title: Next Generation Sequencing Facilitates Quantitative Analysis of Tumor Infiltrating CD8+T Cells Transcriptomes From Control and Manganese(II) Treated C57BL/6 Wild Type Mice

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary:
Purpose: The goals of this study are to compare the differentially expressed genes of tumor infiltrating CD8+T cells between control and Manganese(II) treated mice. We mainliy fouced on the differentiation of trascription and effector related genes.
Methods:C57BL/6 mice were injected subcutaneously in the right flank with B16-F10 and divided into two groups followed by treatment with control (saline) or Manganese(II) respectively. After 14days, mice were euthanized with CO2 and tumor infiltrating CD8+T cells were isolated by FACS. Then RNA of sorted CD8+T cells were generated by deep sequencing using BGISEQ-500. Clean tags were mapped to the mouse genome database (GCF_000001635.25_GRCm38.p5) by HISAT (hierarchical indexing for splicing alignment for transcripts) software.
Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the mouse genome (GCF_000001635.25_GRCm38.p5). The significance of the differential expression of genes was defined by the bioinformatics service of Beijing Genomics Institute according to the combination of the absolute value of log2-Ratio ≥ 1 and false discovery rate ≤ 0.001.
Conclusions: Manganese(II) enhances the function of tumor infiltrating CD8+T cells.

overall_design: mRNA profiles of tumor infiltrating CD8+T cells from control and Manganese (II) treated mice were generated by deep sequencing using  BGISEQ-500.

first: Mengze

last: Lv


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation (MOLM13 HiC)

status: Public on Jan 19 2021

city: New York

first: Hua

last: Zhou

state: NY

address: 550 First Avenue, Smilow 1307

department: PATHOLOGY

country: USA

institute: NYU SCHOOL OF MEDICINE

summary: Genome-wide assessment of TADs in AML cells

overall_design: TAD domains in MOLM13 AML cells

first: Eric

last: Wang

first: Iannis

last: Aifantis


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation (ECCITE-seq)

summary: Single cell CRISPR screen of AML differentiation genes

overall_design: ECCITE-seq analysis of gene candidates in AML


title: LincRNA PVT1 associates with EZH2 and with the androgen receptor in LNCaP prostate cancer cells and inhibits the expression of genes involved with cell death, cell differentiation and cell adhesion

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

summary: Long intergenic non-coding RNA (lincRNA) PVT1 is an oncogene known to be overexpressed in various types of cancer. PVT1 high expression is associated with increased prostate cancer (PCa) risk while androgen-independent PCa progression is correlated with increased androgen receptor (AR) expression. However, the mechanism of PVT1 and AR involvement in the development of prostate cancer is still unclear. Here, we tested the hypothesis that PVT1 participates along with AR and the methyltransferase EZH2 from the Polycomb repressive complex 2 in the repression of gene expression in LNCaP prostate cancer cells. Native RNA-binding proteins immunoprecipitation followed by quantitative PCR of co-precipitated RNAs (RIP-qPCR) revealed that in LNCaP, PVT1 lincRNA is associated both with AR (10 – 12 % of PVT1 input) and EZH2 (36 – 42 % of input) in the presence or absence of androgen. PVT1 knockdown in LNCaP in the presence of androgen increased the expression of 160 genes whose expression was repressed by androgen, including genes involved in regulation of cell differentiation, in inhibition of cell migration/invasion and in triggering apoptosis. Analysis by chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) of the histone marks occupancy at the promoter region of the tumor suppressor gene NOV, one of the genes that had an increased expression upon PVT1 silencing, showed a significant epigenetic remodeling at its promoter and enhancer regions upon PVT1 knockdown. We provide evidence for a genome-wide transcriptional repressive role of PVT1 lincRNA on tumor suppressor genes in prostate cancer cells.

overall_design: Two-color hybridization design. Aliquots of total RNA isolated from LNCaP cells transfected with siCTRL or siPVT1 and treated with androgen R1881 or vehicle controls were labeled with Cy3 or Cy5 and hybridized to Agilent DNA SurePrint G3 Human Gene Expression 8x60k v3 Oligoarray (design ID # 039494) . Biological replicates: 4. No technical replicates.

first: Alexandre

last: Videira

middle: C

first: Sergio

last: Verjovski-Almeida


title: Diabetes severity is reflected by changes in a cardiac gene expression signature characterized by metabolism and cell death processes

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

type: Expression profiling by high throughput sequencing

summary: We tested the impact of a graded reduction in insulin on cardiac gene expression with particular focus on metabolism and energy homeostasis. Wistar rats were made diabetic with a single dose of either 55 (D55) or 100 (D100) mg/kg streptozotocin (STZ). Although both D55 and D100 were equally hyperglycemic compared to control, D100 showed markedly lower plasma insulin and robust increases in plasma FA and TG. D100 demonstrated more significant transcriptomic changes than D55 with enrichment for metabolic processes that direct the heart to use FA, when glucose use is obstructed. Analysis of a protein-protein interaction network identified functional networks in D100 that describe mitochondrial overload, incomplete fatty acid oxidation, and loss of cardiomyocytes. Our data suggests that the differential reduction of insulin produced a dramatic change in cardiac gene expression largely enriched for substrate metabolism functions as well as a gene expression program supporting cell death.

overall_design: We analyzed 4 control samples, 6 D55 samples and 6 D100 samples with RNA-Seq.

first: Karn

last: Puri

first: Nathaniel

last: Lal

first: Fulong

first: Rui

last: Shang

first: Corey

last: Nislow

first: Bahira

last: Hussein

first: Brian

last: Rodrigues


title: ChIP-seq for E4BP4 in CD4+ T cell

city: changsha

first: Zijun

state: hunan

address: N0.139 RENMIN MIDDLE ROAD

department: Dermatology

country: China

institute: Second Xiangya Hospital of Central South university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, using ChIP-seq, we demonstrate that the transcriptional repressor Adenovirus E4 promoter-binding protein (E4BP4) binds directly to the Bcl6 promoter, which a key transcription factor controlling Tfh cell differentiation. By obtaining sequence from chromatin immunoprecipitated DNA of E4BP4 overexpressing CD4+T cells, we generated genome-wide binding gene spectrums of E4BP4. These results reveal that E4BP4 interacts with BCL6 and E4BP4 directly modulated the expression of Bcl6 to reveal the mechanism downstream of E4BP4 that regulates Tfh cell differentiation.

overall_design: We identified the binding patterns of E4BP4 in CD4+T cells using ChIP-seq.

first: Ming

last: Zhao

first: Qianjin

last: Lu


title: RNA-seq analysis of the effects of E4BP4 in Tfh cells

summary: The goal of this experiment is to measure the changes in gene expression in E4BP4 deficient in vitro induced mice Tfh cells.

overall_design: We screened the gene expression profiles of Tfh cells that were differentiated in vitro after isolation from E4BP4-conditional knockout mice and wild-type mice using RNA-seq to further clarify the role of E4BP4 in regulating Tfh cell differentiation.


title: E4BP4 is a transcriptional brake in Tfh cell differentiation

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

overall_design: Refer to individual Series


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 cell line SRC-3 ChIP-seq]

status: Public on Jan 18 2021

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: The role of the androgen receptor (AR) in estrogen receptor alpha (ER) positive breast cancer is controversial, constraining implementation of AR-directed therapies. Using a diverse, clinically relevant panel of cell-line and patient-derived models, we demonstrate that AR activation, not suppression, exerts potent anti-tumor activity in multiple disease contexts, including resistance to standard-of-care ER and CDK4/6 inhibitors. Importantly, AR agonists combined with standard-of-care agents enhanced therapeutic responses. Mechanistically, agonist activation of AR altered the genomic distribution of ER and essential co-activators (p300, SRC-3), resulting in repression of ER-regulated cell cycle genes and up-regulation of AR target genes, including known tumor suppressors. A gene signature of AR activity positively predicted disease survival in multiple clinical ER+ breast cancer cohorts.  These findings provide unambiguous evidence that AR has a tumor suppressor role in ER+ breast cancer and support AR agonism as the optimal AR-directed treatment strategy, revealing a rational therapeutic opportunity.

overall_design: ChIP-seq for SRC-3 in ZR-75-1 cells cultured in steroid-depleted conditions and treated for 6 hours with Vehicle, E2 or E2+DHT (10 nM each).

first: T

middle: E

last: Hickey

first: L

middle: A

first: G

last: Laven-Law

first: W

middle: D

last: Tilley


title: Role of nitric oxide and nitric oxide synthase isoforms in pulmonary emphysema.

city: Kitakyushu

first: Kaori

last: Kato

address: 1-1 Iseigaoka, Yahatanishiku, Kitakyushu city, Fukuoka 807-8555 Japan

country: Japan

institute: University of Occupational and Environmental Health, Japan

summary: The purpose of this study is to comprehensively elucidate the role of nitric oxide and nitric oxide synthase isoforms in pulmonary emphysema using cap analysis of gene expression (CAGE) sequencing.

overall_design: We performed CAGE sequencing using unexposed lung tissue of C57BL/6J (wild type mice) and triply n/i/eNOSs-/- mice at 4 weeks of age (n=4 each).

first: Masato

last: Tsutsui

first: Shingo

last: Noguchi

first: Keisuke

last: Naito

first: Takaaki

last: Ogoshi

first: Masahiro

last: Tahara

first: Ke-Yong

last: Wang

first: Hiroaki

last: Shimokawa

first: Kazuhiro

last: Yatera


title: RNAseq of CD44v6+ and CD44v6- colon cancer cells

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

summary: We previously reported that colorectal cancer sphere cells express CD44v6, which is required for their migration and generation of metastatic tumors. The goal of this study is to compare NGS-derived  transcriptome profiling (RNA-seq) obtained from enriched CD44v6+ and CD44v6- fractions from sphere cells harboring different mutations.

overall_design: Examination of the transcriptome of CD44v6+ and CD44v6- subpopulation obtained from colorectal cancer sphere cells with different mutational background

first: Alessio

first: Sven

last: Beyes


title: The Fetal and Infant Human Testis Cell Atlas via Single-cell RNA-seq

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: Human testis development in prenatal life involves complex changes in germline and somatic cell identity. To better understand, we profiled and analyzed ~32,500 single-cell transcriptomes of testicular cells from embryonic, fetal and infant stages. Our data shows that at 6-7 weeks post-fertilization as the testicular cords are established, the Sertoli and interstitial cells originate from a common heterogeneous progenitor pool, which then resolves into fetal Sertoli cells (expressing tube-forming genes) or interstitial cells (including Leydig-lineage cells expressing steroidogenesis genes). Almost ten weeks later, beginning at 15-16 weeks post-fertilization, the male primordial germ cells exit mitosis, downregulate pluripotent transcription factors and transition into cells that strongly resemble the ‘State 0’ spermatogonia originally defined in the infant and adult testes. Therefore, we termed these fetal spermatogonia ‘State f0’. Taken together, we reveal multiple insights into the coordinated and temporal development of the embryonic, fetal and postnatal male germline together with the somatic niche.

