title: Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress

city: Cleveland

first: Konstantin

last: Leskov

state: OH

address: 2109 Adelbert Rd., WRT205

department: Molecular Biology and Microbiology

institute: Case Western Reserve University

summary: HIV-1 infects lymphoid and myeloid cells, which can harbor a latent proviral reservoir responsible for maintaining lifelong infection. Glycolytic metabolism has been identified as a determinant of susceptibility to HIV-1 infection, but its role in the development and maintenance of HIV-1 latency has not been elucidated. By combining transcriptomic, proteomic and metabolomic analysis, we here show that transition to latent HIV-1 infection downregulates glycolysis, while viral reactivation by conventional stimuli reverts this effect. Decreased glycolytic output in latently infected cells is associated with downregulation of NAD+/NADH. Consequently, infected cells rely on the parallel pentose phosphate pathway and its main product, the antioxidant NADPH, fueling antioxidant pathways maintaining HIV-1 latency. Of note, blocking NADPH downstream effectors, thioredoxin and glutathione, favors HIV-1 reactivation from latency in lymphoid and myeloid cellular models. This provides a “shock and kill effect” decreasing proviral DNA in cells from people-living-with-HIV/AIDS. Overall, our data show that downmodulation of glycolysis is a metabolic signature of HIV-1 latency that can be exploited to target latently infected cells with eradication strategies.

overall_design: The scRNA-Seq analysis of HC69 was performed as follows: immortalized human microglia HC69 cells were left untreated or treated with dexamethasone [DEXA, 1μM (Sigma-Aldrich, St. Louis, MO, USA)] for 72 h. After harvesting, a minimum of 600,000 viable cells per condition was subjected to Drop-Seq as described in (Macosko et al, 2015). After capturing individual cells in the oil droplets with barcoded beads (Chemgenes, Inc. Wilmington, MA, 01887 USA), droplets were broken, and cDNA libraries were generated using Illumina Nextera XT kit (Illumina, Inc., 5200 Illumina Way San Diego, CA, 92122 USA). Next Generation Sequencing and quality control were performed at Medgenome Inc (Foster City, CA, 94404 USA). Drop-Seq Tools v.1.0 and STAR-2.5.1b alignment tools were used to process and map the sequences to the hg18 human reference genome and to the retroviral portion of the HIV-1pNL4-3 construct. As a result, we built digital gene expression matrices (DGE) containing the read counts for human and HIV-1 genes.


title: Role of Gpnmb in response to PFF-induced spreading alpha-synucleinopathy

status: Public on Jun 18 2021

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

type: Expression profiling by high throughput sequencing

summary:
Effect of Gpnmb knockout on development of differential expression in PFF-aSyn model was studied.
The "sample_id" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0036142

overall_design: RNA from ipsilateral whole striatum, midbrain or brainstem of mixed-sex (but balanced) GPNMB WT or knockout mice 60 or 90 days after injection with either aSyn pre-formed fibrils (PFF) or monomer (mono) control.


title: Maternal RNF114 plays critical roles in activation of the early zygotic genome through promoting ubiquitin-mediated degradation of Chromobox protein CBX5

status: Public on Jun 16 2021

city: Nanjing City

first: Haifeng

last: Sun

state: JiangSu province

address: Tianyuan East Road 818

country: China

institute: Nanjing Medical University

summary: Zygotic genomic activation (ZGA) is a landmark event in the maternal-to-zygotic transition (MZT), and the regulation of ZGA by maternal factors remains to be elucidated. In this study, the depletion of maternal RNF114 led to 2-cell embryos developmental arrest in mice. RNF114 was proven to play an important role in major ZGA using ethynyl uridine (EU) incorporation and transcriptome analysis. To study the underlying mechanism, we performed protein profiling in mature oocytes and found a potential substrate for RNF114, Chromobox protein CBX5, whose ubiquitination and degradation was regulated by RNF114. Furthermore, the overexpression of CBX5 prevented embryonic development and impeded major ZGA. In summary, our study reveals that maternal RNF114, as a ubiquitin E3 ligase, plays a precise role in mediating the degradation of repressive protein CBX5 during MZT, the misregulation of which may impede the appropriate activation of major ZGA in mouse embryos.

