title: Generation of the organotypic kidney by integrating pluripotent stem cell-derived renal stroma

status: Public on Dec 05 2021

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Organs consist of not only parenchyma but also stroma, the latter of which coordinates generation of organotypic structures. Despite recent advances in organoid technology, induction of organ-specific stroma and recapitulating the complex organ configurations from pluripotent stem cells (PSCs) has remained challenging. For the kidney, the stromal progenitor coordinates differentiation of the two parenchymal progenitors: nephron progenitor and ureteric bud. By identifying the origin and dorsoventral patterning of the renal stromal progenitor, we established its induction protocol from mouse PSCs. When the three types of progenitors were differentially induced from PSCs and assembled, the all PSC-derived organoids reproduced the complex kidney structures, with multiple types of stromal cells distributed around differentiating nephrons and branching ureteric buds. Thus, integration of PSC-derived stroma into the conventional organoids enables recapitulation of organotypic architecture.

overall_design: Kidney mRNA profiles of embryonic day 9.5, E11.5, E15.5, E13.5, E17.5, postnatal day 0 mice and mouse ES cells-derived kidney organoids at single cell resolution.

first: Etsuko

last: Tanaka

first: Koichiro

last: Miike

first: Akio

last: Kobayashi

first: Ryuichi

last: Nishinakamura


title: Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

status: Public on Dec 03 2021

city: Santa Cruz

first: Manuel

last: Ares

state: CA

address: 1156 High St

country: USA

institute: University of California, Santa Cruz

type: Expression profiling by high throughput sequencing

summary: Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During ribosome biogenesis, modifications are added at various stages of assembly. The existence of differently modified classes of ribosomes in normal cells is unknown because no method exists to simultaneously evaluate the modification status at all sites, within a single rRNA molecule. Using a combination of yeast genetics and nanopore direct RNA sequencing, we developed a reliable method to track the modification status of single rRNA molecules at 37 sites in 18S rRNA and 73 sites in 25S rRNA. We use our method to characterize patterns of modification heterogeneity and identify concerted modification of nucleotides found near functional centers of the ribosome. Distinct undermodified subpopulations of rRNAs accumulate upon loss of Dbp3 or Prp43 RNA helicases, suggesting overlapping roles in ribosome biogenesis. Modification profiles are surprisingly resistant to change in response to many genetic and environmental conditions that affect translation, ribosome biogenesis, and pre-mRNA splicing. The ability to capture single-molecule RNA modification profiles provides new insights into the roles of nucleotide modifications in RNA function.

overall_design: We sequenced 33 samples of 18S and 25S ribosomal rRNA. 3 replicates of wild type yeast and 3 replicates of wild type shifted to cold. We sequenced 2 replicates of snr80 KO, Prp43 mutant, Dbp3 KO and Pxr1 KO.

first: Andrew

middle: D

last: Bailey IV

first: Jason

last: Talkish

first: Hongxu

last: Ding

first: Haller

last: Igel

first: Alejandra

last: Duran

first: Shreya

last: Mantripragada

first: Benedict

last: Paten

last: Ares Jr.


title: Progressively overloaded single-cell RNA-seq with cell hashing

status: Public on Dec 01 2021

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. To evaluate methods for demultiplexing barcode-multiplexed data, we generated a dataset by labeling samples separately with barcode-tagged antibodies, mixing those samples, and progressively overloading a droplet-based scRNA-seq system.

overall_design:
An aliquot of Ficoll-purified human PBMCs was sorted into 3 distinct populations by FACS(Naive T cells, Memory T cells, and Non-T cells), each population was divided into two replicates, and each replicate was stained with a different barcoded antibody (BioLegend TotalSeq-A). Samples were then mixed, and loaded into a Chromium Next GEM Single Cell 3' v3.1 scRNA-seq chip (10x Genomics) at 16,000 to 80,000 cells per well. After library prepraration, well libraries were mixed based on overloading level to obtain an increased number of reads with increased overloading.
NOTE FROM SUBMITTER: Raw files from human subjects will be submitted to dbGaP

first: Elliott

last: Swanson

first: Peter

middle: J

last: Skene

first: Lucas

middle: T

last: Graybuck

first: Olivia

last: Fong


title: RNA sequencing analysis of the hippocampus reveals transcriptomic signatures of PTZ-kindled seizure rats and upon treatment of novel anti-convulsant chemical Q808

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

country: China

institute: Jilin Provincial Academy of Traditional Chinese Medicine

summary: The present study aimed to use RNA sequencing (RNA-seq) to reveal the gene transcriptomic profile of chronic PTZ-kindled seizure rats and the difference of the PTZ model rat before and after treatment with Q808.

overall_design: Rats were randomly divided into vehicle control group (n=3), PTZ + vehicle group (n=3), and PTZ + Q808 group (n=2)

first: Xiang

first: Qing

last: Wang

first: Dianwen

last: Zhang

first: Siwei


title: Mechanical control of innate immune responses against viral infection revealed in a human Lung Alveolus Chip III

city: Boston

first: Haiqing

last: Bai

state: MA

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

summary: Mechanical forces associated with breathing play fundamental role in lung development and disease but the molecular pathways remain largely unknown. Here, we used a mechanically actuatable Human Lung Alveolus Chip that recapitulates human lung alveolar type I and type II cell differentiation, alveolar-capillary interface formation, and genome-wide gene expression profiles characteristic of the distal lung to investigate the role of physical forces associated with cyclic breathing motions in lung innate immune responses to viral infection. When the mechanically active Alveolus Chips are infected with influenza H3N2 virus, a cascade of host responses is elicited on-chip, including increased production of cytokines and expression of inflammation-associated genes in pulmonary epithelial and endothelial cells, resulting in enhanced recruitment of circulating immune cells as occurs during viral infection in vivo. Surprisingly, studies carried out in parallel with static chips revealed that physiological breathing motions suppress viral replication by activating protective innate immune responses in epithelial and endothelial cells. This is mediated at least in part through upregulation of S100 calcium-binding protein A7 (S100A7), which binds to the Receptor for Advanced Glycation End Products (RAGE), an inflammatory mediator that is most highly expressed in the lung alveolus in vivo. This mechano-immunological control mechanism is further supported by the finding that existing RAGE inhibitor drugs can suppress production of inflammatory cytokines in response to influenza virus infection in this model. S100A7-RAGE interactions and modulation of mechanical ventilation parameters could therefore serve as new targets for therapeutic intervention in patients infected with influenza and other potential pandemic viruses that cause life-threatening lung inflammation.

overall_design: This study aims to examine the effect of S100A7 overexpression on gene expression in alveolar epithelial cells culure on human Alvelous Chip

first: Donald

middle: E

last: Ingber


title: Influence of CPM-dependent sorting on the multi-omics profile of hepatocyte-like cells matured in microscale biochips.

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

summary: We investigated the transcriptome of human induced pluripotent stem cells (hiPSCs) differentiated into hepatocyte-like cells (HLCs) in a biochip culture environment with or without carboxypeptidase M positive (CPM+) cells selection using nanoCAGE, a method for promoters, transcription factors, and transcriptome analysis.

overall_design: Comparison of the multi-omics profiles of human induced pluripotent stem cells (hiPSCs) differentiated into hepatocyte-like cells (HLCs) in a biochip culture environment either with or without applying a carboxypeptidase M positive (CPM+) cells sorting step before cell inoculation.

first: Mathieu

last: Danoy

first: Benedikt

last: Scheidecker

first: Rachid

last: Jellali

first: Yannick

last: Tauran

first: Marjorie

last: Leduc

first: Johanna

last: Bruce

first: Francoise

last: Gilard

first: Bertrand

last: Gakiere

first: Hiroshi

last: Arakawa

first: Yukio

last: Kato

first: Soo

middle: H

last: Kim

first: Taketomo

last: Kido

first: Atsushi

last: Miyajima

first: Yasuyuki

last: Sakai

first: Éric

last: Leclerc


title: Mechanical control of innate immune responses against viral infection revealed in a human Lung Alveolus Chip II

first: Haiqing

last: Bai

overall_design: This study examined host transcriptome on-chip following H3N2 infection at MOI = 1 at 48 hours post infection

first: Donald

last: Ingber


title: Transcriptional profiling of TSC2-null cell lines UMB1949 and 621-102 (TRI102)

status: Public on Dec 04 2021

city: Grand Rapids

first: Jeffrey

last: MacKeigan

state: MI

address: 400 Monroe Ave NW

institute: Michigan State University

summary: RNA-sequencing was performed to establish the transcriptional profiles of two cell lines used in our study. 621-102 (TRI102) were originally isolated from a lymphangioleiomyomatosis-associated renal angiomyolipoma. UMB1949 were originally isolated from a male tuberous sclerosis complex (TSC) patient with renal angiomyolipoma and immortalized via SV40 large T antigen and hTERT introduction. These samples were seuqenced as part of a larger study (Martin et al. 2017, Nat. Comm. https://doi.org/10.1038/ncomms15816).

overall_design: two cancer cell lines analyzed

first: Robert

middle: M

last: Vaughan

first: Katie

middle: R

last: Martin


title: Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction

city: Berlin

first: Jorge

last: Ruiz-Orera

state: Berlin

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbruck Center for Molecular Medicine

summary: The northern white rhinoceros (NWR) is probably the earth’s most endangered mammal. To rescue the functionally extinct species, we aim to employ induced pluripotent stem cells (iPSCs) to generate gametes and subsequently embryos in vitro. To elucidate the regulation of pluripotency and differentiation of NWR PSCs, we generated iPSCs from a deceased NWR female using episomal reprogramming, and observed surprising similarities to human PSCs. NWR iPSCs exhibit a broad differentiation potency into the three germ layers and trophoblast, and acquire a naïve-like state of pluripotency, which is pivotal to differentiate PSCs into primordial germ cells (PGCs). Naïve culturing conditions induced a similar expression profile of pluripotency related genes in NWR iPSCs and human ESCs. Furthermore, naïve-like NWR iPSCs displayed increased expression of naïve and PGC marker genes, and a higher integration propensity into developing mouse embryos. As the conversion process was aided by ectopic BCL2 expression, and we observed integration of reprogramming factors, the NWR iPSCs presented here are unsuitable for gamete production. However, the gained insights into the developmental potential of both primed and naïve-like NWR iPSCs are fundamental for in future PGC-specification in order to rescue the species from extinction using cryopreserved somatic cells.