overall_design: We isolated single testicular cell from an infant (5 months old). Two technical replicates were performed.

first: Bradley

middle: R

last: Cairns


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 cell line Bicalutamide study ER ChIP-seq]

first: Luke

last: Selth

overall_design: ChIP-seq for ERα in ZR-75-1 cells cultured in steroid-depleted conditions and treated for 6 hours with Vehicle, 1 nM E2, 1 µM Bicalutamide, E2 + Bicalutamide, or E2 + 1 nM DHT. Bicalutamide was added 1 h prior to any hormone addition.

first: T

first: L

first: E

last: Ebrahimie


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 cell line RNA-seq]

overall_design: RNA-seq of ZR-75-1 cells cultured in steroid-depleted conditions then treated for 4 hours with E2 or E2+DHT (10 nM each).

last: Hickey

first: G

last: Laven-Law

first: W


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [PDX model HCI-005 ChIP-seq]

overall_design: ChIP-seq for AR, ERα, and H3K27ac in the patient-derived xenograft (PDX) tumor model HCI-005 treated for 5 days with either Vehicle, DHT, or Enobosarm.

first: K

middle: M

last: Chia

first: H

middle: H

last: Milioli

first: D

last: Roden

last: Lim

last: Tilley


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [T-47D cell line ChIP-seq]

overall_design: ChIP-seq for AR and ERα in T-47D cells cultured in steroid-depleted conditions and treated for 4 hours with E2 or E2+DHT (10 nM each).


title: MAX-mutant small cell lung cancers sustain impaired activities of the MGA-dependent ncPRC1

city: Hospitalet d'Llobregat

first: manuel

last: torres diz

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: PEBC

country: Spain

institute: IDIBELL

summary: The MYC-axis is disrupted in cancer, mostly by activation of the MYC-oncogenes but also through inactivation of the MYC-partner, MAX, or of the MAX-partner, MGA, both also members of the polycomb repressive complex, ncPRC1.6. Here, we use genetically modified MAX-deficient small cell lung cancer (SCLC) cells and apply genome wide and proteomics analysis to study the tumor suppressor function of MAX. We find that MAX-mutant SCLCs classify as ASCL1-type and lack MYC-transcriptional activities. MAX-restitution triggers pro-differentiation expression profiles that shift when MAX and oncogenic MYC (HMYC/MAX) are co-expressed. Despite the ncPRC1.6 can be formed, the lack of MAX restricts global MGA-occupancy, selectively driving its recruitment towards E2F6-motifs. Conversely, MAX-restitution enhances MGA-occupancy and global gene repression of genes involved in different functionalities, including stem-cell and DNA repair/replication. Collectively, these findings reveal that MAX-mutant SCLCs have ASCL1-characteristics, are MYC-independent and their oncogenic features include a deficient ncPRC1.6-mediated gene repression.

overall_design: 6 cell lines from SCLC were analyzed in triplicates to compare gene expression signature.

first: Montse

last: Sanchez-Cespedes

first: Paula

last: Llabata

first: Manuel

last: Torres-diz

first: Laureano

last: Tomas

first: Antonio

last: Gomez

first: Octavio

last: Romero

first: Joaquim

last: Grego-Bessa

first: Pere

last: Llinas

first: Manel

last: Esteller

first: Biola

last: Javierre


title: Host transcriptional response to TB preventive therapy differentiates two sub-groups of IGRA-positive individuals: in vitro (Quantiferon tube)-stimulated blood

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

summary:
We hypothesized that individuals with immunological sensitization to Mycobacterium tuberculosis (Mtb), conventionally regarded as evidence of latent tuberculosis infection (LTBI), would demonstrate binary responses to preventive therapy. This would reflect the differential immunological consequences of the sterilization of viable infection in those with an active Mtb infection versus no Mtb killing in those who, despite T cell recognition of Mtb antigens, did not harbor viable Mtb bacilli.
We investigated the  blood transcriptional profiles of 18 individuals with a positive IGRA result and known recent exposure to an index person with isoniazid and rifampicin susceptible pulmonary tuberculosis, at baseline, 2  weeks after initiating combined rifampicin/isoniazid (RH) preventive therapy and at treatment completion. Healthy control volunteers with no history of TB exposure and negative IGRA results were also included. RNA from unstimulated and M. tuberculosis peptide stimulated whole blood (from QuantiFERON TB1 and TB2 tubes) was measured using Agilent microarrays.
A set of 474 genes showed the greatest interpersonal and temporal expression variability in antigen-stimulated blood. By performing longitudinal unsupervised clustering analysis with the subset of most variable genes, the IGRA+ participants were separated into two distinct groups. The IGRA-negative controls clustered within one of these groups suggesting that, in contrast to the other subgroup of IGRA+ individuals, RH had no discernible effect in this subgroup. 117 genes were significantly differentially expressed over time between these two groups, with the majority of them associated with immunological pathways known to be important in mycobacterial control. We contend that the different host RNA response reflects lack of Mtb viability in the group that clustered with the IGRA- unexposed healthy controls, and Mtb viability in the one that clustered away.
Gene expression patterns in the blood of IGRA+ individuals emerging during the course of RH treatment which reflect Mtb viability could have major implications in the identification of risk of progression/reactivation, treatment stratification and clinical trials for LTBI therapy.

overall_design: 22 donors (18 IGRA+; 4 IGRA- (healthy controls). All received LTBI preventive treatment. Blood collected at baseline and two weeks for all donors, and after 12-18 weeks for IGRA+ donors. Blood cultured in Quantiferon tubes (nil, TB1, TB2) for 22 hours.

first: Claire

last: Broderick

first: Jacqueline

first: JiSook

last: Lee

first: Myrsini

last: Kaforou

first: David

last: Moore


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer  [ZR-75-1 cell line p300 ChIP-seq]

first: Luke

last: Selth

overall_design: ChIP-seq for p300 in ZR-75-1 cells cultured in steroid-depleted conditions and treated for 6 hours with Vehicle, E2 or E2+DHT (10 nM each).

first: T

last: Hickey

first: L

first: G

last: Laven-Law

first: E

last: Ebrahimie

first: W

last: Tilley


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 cell line AR, ER, and H3K27ac ChIP-seq]

overall_design: ChIP-seq for AR, ERα, and H3K27ac in ZR-75-1 cells cultured in steroid-depleted conditions and treated for 4 hours with E2 or E2+DHT (10 nM each).


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 xenograft RNA-seq]

overall_design: RNA-seq of ZR-75-1 xenograft tumors treated for 5 days with either Vehicle, DHT, Enobosarm, or Enzalutamide.

first: H

last: Milioli

first: D

last: Roden

first: M

last: Hui

first: A

last: Swarbrick

last: Lim


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [Normal and tumor patient-derived explant RNA-seq]

overall_design: RNA-seq of patient-derived explants representing normal breast or ER+ invasive breast cancer tissue treated with E2 or E2+DHT (10 nM each) for 24 hours.

first: S

last: Jindal


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [ZR-75-1 xenograft ChIP-seq]

overall_design: ChIP-seq for AR & ERα on ZR-75-1 xenograft tumors, treated for 5 days with Vehicle, DHT, or Enobosarm.

last: Stelloo

last: Zwart


title: Identification of diverse tumor endothelial cell populations in malignant glioma

status: Public on Jan 17 2021

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Background: Glioblastoma multiform is the most common and aggressive type of primary brain tumor, as most patients succumb to the disease less than two years after their diagnosis. Critically, studies demonstrate that glioma recruits surrounding blood vessels, while some work suggests that tumor stem cells themselves may directly differentiate into endothelial cells, yet the molecular and cellular dynamics of the endothelium in glioma are poorly characterized. The goal of this study was to establish clear molecular and morphological benchmarks for tumor associated vessels (TAVs) and tumor derived endothelial cells (TDECs) during GBM disease progression.  Methods: Using In-Utero Electroporation and CRISPR/Cas9 genome engineering to generate a native, immunocompetent mouse model of glioma, we characterized vascular-tumor dynamics in three dimensions during tumor progression. We also employed bulk and single-cell RNA-Sequencing to elucidate the relationship between TAV and TDECs. We confirmed our findings in a patient derived orthotopic xenograft (PDOX) model.   Results:  Using a mouse model of glioma, we identified progressive alteration of vessel function and morphogenesis over time. We also showed that TDECs exist, and that these cells contribute to vessels within the tumor. Furthermore, transcriptional profiling demonstrates that both TAVs and TDECs are molecularly distinct, and that both populations feature extensive molecular heterogeneity. Finally, the distinct molecular signatures of these heterogenous populations are also present in human glioma.  Conclusions: Our findings show extensive endothelial cell heterogeneity within the tumor and tumor microenvironment, and provide insights into the diverse cellular and molecular mechanisms that drive glioma vascularization and angiogenesis during tumorigenesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Jeff

last: Carlson

last: Cantu-Gutierrez

first: Brittney

last: Lozzi

first: Emmet

last: Huang-Hobbs

first: Williamson

last: Turner

first: Burak

last: Tepe

first: Yiqun

last: Zhang

first: Alexander

last: Herman

first: Ganesh

last: Rao

first: Chad

middle: J

last: Creighton

first: Joshua

last: Wythe

first: Benjamin

last: Deneen


title: Myeloid-derived suppressor cells promote lung cancer metastasis

city: Guagzhou

first: Shouheng

last: Lin

address: 190 Kaiyuan Avenue, Science Park, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Myeloid-derived suppressor cells (MDSCs) suppress antitumor immune activities and facilitate cancer progression. Although the concept of immunosuppressive MDSCs is well established, the mechanism that MDSCs regulate non-small cell lung cancer (NSCLC) progression through the paracrine signals is still lacking. Here, we reported that the infiltration of MDSCs within NSCLC tissues were associated with the progression of cancer status, and were positively correlated with the Patient-derived xenograft (PDX) model establishment, and poor patient prognosis. Intratumoral MDSCs directly promoted NSCLC metastasis and highly expressed chemokines that promote NSCLC cells invasion, including CCL11. CCL11 was capable of activating the AKT and ERK signaling pathways to promote NSCLC metastasis through the epithelial-mesenchymal transition (EMT) process. Moreover, high expression of CCL11 was associated with a poor prognosis in lung cancer as well as other types of cancer. Our findings underscore that MDSCs produce CCL11 to promote NSCLC metastasis via activation of ERK and AKT signaling and induction of EMT, suggesting that the MDSCs-CCL11-ERK/AKT-EMT axis contains potential targets for NSCLC metastasis treatment.