overall_design: RNASeq of MII oocytes,1-cell and 2-cell embryos from Rnf114 Mutant/Control mouse

first: Shuai

last: Zhou

first: Yueshuai

last: Guo

first: Liping

last: Yao

first: Chao

last: Liu

first: Yuanlin

last: He

first: Shanren

last: Chao

first: Cheng

first: Mingrui

last: Li

first: Yumeng

last: Cao

first: Congjing

last: Wang

first: Qianneng

last: Lu

first: Lu

first: Wei

first: Xuejiang

first: Ran

last: Huo


title: Cross-tissue single cell landscape of human monocytes and macrophages in health and disease

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Mononuclear phagocytes (MNP) encompass dendritic cells, monocytes and macrophages (MoMac), which exhibit antimicrobial, homeostatic and immunoregulatory functions. We integrated 178,651 MNP from 13 tissues across 41 datasets to generate a MNP single-cell RNA compendium (MNP-VERSE), a publicly available tool to map MNPs and defined conserved gene signatures of MNP populations. Next, we generated a MoMac-focused compendium that revealed an array of specialised cell subsets widely distributed across multiple tissues. Specific pathological forms were expanded in cancer and inflammation. All neoplastic tissues contained conserved tumour-associated macrophage populations. Particularly, we focused on IL4I1+CD274(PD-L1)+IDO1+ macrophages, which accumulated in the tumour periphery in a T cell-dependent manner via IFNg and CD40/CD40L-induced maturation from interferon-primed monocytes. IL4I1_Macs exhibited immune-suppressive characteristics through tryptophan degradation and promoted entry of regulatory T cell into tumours. This integrated analysis provides a robust online-available platform for uniform annotation and dissection of specific macrophage functions in healthy and pathological states.

overall_design: Indexed single cell RNAseq (scRNAseq) of human dendritic cells and monocytes from Blood, Liver, Lung,  Spleen and Tonsil.

first: Kevin

last: Mulder

first: Amit

last: Patel

first: Wan

last: Kong

first: Cecile

last: Piot

first: Evelyn

last: Halitzki

first: Garett

last: Dunsmore

first: Shabnam

last: Khalilnezhad

first: Sergio

middle: E

last: Irac

first: Agathe

last: Dubiosson

first: Marion

last: Chevrier

first: XiaoMeng

last: Zhang

first: John

middle: K

last: Tam

first: Tony

last: Lim

first: Regina

middle: M

last: Wong

first: Rhea

last: Pai

first: Ahmed

middle: I

last: Khalil

first: Pierce

last: Chow

first: Sunny

middle: Z

last: Wu

first: Ghamdan

last: Al-Eryani

first: Daniel

last: Roden

first: Alexander

last: Swarbrick

first: Jerry

last: Chan

first: Salvatore

last: Albani

first: Lisa

last: Derosa

first: Laurence

last: Zitvogel

first: Ankur

last: Sharma

first: Jinmiao

last: Chen

first: Aymeric

last: Silvin

first: Antonio

last: Bertoletti

first: Camille

last: Blériot

first: Charles

last: Dutertre


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Nanopore]

status: Public on Jun 15 2021

city: Bethesda

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex further reveals widespread splice site selection within introns. We propose and validate a unified theoretical model for transcription and splicing based on pervasive stochastic recursive splicing.

overall_design: Nanopore direct Nascent RNA long read sequencing of Human Bronchial Epithelial Cells

first: Yihan

last: Wan


title: 14-3-3σ represents an intestinal tumor suppressor

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

summary: Although the 14-3-3σ gene was initially identified as a p53 target gene in colorectal cancer (CRC) cells it remained unknown whether it represents a suppressor of intestinal tumorigenesis. Deletion of 14-3-3σ in ApcMin mouse model of intestinal cancer resulted in an increased number and size of adenomas in the small and large intestine. Consequently, the median survival of these mice was shortened. 14-3-3σ-deficient adenomas displayed an increase in proliferation and decreased apoptosis, as well as increased dysplasia. Global expression profiling of adenomas revealed that loss of 14-3-3σ promoted the acquisition of a mesenchymal-like signature, which was associated with poor, relapse-free survival of CRC patients. In addition, numerous cytokines were up-regulated in 14-3-3σ-deficient adenomas, indicating a role of 14-3-3σ in regulating tumor/stroma interactions. Taken together, these results provide genetic proof of a tumor suppressor function of 14-3-3σ in the intestine.