overall_design: Total RNA-sequencing of NWR iPSCs cultured in 3 different conditions: primed mTeSR1 (feeder-free, 4 replicates), naïve N2B27 (on feeder cells, 2 replicates), naïve Rset (on feeder cells, 2 replicates).

first: Vera

last: Zywitza

first: Ejona

last: Rusha

first: Dmitry

last: Shaposhnikov

first: Valentyna

last: Rishko

first: Jan

last: Stejskal

first: Susanne

last: Holtze

first: Frank

last: Göritz

last: Hermes

first: Masafumi

last: Hayashi

first: Zsuzsanna

last: Izsvak

first: Geert

last: Michel

first: Lars

last: Wittler

first: Cesare

last: Galli

first: Katsuhiko

first: Thomas

middle: B

last: Hildebrandt

first: Giovanna

last: Lazari

first: Jichang

last: Wang

first: Silvia

last: Colleoni

first: Sebastian

last: Diecke

first: Micha

last: Drukker


title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis

status: Public on Nov 30 2021

city: Nanchang

first: Junping

last: Yang

state: Jiangxi

address: 56 Yangming Road, Donghu District

department: Laboratory

institute: Jiangxi Chinese Medical University

summary: In order to identify new biomarkers for the diagnosis of rheumatoid arthritis, we used circRNA microarray technology to screen the differential expression of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis. We identified a total of 399 differentially expressed circRNAs in RA patients and healthy controls, of which 149 circRNAs were significantly up-regulated in RA patients and 250 were down-regulated. Among them, hsa_circRNA_101328 may be a potential biomarker for the diagnosis of RA.

overall_design: We performed microarray analysis on the circRNAs expression profiles in PBMCs of 4 RA patients and 4 healthy controls.Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of circRNAs in PBMCs of 20 RA patients,10 systemic lupus erythematosus (SLE) patients and 20 age- and gender-matched controls.

first: Huangxin

last: Lu

first: Yifan

first: Dong

last: Kuang

first: Ping

last: Liu


title: MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice [array]

city: Beijing

first: huimin

last: liu

state: Beijing

address: 38 Xueyuan Rd , Haidian District

department: Peking University Health Science Center

institute: Peking University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Abstract:  Background: Hyposalivation is one of the common symptoms of diabetes. Although the micro ribonucleic acid (miRNA) has recently been identified to play a role in the pathogenesis of diabetes, the specific effects of miRNAs on diabetic salivary glands remain unclear. This work was aimed to investigate the expression profiles of miRNAs and identify miRNA‐mRNA network in submandibular gland (SMG) in db/db mice.     Methods: miRNA and mRNA expressional profiles were analyzed by microarray technology from the SMG of db/db mice and db/m mice. Significant fold changes in miRNAs and mRNAs were confirmed by real-time quantitative reverse transcription-polymerase chain reaction. Bioinformatic analyses were performed to identify the critical biological functions and signaling pathways involved in diabetes-mediated hyposalivation and to identify the functional networks formed between differentially expressed (DE) miRNAs and mRNAs.    Results: A total of 28 DE miRNAs and 1146 DE mRNAs were identified of the SMG in db/db mice and db/m mice. Gene ontology (GO) analysis and KEGG pathway analysis demonstrated that DE miRNAs were highly associated with terms related to diverse biological processes and signaling pathways. Of the related pathways, TGF-beta signaling pathway and tight junction pathway were notable. The constructed network indicated interactions between 11 miRNAs and 42 mRNAs. Autophagy pathway is worth studying, especially the dynamic network of miRNA and mRNA. In addition, AKT3 and PIK3CD may play important roles in the development of diabetes-mediated hyposalivation.    Conclusions: Our research describes the miRNA and mRNA expression profiles and functional networks involved in SMGs from db/db mice. These results provide possible molecular mechanisms and may help to elucidate possible molecular therapeutic targets for the treatment of diabetes-induced hyposalivation.    Key words: diabetes, submandibular gland, miRNA, mRNA, miRNA–mRNA network, microarray

overall_design: Detection of expression profiles of miRNA and mRNA in submandibular glands of db/m and db/db mice, and analysis of GO and KEGG pathways.

first: Ruolan

last: xiang

first: Huimin

first: XiJin

last: Shi


title: MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: MicroRNA-mRNA expression profiles and functional networks of Submandibular Gland in type 2 diabetic db/db mice [seq]

last: Xiang


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (mRNA-seq)

city: Worcester

first: Yue

last: Zhang

state: Massachusetts

address: GeneTherapyCenter, 368 Plantation st

institute: Umass medical school

summary: In this study, we utilized a mouse model of mucopolysaccharidosis type I (MPS-I) carrying a homozygous nonsense mutation in the Idua gene (Idua-W401X, TGG→TAG) to develop rAAV-delivered sup-tRNA therapeutics that can overcome a pathogenic UAG premature termination codon (PTC).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of sup-tRNA treated and untreated in wildtype mice liver and human Idua+/- fibroblast

first: Dan

first: Jiaming


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (tRNA_charging)

overall_design: targeted tRNA amplicon sequencing of sup-tRNA treated and untreated homozygous Idua-W401X mice


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (mim-tRNA)

overall_design: Liver mim-tRNA sequencing of sup-tRNA treated and untreated homozygous Idua-W401X mice.


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (ribosome profiling)

overall_design: Liver ribosome profilings in sup-tRNA treated and untreated homozygous Idua-W401X mice and patient fibroblasts.


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice


title: AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (amplicon)

overall_design: Idua amplicon sequencing of sup-tRNA treatedand untreated heterozygous Idua-W401X mice


title: Transcriptome Analysis of Liver cancer cell Huh-7 Treated with Metformin

city: Baoding

first: Chunqing

last: Li

state: Hebei Province

address: Number 180,  Wusi east street

institute: Hebei University

summary: Metformin is a kind of widely used antidiabetic agent, which regulates glucose homeostasis through inhibiting liver glucose production and increasing glucose uptake in muscle. Recent studies suggest that metformin exhibits anticancer properties in a variety of cancers. Although several antitumor mechanisms have been proposed for metformin action, its mode of action in human liver cancer remains not elucidated. In our study we investigated the underlying molecular mechanisms of metformin’s antitumor effect on Huh-7 cells of hepatocellular carcinoma (HCC) in vitro. RNA sequencing (RNA-seq) was performed to explore the effect of metformin on the transcriptome of Huh-7 cells. The results revealed that 4518 genes (with log2 fold change>1 or < -1, p-adjusted value<0.05) were differentially expressed in Huh-7 cells with treatment of 25mM metformin compared to 0mM metformin including 1812 up-regulated and 2706 down-regulated genes. Gene ontology and KEGG pathway analyses identified 54 classical pathways which were significantly enriched, and 16 pathways are closely associated with cancer, such as cell cycle, DNA replication, ECM-receptor interaction and so on. We selected 11 differentially expressed genes, which are closely associated with HCC to validate their differential expressions through quantitative real-time reverse transcription PCR (qRT-PCR). The result exhibited that the genes of FASN, MCM6, MCM5, MARCKS, FADS2, CXCL1, BMP4, SKP2, KNG1, PCNA were down-regulated and DUSP1 is significantly up-regulated in Huh-7 cells with treatment of 25mM metformin. These differentially expressed genes and pathways might play a crucial part in the antitumor effect of metformin, and might be potential targets of metformin treating HCC. Further investigations are required to evaluate the metformin mechanisms of anti-cancer action in vivo.

overall_design: mRNA profiles of Huh-7 cells treated with metformin and without metformin for 48 hours

first: Duqiang

last: Luo

first: Zhiqin


title: Response to 10 nM dexamethasone in MEF cells expressing GR dimer deficient mutant receptors

status: Public on Nov 29 2021

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The glucocorticoid (GC) receptor (GR) is essential in development and inflammation. Healthy GRdim/dim mice with reduced dimerization propensity due to a point mutation (A465T) at the dimer interface of the GR DNA binding domain (DBD) (here GRD/D) have helped to define GR monomer and dimer functions of GR. Since GRD/D retains residual dimerization capacity, we generated the dimer-nullifying double mutant GRD+L/D+L mice, featuring an additional mutation (I634A) in the ligand binding domain (LBD) of GR. These mice are perinatally lethal, as are GRL/L mice, displaying improper lung and skin formation. We used embryonic fibroblasts, high and low doses of dexamethasone (Dex), nuclear translocation, RNAseq, dimerization assays and ligand binding assays (and Kd values), we suggest that the lethal phenotype is due to insufficient ligand binding. The data suggest cross talk between GR dimerization potential and ligand affinity. We conclude that a mutation as subtle as this I634A, at a position not directly involved in ligand interactions senso stricto, can thus still influence ligand binding and have a lethal outcome.

overall_design: RNA-seq on MEF cells: 4 GR genotypes (GRwt/wt, GRD/D, GRL/L and GRD+L/D+L) after stimulation with vehicle or 10 nM dexamethasone for a total of 8 conditions. 3 primary MEF cultures per genotype were used, each derived from a different mouse to obtain 3 biological replicates.

first: Nicolette

last: Verhoog

first: Kelly

last: Van Looveren

first: Sylviane

last: Dewaele

first: Tino

last: Hochepied

first: Melanie

last: Eggermont

first: Barbara

last: Gilbert

first: Anne

last: Boerema-de Munck

first: Tineke

last: Vanderhaeghen

first: Joke

last: Vanden Berghe

first: Natalia

last: Garcia Gonzalez

first: Yehudi

last: Bloch

first: Mathias

last: Provost

first: Savvas

middle: N

last: Savvides

first: Karolien

last: De Bosscher

first: im

last: Declercq

first: Robbert

last: Rottier

first: Ann

last: Louw

first: Claude

last: Libert


title: Single-cell RNA sequencing of urinary cells from patients with COVID-19 reveals distinct cellular diversity in AKI

city: Birmingham

first: Matthew

middle: David

last: Cheung

state: AL

address: 1825 University Blvd

institute: University of Alabama at Birmingham School of Medicine

summary:
Background: Acute kidney injury (AKI) is a common sequela of infection with SARS-CoV-2 and contributes to the severity and mortality from COVID-19. Here, we tested the hypothesis that kidney alterations induced by COVID-19-associated AKI could be detected in cells collected from urine.
Methods: We performed single-cell RNA sequencing (scRNAseq) on cells recovered from the urine of eight hospitalized COVID-19 patients with (n=5) or without AKI (n=3) as well as four non-COVID-19 AKI patients (n=4) to assess differences in cellular composition and gene expression during AKI.
Results: Analysis of 30,076 cells revealed a diverse array of cell types, most of which were kidney, urothelial, and immune cells. Pathway analysis of tubular cells from patients with AKI showed enrichment of transcripts associated with damage-related pathways compared to those without AKI. ACE2 and TMPRSS2 expression were highest in urothelial cells amongst cell types recovered. Notably, in one patient we detected SARS-CoV-2 viral RNA in urothelial cells. These same cells were enriched for transcripts associated with anti-viral and anti-inflammatory pathways.
Conclusions: We successfully performed scRNAseq on urinary sediment from hospitalized patients with COVID-19 to noninvasively study cellular alterations associated with AKI and established a dataset that includes both injured and uninjured kidney cells. Additionally, we provide preliminary evidence of direct infection of urinary bladder cells by SARS-CoV-2. The urinary sediment contains a wealth of information and is a useful resource for studying the pathophysiology and cellular alterations that occur in kidney diseases.