overall_design: mRNA profiles of 75 human lung cancer samples, 4 MDSCs samples and 15 cell samples were generated by deep sequencing, using BGISEQ-500.

first: Peng

last: Li


title: Tumor-Derived Thymic Stromal Lymphopoietin Expands Bone Marrow B-cell Precursors in Circulation to Support Metastasis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Immature B cells in the bone marrow emigrate into the spleen during adult lymphopoiesis. Here, we report that emigration is shifted to earlier B-cell stages in mice with orthotopic breast cancer, spontaneous ovarian cancer, and possibly in human breast carcinoma. Using mouse and human bone marrow aspirates and mouse models challenged with highly metastatic 4T1 breast cancer cells, we demonstrated that this was the result of secretion of thymic stromal lymphopoietin (TSLP) by cancer cells. First, TSLP downregulated surface expression of bone marrow (BM) retention receptors CXCR4 and VLA4 in B-cell precursors, increasing their motility and, presumably, emigration. Then, TSLP supported peripheral survival and proliferation of BM B-cell precursors such as pre-B–like cells. 4T1 cancer cells used the increased pool of circulating pre-B–like cells to generate metastasis-supporting regulatory B cells. As such, the loss of TSLP expression in cancer cells alone or TSLPR deficiency in B cells blocked both accumulation of pre-B–like cells in circulation and cancer metastasis, implying that the pre-B cell–TSLP axis can be an attractive therapeutic target.  Significance: Cancer cells induce premature emigration of B-cell precursors from the bone marrow to generate regulatory B cells.

overall_design: CD19+ B cells were FACS sorted from spleens of control naive or 4T1 cancer-bearing mice (female, BALB/c mice, N=3 per experimental group). CD19+ B cells of tumor-baring mice were further sorted into CD23+ (follicular B cells) or CD23-, CD25- (pro-B cell) or CD23-, CD25+ (pre-B cell) populations. CD19+ B cells from naïve mice were in vitro stimulated with 4T1 or 4T1-PE cancer cell conditioned media for 2 days, as described in Olkhanud et al., Cancer Research, 2011, to generate TU4T1 and TU4T1_PE cells, respectively. In addition,  CD19+ B cells from naïve mice were in vitro stimulated with BAFF/Blys or with 4T1-P

first: Emeline

last: Ragonnaud

first: Kanako

last: Moritoh

first: Monica

last: Bodogai

first: Fedor

last: Gusev

first: Soizic

last: Garaud

first: Chen

last: Chen

first: Xin

last: Wang

first: Tuvshintugs

last: Baljinnyam

first: Kevin

middle: G

last: Becker

first: Robert

middle: W

last: Maul

first: Karen

last: Willard-Gallo

first: Evgeny

last: Rogaev

first: Arya

last: Biragyn


title: The Androgen Receptor is a Tumor Suppressor in Estrogen Receptor Positive Breast Cancer [PDX model HCI-005 & GAR15-13 RNA-seq]

first: Luke

last: Selth

overall_design: RNA-seq of patient-derived xenograft (PDX) tumor models HCI-005 & GAR15-13 treated for 5 days with either Vehicle, DHT, or Enobosarm.

first: T

last: Hickey

first: L

first: K

last: Chia

first: H

last: Milioli

first: D

last: Roden

first: G

last: Laven-Law

first: W

last: Lim

last: Tilley


title: Histone demethylase KDM4A-mediated promotion of PAF1/NFATC2 expression is required for oncogenesis in MLL-AF9 acute myeloid leukemia [RNA-seq]

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

institute: Paul O' Gorman Leukaemia Research Centre

summary: In this study we identified the histone demethylase KDM4A as an essential and selective regulator of AML oncogenic potential. RNAseq was used to follow the changes in gene expression following KDM4A knockdown in MLL-AF9 human AML THP-1 cells

overall_design: Human MLL-AF9 AML THP-1 cells were spinoculated with two separate and distinct lentiviruses, each resulting in the expression of a shRNA targeting  the KDM4A transcript. A third lentivirus was included as a negative control, which causes the expression of a non-targeting control (NTC) shRNA. Puromycin selection was used to select cells which had been infected 48 hours following spinoculation. Total RNA was harvested 72 hours following puromycin selection. There are biological replicates for each condition.

first: Xu

last: Huang

first: Matthew

last: Massett


title: Histone demethylase KDM4A-mediated promotion of PAF1/NFATC2 expression is required for oncogenesis in MLL-AF9 acute myeloid leukemia

overall_design: Refer to individual Series


title: Establishment of intestinal organoid cultures modeling injuryassociated epithelial regeneration [ChIP-seq]

status: Public on Jan 16 2021

city: Beijing

first: Yulin

last: Lyu

department: School of Life Sciences

summary: The capacity of 3D organoids to mimic physiological tissue organization and functionality has provided an invaluable tool to model development and disease in vitro. However, conventional organoid cultures primarily represent the homeostasis of self-organizing including VPA, EPZ6438, LDN193189, and R-Spondin 1 conditioned medium, which mimics the gut epithelium regeneration that produces hyperplastic crypts following injury; therefore, these organoids were designated hyperplastic intestinal organoids (Hyperorganoids). Single-cell RNA sequencing identified different regenerative stem cell populations in our Hyper-organoids that shared molecular features with in vivo injury-responsive Lgr5+ stem cells or Clu+ revival stem cells. Further analysis revealed that VPA and EPZ6438 were indispensable for epigenome reprogramming and regeneration in Hyper-organoids, which functioned through  epigenetically regulating YAP signaling. Furthermore, VPA and EPZ6438 synergistically promoted regenerative response in gut upon damage in vivo. In summary, our results demonstrated a new in vitro organoid model to study epithelial regeneration, highlighting the importance of epigenetic reprogramming that pioneers tissue repair.

overall_design: H3K27me3 ChIP-seq of intestine organoids with different conditions in vitro and mouse crypts with different treatments in vivo.

first: Molong

last: Qu

first: Liang

last: Xiong

first: Cheng

last: Li

first: Jun

last: Xu

first: Hongkui

last: Deng


title: Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes

city: Xinxiang

first: Qiu

last: Zongbo

state: Henan

address: 147 Jianshe Road

department: College of Life Science

institute: Henan Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of Paulownia tomentosa cambial tissues at gene expression level. The hypothesis tested in the present study was that miRNAs can regulate the development of the vascular cambium.The results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers.

overall_design: Examination of 3 different periods in Paulownia tomentosa cambial tissues

first: Zongbo

last: Qiu

first: Yanyan

last: He


title: Temporal changes of gene expression in bovine endometrium after parturition

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

institute: Nagoya University

summary: To clarify the regenerative mechanism of endometrium after parturition in cows, mRNA expression profiles in bovine endometrium were investigated during postpartum period. after PVP-I treatment in cows. The differentially expressed genes in the endometrium between postpartum days 49-52 and days 99-101 were 23 genes, and they were much lower than those before postpartum days 49-52. This result suggests that endometrial regeneration after parturition is completely accomplished until postpartum days 49-52.

overall_design: To clarify the gene expression in bovine endometrium at different period after parturition, 4 female cows were used. The endometrial tissues were collected 4 times from the same individual. Several endometrial tissues were biopsied using uterine biopsy forceps from the uterine horns on 9-11, 29-32, 49-52, and 99-101 days after parturition.

first: Ryoki

last: Tatebayashi

first: Sho

last: Nakamura

first: Yasuhiro

last: Morita

first: Satoshi

last: Ohkura

first: Koji

last: Kimura


title: Changes in proportion of side population cells and gene expression in bovine endometrium after Intrauterine administration of povidone-iodine

summary: To clarify whether the regenerative mechanism of endometrium after PVP-I treatment is similar to that after parturition in cows, mRNA expression profiles in bovine endometrium were investigated after PVP-I treatment in cows. Common differentially expressed genes between after PVP-I administration and parturition were few. The difference of the pattern of gene expression changes between after PVP-I administration and postpartum period suggests that the endometrial regeneration after PVP-I administration had different mechanism from parturition.

overall_design: To clarify the changes of gene expression in bovine endometrium after PVP-I treatment, 3 female cows were used. The endometrial tissues were collected 4 times from the same individual. Several endometrial tissues were alternately biopsied using uterine biopsy forceps from the left and right uterine horns on day 0 , 2, 7 and 14 after PVP-I treatment.


title: Histone demethylase KDM4A-mediated promotion of PAF1/NFATC2 expression is required for oncogenesis in MLL-AF9 acute myeloid leukemia [ChIP-seq]

first: Tae Ju

last: Park

summary: In this study we identified the histone demethylase KDM4A as an essential and selective regulator of AML oncogenic potential. ChIPseq was used to identify KDM4A bound genes and follow changes in H3K9me2/3 and H3K27me3 following KDM4A knockdown in MLL-AF9 human AML THP-1 cells

overall_design: Human MLL-AF9 AML THP-1 cells were spinoculated with a lentivirus,  resulting in the expression of a shRNA targeting the KDM4A transcript. Another lentivirus was included as a negative control, which causes the expression of a non-targeting control (NTC) shRNA. Puromycin selection was used to select cells which had been infected 48 hours following spinoculation. There is one biological replicate for each condition. Chromatin immunoprecipitation was performed 48 hours following puromycin selection.  ChIP-grade antibodies against H3K9me2/3 and H3K27me3 were utilised for IP. The genomic binding sites of KDM4A were determined in wild type THP-1 cells.

first: Xu

last: Huang


title: Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress  Biology

institute: Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing


title: Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (RNA-Seq)

summary: Using RNA-Seq to to analyse the gene expression pattern in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

overall_design: RNA-Seq:   Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

first: Wenjie

last: Zeng

first: Huan

first: Jian-Kang

last: Zhu

first: Miki

last: Daisuke


title: Gene expression analysis in HeLa Kyoto cells upon knockdown of JAZF1

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: The goal was the investigation of JAZF1's possible role in regulating gene expression. RNA-seq analysis revealed that depletion of JAZF1 results in transcriptome changes that affect, among others, ribosome biogenesis.