overall_design: Intestinal adenomas from ApcMin/+ and ApcMin/+/14-3-3σ-/- mice were subjected to RNA-seq analyses. For each genotype, four mice were analyzed.

first: Markus

last: Winter

first: Heiko

last: Hermeking


title: Neuronal VCP loss of function recapitulates FTLD-TDP pathology

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

summary: The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear.  To explore this, we inactivated VCP in murine postnatal forebrain neurons (VCP cKO).  VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction and TDP-43 inclusions resembling FTLD-TDP pathology.  Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulated features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic.  Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles.  These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency.

overall_design: Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.

first: Conrad

last: Weihl

middle: D

first: Abukar

last: Wani


title: Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [RNA-seq]

city: St Louis

first: Thorold

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

department: Developmental Biology

institute: Washington Unversity School of Medicine

summary:
Background: Naïve human embryonic stem cells (hESCs) have been isolated that more closely resemble the pre-implantation epiblast compared to conventional “primed” hESCs, but the signaling principles underlying these discrete stem cell states remain incompletely understood.
Methods:Here we performed high-throughput screening using a library of >3,000 well-annotated compounds to identify essential signaling requirements for naïve human pluripotency.
Results:We report that MEK1/2 inhibitors can be replaced during maintenance of naïve human pluripotency by inhibitors targeting either upstream (FGFR, RAF1) or downstream (ERK1/2) kinases. Naïve hESCs maintained under these alternative conditions display elevated levels of ERK phosphorylation but retain genome-wide DNA hypomethylation and a transcriptional identity of the pre-implantation epiblast. In contrast, dual inhibition of MEK and ERK promotes efficient primed-to-naïve resetting in combination with PKC, ROCK, and TNKS inhibitors and Activin A.
Conclusions: This work demonstrates that induction and maintenance of naïve human pluripotency are governed by distinct signaling requirements.

overall_design: Bulk RNA-seq analysis of primed and naïve hESCs induced and maintained under alternative conditions

first: Shafqat

last: Khan

first: Sabine

last: Dietmann


title: The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct from its DNA-binding function in Ewing sarcoma

city: Columbus

first: Megann

middle: A.

last: Boone

address: 700 Children's Drive, WA5011

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide atlas of promoters expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy of skeletal muscles

status: Public on Jun 17 2021

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Here we report genome wide estimation of expression profiles at promoter level in Soleus and EDL muscles in rat hindlimbs under unloading conditions.

overall_design: Samples were collected from rat hindlimbs at normal state, after unloading for 24 hours, 3 days, 7 days; recovery after 7 days unloading for 24 hours, 3 days, 7 days. Extracted total RNA were proceeded into cDNA and submitted to nAnTi-CAGE libraries preparation with subsequent sequencing on Illumina HiSeq2500 (SE, 50bp)

first: Sergey

last: Pintus

first: Ilya

last: Akberdin

first: Ivan

last: Yevshin

first: Pavel

last: Makhnovskii

first: Oksana

last: Tyapkina

first: Islam

last: Nigmetzyanov

first: Leniz

last: Nurullin

first: Elena

last: Shagimardanova

first: Daniil

last: Popov

first: Fedor

last: Kolpakov

first: Oleg

last: Gusev

first: Guzel

last: Gazizova


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Lariat seq]

first: Daniel

last: Larson

overall_design: improved lariat sequencing in HEK293 cells

first: Dimitrios

last: Anastasakis

first: Markus

last: Hafner


title: Transcriptome profiling of Mature B cells residing in the bone marrow.

city: Clayton

first: Stephane

last: Chappaz

state: Victoria

address: Monash Biomedicine Discovery Institute, Level 3, Building 76, 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary:
Purpose: The role of intrinsic apoptosis in mature B cell homeostasis is still elusive. The aim of this study is to compare the transcriptome of mature B cells that are either sensitive or resistant to intrinsic apoptosis.
Methods: Bone marrow-residing Mature B cells were FACS-sorted as B220high CD93- IgM+ with >99.8% purity.  RNA was extracted with Qiagen RNA extraction kit.

overall_design: 12 samples in total, n=3 biological replicates per experimental group.

first: Charity

middle: W

last: Law

first: Anna

last: Lieschke

first: Benjamin

middle: T

last: Kile


title: Array-based genome-wide transcriptome analysis of Ductal carcinoma in situ (DCIS)

status: Public on Jun 14 2021

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

summary:
Ductal carcinoma in situ (DCIS) is the presence of abnormal cells inside a milk duct in the breast. DCIS is considered the earliest form of breast cancer.
DCIS is noninvasive, meaning that it does not spread out of the milk duct and has a low risk of becoming invasive.