overall_design: Single-cell RNA sequencing of cells obtained from urine of patients with COVID-19. There are 12 total samples from 12 separate patients, 5 with COVID19 AKI, 3 with COVID19 without AKI, and 4 with non COVID19 AKI

first: Elise

last: Erman

first: Shanrun

last: Liu

first: Nathaniel

last: Erdmann

first: Gelare

last: Ghajar-Rahimi

first: Kyle

last: Moore

first: Jeffrey

middle: C

last: Edberg

first: James

middle: F

last: George

first: Anupam

last: Agarwal


title: CDK16 is a vulnerable target for triple negative breast cancer therapy

city: Wuhan

first: xiao

last: Li

address: No. 115, Donghu Road

institute: Wuhan University

summary:
Background: CDK16 is an atypical PCTAIRE kinase, and its activity is dependent on Cyclin Y (CCNY) family. CCNYs have been reported to regulate mammary stem cell activity and mammary gland development, and CCNY plays an oncogenic role in a variety of cancers including breast cancer. However, whether CDK16 plays a role in breast cancer and whether CDK16 can be served as a therapeutic target for breast cancer remains unknown.
Methods: TCGA/GEO database analysis and KM survival analysis were used to examine the mRNA expression and the clinical relevance of PFTAIRE and PCTAIRE kinases in breast cancer. The expression of CDK16 protein was determined by CPTAC dataset output and immunohistochemical analysis of breast cancer tissue microarray and immunoblot analysis of additional clinical samples. Knockdown and overexpression of CDK16 were mediated by shRNA and lentivirus vectors, respectively. Cell proliferation was assessed by colony formation and MTT analysis. The cell cycle and apoptosis were examined by FACS analysis. Wound-healing and trans-well invasion assay were conducted to test cell migration ability. The functions of CDK16 on tumorigenesis and metastasis were evaluated by cell line-derived xenograft, patient-derived organoid/xenograft, lung metastasis and systemic metastasis mouse models. RNA-sequencing analysis was performed to reveal the potential molecular mechanisms involved in the function of CDK16. Pharmacological inhibition of CDK16 was achieved by its inhibitor Rebastinib to further assess the anti-tumor effect of targeting CDK16.
Results: CDK16 is highly expressed in breast cancer, especially in triple-negative breast cancer (TNBC). The elevated CDK16 expression is correlated with poor outcomes in breast cancer patients. CDK16 promotes the proliferation and migration of TNBC cells in vitro and tumorigenesis and metastasis of TNBC tumors in vivo. Both gene knockdown and pharmacological inhibition of CDK16 significantly repress tumor progression of TNBC. Mechanically, CDK16 not only regulates spindle formation by phosphorylating PRC1 at the T481 site, but also regulates the Rb-E2F pathway by phosphorylating Rb, which are essential for cell cycle progression and cell proliferation of tumor cells.
Conclusion: CDK16 plays an oncogenic role in TNBC and can be served as a novel potential therapeutic target for TNBC.

overall_design: mRNA profiles of TNBC cell line MDA-MB-231 with CDK16 knockdown or Rebastinib treatment.

first: Xiao

first: Jinpeng


title: Bmp2 -driven terminal differentiation of the stomach epithelium is induced by an autocrine Bmp2 positive feedback loop and inhibited by H. pylori via Interferon gamma signaling [RNA-seq]

first: Thomas

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

summary: We find that Bmp2 expression in the surface epithelium of the stomach provides a decisive, dominant fate-determining signal in the gland resulting in terminal differentiation. Terminal differentiation is induced by Bmp2 expression controlled by Bmp2 itself, creating an auto- and paracrine loop that maintains the cells in the differentiated state. Infection with H. pylori leads to a loss of stromal and epithelial Bmp2 expression resulting in gland hyperplasia and impaired differentiation. We demonstrate that Interferon gamma blocks endogenous Bmp2 expression and therefore Bmp2 signaling. Its effect on differentiated cells via Bmp2 inhibition maintains plasticity in this compartment, allowing for recruitment of differentiated cells to the stem cell pool, accounting for the rearrangement of stem cell compartment and increased plasticity in the epithelium in the context of epithelial damage in the gastrointestinal tract.

overall_design: RNAseq of Myh11+ myofibroblasts from 3x uninfected and 3x H. pylori infected mice

first: Marta

last: Jablonska

first: Michael

last: Sigal

first: Hans

last: Mollenkopf

first: Jeroen

last: Maertzdorf

first: Hilmar

last: Berger


title: Bmp2 -driven terminal differentiation of the stomach epithelium is induced by an autocrine Bmp2 positive feedback loop and inhibited by H. pylori via Interferon gamma signaling [microarray]

overall_design: Hpy infection: Microarray of uninfected and 2 months H. pylori infected antral tissue from BL6 mice. IFNy treatment: Microarray of organoids untreated and treated with recombinant Interferon-γ


title: Bmp2 -driven terminal differentiation of the stomach epithelium is induced by an autocrine Bmp2 positive feedback loop and inhibited by H. pylori via Interferon gamma signaling


title: Coupled Single Cell RNA Sequencing and TCR Profiling of T Cells in Large Granular Lymphocytosis to Infer Pathophysiology and Mechanism of Drug Action

status: Public on Nov 22 2021

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary:
Background and methods:  T-cell large granular lymphocytosis (T-LGL) is a lymphoproliferative disease usually presenting with cytopenia, and typically characterized by clonal expansion of terminally differentiated effector-memory cytotoxic T lymphocytes (CTLs). Conventional methods including flow cytometry and sequencing of Vb chains provided incomplete signature of TCR repertoire. Efforts to characterize transcriptome of clonal CTLs using whole peripheral blood or after enrichment of specific clones by flow cytometry have not provided satisfying resolution and scale due to heterogeneity among individual patients. We applied single cell TCR-sequencing coupled with single cell RNA sequencing to CD3+ T cells from a relatively large cohort (N=13) of T-LGL patients in a clinical protocol to prospectively test therapy with alemtuzumab in refractory disease, to characterize TCR repertoire and to define pathophysiologic mechanism at the single cell level, and to determine mechanisms of response and non-response to therapy.
Results: T cells have less clonal diversity in T-LGL patients, compared with that in healthy donors. TCR repertoires in T-LGLL follow power law distribution but at a larger scale. There are no significant evidence of common TCR clonotypes among T-LGLL patients. TCR usage and T cell activation states shape T cell phenotypes. Cell survival and apoptosis gene programs are deregulated in T-LGL. Immunosuppressive treatment modulates clonality and gene expression in T-LGL.
Conclusion: Our work complements and adds to previous modeling of T cell clonal expansion. Single cell sequencing of  transcriptomes supports a theory of fluctuation in clone fitness, antigenic and environmental factors in concert with clone-specific and cell-specific germline and somatic genetic factors (HLA and STAT3).

overall_design: We applied scTCR-seq coupled with scRNA-seq to CD3+ T cells obtained from a relatively large cohort of T-LGLL patients and 7 healthy donors

first: Zhijie

last: Wu


title: Extracellular Nicotinamide Phosphoribosyltransferase (eNAMPT) boosts IFNγ-induced macrophage polarization

status: Public on Nov 20 2021

city: Novara

first: Giorgia

last: Colombo

state: NO

address: Via Bovio 6, Presso Fondazione Novara Sviluppo

department: Department of Pharmaceutical Sciences

country: Italy

institute: UNIUPO

summary: Nicotinamide phosphoribosyltransferase (NAMPT), alongside being a crucial enzyme to synthesize NAD in cells, has also been shown to be a secreted protein (eNAMPT). In this respect, this protein is found increased in plasma of cancer patients as well as in patients suffering from immune-mediated disorders and preclinical models have demonstrated that it is involved in their pathogenesis (e.g. (inflammatory bowel disease). In the present contribution, we evaluated the effect of this protein on macrophages performing a comprehensive RNAseq analysis, coupled to functional assays. Using peritoneal exudate cells (PECs), we now report that eNAMPT has chemoattractive and M1-skewing properties in macrophages and this holds true also in human monocyte-derived macrophages. Furthermore, we report that this protein is able to boost the responses to IFNγ, and this is likely to be mediated by STAT1-STAT3-activation. Importantly, IFNγ triggers the upregulation and secretion of eNAMPT, thereby providing evidence of a positive feedback loop upon cytokine activation. Last, we report that these phenomena are not a result of TLR4 activation, the only eNAMPT receptor that has been recognised until now, prompting the knowledge that other receptors may be involved.

overall_design: We used 5 replicates of 4 samples (CTRL, eNAMPT, IFNγ and IFNγ+eNAMPT treated) using Illumina NextSeq 500

first: Colombo

last: Giorgia

first: Cristina

last: Travelli

first: Chiara

last: Porta

first: Armando

middle: A

last: Genazzani


title: ChIP analysis trial of human TFB2M and POLRMT interaction with mtDNA

status: Public on Nov 21 2021

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In many mammalian tissues and cells, two classes of mitochondrial DNA (mtDNA) replication intermediates have been observed. One involves leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Surprisingly, removal of either protein resulted in the complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for human mtDNA maintenance. Moreover, the lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of strand-coupled replication initiation.