overall_design: Gene expression profiles of HeLa Kyoto cells upon knockdown of JAZF1 compared to control treatment (with biological replicates) were generated by RNA-sequencing

first: Marek

last: Bartkuhn

first: Tara

last: Procida


title: Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (BS_Seq)

summary: Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

overall_design: BS-Seq:   Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)


title: Local Translation in Nuclear Condensate Amyloid-bodies

status: Public on Jan 15 2021

city: Miami

first: Stephen

last: Lee

state: Florida

department: Biochemistry & Molecular Biology

institute: University of Miami

summary: We report that solid-like condensates Amyloid-bodies are hubs of stress-resistant local nuclear translation in cells responding to high temperature. RNA-seq. analysis of purified Amyloid-bodies confirms that HSF1-transcribed mRNAs accumulate in these solid-like condensates during stress.

overall_design: Transcriptome comparisons of purified nucleoli and Amyloid-bodies obtained from untreated or 60min heat shocked MCF7 cells, respectively.

first: Xianzun

last: Tao

first: Miling

last: Wang


title: MCF10 series 3D cultures: gene expression in association with epithelial p53 status and stromal milieu

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

summary: Basal-like breast cancers (BBC) exhibit subtype-specific phenotypic and transcriptional responses to stroma, but little research has addressed how stromal-epithelial interactions evolve during early BBC carcinogenesis. It is also unclear how common genetic defects, such as p53 mutations, modify these stromal-epithelial interactions. To address these knowledge gaps, we leveraged the MCF10 progression series of breast cell lines (MCF10A, MCF10AT1, and MCF10DCIS) to develop a longitudinal, tissue-contextualized model of p53-deficient, pre-malignant breast. Acinus asphericity, a morphogenetic correlate of cell invasive potential, was quantified with optical coherence tomography imaging, and gene expression microarrays were performed to identify transcriptional changes associated with p53 depletion and stromal context. Co-culture with stromal fibroblasts significantly increased the asphericity of acini derived from all three p53-deficient, but not p53-sufficient, cell lines, and was associated with the upregulation of 38 genes. When considered as a multigene score, these genes were upregulated in co-culture models of invasive BBC with increasing stromal content, as well as in basal-like relative to luminal breast cancers in two large human datasets. Taken together, stromal-epithelial interactions during early BBC carcinogenesis are dependent upon epithelial p53 status, and may play important roles in the acquisition of an invasive morphologic phenotype.

overall_design: All samples were run in duplicate (2 independent experiments), with the exception of RMF mono-cultures: due to low sample concentrations, RNA from 4 wells from 2 independent experiments was pooled, concentrated, and applied to each of 4 microarrays. Total sample number = 28.

first: Ashley

last: Fuller


title: Viral N6-methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus [SeV]

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most abundant internal RNA modification catalyzed by host RNA methyltransferases. As obligate intracellular parasites, many viruses acquire m6A methylation in their RNAs. However, the biological functions of viral m6A methylation are poorly understood. Here, we found that viral m6A methylation serves as a molecular marker for host innate immunity to discriminate self from nonself RNA and that this novel biological function of viral m6A methylation is universally conserved in non-segmented negative-sense (NNS) RNA viruses. Using m6A methyltransferase (METTL3)-knockout cells, we produced m6A-deficient virion RNA from the representative members of the families Pneumoviridae, Paramyxoviridae, and Rhabdoviridae and found that these m6A-deficient viral RNAs triggered significantly higher levels of type I interferon compared to the m6A-sufficient viral RNAs, in a RIG-I dependent manner. Reconstitution of the RIG-I pathway revealed that m6A-deficient virion RNA induced higher expression of RIG-I, bound to RIG-I more efficiently, enhanced RIG-I ubiquitination, and facilitated RIG-I conformational rearrangement and oligomerization. Furthermore, the m6A binding protein YTHDF2 sequesters m6A-sufficient virion RNA which suppresses type I interferon signaling pathway. Collectively, our results suggest that NNS RNA viruses acquire m6A in viral RNA as a common strategy to evade host innate immunity.

sample_organism:
Homo sapiens
Respirovirus muris

platform_organism:
Homo sapiens
Respirovirus muris

overall_design: A few other (NNS) RNA viruses including RSV and hMPV has been sequenced and published before by us. Here, we performed m6A-seq of Sendai virus (SeV). Total RNA were purified from SeV-infected A549 cell lines and subject to m6A-IP-MeRIP-seq.

first: Mijia

last: Lu

first: Jianrong

last: Li


title: Microarray data of differentiated human keratinocytes treated with and without AMD1 inhibitor EGBG and rescued with spermidine/ spermine.

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Maintaining tissue homeostasis depends on a balance of cell proliferation, differentiation and apoptosis.   Polyamine regulator, AMD1, is a crucial regulator of keratinocyte differentiation and AMD1 protein is upregulated on differentiation and highly expressed in the suprabasal layers of the human epidermis. During keratinocyte differentiation, elevated AMD1 promotes decreased putrescine and increased spermine levels.  Inhibition of AMD1 results in reduced spermine levels and inhibition of keratinocyte differentiation. Supplementing AMD1 inhibited keratinocytes with exogenous spermidine/spermine rescued aberrant differentiation.  Undifferentiated and differentiated keratinocytes that had been treated with and without AMD1 inhibitor EGBG in the presence or absence of spermidine/ spermine supplementation were subjected to microarray analysis. These data show that AMD1 up regulation is required for keratinocyte differentiation and that inhibition of AMD1 can be rescued by supplementation with the polyamines spermidine and spermine.

overall_design: Human NTERT1 keratinocytes were differentiated with high calcium for six days. Cells were treated with or without AMD1 inhibitor EGBG from day 3. Cells were further treated with and without 1mM Spermine/ Spermidine. Cells were harvested at 6 days of differentiation. Undifferentiated keratinocytes were also harvested.  4 biological replicates were harvested for each sample.

first: Anisa

middle: B

last: Rahim

first: Leah

last: Vardy

first: Li

last: Jia


title: Deletion of Lats1/2 in adult kidney epithelia leads to renal cell carcinoma

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: We characterized the transcriptomes of  both primary tumors and lung metastases tha developed in mice following deletion of Lats1 and Lats2 from Slc34a1-expressing cells as well as tumors arising from kidney allografts of and immortalized Lats1-/-;Lats2-/- cell line derived from the renal papilla.

overall_design: 1. Primary tumors lung metastases were collected by dissection 4 months following injection of  Slc34a1CreERT2;Lats1/2flox/flox mice mice with tamoxifen and processed for RNA-sequencing. 2. Proximal tubule cells were isolated by FACS from the kidneys of Slc34a1CreERT2;Lats1c/c;Lats2c/+;RosaTomato adult mice and processed for bulk RNA-sequencing. 3. Tumors were dissected from the kidneys of NOD/scid mice 6 weeks after injection of Lats1-/-;Lats2-/- cells under the renal capsule and processed for RNA-sequencing.

first: Phoebe

last: Carter

first: Christopher

last: Chaney


title: Macrophage polarization in response to Piceatannol

city: New York

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: Gene ontology analysis suggested that targeting syk signaling induced changes in diverse innate inflammatory processes.

overall_design: Compare the landscape of transcriptome of bone marrow derived macrophage following treatment of Piceatannol vs. control

first: Wei

first: George

last: Miller


title: Potential Mechanism of Wavelength Defocus in Bidirectional Regulation of Refractive Development in Guinea Pigs

city: Hangzhou

first: Yingying

last: Wen

address: 79 Qingchun Road

department: Department of Ophthalmology

institute: First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China

summary: Wavelength defocus plays an important role in the process of emmetropization. This study aim to explore the potential mechanism underlying retinal response to the wavelength defocus of different signs.

overall_design: to explore the Potential Mechanism of Wavelength Defocus in Bidirectional Regulation of Refractive Development in guinea pigs

first: Le

last: Jin

first: Chen

last: Xie

first: Ye

last: Shen


title: Expression profiles of miRNAs in cholestasis mice and normal mice.

city: Nanjing

last: jie

address: No. 24, Tong Jia Lane

institute: China Pharmaceutical University

summary: We report differences in miRNA expression between cholestasis mice and LIX1L knockout cholestasis mice.Liver samples were obtained from mice from different groups, and the liver samples were detected using the Agilent Mouse miRNA Microarray, Release 21.0 (8*60K,Design ID:070155) chip. After the samples were qualitatively controlled, the data were standardized using the Quantile algorithm. According to the analysis confirmation, a total of three groups of differences were compared and the corresponding GO and KEGG were performed.miR-191-3p displayed the most significant reduction in the liver of WT-BDL mice, and the reduced expression of miR-191-3p was restored in Lix1l-/--BDL mice. We demonstrated that miR-191-3p targets and downregulates LRH-1.Finally, we demonstrated that miR-191-3p further alleviated cholestatic liver injury by inhibiting the expression of LRH-1 to inhibit bile acid synthesis.This study provides a reference for the application of a comprehensive miRNA Microarray to characterize differential miRNA expression in cholestasis mice.

overall_design: Microarray analysis of miRNA expression profiles in cholestasis mice.

first: Jie

first: Xiaoyun

last: Zhu

first: Hao


title: In vitro model of urothelial cell differentiation using bladder cancer cell lines with various degree of epithelial mesenchymal transition

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
Cancer cell lines  frequently lose epithelial characters (epithelial mesenchymal transition or EMT) but some cell lines retain them without EMT.
Here we performed microarray analysis of two different types of human bladder cancer cell lines to characterize urothelial differentiation from stem cells.

overall_design:
BOY12E, JMSU1 and T24 displayed EMT and were classified as M-type cell lines. HuB6, HuB15 and 5637 retained urothelial characters such as E-cadherin and uroplakin syntheses and were classified as E-type cell lines.
E-type cells were further differentiated by the treatment of all-trans-retinoic acid (ATRA). Expression profile of each cell line was analyzed.

first: Ken-ichi

last: Inoue

first: Tomohiko

last: Kamasako


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [icell8]

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

summary: We systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes.  We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type.  We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods.  We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.

overall_design: Various single-cell RNA-seq methods used to generate libraries using a 1:1:1:1 mixture of four lymphocyte cell lines (Jurkat, TALL-104, EL4, IVA12).

first: Daniel

last: Lu

last: Ellwanger

first: Dev

last: Bhatt

first: Paolo

last: Manzanillo

first: Vanessa

last: Arias

first: Hong

last: Zhou

first: Oh-Kyu

last: Yoon

first: Oliver

last: Homann

first: Songli

last: Wang

first: Chi-Ming

last: Li


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [DS]


title: The UPR Transducer IRE1 Promotes Breast Cancer Malignancy by Degrading Tumor Suppressor microRNAs

city: Detroit

first: Zeng-Quan

last: Yang

state: MI

address: 4100 John R HWCRC 815

department: Oncology

institute: Karmanos Cancer Institute

summary: To understand the mechanistic basis by which inositol-requiring enzyme 1 (IRE1) is involved in luminal breast cancer malignancy, we analyzed the transcriptomic signature that IRE1 regulates in breast cancer. We suppressed the activity of IRE1 RNase in luminal breast cancer SUM52 line by adenoviral-based over-expression of the IRE1 dominant-negative K599A or K907A, and then performed RNA-sequencing (RNA-seq) analysis with IRE1 dominant-negative and control SUM52 cells. Through the RNA-seq analysis, we identified 98 genes that were commonly upregulated (65 genes) or downregulated (33 genes) in K599A-expressing SUM52 (SUM52-K599A) or K907A-expressing SUM52 (SUM52-K907A) cells.