overall_design: The tumorous and non-tumorous regions of mammary gland specimens from 3 DCIS patients.

first: Masujiro

last: Makita

first: Tomoo

last: Jikuzono

first: Tomoko

last: Ishikawa

first: Iwao

last: Sugitani

first: Osamu

last: Ishibashi


title: Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

summary: Integrative analysis of colorectal cancer (CRC) ATAC-seq and RNA-seq revealed an epigenomic and transcriptomic remodeling during liver metastasis.

overall_design: Examination of CRC liver metastases and primary tumor from an in vivo model.

first: Lihua

first: Jorge

middle: P

last: Balcazar

first: Zhenzhen

last: Wu

first: Kun

last: Xiang

first: Yi

first: Qiang

last: Huang

first: Marcos

last: Negrete

first: Kai

middle: Y

last: Chen

first: Wei

last: Li

first: Yujie

last: Fu

first: Anders

last: Dohlman

first: Robert

last: Mines

first: Liwen

last: Zhang

first: Yoshihiko

last: Kobayashi

first: Tianyi

first: Guizhi

last: Shi

first: John

last: Shen

first: Scott

last: Kopertz

first: Purushothama

last: Tata

first: Charles

last: Gersbach

first: Greory

last: Crawford

first: David

last: Hsu

first: Emina

first: Pengcheng

last: Bu

first: Xiling


title: Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [pulse_chase_nascent RNA]

first: Daniel

last: Larson

overall_design: Pulse Chase Nascent RNA profiling in HBEC cells

first: Yihan

last: Wan


title: CRY2 missense mutations suppress P53 and enhance cell growth

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: Disruption of circadian rhythms increases the risk of several types of cancer. Mammalian cryptochromes (CRY1 and CRY2) are circadian transcriptional repressors that are related to DNA repair enzymes. While CRYs lack DNA repair activity, they modulate the transcriptional response to DNA damage, and CRY2 can promote SCFFBXL3-mediated ubiquitination of c-MYC and other targets. Here, we characterize five mutations in CRY2 observed in human cancers in The Cancer Genome Atlas. We demonstrate that two orthologous mutations of mouse CRY2 (D325H and S510L) accelerate the growth of primary mouse fibroblasts expressing high levels of c-MYC. Neither mutant affects steady state levels of overexpressed c-MYC, and they have divergent impacts on circadian rhythms and on the ability of CRY2 to interact with SCFFBXL3. Unexpectedly, stable expression of either CRY2 D325H or of CRY2 S510L robustly suppresses P53 target gene expression, suggesting that this is the primary mechanism by which they influence cell growth.

overall_design: Comparisons of the transcriptomes of Cry2−/− mouse embryonic fibroblasts (MEFs) expressing c-MYC and WT or mutant Cry2 (D325H, S510L, or F428D), at low or high cell density.

first: Alanna

middle: B

last: Chan

first: Katja

last: Lamia

middle: H

first: Michael

last: Bollong


title: Epigenetic profiling of young and aged spermatogonial stem cells (RRBS)

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Methylation profiling by high throughput sequencing

summary: Spermatogonial stem cells (SSC), the foundation of spermatogenesis and male fertility, possess lifelong self-renewal activity. Aging leads to the decline in stem cell function and increased risk of paternal age-related genetic diseases. Aged SSCs exhibited gene body hypomethylation, which is accompanied by an elevated 5hmC level.

overall_design: We separated stem cells (Oct4-GFP+/KIT-) and their immediate proliferating daughter cells (Oct4-GFP+/KIT+) using FACS from adult (6-8 months) and aged mice (15-18 months), which were subjected to RRBS and oxRRBS analysis.

first: Tin-Lap

last: Lee


title: Acinetobacter baumannii Fatty Acid Desaturases Facilitate Survival in Distinct Environments

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

institute: Macquarie University

summary: RNA sequencing transcriptomics was performed on a highly multidrug resistant A. baumannii strain belonging to international clone I, AB5075_UW and a transposon insertion inactivated mutant of ABUW_1103 (DesT1), which encodes for a TetR family regulator. Transcriptomics revealed that DesT1 might function as a global regulator controlling expression of various genes involved in fatty acid metabolism and transport and  a range of outer membrane proteins. Genes encoding acyl-CoA desaturase and ferredoxin reductase were found to be significantly upregulated when DesT1 regulator was inactivated. Aerobic desaturases are known to play an important role in maintaining membrane homeostasis.

