR1 -, and DBR1 - +DBR1 addback HEK293T cells

first: Nathaniel

last: Clark


title: Cohesin and CTCF control chromosomal contact dynamics in living cells [integration sites]

first: Luca

last: Giorgetti

overall_design: Integration site mapping using biotinylated probes against the piggyBac inverted terminal repeats

first: Pia

last: Mach

first: Pavel

last: Kos

first: Yinxiu

last: Zhan

first: Julie

last: Cramard

first: Simon

last: Gaudin

first: Jana

last: Tünnermann

first: Jan

last: Eglinger

first: Jessica

last: Zuin

first: Mariya

last: Kryzhanovska

first: Sebastien

last: Smallwood

first: Laurent

last: Gelman

first: Edoardo

last: Marchi

first: Elphège

last: Nora

first: Guido

last: Tiana


title: Cohesin and CTCF control chromosomal contact dynamics in living cells

overall_design: Refer to individual Series


title: HUVEC cell transcriptome response to Zaire Ebola virus (EBOV) and mutant lacking the mucin domain (deltamucin-EBOV)

status: Public on Aug 02 2022

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

summary: The purpose is to obtain samples for mRNA analysis in HUV-EC-C cells, a human endothelial cell line isolated from the vein of the umbilical cord, using the following viruses obtained by reverse genetics: Zaire Ebola virus wild-type in the ΔVP30 background (deltaVP30-WT) and mutant lacking the mucin domain (deltaVP30-deltamucin).

overall_design: HUVEC cells were infected with a MOI=500 adenovirus VP30 overnight.  24 hours post adeno-infection cells were either Mock, deltaVP30-WT-EBOV (MOI=10), or deltaVP30-delta-mucin-EBOV (MOI=10) infected.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 8, 24, 48, and 72 h post-infection.

first: Danielle

last: Westhoff Smith

first: Katrina

last: Waters

first: Amie

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Effect of high-dose cyclophosphamide gene expression profiles in cardiomyocytes of C57BL/6J mice

status: Public on Jan 21 2022

city: Kagoshima

first: Takuro

last: Nishikawa

address: Sakuragaoka 8-35-1

department: Pediatrics

institute: Kagoshima University

summary: To clarify the mechanisms of cyclophosphamide (CY)-induced myocardial damage, we have analyzed the genome-wide expression profiles of C57BL/6J mice received CY, one of CY metabolites acrolein, and CY with N-acetyl cysteine (NAC). The microarray analysis revealed that the gene expression of L-type calcium channel (DHPR), ryanodine receptor 2 (RyR2), and Troponin C (TnC) were suppressed by CY administration. DHPR, RyR2 and TnC are responsible for control of intracellular calcium ion concentration and important for myocardial contraction. On the other side, the gene expression profiles after administration of acrolein differed from CY administration. Furthermore, the gene expression profiles after administration of NAC and CY, NAC did not inhibit the DHPR, RyR2 and TnC gene expression suppression.

overall_design: Six-week-old female mice were intraperitoneally injected with cyclophosphamide (CY, 400 mg/kg), acrolein (5 mg/kg), or N-acetyl cysteine (200 mg/kg) + CY once a daily for two days. Normal saline-treated mice were used as controls. Gene expression changes were measured 3 hours after the second dose. 3 independent studies were performed.

first: Emiko

last: Miyahara


title: Comparing expression profiles : among comparable samples in which target genes are knocked down

first: Jae

last: Song


title: Transcriptome analysis of M07e cells and patient derived AMKL cells upon SEKIT inhibition by CRISPRi

first: Camille

last: Lobry

overall_design: PolyA+ RNA from M07e cell line and patient derived cells following  CRISPRi inhibition of SEKIT was sequenced on HiSeq4000 to assess for transcriptome variations


title: Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment

status: Public on Aug 07 2022

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Cancer-associated fibroblasts (CAFs) are the dominant components of stroma in the tumor microenvironment (TME), and they influence cancer hallmarks by interacting with other TME components. However, the heterogeneity and dynamics of CAFs have not been systematically characterized across different cancer types. Here, we performed pan-cancer analysis on 226 samples from 164 donors across 10 types of solid cancers to profile the TME at single-cell resolution. The activation trajectory of fibroblasts into various major types of CAFs was divided into three distinct differentiated states and was capable of sculpting the TME, which was associated with the prognosis of immunotherapy. On the other hand, except for activation, minor CAF components represented the dynamic transition between fibroblasts and other TME components (i.e., macrophages, peripheral nerve and endothelial cells) and delineated the alternative origins of CAFs. Particularly, the ubiquitous presentation of CAFEndoMT (endothelial-mesenchymal transition), which may be stimulated by proximal SPP1+ tumor-associated macrophages, played a role in angiogenesis and patient survival stratifications. Our study comprehensively profiled the heterogeneity and plasticity of CAFs, implied a potential divergent origin of different CAF populations, and highlighted its generalized key role in the TME across different cancer types.