overall_design: Total RNAs from SUM52 cells transducted with the IRE1 dominant-negative K599A, K907A, or control adenovirus were harvested, frozen, and sent to the LC Sciences (Houston, TX, USA) for next-generation sequencing.

first: Kezhong

last: Zhang


title: Efficient IL-2R signaling differentially affects stability, function, and composition of the regulatory T cell pool

city: Hannover

first: Berislav

last: Bosnjak

address: Carl-Neuberg Straße 1

department: Institute of Immunology

country: Germany

institute: Hannover Medical School

summary: Signaling via the interleukin 2 receptor (IL-2R) is a requisite for Treg cell identity and function. However, it is not completely understood to what degree IL-2R signaling is required for Treg cell homeostasis, lineage stability and function during both resting and inflammatory conditions. Here, we characterized a spontaneous mouse mutant endowed with a hypomorphic Tyr129His variant of CD25, the a chain of the IL 2R, which resulted in diminished receptor expression and reduced IL-2R signaling. Under non-inflammatory conditions Cd25-Y129H mice harbored substantially lower numbers of peripheral Treg cells with stable Foxp3 expression that prevented the development of spontaneous autoimmune diseases. In contrast, Cd25-Y129H Treg cells failed to efficiently induce immune suppression and lost linage commitment in a T cell transfer colitis model, indicating that unimpaired IL-2R signaling is critical for Treg cell function in inflammatory environments. Moreover, single-cell RNA sequencing of Treg cells revealed that impaired IL-2R signaling profoundly affected the balance of central and effector Treg cell subsets. Thus, partial loss of IL-2R signaling differentially interferes with maintenance, heterogeneity and suppressive function of the regulatory T cell pool.

overall_design: CD4+Foxp3+ Treg cells were sorted from spleens of WT or CD25-Y129H Foxp3-GFP mice by flow cytometry and subjected to single-cell RNA sequencing (10x genomics).

first: Marc

last: Permanyer

last: Bošnjak

first: Reinhold

last: Förster


title: Post-translational modification of Sox11 regulates RGC survival and axon regeneration

city: Palo Alto

first: Jeffrey

middle: L

last: Goldberg

state: CA

address: 1651 Page Mill Road

department: Opthalmology

institute: Stanford University

summary: The failure of adult CNS neurons to survive and regenerate their axons after injury or in neurodegenerative disease remains a major target for basic and clinical neuroscience. Recent data demonstrated in the adult mouse that exogenous expression of Sry-related high-mobility-box 11 (Sox11) promotes optic nerve regeneration after optic nerve injury, but exacerbates the death of a subset of retinal ganglion cells, alpha-RGCs. During development, Sox11 is required for RGC differentiation from retinal progenitor cells (RPCs), and we found that mutation of a single residue to prevent sumoylation at K91 increased nuclear localization and RGC differentiation in vitro. Here we explored whether this Sox11 manipulation similarly has stronger effects on RGC survival and optic nerve regeneration. In vitro, we found that non-SUMOylatable Sox11 K91A leads to RGC death and suppresses axon outgrowth in primary neurons. We furthermore found that Sox11 K91A more strongly promotes axon regeneration but also increases RGC death after optic nerve injury in vivo in adult mouse. RNA-seq data showed that Sox11 and Sox11 K91A increase the expression of key signaling pathway genes associated with axon growth and regeneration but downregulated Spp1 and Opn4 expression in RGC cultures, consistent with negatively regulating the survival of α-RGCs and ipRGCs. Thus Sox11 and its sumoylation site at K91 regulate gene expression, survival and axon growth in RGCs and may be explored further as potential regenerative therapies for optic neuropathy.

overall_design: The changes in the gene expression profiles were investigated by RNA-seq

first: Kun-Che

last: Chang

first: Ankush

last: Madaan

first: Bogdan

last: Tanasa


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [ddSEQ]

first: Tracy

last: Yamawaki

first: Daniel

last: Lu

last: Ellwanger

first: Dev

last: Bhatt

last: Manzanillo


title: Vanillin Ameliorated Azoxymethane/Dextran Sodium Sulfate-Induced Murine Colorectal Cancer: the Involvement of Proteasome/Nuclear factor-κB/Mitogen-Activated Protein Kinase Pathway

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: Vanillin is a natural dietary flavoring. Colorectal cancer (CRC) is one of the common malignancies in the world. Chronic intestinal inflammation is a risk factor for the development of CRC. We have previously found that vanillin improves and prevents the colitis in mice. Here, we evaluated the inhibitory activities of vanillin on a mouse model of colitis-induced colon cancer.

overall_design: Mice were challenged intraperitoneally with azoxymethane (AOM) and orally with dextran sodium sulfate (DSS). Various amounts of vanillin were orally administered for 91 consecutive days.


title: Comparing the transcriptome of imatinib-resistant chronic myeloid leukemia K562/G01 cells with or without treatment of imatinib and TCF7 knockdown

city: Chongqing

first: Hui

state: Chongqing

address: Yixueyuan road 1#

department: School of Laboratory Medicine

institute: Chongqing Medical University

summary: Knockdown of TCF7 increases the drug sensitivity of chronic myeloid leukemia to imatinib‑based therapy.

overall_design: K562/G01 cells were stable transfected with the lentiviral vector carrying a scramble and a TCF7-targeting shRNA sequences, respectively. Subsequently, the stable transfected K562/G01 cells were treated with or without imatinib at concentrations of 1 μM for 48 hours. Total RNAs from four groups of K562/G01 cells with scramble, imatinib, TCF7_KD, and TCF7_KD combine with imatinib treatment were extracted. In total, four samples were sequenced.

first: Wenli

last: Feng

first: Jiwei

last: Li


title: The Fem system in Pseudomonas aeruginosa functions as an ExsA-regulated  interspecies signaling pathway

status: Public on Jan 14 2021

city: Winnipeg

first: Kangmin

last: Duan

state: MB

address: 66 Chancellors Cir

institute: University of Manitoba

summary: Bacterial interspecies interactions shape the function and structural dynamics of microbial communities and affect disease progression of polymicrobial infections. Here, we present data suggesting that the FemA-FemR-FemI (Fem) cell surface signaling system in P. aeruginosa serves as an interspecies signaling pathway between P. aeruginosa and Mycobacterium species. The Fem system is regulated by the type three secretion system (T3SS) regulator ExsA. Fem system significantly influenced virulence factors in P. aeruginosa, including the quorum sensing systems, pyocyanin production, biofilm formation and the type six secretion systems (T6SSs). Our study using a Galleria mellonella infection model indicates femA deletion significantly increased the host survival rate while femI over-expression decreased it, demonstrating that the Fem system’s role in bacterial pathogenicity in vivo. We propose that the Fem system functions as an interspecies signaling pathway enabling P. aeruginosa to alter its behaviours in response to the presence of mycobacteria.

overall_design: Gene expression was compared between wild-type P. aeruginosa PAO1 and femI deletion mutant in the presence and absence of Mycobactin J.

first: K


title: Acute perturbation strategies in interrogating RNA Polymerase II elongation factor function in gene expression

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The regulation of gene expression catalyzed by RNA Polymerase II (Pol II) requires a host of accessory factors to ensure cell growth, differentiation, and survival under environmental stress. Here, using the auxin-inducible degradation (AID) system to study transcriptional activities of the bromodomain and extra terminal domain (BET) and Super Elongation Complex (SEC) families, we found that the CDK9-containing BRD4 complex is required for the release of Pol II from promoter-proximal pausing for most genes, while the CDK9-containing SEC is required for activated transcription in the heat shock response. By using both the Proteolysis-targeting chimera (PROTAC) dBET6 and the AID system, we found that dBET6 treatment results in two major effects: the increased pausing due to BRD4 loss, and reduced enhancer activity attributable to BRD2 loss. In the heat shock response, while auxin-mediated depletion of the AFF4 subunit of SEC has a more severe defect than AFF1 depletion, simultaneous depletion of AFF1 and AFF4 leads to a stronger attenuation of the heat shock response, similar to treatment with the SEC inhibitor KL-1, suggesting a possible redundancy among SEC family members. This study highlights the usefulness of orthogonal acute depletion/inhibition strategies to identify distinct and redundant biological functions among Pol II elongation factor paralogs.

overall_design: Examination of RNA Pol II dynamics by ChIP-seq in human cells subjected to rapid depletion of AFF1, AFF4 or BET bromodomain proteins using an auxin-inducible degron. The PROTAC dBET6 was used to degrade all BET proteins and the SEC disruptor KL-1 was used to target AFF1 and AFF4 containing P-TEFb complexes. RNA-seq +/- auxin was also performed for BRD4 degron cells and for AFF1/AFF4 double degron cells.

first: Bin

last: Zheng

first: Edwin

last: Smith

first: Marta

last: Iwanaszko


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [bulk]

overall_design: Bulk RNA-seq data used as baseline for benchmarking single-cell RNA-seq methods.

first: Paolo

first: Vanessa

last: Arias

first: Hong

last: Zhou

first: Oh-Kyu

last: Yoon

first: Oliver

last: Homann

first: Songli

last: Wang

first: Chi-Ming


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [10x]

first: Tracy

last: Yamawaki

first: Daniel

last: Lu

first: Dev


title: Checkpoint inhibition of origin firing prevents inappropriate replication in G2/M phase.

city: Cambridge

first: Philip

last: Zegerman

address: 80, Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

summary: Across eukaryotes, checkpoints maintain the order of cell cycle events in the face of DNA damage or incomplete replication. Although a wide array of DNA lesions activates the checkpoint kinases, whether and how this response differs in different phases of the cell cycle remains poorly understood. The S-phase checkpoint for example results in the slowing of replication, which in the budding yeast Saccharomyces cerevisiae is caused by Rad53 kinase-dependent inhibition of the initiation factors Sld3 and Dbf4. Despite this, we show here that Rad53 phosphorylates both of these substrates throughout the cell cycle at the same sites as in S-phase, suggesting roles for this pathway beyond S-phase. Indeed we show that Rad53-dependent inhibition of Sld3 and Dbf4 limits re-replication in G2/M phase, preventing inappropriate gene amplification events. In addition we show that inhibition of Sld3 and Dbf4 after DNA damage in G1 phase prevents premature replication initiation at all origins at the G1/S transition. This study redefines the scope and specificity of the ‘S-phase checkpoint’ with implications for understanding the roles of this checkpoint in the majority of cancers that lack proper cell cycle controls.