overall_design: After 1% formaldehyde crosslinking of cells (containing mitochondria), immunoprecipitation was carried out. DNA fragments obtained were subjected to deep sequencing to examine the binding sites for TFB2M (a mitochondorial transcription initiation factor) and POLRMT (the mitochondorial RNA polymerase).  Although the obtained data showed strong enrichment of ChIP reads in the NCR for TFB2M, POLRMT, and HA (for HA-tagged TFB2M), such enrichment was also seen in the respective negative cntorol samples (control IgG).  Therefore, we note that the ChIP-seq data may contain artificial enrichments with unknwon reasons.

first: Teppei

last: Inatomi

first: Shigeru

last: Matsuda

first: Takashi

last: Ishiuchi

first: Shusaku

last: Abe

first: Yura

last: Do

first: Takehiro

last: Yasukawa


title: A sex-specific evolutionary interaction between ADCY9 and CETP

status: Public on Nov 24 2021

city: Montreal

first: Julie

last: Hussin

state: QC

address: 5000, rue Bélanger

country: Canada

institute: Montreal Heart Institute

summary: Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the cholesteryl ester transfer protein (CETP) modulator dalcetrapib, however, the mechanism behind this interaction is still unknown. Here, we characterized selective signals at the locus associated with the pharmacogenomic response in human populations and we show that rs1967309 region exhibits signatures of natural selection in several human populations. Furthermore, we identified a variant in CETP, rs158477, which is in long-range linkage disequilibrium with rs1967309 in the Peruvian population. The signal is mainly seen in males, a sex-specific result that is replicated in the LIMAA cohort of over 3,400 Peruvians. We further detected interaction effects of these two SNPs with sex on cardiovascular phenotypes in the UK Biobank, in line with the sex-specific genotype associations found in Peruvians at these loci. Analyses of RNA-seq data further suggest an epistatic interaction on CETP expression levels between the two SNPs in multiple tissues. We propose that ADCY9 and CETP coevolved during recent human evolution, which points towards a biological link between dalcetrapib’s pharmacogene ADCY9 and its therapeutic target CETP.

overall_design: RNAseq: HepG2 ADCY9 knock down

first: Isabel

last: Gamache

first: Marc-André

last: Legault

first: Jean-Christophe

last: Grenier

first: Rocio

last: Sanchez

first: Eric

last: Rhéaume

first: Samira

last: Asgari

first: Amina

last: Barhdadi

first: Yassamin

last: Zada

first: Holly

last: Trochet

first: Yang

last: Luo

first: Leonid

last: Lecca

first: Megan

last: Murray

first: Soumya

last: Raychaudhuri

first: Jean-Claude

last: Tardif

first: Marie-Pierre

last: Dubé

middle: G


status: Public on Nov 19 2021

city: Hangzhou

first: XIN

last: GUO

state: Zhejiang

address: yuhangtang road

institute: Zhejiang University

summary: Chimeric antigen receptor (CAR) T cells are known to be potent in recognizing and eliminating tumor elimination, and effector functions. They induce marked responses in patients with refractory leukemia and lymphoma, but dysfunction of T cells is an inevitable obstacle for persistent curative effect. Extending the persistence of these cells without compromising their potency is supposed to improve treatment outcomes. We demonstrated that the SOCE (Store-Operated Calcium Entry) inhibitor BTP-2, rather than calcium chelator BAPTA-AM, diminished exhaustion and terminal differentiation of CAR-T cells both in tonic signaling and tumor antigen exposure models. And BTP-2 pretreated CAR-T cells showed improved antitumor potency and prolonged survival in NSG mice. To further investigate the biological impact of calcium signaling at the molecular level, we performed RNA-seq on CAR-T cells and CAR-T cells exposed to Nalm6 stimulation followed by treatment with DMSO, BAPTA and BTP-2.The high-throughput RNA sequencing (RNA-Seq) revealed that treatment with BTP-2 downregulates glycolysis pathway.

overall_design: We performed RNA-Seq differential expression analysis of CAR T and CAR T exposed to Nalm6 stimulation  followed by treatment with DMSO, BAPTA and BTP-2.

first: Mi

last: Shao

first: Xinyi

last: Teng

first: Xin

last: Guo


title: The effect of photobiomodulation (PBM) on mouse bone marrow-derived macrophages activated by LPS and IFN-γ

city: Xi’an

first: Yangguang

last: Ma

address: Changle West Road No. 127

institute: Department of Orthopedics, The First Affiliated Hospital of Air Force Military Medical University

summary: Purpose: This study uses transcriptome analysis (RNA-seq) to study the effects of photobiomodulation therapy on classically activated M1 macrophages induced by LPS and  IFN-γ.

overall_design: After 12 hours of LPS and IFN-γ induction, the differentially expressed genes of classically activated macrophages in the blank control group and the PBM treatment group were examined.  Total RNA was isolated from macrophage sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina HiSeq X Ten instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

first: Xiaoshuang

last: Zuo

first: Cheng

last: Ju


title: Tormentic Acid Ameliorates Hepatic Fibrosis in vivo by Inhibiting Glycerophospholipids Metabolism and PI3K/Akt/mTOR and NF-κB Pathways: Based on Transcriptomics and Metabolomics

status: Public on Nov 13 2021

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the effects and underlying mechanisms of tormentic acid (TA) on carbon tetrachloride (CCl4)-induced liver fibrosis in rats. The rats were intragastrically administered with 50% CCl4 for 9 weeks to induce hepatic fibrosis, followed by various agents for 6 weeks. Transcriptomic analysis was carried out to predict the potential targets, and then multiple examinations were performed to verify the prediction. The results showed that TA significantly alleviated liver injury and fibrosis, as evidenced by the ameliorative pathological tissue, low transaminase activity, and decreased collagen accumulation. Besides, TA markedly reduced hepatocyte apoptosis by regulating the expression of caspase-3 and Bcl-2 families. The transcriptomic analysis revealed 2,173 differentially expressed genes (DEGs) between the TA and model groups, which could be enriched in the metabolic pathways and the PI3K/Akt and NF-κB signaling pathways. The metabolomics analysis showed that TA could regulate the glycerophospholipid metabolism pathway by regulating the synthesis of phosphatidylserines, phosphatidylethanolamines and phosphatidylcholines. Moreover, the integrative analysis of the transcriptomics and metabolomics data indicated that TA inhibited the glycerophospholipid metabolism pathway by inhibiting the expression of LPCAT4, PTDSS2, PLA2G2A and CEPT1. In addition, the relevant signaling pathways analysis confirmed that TA inhibited HSCs activation by blocking the PI3K/Akt/mTOR pathway and ameliorated inflammatory injury by inhibiting the NF-κB pathway. In conclusion, TA significantly alleviates liver fibrosis in vivo by inhibiting the glycerophospholipid metabolism pathway and the PI3K/Akt/mTOR and NF-κB signaling pathways.

overall_design: Male Sprague–Dawley (SD) rats were intragastrically administered with 2 ml/kg CCl4 (50% oil solution) twice a week for 9 weeks to induce liver fibrosis, followed by Tormentic acid (TA) treatment for 6 weeks. At the end of the treatment, all animals were fasted for 12 h and then anesthetized by intraperitoneal injection of 3% sodium pentobarbital (1.0 ml/kg). The liver samples were collected immediately. The samples for the analysis were obtained from the normal group, model group, and SCL group (3.0 mg/kg TA group; SCL means the special concentration of liver homogenate (<1μg/mL) from the 3.0 mg/kg TA-treated group).

first: Xing

last: Lin

first: Yuanyuan

last: Wei

first: Yan

last: Li

first: Yuhua

last: Xiong


title: Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.

status: Public on Nov 16 2021

city: Seattle

first: David

last: Beier

state: WA

address: 1900 9th Avenue

department: CDBRM

institute: Seattle Children's Research Institute

summary: Cis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. These analyses allowed us to identify cell-class-specific CREs, enriched transcription factor binding motifs, putative target genes, and to examine how these features change over development. By comparing DNA accessibility between the human retina and retinal organoids we found that CREs in organoids are highly correlated at the single-cell level, validating the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we studied the function of a disease-associated CRE at 5q14.3 in organoids, identifying its principal target gene as the miR-9-2 primary transcript and demonstrating a dual role for this CRE in regulating neurogenesis and gene regulatory programs in mature glia. This study provides a rich resource for characterizing cell-class-specific CREs in the human retina and showcases retinal organoids as a model in which to study the function of retinal CREs that influence retinal development and disease.

overall_design: Single-nucleus ATAC-Seq and RNA-Seq of the adult and developing human retina and human iPSC-derived retinal organoids using the 10X Genomics library preparation reagents and workflow.

first: Timothy

last: Cherry

first: Eric

last: Thomas

first: Andrew

last: Timms


title: Expression data from ethanol extract of Aurantiochytrium Sp. (EEA)-treated human amnion epithelial cells (hAECs)

status: Public on Nov 11 2021

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of EEA in neural induction and neuronal differentiation of hAECs.
hAECs were isolated from discarded term placenta and were treated with EEA at the concentration of 20 µg/ml for seven days. Microarray gene expression profiling was conducted for three biological replicates of EEA-treated and untreated control cells.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Cellular Architecture of Human Brain Metastases

status: Public on Nov 12 2021

city: San Francisco

first: Hugo

last: Gonzalez

state: California

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

summary: Here we present an integrative analysis  of 15 human parenchymal BrMs as a resource, generated by single-cell transcriptomics,  and complemented with two mouse models- and in silico- approaches. We interrogated the composition of BrM niches, molecularly defined the blood-tumor interface, and reveal stromal immunosuppressive states, enriched with infiltrated T cells and macrophages. Specific single-cell interrogation of metastatic tumor cells provides a novel framework of 8 functional cell programs that coexist or anticorrelate. Collectively, these programs delineate two functional BrM archetypes, one proliferative and the other inflammatory, that are evidently shaped through tumor-immune interactions. Our resource provides a foundation to understand the molecular basis of BrM in patients with tumor cell-intrinsic and host environmental- traits.