relation:
Reanalysis of: GSM3980125
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overall_design: In total, we included 232 single cell transcriptome samples (normal = 31; adjacent = 54; tumor = 148) from 12 articles for pancancer's analysis. Of these, 31 GSM samples were derived from GSE134355; 11 GSM samples were related to GSE141445; 49 samples were derived from the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-8107; 2 GSM samples were associated with GSE157703; 22 GSM samples were derived from GSE131907; 7 GSM samples were derived from GSE138709; 31 samples were derived from the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-6149 and E-MTAB-6653; 32 CRR samples were related to GSA database under accession number CRA001160; 10 GSM samples were related to GSE154778; 7 HRR samples were available in GSA-Human under the accession code HRA000212; 10 thyroid samples were derived from GSA-Human database under accession number HRA000686; 20 gastric samples were download from http://dna-discovery.stanford.edu/download/1401/;

first: Han

last: Luo

first: Xuyang

last: Xia

first: Li-Bin

last: Huang

first: Hyunsu

last: An

first: Minyuan

last: Cao

first: Hai-Ning

last: Chen

first: Wei-Han

last: Zhang

first: Yang

last: Shu

first: Xiangyu

last: Kong

first: Zhixiang

last: Ren

first: Pei-Heng

last: Li

last: Liu

first: Huairong

last: Tang

first: Ronghao

last: Sun

first: Chao

first: Bing

last: Bai

first: Weiguo

last: Jia

first: Yi

first: Wei

first: Li

last: Yang

first: Yong

last: Peng

first: Lunzhi

last: Dai

first: Hongbo

last: Hu

last: Jiang

first: Yiguo

first: Jingqiang

last: Zhu

first: Hong

first: Zhihui

first: Carlos

last: Caulin

first: Jihwan

last: Park


title: Analysis of chromatin interactions in M07e cells around SEKIT locus

first: Camille

last: Lobry

summary: In the recent years, massively parallel sequencing approaches identified hundreds of mutated genes in cancer providing an unprecedented amount of information about mechanisms of cancer cell maintenance and progression. However, while (it is widely accepted that) transformation processes result from oncogenic cooperation between deregulated genes and pathways, the functional characterization of candidate key players is mostly performed at the single gene level which is generally inadequate to identify these oncogene circuitries. In addition, studies aimed at depicting oncogenic cooperation involve the generation of challenging mouse models or the deployment of tedious screening pipelines. Genome wide mapping of epigenomic modifications on histone tails or binding of factors such as MED1 and BRD4 allowed identification of clusters of regulatory elements, also termed Super-Enhancers (SE). Functional annotation of these regions revealed their high relevance during normal tissue development and cancer ontogeny. An interesting paradigm of the tumorigenic function of these SE regions comes from ETO2-GLIS2-driven acute megakaryoblastic leukemia (AMKL) in which the fusion protein ETO2-GLIS2 is sufficient to promote an aberrant transcriptional network by the rewiring of SE regions4. We thus hypothesized that important regulatory regions could control simultaneously expression of genes cooperating in functional modules to promote cancer development. In an effort to identify such modules, we deployed a genome-wide CRISPRi-based screening approach and nominated SE regions that are functionally linked to leukemia maintenance. In particular, we pinpointed a novel SE region regulating the expression of both tyrosine kinases KIT and PDGFRA. Whereas the inhibition of each kinase alone affected modestly cancer cell growth, combined inhibition of both receptors synergizes to impair leukemia cell growth and survival. Our results demonstrate that genome-wide screening of regulatory DNA elements can identify co-regulated genes collaborating to promote cancer and could open new avenues to the concept of combined gene inhibition upon single hit targeting.