overall_design: Examination of re-replication by high-throughput sequencing of DNA in two strains (PGAL-Mcm7-NLS PGAL-Orc6-4A PGAL-Cdc6 and sld3-A dbf4-A PGAL-Mcm7-NLS PGAL-Orc6-4A PGAL-Cdc6) in G2/M phase.

first: Mark

last: Johnson


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

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

overall_design: Refer to individual Series


title: Effect of hepatocyte-specific PPARgamma knock out in the regulation of hepatic gene expression in mice fed a low fat diet or and high fat, cholesterol and fructose diet that induces NASH

first: Jose

last: Cordoba-Chacon

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

summary:
In this study we sought to determine how hepatocyte-specific PPARgamma expression regulates hepatic gene expression in normal (healthy) mice fed a LFCF diet, or mice that were fed a HFCF diet for 24 weeks to induce non-alcoholic steatohepatitis (NASH).
Specifically, we used chow-fed adult (10 week-old) PPARgamma floxed male mice and injected them with AAV8-TBG-Cre to knockout PPARgamma in hepatocytes (KO). A subset of PPARgamma floxed mice were injected with AAV8-TBG-Null to generate controls (C). Two weeks after AAV injections, half of the mice in each group were fed a low fat, cholesterol and fructose (LFCF) diet, or a high fat, cholesterol and fructose (HFCF) diet for 24 weeks.  Livers were collected at the end of the study to assess hepatic gene expression with RNA-seq (performed by Novogen, Inc.)

overall_design:
There are 4 groups:

Group 1. LFCF-fed control mice: LF-C (4 samples: PG-413, PG-419, PG-437, PG-442).
Group 2. LFCF-fed hepatocyte-specific PPARgamma knock out mice: LF-KO (4 samples: PG-412, PG-417, PG-436, PG-440).
Group 3. HFCF-fed control mice: HF-C (5 samples: PG-399, PG-411, PG-398, PG-405, PG422).
Group 4. HFCF-fed hepatocyte-specific PPARgamma knock out mice: HF-KO (6 samples: PG-396, PG-429, PG-425, PG-426, PG-427, PG-404).

We have compared the gene expression levels between the following groups:
- LF-C vs HF-C, and LF-KO vs HF-KO to assess the effect of HFCF-mediated NASH in the regulation of hepatic gene expression in control (C) and hepatocyte-specific PPARgamma knock out (KO) mice, respectively
- LF-C vs LF-KO, and HF-C vs HF-KO to assess the effect of hepatocyte PPARgamma knock out in LFCF- and HFCF-fed mice respectively.

Readcounts and FPKM of each sample are included in the processed files (comparisons indicated above), along with the Log2 fold change, p-value and p-adjusted.


title: Effect of hepatocyte-specific PPARgamma knock out with and without rosiglitazone treatment in hepatic gene expression of mice with diet-induced NASH

summary:
In this study we sought to determine if the knockout of hepatocyte PPARgamma expression alter transcriptomics of the livers of mice with diet-induced NASH, and if there was a hepatocyte-specific PPARgamma dependent regulation of gene expression in TZD treated mice.

Specifically, adult PPARg floxed male mice were fed a high fat, cholesterol and fructose (HFCF) diet for 24 weeks. After this period of time, half of the mice were injected with AAV8-TBG-Cre to knockout PPARgamma in hepatocytes (KO mice). The other half of the mice were injected with AAV8-TBG-Null, and served as controls (C mice). A subset of PPARg floxed mice were fed a low fat, cholesterol and fructose (LFCF) diet, and they were injected with AAV8-TBG-Null to generate LFCF-controls. Two weeks after AAV8 injections, half of the HFCF-fed mice in each group (C and KO) were switched to a HFCF diet containing rosiglitazone maleate (TZD, 50mg/kg of diet) for eight additional weeks. Mice were kept in their respective diets for 8 additional weeks too. At the end of the study, the livers were collected to assess hepatic gene expression with RNA-seq (performed by Novogen, Inc.)

overall_design:
There are five groups:
Group 1, LFCF-fed control mice: LF-C (4 mice: PG-783, PG-784, PG-785, PG-787)
Group 2, HFCF-fed control mice: HF-C (5 samples: PG-721, PG-777, PG-734, PG-764, PG-780)
Group 3, HFCF-fed hepatocyte-specific PPARgamma knock out mice: HF-KO (5 samples: PG-722, PG-748, PG-750, PG-765, PG-781)
Group 4, TZD treated HFCF-fed control mice: HF/TZD-C (5 samples: PG-728, PG-731, PG-753, PG-768, PG-774)
Group 5, TZD-treated HFCF-fed hepatocyte-specific PPARgamma knock out mice: HF/TZD-KO (5 samples: PG-754, PG-763, PG-770, PG-772, PG-776).

We have compared the gene expression levels between the following groups:
- LF-C vs HF-C to assess the effect of HFCF diet (34 weeks) in the regulation of hepatic gene expression in control mice.
- HF-C vs HF-KO, to assess the effect of hepatocyte-specific PPARgamma knockout for 10 weeks in mice that were fed a HFCF diet.
- HF-C vs TZD/HF-C  and HF-KO vs TZD/HF-KO to assess the effect that TZD (rosiglitazone maleate) has in the regulation of hepatic gene expression in control (C) and hepatocyte-specific PPARgamma knock out (KO) mice with HFCF-induced NASH, respectively.
- TZD/HF-C vs TZD/HF-KO to assess the effect that hepatocyte PPARgamma knock out had in mice with HFCF-induced NASH treated with TZD.

Readcounts and FPKM of each sample are included in the processed files (comparisons indicated above), along with the Log2 fold change, p-value and p-adjusted.


title: Overexpression of b-Arrestins in triple negative breast cancer cells.

city: Ankara

first: Hakan

last: Gurdal

address: A. Adnan Saygun Cad.

department: Faculty of Medicine

country: Turkey

institute: Ankara University

summary: Beta-Arrestins (βArrs) are intracellular signal regulating proteins. Their expression level varies in some cancers and they have significant impact on cancer cell function. In general, the significance of βArrs in cancer research comes from studies examining GPCR signalling. Given the diversity of different GPCR signals in cancer cell regulation, contradictory results are inevitable regarding the role of βArrs. Our approach examines the direct influence of βArrs on cellular function and gene expression profiles by changing their expression levels in breast cancer cells, MDA-MB-231.

overall_design: MDA-MB-231 human triple negative breast cancer cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) and Eagle’s minimal essential medium (EMEM), supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 5% CO2, 37˚C with 90-95 % humidity. The cells (2.5x105) were cultured in a 6 well plate and left for 24 h to reach 70-80 % confluency for cDNA transfections. DNA transfections were performed according to the manufacturer’s protocol using, for each well, 4 µl of TurboFectin Transfection 8.0 Reagent and 2µg of control nontarget DNA (Cloning vector PCMV6XL5), and Human βArr1cDNA or Human βArr2 cDNA. After transfection for 48 h at 37˚C, the medium was replaced, and the cells were cultured for an additional 12 h.


title: IRE1 modulates expression of a set of tumor suppressor miRNAs in luminal breast cancer cells.

first: Zeng-Quan

last: Yang

summary: To explore the regulatory mechanism by which inositol-requiring enzyme 1 (IRE1) regulates oncogenic factors, particularly RAB3B, in luminal breast cancer cells, we blocked IRE1 activity in breast cancer cell lines by using the IRE1 inhibitor 4μ8C or expressing IRE1 dominant-negative for miRNA microarray analysis. SUM52 and SUM225 lines with high-level IRE1 expression were treated with 4μ8C for 2 days. The IRE1 kinase dominant-negative mutant K599A or K907A was also used to suppress IRE1 kinase or RNase activity in SUM52 cells. The miRNA microarray analysis revealed a landscape change in miRNA expression profiling in IRE1-inhibited luminal breast cancer cells. Using a criterion of p < 0.05 in miRNA analysis, we identified 41 miRNAs in both SUM52 and SUM225 cells that were altered after inhibiting IRE1 activity. Additionally, we exogenously overexpressed wild-type IRE1 in human nontumorigenic mammary epithelial MCF10A cells and then performed miRNA array assays. When we combined miRNA data from both IRE1 inhibition models in breast cancer cells and exogenous overexpression of IRE1 in MCF10A cells (p<0.05), we identified 5 miRNAs (3607-3p, 374a-5p, 4764-3p, 516a-3p, and 6073) that were upregulated in IRE1-inhibited breast cancer cells and downregulated in MCF10A-IRE1 cells.

overall_design: Total RNAs from SUM52, SUM225, or MCF10A cells that were treated with IRE1 inhibitor 4μ8C or transducted with the IRE1 dominant-negative K599A, K907A, or wild-type IRE1 were harvested, frozen, and sent to the LC Sciences (Houston, TX, USA) for miRNA analysis.

first: Kezhong

last: Zhang


title: ATAC-seq of squamous cell carcinoma cells varying in FAK status

city: Edinburgh

first: Billie

middle: Georgina Cooper

last: Griffith

address: Crewe road south

department: IGMM, ECRC

institute: University of Edinburgh

summary: Focal adhesion kinase (FAK) localizes to focal adhesions and is overexpressed in many cancers. FAK can also translocate to the nucleus, where it binds to, and regulates, several transcription factors, including MBD2, p53 and IL-33, to control gene expression by unknown mechanisms. We have used ATAC-seq to reveal that FAK controls chromatin accessibility at a subset of regulated genes. Integration of ATAC-seq and RNA-seq data showed that FAK-dependent chromatin accessibility is linked to differential gene expression, including of the FAK-regulated cytokine and transcriptional regulator interleukin-33 (Il33), which controls anti-tumor immunity. Analysis of the accessibility peaks on the Il33 gene promoter/enhancer regions revealed sequences for several transcription factors, including ETS and AP-1 motifs, and we show that c-Jun, a component of AP-1, regulates Il33 gene expression by binding to its enhancer in a FAK kinase-dependent manner. This work provides the first demonstration that FAK controls transcription via chromatin accessibility, identifying a novel mechanism by which nuclear FAK regulates biologically important gene expression.