overall_design:
We obtained fresh surgically resected BrM specimens from fifteen patients with diagnosis of melanoma (n=3), breast cancer (n=3), lung cancer (n=3), ovarian cancer (n=2), CRC (n=1), renal cell carcinoma (n=1), unknown primary carcinoma (n=1) and a case of adult rhabdomyosarcoma that was a non-carcinoma, non-melanoma sample used for comparison. All cases were diagnosed as parenchymal BrM, located predominantly in brain cortex. Each tumor was dissociated into single cell suspensions, dead cells were removed, and live cells were profiled by single cell RNA sequencing (scRNAseq) with the 10x drop-seq platform (10x Genomics). For the experimental brain metastasis models, 0,25x106/100ml MDAMB231Br (nude mice) and 0,2X10^6 4T1Br (Balb/c mice) cells were injected into the left ventricle of the heart under anesthesia. After reaching ethical end-point, Viable (Ghost Dye negative), hCD298+ (Just MDAMB231Br), mCherry+, mCD45-, mTer119-, mCD31- single cells were sorted by FACS and processed using 10x drop-seq platform (10X Genomics). For more details, refer to the original study DOI:10.1016/j.cell.2021.12.043, PMID:35063085
Note from submitter: we did not upload the human raw data files because of confidentiality and patient privacy issues with clinical samples.


title: Comparison of transcriptomes reveals differential regulation at four different ages in Sika Deer testes

status: Public on Nov 10 2021

city: Changchun

first: Boyin

last: Jia

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

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

overall_design: Refer to individual Series


title: Comparison of mRNA transcriptomes reveals differential regulation at four different ages in Sika Deer testes

summary: To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of mRNA profiles in the four developmental stages of testis the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old) and aged (10-year-old) stages. The results showed that total total of 23558 differentially expressed (DE) unigenes were obtained. 14918 (8413 up and 6505 down), 4988 (2453 up and 2535 down), 5681 (2929 up and 2752 down) DE unigenes were identified in 3-vs.1-, 5-vs.3- and 10-vs.5-year-old testes, respectively. By integrating mRNA expression profiles, we predicted 10790 mRNA-mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE mRNA (ALKBH5, Piwil, HIF1A, BRDT, etc.), which play an important role in testis development and spermatogenesis. The data show that DE mRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. It provides a useful resource for future studies on the role of genes regulation in testis development and spermatogenesis.

overall_design: The gene expression profiles of testicular tissues at 1, 3, 5, and 10-year-old in sika deer were generated by Illumina HiSeq2500 sequencing

first: Rui

last: Du

first: Fuhe

last: Yang


title: Comparison of miRNA transcriptomes reveals differential regulation at four different ages in Sika Deer testes

summary: To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of miRNA profiles in the four developmental stages of testis the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old) and aged (10-year-old) stages. The results showed that total total of 198 mature and 66 novel miRNAs were obtained. 88 (43 up and 45 down), 102 (44 up and 58 down), 54 (18 up and 36 down) DE miRNAs were identified in 3-vs.1-, 5-vs.3- and 10-vs.5-year-old testes, respectively. By integrating miRNA  expression profiles, we predicted 69883 miRNA-mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE miRNA (miR-145, miR-140, miR-7, miR-26a, etc.), which play an important role in testis development and spermatogenesis. The data show that DE miRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. It provides a useful resource for future studies on the role of miRNA regulation in testis development and spermatogenesis.

overall_design: The miRNA expression profiles of testicular tissues at 1, 3, 5, and 10-year-old in sika deer were generated by Illumina HiSeq2500 sequencing


title: Endothelial GNAQ p.R183Q activates phospholipase-Cbeta3, increases angiopoietin-2 and drives formation of enlarged blood vessels

status: Public on Nov 09 2021

first: Jonathan

last: Pevsner

address: 6001 Executive Blvd

institute: NIMH

summary:
Introduction: Capillary malformation (CM) occurs sporadically and is associated with Sturge-Weber syndrome (SWS). The somatic mosaic mutation in GNAQ (c.548GàA, p.R183Q) is enriched in endothelial cells (EC) in skin CM and SWS brain CM. Our goal was to investigate how the mutant G-protein a-q subunit (Gaq) alters EC signaling and disrupts capillary morphogenesis.
Approach and results: We used lentiviral constructs to express p.R183Q or wild-type GNAQ in normal human endothelial colony forming cells (EC-R183Q and EC-WT respectively). EC-R183Q constitutively activated phospholipase-C β3 (PLCβ3), a downstream effector of Gαq. Activated PLCβ3 was also detected in human CM tissue sections. Bulk RNA-seq analyses of mutant versus wild-type EC indicated constitutive activation of protein kinase C (PKC), NF-κB and calcineurin signaling in EC-R183Q. Increased expression of downstream targets in these pathways, Angiopoetin-2 (ANGPT2), C-X-C Motif Chemokine Ligand 5 (CXCL5) and Down Syndrome Critical Region Protein 1.4 (DSCR1.4) were confirmed by qPCR and immunostaining of human CM tissue sections. The Gαq inhibitor YM-254890 reduced mRNA expression levels of these targets in EC-R183Q while the pan-PKC inhibitor AEB071 reduced ANGPT2 and CXCL5 but not DSCR1.4. EC-R183Q formed enlarged blood vessels in mice, reminiscent of those found in human CM, with robust endothelial ANGPT2.
Conclusions: Gaq-R183Q, when expressed in ECs, establishes constitutively active PLCb3 signaling that leads to a pro-angiogenic, pro-inflammatory phenotype. EC-R183Q are sufficient to form CM-like vessels in mice which provides the first evidence that endothelial Gaq-R183Q is causative for CM.

overall_design: Examination of the effects of the p.R183Q mutation in GNAQ on gene expression and blood vessel function in human endothelial colony-forming cells (ECs).

first: Joyce

last: Bischoff

first: Lan

last: Huang


title: Native MOWChIP-seq: Genome-wide profiles of key protein bindings reveal functional differences among various brain regions

status: Public on Nov 05 2021

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Here we developed a low-input ChIP-seq technology and associated protocol for profiling RNA Polymerase II, transcription factor, or enzyme binding at the genome scale. The new approach, termed native MOWChIP-seq or nMOWChIP-seq, produces genome-wide binding profiles using as few as 1000 cells.

overall_design: We show that MNase digestion is effective for preserving the links between protein and genome and facilitating low-input profiling. We show that native MOWChIP-seq is universally effective for profiling genome-wide protein bindings. We generated high-quality ChIP-seq data using as few as 1,000 GM12878 cells for studying RNA Pol II, 5,000 cells for TF EGR1, and 10,000 cells for HDAC2. We applied this method to study genome-wide binding of RNA Pol II, EGR1 and MEF2C in two functional regions of the mouse brain: prefrontal cortex (PFC) and cerebellum. The filename contains information on the nature of sample (GM12878 cell line, mouse PFC, mouse cerebellum), the target being profiled, number of cell/nuclei used per assay, special condition of the sample, and replicate number. 2 technical replicates were conducted each sample. For example, "GM12878-Pol2-S5-10K-1" refers to technical replicate 1 of the assay using 10,000 GM12878 cells, profiling Pol2 (S5).

first: Zhengzhi

last: Liu


title: Genome-wide gene expression prolifing post-valproic acid exposure in human forebrain organoids

city: Hengyang

first: Qingtuan

last: Meng

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: Human forebrain organoids (day 42) derived from U1M and U2F iPS cell lines were exposed with or without 1 mM valproic acid (VPA) for 72h. Organoids were then randomly selected for RNA sequencing, we found that differentially expressed genes (DEGs) induced by VPA exposure that shared in both U1M and U2F were enriched with neural development, synaptic transmission, calcium and potassium signaling pathways. The DEGs were also significantly enriched with autism spectrum disorder (ASD)-associated genes, including genes dysregulated in brains or organoids derived from ASD patients, and known ASD risk genes, as well as genes in ASD risk-associated gene coexpression modules.

overall_design: We generated human forebrain organoids from U1M and U2F iPS cell lines. On day 42, human forebrain organoids derived from both U1M and U2F were exposed with or without 1 mM VPA for 72h. Three organoids in each group were randomly selected for RNA-seq (Illumina NovaSeq 6000, paired-end 150 bp) to identify genes affected by VPA exposure. DEGs (adjusted P value < 0.05) that identified in both U1M and U2F were used for Gene Ontology and KEGG pathway analysis.

first: Chuan

last: Jiao


title: H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [CUT&Tag_H3K4me2_FLAG]

status: Public on Nov 08 2021

city: Pittsburgh

first: Delphine

last: Gomez

state: PA

address: 200 Lothrop Street

department: Medicine, division of Cardiology

institute: University of Pittsburgh

summary: Epigenetic control of lineage-specific gene expression is essential for cell differentiation, acquisition of specialized functions, and tissue homeostasis. Here, we uncovered a unique epigenetic pathway critical for governing lineage identity in cells presenting milieu-dependent phenotypic modulation in adult organisms, by using vascular smooth muscle cells (SMC) as a model of highly specialized and differentiated cell type retaining phenotypic plasticity. We found that the histone modification H3K4me2 is essential for the maintenance of vascular SMC lineage identity and functions by performing H3K4me2 demethylation selectively on a SMC lineage-specific subset of genes. Removal of H3K4me2 on the myocardin-regulated genes led to a marked loss of contractility and alteration in SMC adaptive response capacities during vascular remodeling. Rather than presenting intrinsic gene activation properties, H3K4me2 serves as a stable preferential hub for the dynamic recruitment of the DNA methylcytosine dioxygenase Ten-Eleven Translocation 2 (TET2). Besides the SMC contractile apparatus, the H3K4me2/TET2 complex controls the expression of miR-145, a central microRNA promoting SMC differentiation and participation in vascular remodeling. Finally, H3K4me2 editing induced a profound loss of SMC lineage identity and gain of plasticity, characterized by the redistribution of H3K4me2 on genes associated with stemness and developmental programs and the greater ability of H3K4me2 edited SMC to transdifferentiate into other lineages. These studies identified H3K4me2 as a central epigenetic mechanism controlling lineage identity and cell-specific specialized functions. Our findings may have broad implications for the understanding of mechanisms controlling multiple plastic cell type behaviors and functions in various pathophysiological processes.

overall_design: Compare H3K4me2 distribution in control, Myocd-LSD1 and Myocd-LSD1NF SMC by CUT &Tag seq targeting H3K4me2. FLAG-tagged Mycod-LSD1 binding sites were assessed by CUT&Tag-seq targeting FLAG in Mycod-LSD1 SMC.