overall_design: 4Cseq has been performed in M07e cells using a bait in SEKIT locus

first: Julie

last: Chaumeil


title: ATACseq analysis of M07e cells and patient derived AMKL cells

overall_design: ATACseq was performed on M07e cells, AMKL patient derived cells and M07e cells upon CRISPRi inhibition of SEKIT


title: Profiling of H3K27ac in ETO2-GLIS2 positive AMKL cells and ETO2-GLIS2 binding

overall_design: ChIPseq for H3K27ac in cord blood CD34 cells, patient derived AMKL cells and inducible HEL_5j20 cell line

first: Thomas

last: Mercher


title: Genetic knockout of adiponectin receptor 1 (Adipor1) in mouse leads to progressive retinal degeneration

status: Public on Mar 02 2022

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina of AdipoR1-/- (KO) mice, we collected samples from KO and WT animals at day 19, 25 and 30, generated single-cell suspensions, and performed scRNA-Seq (10X Genomics). Additionally, we collected samples from a bulk population and performed bulk RNA-seq of WT and AdipoR1-/- at P30 (Illumina NextSeq 500 platform).

overall_design: Single-cell RNAseq:  In each of the six experimental groups (WT and AdipoR1-/- at P19, P25, and P30), four retinae were used to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. For each group, freshly dissociated cells (~10,000) were loaded into a 10x Genomics Chromium Single Cell system using v2 chemistry following the manufacturer's instructions.  Bulk RNAseq:   We analyzed a total of 16 samples derived from mice at P30: Four samples for each AdipoR1-/- KO retina, AdipoR1-/- KO RPE, WT retina, and WT RPE.

first: Dominik

last: Lewandowski

first: Elliot

last: Choi

first: Susie

last: Suh


title: Single-cell genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

status: Public on Dec 21 2021

city: Los Angeles

first: Janos

last: Peti-Peterdi

address: 1501 San Pablo Street

institute: University of Southern California

summary: Single cell based gene expression analysis of the rare kidney cell type, the macula densa in control and physiological stimulatory conditions. The hypothesis tested in the study was that macula densa cells utilize unique and cell-specific molecular networks that play important roles in sensory, regulatory, and secretory functions, and in the physiological stimulation of these cells by environmental clues such as low salt condition. Results provide important information of the identity, biological and physiological functions of macula densa cells consistent with their chief role in the regulation of kidney functions.

overall_design: RNA obtained from freshly isolated single mouse macula densa cells. Mice were  subjected to 14 days of normal salt (control) or low salt (LS) diet.

first: Georgina

last: Gyarmati

first: Yibu

last: Chen


title: Genome-wide analysis of macula densa cell gene expression in control and physiological stimulatory conditions

summary: Analysis of the function and physiological regulation of the rare kidney cell type of the macula densa at gene expression level. The hypothesis tested in the study was that macula densa cells utilize unique and cell-specific molecular networks that play important roles in sensory, regulatory, and secretory functions, and in the physiological stimulation of these cells by environmental clues such as low salt condition. Results provide important information of the identity, biological and physiological functions of macula densa cells consistent with their chief role in the regulation of kidney functions.

overall_design: Total RNA obtained from freshly isolated mouse macula densa cells. Mice were  subjected to 14 days of normal salt (control) or low salt diet combined with ACE inhibition.


title: Distinct TNF Receptors Dictate Stem Cell Fitness Versus Lineage Output in Clonal Hematopoiesis of Aging

status: Public on Nov 25 2021

city: Bar Harbor

first: Jennifer

last: Trowbridge

address: 600 Main Street

institute: The Jackson Laboratory

summary: Clonal hematopoiesis of aging results from enhanced fitness of mutant hematopoietic stem cells (HSCs) and associates with both favorable and unfavorable health outcomes related to lineage cell types produced by mutant HSCs. The extent to which lineage output can be controlled in clonal hematopoiesis is unknown. Using a mouse model of DNMT3AR882/+ clonal hematopoiesis (Dnmt3aR878H/+), we find that aging-induced TNFα signaling drives selective advantage of mutant HSCs concomitant with B lymphoid lineage production. Genetic loss of TNFα receptor TNFR1 impaired mutant HSC fitness while loss of TNFR2 abrogated lymphoid production and resulted in unrestrained myeloid cell production from mutant HSCs. These results support a model where clone size and lineage output can be independently targeted to harness potential beneficial aspects of clonal hematopoiesis.