overall_design: To identify which transcription factors may be candidate mediators of FAK-dependent gene expression, we used ATAC-seq to analyze active (accessible) chromatin in FAK-deficient SCC cells or cells expressing different FAK mutant proteins. Specifically, we compared SCC cells in which FAK had been depleted by Cre-lox-mediated Ptk2 (which encodes FAK) gene deletion (FAK-/- cells) with the same cells re-expressing wild-type FAK (FAK-WT-expressing cells) or FAK mutants that were impaired in nuclear localization (FAK-nls-expressing cells) or deficient in kinase activity (FAK-kd-expressing cells) (cell lines generated previously in Serrels et al., 2012 and Serrels et al., 2015). These permitted the identification of FAK-dependent, FAK nuclear localization-dependent and FAK kinase-dependent alterations in chromatin accessibility and transcription factor motif enrichment in accessible regions of chromatin across the genome.

first: Rosanna

last: Upstill-Goddard

first: Holly

last: Brunton

first: Graeme

last: Grimes

first: Andrew

middle: V

last: Biankin

first: Bryan

last: Serrels

first: Adam

last: Byron

first: Margaret

last: Frame


title: Time-resolved transcriptional profiling of epithelial cells infected by intracellular Acinetobacter baumannii

city: Barcelona

first: Marc

last: Torrent Burgas

address: Carrer de la Vall Moronta

department: Biochemistry and Molecular Biology

institute: Universitat Autònoma de Barcelona

summary: The increasing rate of antibiotic-resistant bacteria has become a serious health threat. Thus, it is important to discover, characterize, and optimize new molecules to overcome infections caused by these bacteria. It is known that Acinetobacter baumannii has a high capacity to avoid antibacterial drugs. Consequently, these bacteria have emerged as one of responsible for hospital and community-acquired infections. However, how this pathogen infects and survives inside the host cell is unknown. Here we analyze the time-resolved transcriptional profile changes on human epithelial HeLa cells after A. baumannii. Our results show how A.baumannii can survive in host cells and starts replication at 4 hours post infection. We sequenced RNA to obtain a set of differentially expressed gen (DEGs) used for a Gene Ontology (GO) and KEGG pathway analysis. The results show us how host bacteria is altering the host cells environment for their own benefit. We also determine chromosomal regions affected by our set of genes. Furthermore, we obtain protein-protein networks that reveal highly interacted proteins. The combination of these results will pave the way to discover new antimicrobial candidates for multidrug-resistant bacteria.

overall_design: Examination of 3 different post infection times in HeLa cells infected by Acinetobacter baumannii

first: Nuria

last: Crua Asensio

first: Javier

last: Macho Rendón


title: Intracellular pathways for lignin catabolism in white-rot fungi

city: Golden

first: Davinia

last: Salvachua

state: CO

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

summary: Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.

sample_organism:
Trametes versicolor
Gelatoporia subvermispora

overall_design: Examination of the effects of aromatic compounds, lignin, and lignocellulose on two different white rot fungi.

first: Carlos

last: del Cerro

first: Lye

last: Markillie

first: Matthew

last: Gaffrey

first: Hugh

last: Mitchell


title: Ribosome profiling on heat shocked wild type and Mettl14 -/- mES cells

city: New York

first: Pierre

last: Klein

state: NY

address: 1300 York Avenue

department: Department of Pharmacology

institute: Weill Medical College, Cornell University

summary: Abstract : "A hallmark of the cellular response to environmental stress is the formation of stress granules.  Stress granules are RNA-protein assemblies that provide an adaptive response to stress; however, the basis for their formation and how they contribute to the stress response remains incompletely understood.  Here we show that the mRNA modification N6-methyladenosine (m6A) is a mark that targets mRNAs to stress granules.  We find that m6A mRNAs are highly enriched in stress granules, and this is mediated by m6A-induced liquid-liquid phase separation of the YTHDF family of m6A-binding proteins.  These proteins bind poly-methylated m6A mRNAs, causing them to form liquid droplets that partition into stress granules. Moreover, disrupting either m6A or YTHDF proteins prevents stress granule formation."  The goal of this experiment is to understand how recruitment of m6A mRNA to stress granules influences the translational response to heat shock. Result: we found that m6A-containing mRNA are preferentially repressed during stress, and that m6A is required for translational recovery after heat shock

overall_design: Ribosome profiling were generated from two biological replicates of wild type and Mettl14 -/- mES cells heat socked at 42°C for 30 min or not and at a recovery time point of 1h after heat shock

first: Samie

last: Jaffrey


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer [mRNAseq_PDX]

city: Rochester

first: Steven

last: Johnsen

state: MN

address: 200 First Street SW

department: Gastroenterology Research

institute: Mayo Clinic

summary: We characterized Gemcitabine resistant pancreatic cancer tumors and show that the co-amplification of RRM1 and STIM1 confers novel and independent properties to gemcitabine resistant cells. The upregulation of RRM1 drives gemcitabine resistance, while the amplification of STIM1 leads to increased cytosolic calcium upon stress, eliciting ER stress resistance and NFAT activation.

overall_design: We performed mRNAseq from vehicle or Gemcitabine and nab-Paclitaxel treated pancreatic cancer patient-derived xenografts.

first: Ana

middle: P

last: Kutschat

first: Xin

last: Wang

first: Elisabeth

last: Hessmann


title: DNA damage contributes to cGAS-STING activation in colon cancer

city: Nanjing

first: Bin

last: Wei

state: Jiangsu

address: 101 Longmian Avenue

institute: Nanjing medical university

summary: This study aimed to investigate the role of DNA damage contributes in STING pathway activation and its implication in colorectal cancer.

overall_design: Role of chemotherapy in STING pathway in colon cancer

first: Lingyan

last: Xu

first: Xiaofei

last: Li

first: Xiaomin

last: Cai

first: Meijing

first: Wenjie

last: Guo

first: Qiang

first: Wen

last: Liu

first: Yanhong

last: Gu


title: Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase

first: Philip

last: Zegerman

overall_design: Examination of replication progression by high-throughput sequencing of DNA in two strains (swi4-t and swi4-t/sld3-A/dbf4-A) after DNA damage in G1 phase.

first: Mark

last: Johnson


title: Activation of YAP-dependent Proliferation by a Small Molecule Targeting Annexin A2

city: San Diego

first: Lara

last: Ibrahim

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: The transcriptional coactivator YAP orchestrates a pro-proliferative transcriptional program that controls the fate of somatic stem cells and the regenerative responses of certain tissues. As such, agents that activate YAP may hold therapeutic potential in disease states exacerbated by insufficient proliferative repair. Here we report the discovery of a small molecule, termed PY-60, which robustly activates YAP transcriptional activity in vitro and promotes YAP-dependent expansion of epidermal keratinocytes in mouse upon topical administration of drug. Chemical proteomics revealed the relevant target of PY-60 to be Annexin A2 (ANXA2), a protein that directly associates with YAP at the cell membrane in response to increased cell density. PY-60 treatment liberates ANXA2 from the membrane, ultimately promoting a phosphatase bound, non-phosphorylated, and transcriptionally active form of YAP. This work reveals ANXA2 to be a previously undescribed, druggable component of the Hippo pathway and suggests a mechanistic rationale for promoting YAP-dependent regenerative repair in disease.

overall_design: Comparisons of the transcriptomes of 293A cells treated with DMSO vs PY-60

first: Edyta

last: Grzelak

first: Michael

last: Bollong


title: SARS-CoV-2 infection dynamics in lungs of African green monkeys

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Detailed knowledge about dynamics of SARS-CoV-2 infection in vivo is important for unraveling the viral and host response factors that contribute to COVID-19 pathogenesis. The unknown dose and exposure timing in human infections makes the needed well-controlled time course studies impossible and thus animal models of disease are essential to fill in the gaps in our understanding of disease progression. Old-World nonhuman primate species recapitulate mild COVID-19 cases, thereby serving as important models for studying disease pathogenesis. In this study, we compare African green monkeys (AGM; Chlorocebus sabaeus) inoculated with SARS-CoV-2 to AGM inoculated with a gamma-irradiated form of the virus to study the dynamics of virus replication throughout the respiratory tract and other target tissues. RNA sequencing of single cells from the lungs and mediastinal lymph nodes allowed a high-resolution, simultaneous analysis of virus replication and the host response in these tissues over time. Viral replication was mainly localized to the lower respiratory tract, especially the pneumocyte population. However, even in the absence of active replication, viral genomic RNA is was highly stable, especially in the upper respiratory tract. Macrophages play a vital and dynamic role in initiating a pro-inflammatory state in the lungs, while also interacting with infected pneumocytes. Together, our dataset provides a detailed view of changes in host and virus replication dynamics over the course of a mild COVID-19 infection and serves as a valuable resource to identify new therapeutic targets.

overall_design: 10 african green monkeys, 2 inoculated with irradiated SARS-CoV-2, 8 with active SARS-CoV-2, single cell sequencing

first: Emily

last: Speranza

first: Brandi

middle: N

last: Williamson

first: Friederike

last: Feldmann

first: Gail

last: Sturdevant

first: Lizzette

last: Perea-Perez

first: Kimberly

last: Meand-White

first: Brian

last: Smith

first: Vincent

last: Munster

first: Atsushi

last: Okumura

first: Carl

last: Shaia

first: Heinz

first: Sonja

last: Best

first: Emmie

last: de Wit


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer [mRNAseq_siSTIM1_Thap]

first: Steven

last: Johnsen

overall_design: We performed mRNAseq from L3.6pl (Par) and gemcitabine resistant L3.6pl cells (GemR) depleted of STIM1 and treated with 500nM thapsigargin. For this, Par were treated with siControl (siCont) and with DMSO (Veh) or 500nM thapsigargin (Thap), while GemR were depleted or not of STIM1 (siCont or siSTIM1) and treated either with DMSO (Veh) or with 500nM thapsigargin (Thap). The siRNA mediated depletion was perfomed for 48h, while the thapsigargin treatment lasted for 3h.

first: Ana

last: Kutschat

first: Xin

last: Wang


title: Infant Circulating MicroRNAs as Biomarkers of Effect in Fetal Alcohol Spectrum Disorders

city: Bryan

first: Amanda

last: Mahnke

state: TX

address: 8447 Riverside Parkway

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University Health Science Center

summary: Infant plasma miRNAs were isolated at 2 weeks and 6.5 months of age from prenatal alcohol exposed and control infants

overall_design: qPCR array miRNA expression profiling from 25ng input RNA from each sample. Samples were excluded for hemolysis or panel performance as indicated.