first: Mingjun

first: Cristina

last: Espinosa-Diez

first: Sidney

last: Mahan

first: Mingyuan

first: Anh

last: Nguyen

first: Scott

last: Hahn

first: Adam

last: Straub

first: Raja

last: Chakraborty

first: Kathleen

last: Martin

first: Gary

middle: K

last: Owens


title: H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [CUT&Tag_HA-TET2]

overall_design: HA-tagged TET2 was overexpressed in Mycod-LSD1 SMC and control SMC by adenovirus. CUT&Tag seq targeting HA-TET2 was performed to assess Tet2 binding sites in Myocd-LSD1 and Control SMC

last: Du


title: Transcriptional reprogramming of somatic cells after nuclear transfer to mouse 4-cell embryos

status: Public on Nov 03 2021

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

institute: Kyushu University

summary: We have developed a nuclear transfer (NT) system in which somatic nuclei are transplanted into mouse embryos arrested at the 4-cell stage. The transplanted somatic nuclei show swelling and epigenetic reprogramming towards 4-cell-like nuclei. To assess genome-wide transcriptional reprogramming of the injected nuclei, the newly transcribed genes in NT embryos were examined by RNA-seq analyses. As a control, NT was also performed using mouse embryos at the 2-cell stage.

sample_organism:
Mus musculus
Oryx dammah

platform_organism:
Mus musculus
Oryx dammah

overall_design: Mouse C2C12 cells or primary Oryx dammah cells were fused with mouse 4-cell embryos arrested at G2/M phase with 0.1 µg/ml demecolcine. The reconstructed NT embryos were incubated in mouse embryo culture medium containing 0.1 µg/ml demecolcine with or without alpha-amanitin. After 24 hours of culture, the NT embryos were subjected to RNA-seq analyses to detect newly transcribed genes in a RNA polymerase II-dependent manner by comparing embryos without alpha-amanitin and those with alpha-amanitin. Furthermore, to examine the effect of DNA replication, nuclear transfer of C2C12 cells to 4-cell embryos was performed before and after DNA replication at the 4-cell stage (40 hours post insemination [hpi] and 46 hpi, respecitively, followed by 24 hours of culture). Then, transcriptomes of these embryos with or without DNA replication were compared. Reprogramming ability of 2-cell embryos was also examined by transplanting C2C12 cells to early (21 hpi) or late 2-cell embryos 30 hpi).

first: Junko

last: Tomikawa

first: Christopher

last: Penfold


title: H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [hMeDIP-seq]

type: Methylation profiling by high throughput sequencing

overall_design: human SMC were treated with rapamycin to enhance TET2-mediated DNA hydroxymethylation. Global 5hmC distribution was assessed by hMeDIP-seq


title: Single cell RNA-seq post valproic acid exposure in human forebrain organoids

status: Public on Oct 31 2021

summary: Human forebrain organoids (day 50) derived from U1M and U2F iPS cell lines were exposed with or without 1 mM valproic acid (VPA) for 72h. Organoids were then used for single cell RNA sequencing (scRNA-seq). Through data processing, ten major cell types including astrocyte, choroid plexus, endothelia, intermediate progenitor cells, medial ganglionic eminence, radial glia, immature neuron, excitatory and inhibitory neuron, and microglia-like cells were identified. We found that VPA affected gene expression in choroid plexus, excitatory neuron, immature neuron, and medial ganglionic eminence cells. The cell type-specific DEGs were enriched with mitotic nuclear division, multiple neuronal functions, and response to type I interferon and virus.

overall_design: We generated human forebrain organoids from U1M and U2F iPS cell lines. On day 50, human forebrain organoids derived from both U1M and U2F were exposed with or without 1 mM VPA for 72h. Three organoids in each group were randomly pooled together to prepare single cell suspension using Accutase. 2x104 cells per sample were used for cell capture using the 10x Genomics system. The captured cells were then used for reverse-transcription and library constructions based on the standard Illumina protocols. The constructed libraries were then sequenced on Illumina NovaSeq 6000 (paired-end 150 bp). We then performed differential gene expression analysis to identify genes affected by VPA exposure in each cell type identified in the organoids.

first: Xuan

last: Wang


title: Prolonged cadmium exposure alters benign uterine fibroid cell behavior, extracellular matrix components, and TGFB signaling [CanPath]

status: Public on Oct 29 2021

city: RTP

first: Rick

last: Fannin

state: NC

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

summary: In our lab, Cadmium treatment of human fibroid cells induced a cancer phenotype and altered glycogen metabolism.  In this study we treated fibroid cells with cadmium continuously for 2 or 6 months. Cancer progression and pathway gene expression were investigated using NanoString Technologies.

overall_design: A human uterine leiomyoma cell line immortalized via retroviral transfection of telomerase (ht-UtLM) was generated by our laboratory. For 2 or 6 month Cd-exposure, the ht-UtLM cultures were maintained continuously in ht-UtLM culture medium supplemented with 10 uM CdCl2 for 16 weeks. The culture medium was replaced with fresh medium with 10 ?M CdCl2 every 3 days. Passage-matched control ht-UtLM cultures were run concurrently with Cd exposed cells. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2

first: Darlene

last: Dixon

first: Yitang

last: Yan

first: Kevin

last: Gerrish

first: Jingli

last: Liu

first: Arriana

last: Lawrence

first: Michael

last: Dykstra

first: Rickie

first: C

last: Tucker

first: Erica

last: Scappini


title: Single-Cell RNA-Seq reveals cellualr heterogeneity and gene expression difference between ischemic and hemorrhagic stroke brain

city: Shanghai

first: Xiaojing

last: Shi

state: Please Select

address: 1954 Huashan Rd.

institute: Shanghai Jiao Tong University

summary: Cluster analysis using nonlinear dimensionality reduction ([tSNE]) revealed the differences in global gene expression profiles of healthy and injured striatum, and identified clusters of cells with unique genetic signatures in both ischemic brain and hemorrhagic brain. Genes with p-value < 0.05 and fold change ≥1.5 were regarded as differentially expressed genes (DEGs). For astrocytes, 135 DEGs were downregulated in hemorrhagic stroke compared to ischemic stroke. The secondary profiling of astrocytic subtypes yielded 10 different subtypes with distinct functional cell identities. For microglia, tSNE map indicated the distribution and proportion of microglia/macrophage were very similar in in the ischemic and hemorrhagic stroke models.  We obtained 75 DEGs in total (hemorrhagic stroke vs. ischemic stroke, 54 were upregulated, 21 were downregulated) .

overall_design: comparison of gene exprssion difference between ischemic and hemorrhagic brain in mice

first: Yaohui

last: Tang

first: Guo-yuan

last: Yang


title: Transcriptional profiling of macrophages in skin wounds

status: Public on Oct 28 2021

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Macrophages were isolated from wounded skin 4 and 14 days post wounding. Monocytes were adoptively transferred on days 2 and 12 and traced into the wound.

overall_design: Mice were anesthetized by i.p. injection of Ketanest/Rompun. Back skin was shaved and full-thickness excisional wounds were created using a standard biopsy puncher. Mice were housed individually during the entire time course of healing. Monocytes from female B6.RFP mice were isolated from B6.RFP mice via Immuno-magnetic depletion of whole bone marrow, counted and then 3x10^6 cells were adoptively transferred into each previously wounded C57/BL6 recipient via intravenous injection, either 2 or 12 days after injury. Wounds were excised 4 or 14 days after injury. Wounds from several mice were pooled in two separate experiments (2 biological replicates of several mice each).

first: David

last: Sanin

first: Yan

last: Ge

first: Emilija

last: Marinkovic

first: Sebastian

last: Willenborg

first: Susanne

last: Reinhardt

first: Andreas

last: Dahl

first: Erika

middle: L

last: Pearce

first: Sabine

last: Eming

first: Alexander

last: Gerbaulet

first: Axel

last: Roers

first: Peter

last: Murray

first: Edward


title: Transcript analysis under phosphate and iron deprivation in 7 day old Arabidopsis thaliana seedlings

city: Stanford

first: Yanniv

last: Dorone

address: 371 Jane Stanford Way

institute: Stanford University

summary: Arabidopsis wild-type plants (Col-0 accession) were grown on control (+Fe+P) for 7 days on 0.1X MS then transferred to three different medium: control (+Fe+P), iron deficiency (-Fe+P), and iron and phosphate deficiency conditions (-Fe-P). Shoots were collected 39 h, 52 h and 76 h after the transfer. For RNA-seq experiments, three biological replicates were used for each time point (39h, 52h and 76h) and each condition (+Fe+P, -Fe+P and -Fe-P) for a total of 27 samples.

overall_design: Transcrip analysis of 7do Arabidospsis thaliana seedlings under three conditions (+P+Fe, +P-Fe, -P-Fe) at three time points: 39h, 52h and 76h


title: PPARdelta signaling induces metabolic maturation in human pluripotent stem cell-derived cardiomyocytes

status: Public on Nov 01 2021

city: New York

first: Nadeera

last: Wickramasinghe

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) provide an unprecedented opportunity to study human heart development and disease. A major caveat however is that they remain functionally and structurally immature in culture, limiting their potential for disease modeling and regenerative approaches. Here we address the question of how different metabolic pathways can be modulated in order to induce efficient cardiac maturation of hPSC-CMs. We show that PPAR signaling acts in an isoform-specific manner to balance the glycolysis and fatty acid oxidation (FAO) pathways. PPARd activation or inhibition results in efficient respective up- or down-regulation of the gene regulatory networks underlying FAO in hPSC-CMs. PPARd induction further increases mitochondrial and peroxisome content, enhances mitochondrial cristae formation and augments FAO flux. Lastly PPARd activation results in enhanced myofibril organization and increased numbers of bi-nucleated hPSC-CMs. Transient lactate exposure, commonly used in hPSC-CM purification protocols, induces an independent program of cardiac maturation, but when combined with PPARd activation equally results in a metabolic switch to FAO. In summary, we identify multiple axes of metabolic modifications of hPSC-CMs including a role for PPARdelta signaling in inducing the metabolic switch to FAO in hPSC-CMs. Our findings provide new opportunities to generate and use metabolically mature hPSC-CMs including for disease modeling and regenerative therapy.

overall_design: 105 total samples were analyzed, consisting of 34 treatment conditions with a minimum of 3 biological replicates each. Control samples are included for monolayers (Samples 1-3), EHTs (Samples 88-90) and Ebs (Samples 103-105).