overall_design: Mx1-Cre (control) or Dnmt3a-mutant (D3a-mut) bone marrow from young donors was tranplanted into young or aged recipient CD45.1 mice. 4 months post-transplant, LT-HSCs or MPP3s were re-isolated from the recipients and submitted for RNA-seq analysis. Aged Control LT-HSCs (n = 3), Aged Control MPP3s (n = 4), Aged D3Amut LT-HSCs (n = 4), aged D3Amut MPP3s (n=4),  young control LT-HSCs (n = 4), young control MPP3s (n =4), young D3Amut LTHSCs (n =2), young D3amut MPP3s (n = 3)

last: SanMiguel


title: Molecular Cooperativity of Dnmt3a and Npm1 Mutations in Transformation from Clonal Hematopoiesis to Myeloid Malignancy

summary: Driver somatic mutations in adult acute myeloid leukemia (AML) may be preceded by a benign state termed clonal hematopoiesis (CH). To develop therapeutic strategies to prevent leukemia development from CH, it is important to understand the mechanisms by which CH-driving and AML-driving mutations cooperate. Here, we utilize mice with inducible mutant alleles common in CH (DNMT3AR882; mouse Dnmt3aR878H/+) and AML (NPM1c; mouse Npm1cA/+). We find that Dnmt3aR878H/+ hematopoietic stem cells (HSCs), but not multipotent progenitor cell (MPP) subsets, have reduced expression of cytokine and pro-inflammatory transcriptional signatures and a functional competitive advantage over their wild-type counterparts. These Dnmt3aR878H/+ HSCs are transformed by activation of Npm1cA/+, generating myeloid malignancies in which few additional cooperating somatic mutation events were detected. At a molecular level, Npm1cA/+ acutely increased accessibility of a distinct set of promoters in cooperation with Dnmt3aR878H/+ than it did as a single mutation. These promoters were enriched for pro-inflammatory response signatures, p53 pathway, DNA repair and targets of transcription factors implicated in AML, including Hmgb1 and Pax4. These results suggest cooperativity between pre-existing Dnmt3a mutation and Npm1 mutation at the chromatin level, where specific loci altered in accessibility by the Npm1 mutation are dependent on Dnmt3a mutation status. These findings have implications for biological understanding and therapeutic intervention of the transformation from CH to AML.

overall_design: 1 x 10^6 whole bone marrow cells from young WT (Mx-Cre), Dnmt3a-flR878H/+, Npm1-frt/+, or Dnmt3a-flR878H/+;Npm1-frt/+ were transplanted into young, lethally irradiated CD45.1 recipients. 4 wks post-transplant, all recipient mice received poly(I:C), and 4 wks post-poly(I:C), all mice recieved tamoxifen. 4 wks post-tamoxifen, the bone marrow was harvested and LT-HSCs and MPP3s were sorted via FACS and used for ATAC-library prep.


title: Mesenchymal cell-derived septoclasts resorb cartilage during endochondral ossification and fracture healing

status: Public on Dec 10 2021

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: For scRNA-seq of fracture bone , 14 days post-fracture (PFD14) femur and control bones were harvested, cleaned surrounding tissue and the nail insert was removed from fracture bone. Control and PFD14 bone single cell suspension and non-hematopoietic stromal cells were prepared for scRNA-seq .

overall_design: Fracture bone single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC)  using  10X genomics

first: Kishor

middle: K

last: Sivaraj

first: Ralf

middle: H

last: Adams


title: In vivo partial reprogramming in 4F mice

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

summary:
Partial reprogramming by expression of reprogramming factors (Oct4, Sox2, Klf4 and cMyc) for short periods of time restores a youthful epigenetic signature to aging cells and extends the lifespan of a premature aging mouse model. However, the effects of longer-term partial reprogramming in physiologically aging wild-type mice are unknown. Here, we have performed various long-term partial reprogramming regimens, including different onset timings, during physiological aging in different mouse strains. n=239 tissues from mice.
The study involves different conditions (treated and untreated samples) and leads to 7 groups:   1) Black6 mouse +Doxocycline  2) 4 factor mouse+1 month of Doxocycline.  3) 4F mice+7month of Dox 4) 4F+10 months of Dox    5) 4F mice which are relatively old    6) B6 mice that are relatively old  7) 4F mice which are relatively young.

overall_design: n=168 mouse tissues (liver, spleen, skeletal muscle, lung).  Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Pradeep

last: Reddy

first: Juan

last: Belmonte


title: Methylation studies in horses

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses
We generated DNA methylation data from n=333 horse tissue samples representing tissues.  Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.

overall_design: N=333 tissue samples from horses. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Carrie

last: Finno


title: chip-seq for MoIug4 in rice

status: Public on Nov 17 2021

city: Nanjing

first: Zhengguang

last: Zhang

address: Weigang No.1

institute: Nanjing agricultural university

summary: chip-seq for MoIug4 in rice, putative transcription factor MoIug4 was secrected from M. oryzae to the nucleus of rice. Here, we performed of MoAtf1 chip-seq assays to uncovered the regulation network

overall_design: MoIug4-GFP binding with the whole promoters in rice

first: Xinyu

last: Liu