first: Rajesh

middle: C

last: Miranda


title: SIX1 and SIX4 double knockout transcriptome profiling in 2D cell lines derived from murine pancreatic tumors

city: Salt Lake City

first: Soledad

last: Camolotto

address: 201 Presidents' Cir

institute: University of Utah

summary: Pancreatic ductal adenocarcinoma is aggressive disease with a dismal five-year survival of 5%. Gene expression profiling has been instrumental for subtype classification in cancer, highlighting fundamental differences in tumors at the molecular level. Over the last years, multiple genomics studies have led to the classification of PDAC into two major subtypes: classical and basal-type. The classical subtype expresses higher levels of endodermal lineage specifiers, including HNF4A, GATA6, FOXA2, FOXA3 than the basal-type. The basal-type confers a worse prognosis, raising the possibility that loss of these lineage specifiers might enhance the malignant potential of PDAC. We found that the lineage specifier HNF4a plays a key role in maintaining a transcriptional network that characterizes the classical subtype, restraining growth in different PDAC models. Additionally, we demonstrated that HNF4a controls PDAC cell identity and proliferation, and represses the expression of SIX family members, two mesodermal lineage specifiers highly expressed in basal-type.

overall_design: The study was designed to compare transcriptome profiles in control versus CRISPR-mediated SIX1/4 double knockout murine pancreatic cancer cell lines.

first: Veronika

middle: K

last: Belova

first: Luke

last: Torre-Healy

first: Hannah

last: Conway

first: Chris

last: Stubben

first: Richard

last: Moffit

first: Eric

last: Snyder


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer [ChIPseq_siSTIM1_Thap]

middle: A

overall_design: We performed ChIPseq in L3.6pl (Par) and gemcitabine resistant L3.6pl cells (GemR) depleted of STIM1 and treated with 500nM thapsigargin. For this, Par were treated with siControl (siCont) and with DMSO (Veh) or 500nM thapsigargin (Thap), while GemR were depleted or not of STIM1 (siCont or siSTIM1) and treated either with DMSO (Veh) or with 500nM thapsigargin (Thap). The siRNA mediated depletion was perfomed for 48h, while the thapsigargin treatment lasted for 3h. H3K27ac ChIPseq was performed for all conditions, while ATF4 ChIPseq was only generated for thapsigargin treated Par.


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer [mRNAseq_Par_GemR]

overall_design: We performed mRNAseq from 24h vehicle (DMSO) treated only L3.6pl (Par) and gemcitabine resistant L3.6pl (GemR) cells.

first: Feda

last: Hamdan


title: Reciprocal Regulation of Pancreatic Ductal Adenocarcinoma Growth and Molecular Subtype by HNF4a and SIX1/4

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

overall_design: Refer to individual Series


title: Hnf4a chromatin interactions in PDAC [ChIP-seq]

overall_design: Study of Hnf4a genomic occupancy in murine PDAC cell lines

first: Jeffery

last: Vahrenkamp

first: Kristofer

last: Berrett


title: miR-193 inhibits bladder cancer progression by targeting N-myc

status: Public on Jan 13 2021

city: Shenyang

first: Liping

last: Shan

state: Liaoning

address: 36 Sanhao street

institute: Shenjing hospital of China Medical University

summary: Growing evidence has indicated that miR-193 is involved in the initiation and progression of malignancy, such as bladder cancer, hepatocellular carcinoma, renal cell carcinoma, and colorectal cancer. Nevertheless, the mechanisms of miR-193 in the development of metastatic bladder cancer remains unknown. In the current study, we clarified the association of miR-193/N-myc was implicated in cancer metastasis. miR-193 expression increased in metastatic bladder cancer biopsies compared to the primary cases. Moreover, the elevation of miR-193 was correlated with the invasiveness, lymph node metastasis, and advanced stages of bladder cancer significantly. Downregulation of miR-193 by shRNA hampered proliferation and migration while inducing cell apoptosis. Furthermore, miR-193 sponged N-myc and diminished miR-103 expression. Overexpression of miR-193 released oncogene N-myc expression, leading to the promotion of cell proliferation and migration. Besides, knockout of miR-193 suppressed tumor growth in the human T24 mice models. Briefly, the present findings suggested that miR-193-N-myc were novel promising pathways for conquering bladder cancer progression.

overall_design: Bladder cancer samples and the adjacent tissues were recruited in the present study. Microarray-based miRNA expression profiles were obtained with Qiagen custom miScript miRNA PCR Arrays.

first: Wei

last: Liu


title: Changes in chromatin accessibility landscape induced by Hnf4a in PDAC [ATAC-seq]

overall_design: Study designed to compare chromatin accesibility profiles of Hnf4a-negative and isogenic murine PDAC cells in which Hnf4a expression was restored


title: OsMre11 is required for mitosis during rice growth and development

city: Wuhan

first: Jie

last: Zhao

address: No. 299, Bayi Road, Wuchang District,

institute: Wuhan University

summary: Meiotic recombination 11 (Mre11) is a relatively conserved nuclease in various species. Mre11 plays important roles in meiosis and DNA damage repair in yeast, humans and Arabidopsis, but little research has been done on mitotic DNA replication and repair in rice. Here, it was found that Mre11 was an extensively expressed gene among the various tissues and organs of rice, and loss-of-function of Mre11 resulted in severe defects of vegetative and reproductive growth, including dwarf plants, abnormally developed male and female gametes, and completely abortive seeds. The decreased number of cells in the apical meristem and the appearance of chromosomal fragments and bridges during the mitotic cell cycle in rice mre11 mutant roots revealed an essential role of OsMre11. Further research showed that DNA replication was suppressed, and a large number of DNA strand breaks occurred during the mitotic cell cycle of rice mre11 mutants. The expression of OsMre11 was up-regulated with the treatment of hydroxyurea and methyl methanesulfonate. Moreover, OsMre11 could form a complex with OsRad50 and OsNbs1, and they might function together in non-homologous end joining and homologous recombination repair pathways. These results indicated that OsMre11 plays vital roles in DNA replication and damage repair of the mitotic cell cycle, which ensure the development and fertility of rice by maintaining genome stability.

overall_design: mRNA from 7-day-old wild-type rice seedlings and mre11 rice seedlings

last: zhao

first: Miaomiao

last: Shen


title: Targeting In Vivo Metabolic Vulnerabilities of Th2 and Th17 Cells Reduces Airway Inflammation

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: T cells promote inflammation in asthmatic patients and both Th2 and Th17 CD4 T cells have been implicated in severe forms of the disease. The metabolic phenotypes and dependencies of these cells, however, remain poorly understood in the regulation of airway inflammation. Here we show the bronchoalveolar lavage fluid of asthmatic patients had markers of elevated glucose and glutamine metabolism. Further, peripheral blood T cells of asthmatics had broadly elevated expression of metabolic proteins when analyzed by mass cytometry compared to healthy controls. Therefore, we hypothesized that glucose and glutamine metabolism were important in allergic airway inflammation. We tested this hypothesis in two murine models of airway inflammation. T cells from lungs of mice sensitized with Alternaria alternata extract displayed genetic signatures for elevated glucose and oxidative metabolism by single cell RNAseq.  This result was most pronounced when protein levels were measured in IL17 producing cells and was recapitulated when airway inflammation was induced with House Dust Mite plus lipopolysaccharide (HDM+LPS), a model which led to abundant IL4 and IL17 producing T cells. Importantly, inhibitors of the glucose transporter 1 (Glut1) or glutaminase (GLS) in vivo attenuated HDM+LPS eosinophilia, T cell cytokine production, and airway hyperresponsiveness as well as augmented the immunosuppressive properties of dexamethasone. These data show that T cells induce markers to support metabolism in vivo in airway inflammation and that this correlates with inflammatory cytokine production. Targeting metabolic pathways may provide a new direction to protect from disease and enhance the effectiveness of steroid therapy.

overall_design: Adult mice were administered Alt Ext Ext (7.5ug) or vehicle control (PBS) on days 0, 3, 6. Lung were harvested on day 7 and digested using DNAse (0.1%) and collagenase (2mg/ml) for 30 minutes at 370C. Single cell lung suspensions were enriched for CD45+ cell using Miltenyi  microbeads (Catalog #130-052-301) using manufacturer’s protocol. CD45+ cells were further purified by cell sorting and then loaded onto 10X Genomics Chromium Controller for single cell RNA sequencing.

first: Dawn

last: Newcomb


title: Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids

city: Boston

first: Allon

last: Klein

state: MA

address: 210 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

summary: We apply single cell RNA-sequencing (scRNA-seq) to murine intestinal organoids in two experiments: 1) Comparing the transcriptomic landscape of organoids cultured in dome and sandwich culture systems (as described in the accompanying paper for this GEO submission), and 2) Assessing the transcriptomic landscape of organoids perturbed with CFTRinh-172 to inhibit inflation events, and with Forskolin to activate inflation events in the sandwich culture system, with respective controls. We find that the dome and sandwich culture systems produce similar abundance levels of each major specialized cell type, with similar marker gene expression shared across culture types. We find in the perturbation experiments a stretch-responsive cell state, similar in gene expression to several previously reported cell states, which is significantly more abundant in the Forskolin treated organoids compared to controls, and significantly less abundant in CFTRinh-172 treated organoids compared to controls. Additionally, we find that Stem and Enterocyte cell states are respectively, significantly less abundant, and more abundant in the Forskolin treated organoids compared to controls.

overall_design: Examination of transcriptomic landscapes of two murine intestinal organoid culture types: dome and sandwich culture systems; examination of transcriptomic landscape changes in murine intestinal organoids as a result of inflation perturbations.

first: Naren

last: Tallapragada

first: Hailey

last: Cambra

first: Tomas

last: Wald

first: Samantha

last: Keough Jalbert

first: Diana

last: Abraham

first: Ophir

middle: D


title: RNA sequencing on stem cell-derived endothelial cells

city: Leuven

first: Jonathan

last: De Smedt

address: ON4 - Herestraat 49 PB804

department: Development and Regeneration

country: Belgium

institute: Stem Cell Institute Leuven

summary: We generated a stable H9 stem cell line with an FRT cassette in the AAVS1 safe harbour locus, which allows recombinase-mediated cassette exchange. We used this system to overexpress ETV2, a master regulator of endothelial fating. This study contains gene expression characterisation of endothelial cells derived through overexpression of ETV2, at day 10 of differentiation. These endothelial cells are referred to as ETV2-ECs.

overall_design: Expression characterisation of ETV2-ECs

first: Elise

last: van Os

first: Irene

last: Talon

first: Sreya

last: Ghosh

first: Burak

last: Toprakhisar

first: Rodrigo

last: Furtado Madeiro Da Costa

last: Zaunz

first: Marta

last: Aguirre Vazquez

first: Ruben

last: Boon

first: Pieter

last: Baatsen

first: Ayla

last: Smout

first: Stefaan

last: Verhulst

first: Leo

last: van Grunsven

first: Catherine

last: Verfaillie