last: Sachs

first: Priyanka

last: Dhanan-Krishnan

first: Denis

last: Torre

first: Serena

last: Raimo

first: Madhavika

last: Serasinghe

first: Joshua

last: Mayourian

first: Deborah

last: French

first: Arne

last: Hansen

first: Thomas

last: Eschenhagen

first: Jerry

last: Chipuk

first: Eric

last: Sobie

first: Adam

last: Jacobs

first: Harry

last: Ischiropoulos

first: Avi

last: Ma'ayan

first: Sander

last: Houten

first: Kevin

last: Costa

first: Nicole

last: Dubois


title: Prolonged cadmium exposure alters benign uterine fibroid cell behavior, extracellular matrix components, and TGFB signaling

first: Rick

last: Fannin


title: Prolonged cadmium exposure alters benign uterine fibroid cell behavior, extracellular matrix components, and TGFB signaling [CanProg]

first: Darlene

last: Dixon

first: Yitang

last: Yan

last: Gerrish

first: Jingli

last: Liu

first: Arriana

last: Lawrence

first: Michael

last: Dykstra

first: Rickie

first: C

last: Tucker

first: Erica

last: Scappini


title: Identification of miRNA and noncoding RNA expression profiles following traumatic spinal cord injury by  high-throughput sequence analysis

status: Public on Oct 27 2021

city: Jinan

first: Bin

last: Ning

address: Jiefang Road #105

institute: Shandong University


title: Cytokine Signaling Co-opts the CREB/CRTC Pathway in Obesity

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

summary: Obesity stimulates the infiltration of adipose tissue by innate immune cells, which in turn promote insulin resistance via the NFkB mediated induction of pro-inflammatory cytokines, which interfere with triglyceride metabolism. The cAMP responsive factor CREB has also been implicated in adipose tissue inflammation and insulin resistance, although the underlying mechanism is unclear. Here, we show that high fat diet (HFD) feeding triggers activation of the CREB cofactors CRTC2 and CRTC3, which bind to CREB and mediate induction of CXCL1 and other cytokine genes in cooperation with NFkB. HFD feeding reduced adipocyte C/EBPa expression in adipose, leading to decreases in the expression of Salt Inducible Kinase 2 (SIK2), which otherwise phosphorylates and sequesters CRTCs in the cytoplasm. Depletion of SIK2 in adipose led to dephosphorylation of CRTC2 and CRTC3 (CRTC2/3) and to the induction of CXCL1 and other cytokine genes in adipocytes. Indeed, CRTC2/3 were found to stimulate the expression of a subset of cellular genes cooperatively with NF-kB in adipocytes. Knockout of both CRTC2 and CRTC3 in adipose decreased the expression of CXCL1/2 and thereby reduced neutrophil and macrophage infiltration. As depletion of CXCL1/2, with neutralizing antiserum or by KO of the CXCL1 gene restored glucose tolerance and insulin sensitivity in the setting of diet induced obesity, our results demonstrate that NF-kB and CREB/CRTC pathways modulate adipose tissue function in part via cooperative effects on target gene expression.

overall_design: ChIP-seq for CRTC2, p65, Histone H3 Acetyl K27 in 3T3L1 adipocytes untreated or treated with 10 uM forskolin, TNFa or both.


title: TET2-mediated deprogramming of breast cancer cells

status: Public on Oct 26 2021

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

summary: Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression through controlling chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function.

overall_design: MCF-7 cells stably transfected with an empty vector or with plasmids encoding either wild type mouse TET2 catalytic domain (CD - aa916-1921, pcDNA3-Flag-TET2 CD, addgene #72219) or the catalytically dead mutant H1304Y, D1306A mutant (pcDNA3-Flag-TET2 mCD, addgene #72220)  were analyzed for gene expression by RNA-seq and for chromatin marks by ChIP-seq (H3K4me3 and H3K27me3) and selective chemical labeling (5hmC).

first: Stéphane

last: Avner


title: Identification of noncoding RNA expression profiles following traumatic spinal cord injury by  high-throughput sequence analysis

summary: To systematically profile and characterize the noncoding RNA (ncRNA) expression pattern in the lesion  epicenter of spinal tissues after traumatic spinal cord injury (TSCI). We used RNA-Seq to profle the expression and regulation patterns of noncoding RNAs and mRNAs of mice  models after TSCI. A total of 498 circRNAs and 1203 mRNAs were identified in TSCI mice  models to be differentially expressed. noncoding RNAs might play important roles via the competing endogenous RNA regulation pattern  after TSCI, further findings arising from this study will not only expand the understanding of potential ncRNA  biomarkers but also help guide therapeutic strategies for TSCI.

overall_design: Spinal cord ncRNA profiles of 8-week old C57BL/6 mice with/without traumatic spinal cord injury

first: Jianan

last: Chen

first: Wenzhao

last: Wang

first: Yanlin

last: Su


title: Gut microbiota-driven brain Ab amyloidosis requires Microglia

status: Public on Oct 25 2021

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: Recent evidence suggests an important role of the gut microbiome in early life on immune cell entraining. Using two independent transgenic (Tg) lines of Alzheimer’s disease, we have demonstrated that life-long antibiotic (ABX)-perturbation of the gut microbiome is associated with reduced amyloid beta (Ab) plaque pathology and microglial phenotypes in male mice. Furthermore, fecal microbiota transfer (FMT) from age-matched APPPS1-21 Tg mice into long-term ABX-treated male APPPS1-21 mice partially restored amyloidosis and microgliosis, thus establishing causality. in the current studies, we planned to investigate the transcriptome profiles in APPPS1-21 mice treated with short-term abx (PND14-21) compared with vehicle treated groups in genotype-, sex- and time -dependent manner. Most importantly, we also investigated if fecal microbiota transplants from age-matched Tg male mice into short-term abx (PND14-21)-treated male mice restores brain transcriptomes to that of obsreved in vehicle-treated male mice at 9 weeks of age.

overall_design: Pups receiving the antibiotic cocktail were gastric gavaged with 200ml of antibiotic cocktail (4 mg/ml kanamycin (Sigma-Aldrich K4000-5g), 0.35 mg/ml gentamicin (Sigma-Aldrich G1914-250mg), 8,500 U/ml colistin (Sigma-Aldrich C4461-1g), 2.15 mg/ml metronidazole (Sigma-Aldrich M1547-25g), and 0.45 mg/ml vancomycin (Sigma-Aldrich V2002-1g)) from post-natal day (PND) 14 to PND 21 followed by an ad libitum access to regular drinking water until the time of sacrifice at 9 weeks of age. Both WT-littermates and APPPS1-21 Tg-littermates were employed to investigate effects of early-life microbiome perturbations on the brain transcriptome profile at 9 weeks of age. Additonally, we sacrfiiced a cohort of WT and APPPS1-21Tg male pups at the age of PND24 to evaluate brain transriptome changes immediately after a completion of large-dose ABX treatments (PND14-PND21).

first: Hemraj

last: Dodiya

first: Sangram

middle: S

last: Sisodia


title: RNA-sequencing of E2a-deficient or E2a and Lef1-deficient leukemia cell lines

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: We compared the transcriptome of leukemia cell lines generated from 7 E2a-/- and 8 E2a-/-Lef1f/fLckCre+ mice

overall_design: Comparison of RNA-seq from cell lines with two distinct genotypes

first: Tiffany

last: Carr

first: Elizabeth

last: Bartom


title: TPL-2 inhibits interferon-beta expression via an ERK1/2-TCF-FOS axis in TLR4-stimulated macrophages

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

country: United Kingdom

institute: University College London

summary: Studies in mice have indicated that TPL2 kinase plays important roles in immune responses to pathogens and in various models of inflammatory disease. We set out to determine how TPL2 (Map3k8) regulates transcription using an in vitro system of LPS-stimulated primary macrophages. TPL2 regulated genes are involved in a number of different processes including inflammation as well as reproduction, cell cycle and signal transduction. Differentially expressed genes were used in a K means analysis, grouping based on expression profile, which identified 12 different expression profiles. There was a strong correlation between rapidly-induced genes regulated by TPL2 kinase activity and their expression in cells treated with the MKK1/2 inhibitor (PD032590)1 or from cells where phosphorylation of P105 by IKK2 is blocked. Cluster 1 genes were found to be enriched for TCF family members. TPL2 was shown to regulate ELK1 phosphorylation and known TCF targets genes such as Egr1. TPL2 is known to regulate transcription of multiple cytokines and chemokines including IFNb. Like Map3k8[D270A] macrophages, expression of Ifnb1 was increased in Elk1-/-Elk4-/- macrophages compared to WT macrophages following LPS stimulation. In fact, this increase was also seen in MKK1/2 inhibitor treated macrophages. Expression of Fos was decreased in both Map3k8[D270A] and Elk1-/-Elk4-/- macrophages. Macrophages generated from mice with myeloid-specific deletion of Fos also had elevated levels of Ifnb1 compared to controls. Similar results were obtained following activation of TLR1/2, TLR9 and TNF-R in macrophages. Furthermore, LPS or TNF stimulation of MEFs lacking Elk1, Elk3 and Elk4 had reduced FOS protein levels and increased Ifnb1 mRNA suggesting a general role for ERK1/2 > TCF pathway regulating Ifnb1 levels through Fos expression.

overall_design: Bone marrow derived macrophages (BMDMs) from LysM-Cre (LysM, control) and LysM-Cre Fos-fl/fl (FosKO) mice were generated and stimulated with LPS to determine the genes and processes controlled by FOS. BMDMs were stimulated with LPS (100ng/ml) for various times up to 2 hours or left unstimulated.

first: Michael

last: Pattison

first: Louise

last: Blair

first: Probir

last: Chakravarty


title: RNAseq of engineered S. cerevisiae strains for isobutanol production

status: Public on Oct 22 2021

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketoacid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses indicated that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2-null strain harboring a cytosolic localized isobutanol pathway outperformed the strain with the mitochondrial localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.

overall_design: Strains were grown in MMAS 10% glucose media for 48 hours under anaerobic conditions in triplicate (replicate cultures were started from different colonies, grown on the same day), originally for a total of 36 samples to be analyzed by RNAseq. Three samples were lost during extraction steps, leading to only 33 samples sent for sequencing. Y795 is the parental strain used as a reference. Samples for RNAseq were collected at 4 (T3), 10 (T6), and 26 (T14) hours post inoculation to represent the different phases of cell growth: early-exponential phase, mid-exponential phase, and early stationary phase. The engineered strain descriptions are as follows: mIBAILV5 or Y797, a strain harboring a mitochondria localized isobutanol pathway with a NADPH-dependent Ilv5p ketoacid reductoisomerase (KARI); cIBAILV5 or Y812, a strain harboring a cytosolic localized isobutanol pathway with a NADPH-dependent Ilv5p KARI; and cIBAIlvC6E6 or Y799, a strain harboring a cytosolic localized isobutanol pathway with a NADH-dependent IlvC6E6p KARI.

first: Francesca

middle: V

last: Gambacorta

first: Ellen

last: Wagner

first: Tyler

last: Jacobson

first: Mary

last: Tremaine

first: Laura

last: Muehlbauer

first: Mick

last: McGee

first: Justin

last: Baerwald

first: Russell

last: Wrobel

first: John

last: Wolters

first: Mike

last: Place

first: Dan

last: Xie

first: Jose

last: Serate

first: Shabda

last: Gajbhiye

first: Lisa

last: Liu

first: Maikayeng

last: Vang-Smith

first: Yaoping

last: Zhang

first: Chris

last: Hittinger

first: Joshua

last: Coon

first: Daniel

last: Amador-Noguez

first: Trey

last: Sato

first: Brian

last: Pfleger


title: Whole genome expression profiling of Artemsinin resistant Plasmodium falciparum field isolates II

status: Public on Nov 04 2021

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: The objective of this study is to characterize gene expression signatures associated with in vivo artemisinin resistance phenotype and its transcriptional response to Artemisinin Combination Therapy (ACT) treatment . To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 680 patients prior to ACT treatment and 659 patients after the ACT treament.

overall_design: P. falciparum isolates were sampled from the whole blood of 680 patients from 6 countries and 13 sites across Southeast Asia (Ramu in Bangladesh; Thabeikkyin, Pyay, Pyin Oo Lwin and Ann in Myanmar; Phusing and Khun Han in Thailand; Pailin, Pursat, Ratanakiri and Preah Vihear in Cambodia; Sekong in Laos; Bin Phuoc in Vietnam) from 2015 to 2018. RNA was extracted and synthesis and amplification of cDNA were carried out to generate sufficient material for hybridizations against the RNA reference pool of 3D7 strain using a custom made microarray platform.

first: Lei

last: Zhu

first: Michal

last: Kucharski

first: Jaishree

last: Tripathi


title: Parallel functional assessment of m6A sites in human endodermal differentiation with base editor screens

status: Public on Oct 21 2021

city: Guangzhou

first: Zhijun

last: Ren

address: 74 Zhongshan Rd.2

institute: Sun Yat-sen University

summary: N6-methyladenosine (m6A) plays important role in lineage specifications of embryonic stem cells. However, it is still difficult to systematically dissect the specific m6A sites that are essential for early lineage differentiation. Here, we develop an adenine base editor-based strategy to systematically identify functional m6A sites that control lineage decisions of human embryonic stem cells. We design 7999 sgRNAs targeting 6048 m6A sites to screen for m6A sites that act as either boosters or barriers to definitive endoderm specification of human embryonic stem cells. We identify 78 sgRNAs enriched in the non-definitive endoderm cells and 137 sgRNAs enriched in the definitive endoderm cells. We successfully validate two definitive endoderm promoting m6A sites on SOX2 and SDHAF1 as well as a definitive endoderm inhibiting m6A site on ADM. Our study provides a functional screening of m6A sites and paves the way for functional studies of m6A at individual m6A site level.

overall_design: CRISPR screening m6A site affect A549 cell proliferation and H1 cell endodermal differentiation

first: Weisheng

last: Cheng

first: Fang

last: Cao

first: Jinkai

last: Wang


title: RNA-seq analysis of HeLa cells following MYC inhibition with ASO

status: Public on Oct 19 2021

city: Charlestown

first: Christopher

middle: J

last: Ott

state: MA

address: 149 13th Street, Rm 6614

institute: Mass Gen Hospital/Harvard Medical School

summary: We performed RNA-seq on HeLa cells treated with MYCASO-3, a non-targeting ASO (NT-ASO), Lipofectamine alone, and untreated cells

overall_design: Cells were treated for 4h or 18h with 10 nM ASO (formulated with Lipofectamine 2000 reagent). RNA was extracted with the QIAGEN RNeasy Kit, followed by library preparation and sequencing.


title: RNA-seq of mimic miR-34a transfected H1299 and DDX21 KO cell lines.

status: Public on Oct 18 2021

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

summary: In order to investigate the role of DDX21 in RNA activation by miR-34a, next-generation sequencing analysis of RNA extracted from miR-34a transfected H1299 and DDX21 knock-out cell line was performed.

overall_design: RNA profiles were generated by deep sequencing, using Illumina HiSeq 4000.

first: Masahiko

last: Kuroda


title: Sequencing of Caenorhabditis elegans at 4 time points treated with RNAi

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Comparison of gene expression profiles from C. elegans treated with RNAis. (L4440, prp-19, skp-1) at different time points (1, 5, 10 and 15 days). The RNA-seq data comprise 12 groups.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 36 samples in 12 groups: 1 day L4440 (3 Samples), 1 day prp-19 (3 Samples), 1 day skp-1 (3 Samples), 5 days L4440 (3 Samples), 5 days prp-19 (3 Samples), 5 days skp-1 (3 Samples), 10 days L4440 (3 Samples), 10 days prp-19 (3 Samples), 10 days skp-1 (3 Samples), 15 days L4440 (3 Samples), 15 days prp-19 (3 Samples), 15 days skp-1 (3 Samples)

first: Michael

last: Ristow

first: Kim

last: Zarse

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Dual checkpoint blockade of CD47 and PD-L1 using a novel affinity-tuned bispecific antibody maximizes anti-tumor immunity

status: Public on Oct 15 2021

city: San Diego

first: Wenjing

last: Yanf

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

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

overall_design: Refer to individual Series


title: H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis

city: Pittsburgh

first: Delphine

last: Gomez

address: 200 Lothrop Street

institute: University of Pittsburgh

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: SFPQ-ABL1 and BCR-ABL1 utilise different signalling networks to drive B-cell acute lymphoblastic leukaemia

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: We identified a rare instance of the SFPQ-ABL1 in a child with Ph-like ALL. The overall purpose of this study was to compare the structure and function of the SFPQ-ABL1 fusion to the well characterised BCR-ABL1 fusion. We used phosphoproteomics, transcriptomics and functional assays to determine the transforming capacity, subcellular localisation, and signalling networks of these two fusions. Given the known function of SFPQ in mRNA splicing, transcriptomic analysis was performed to analyse the effect of BCR-ABL1 or SFPQ-ABL1 expression on gene splicing.
Methods:  mRNA profiles of Ba/F3 cells expressing BCR-ABL1, SFPQ-ABL1, and empty vector control (MSCV) were generated by deep sequencing, in four biologically independent cell lines, using Illumina GAIIx. The sequences were aligned by subread and quantified by featureCounts.
Results: In contrast to BCR-ABL1, SFPQ-ABL1 localised to the nuclear compartment and was a weaker driver of cellular proliferation. Phosphoproteomics analysis showed upregulation of cell cycle, DNA replication and spliceosome pathways, and downregulation of signal transduction pathways, including ErbB, NF-kappa B, VEGF, and MAPK signalling in SFPQ-ABL1-, compared to BCR-ABL1-expressing cells. SFPQ-ABL1 expression did not activate PI3K/AKT signalling and was associated with phosphorylation of G2/M cell cycle proteins. We identified no difference in overall splicing between cells expressing BCR-ABL1 and SFPQ-ABL1.
Conclusions: SFPQ-ABL1 has functionally distinct mechanisms by which it drives ALL, including subcellular localisation, proliferative capacity, and activation of cellular pathways, highlighting the role that fusion partners have in mediating the function of ABL1 fusions.

overall_design: mRNA profiles of four biologically independent lines of Ba/F3 cells expressing BCR-ABL1, SFPQ-ABL1, and empty vector (MSCV)

first: Soroor

last: Hediyeh-zadeh

first: Lauren

last: Brown


title: H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [RNAseq]

summary: Epigenetic control of lineage-specific gene expression is essential for cell differentiation, acquisition of specialized functions, and tissue homeostasis. Here, we uncovered a unique epigenetic pathway critical for governing lineage identity in cells presenting milieu-dependent phenotypic modulation in adult organisms, by using vascular smooth muscle cells (SMC) as a model of highly specialized and differentiated cell type retaining phenotypic plasticity. We found that the histone modification H3K4me2 is essential for the maintenance of vascular SMC lineage identity and functions by performing H3K4me2 demethylation selectively on a SMC lineage-specific subset of genes. Removal of H3K4me2 on the myocardin-regulated genes led to a marked loss of contractility and alteration in SMC adaptive response capacities during vascular remodeling. Rather than presenting intrinsic gene activation properties, H3K4me2 serves as a stable preferential hub for the dynamic recruitment of the DNA methylcytosine dioxygenase Ten-Eleven Translocation 2 (TET2). Besides the SMC contractile apparatus, the H3K4me2/TET2 complex controls the expression of miR-145, a central microRNA promoting SMC differentiation and participation in vascular remodeling. Finally, H3K4me2 editing induced a profound loss of SMC lineage identity and gain of plasticity, characterized by the redistribution of H3K4me2 on genes associated with stemness and developmental programs and the greater ability of H3K4me2 edited SMC to transdifferentiate into other lineages. These studies identified H3K4me2 as a central epigenetic mechanism controlling lineage identity and cell-specific specialized functions. Our findings may have broad implications for the understanding of mechanisms controlling multiple plastic cell type behaviors and functions in various pathophysiological processes.

overall_design: SMC H3K4me2 signature was demethylated by Myocd-LSD1 fusion protein. Whole transcriptome analysis of Control, Myocd-LSD1, Myocd-LSD1NF SMC and PDGF-BB (30 ng/ml) treated SMC was performed by RNA-seq to assess effects of H3K4me2 editing.

first: Mingjun

last: Liu

first: Cristina

last: Espinosa-Diez

first: Sidney

last: Mahan

first: Mingyuan

last: Du

first: Anh

middle: T

last: Nguyen

first: Scott

last: Hahn

first: Adam

last: Straub

first: Raja

last: Chakraborty

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