overall_design:
Global transcriptomic profiles of the regulator mutant and the parental A. baumannii strain were compared. The parental and mutant cells were grown to mid exponential phase at 37°C, with shaking. Cell pellets were harvested and the total RNA was extracted from three biological replicates. Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using Truseq stranded RNA preparation kit (Illumina, Inc., USA). RNA libraries were prepared for sequencing using standard Illumina protocols.

The processed data columns correspond to the samples as below:
Parental AB5075_Rep1 = WT1.rpkm_1
Parental AB5075_Rep2 = WT2.rpkm_1
Parental AB5075_Rep3 = WT3.rpkm_1
ABUW_1103-112:T26_Rep1 = M1.rpkm_1
ABUW_1103-112:T26_Rep2 = M2.rpkm_1
ABUW_1103-112:T26_Rep3 = M3.rpkm_1

first: Alaska

last: Pokhrel

first: Liping

last: Li

first: Felise

last: Adams

first: Bart

last: Eijkelkamp


title: Transcriptomic  profiling of young and aged spermatogonial stem cells (RNA-Seq)

summary: Spermatogonial stem cells (SSC), the foundation of spermatogenesis and male fertility, possess lifelong self-renewal activity. Aging leads to the decline in stem cell function and increased risk of paternal age-related genetic diseases. In the present study, we performed a comparative genomic analysis of mouse SSC (Oct4-GFP+/KIT-) and differentiating progenitors (Oct4-GFP+/KIT+) isolated from young and aged testes. Our transcriptome data revealed enormous complexity of expressed coding and non-coding RNAs and alternative splicing regulation during SSC differentiation. Further comparison between young and aged SSCs suggested these differentiation programs were affected by aging. We identified aberrant expression of genes associated with meiosis and TGF-β signaling , alteration in alternative splicing regulation and differential expression of specific lncRNAs such as Fendrr.

overall_design: We separated stem cells (Oct4-GFP+/KIT-) and their immediate proliferating daughter cells (Oct4-GFP+/KIT+) using FACS from postnatal (6 days), adult (6-8 months) and aged mice (15-18 months), which were subjected to RNA-Seq analysis.


title: Gene Expression Changes during Chronic Social Isolation in Drosophila melanogaster

city: New York

first: Wanhe

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: To investigate gene expression changes in Drosophila head tissues during social isolation, we performed RNA-sequencing on fruit fly head samples obtained from male flies that have been group-reared for 7 days (Grp), isolated (single-housed) for 7 days (Iso7) and isolated (single-housed) for only 1 day (Iso1). Using differential gene expression analysis, we found a group of candidate genes that are specific to chronic social isolation: they exhibited significant gene expression change in both comparisons of “Grp vs Iso1” and “Iso1 vs Iso7”.

overall_design: Heads of wild type flies with group/isolation experience were collected at ZT0.5-2. Flies of three treatment conditions were collected: socially enriched animals (group reared for 7 days, “Grp”), chronic isolation animals (isolated for 7 days, “Iso7”) and acute isolation animals (isolated for 1 day, “Iso1”). For each condition, 3 replicated samples were collected and each sample contains 200 fly heads.

last: Young


title: Single cell RNA sequencing of skeletal muscle endothelial cells in sedentary and exercised mice

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: Skeleteal muscle is composed of different fiber types, which classically have been defined by their myosin heavy chain content, but they also substantially differ in their metabolic properties and the nutrients they use for energy generation. Within skeletal muscle, blood vessels (endothelium) lie in parallel with muscle fibers. What is less well described is whether the functional properties of muscle ECs (mECs) are dependent on the specific fiber (and thus microenvironment) they interact with. Furthermore, the mechanisms of exercise-induced vascular expansion however are poorly understood. Here, we use single cell RNA sequencing to map angiodiversity in skeletal muscle and investigate the mechanism of excercise induced muscle angiogensis.

overall_design:
1. Single cell RNA sequencing of endothelial cell that FACS sorted from gastrocnemius muscle of wild type C57BL6N mice.
2. Compare scRNAseq data of ECs isolated from the gastrocnemius of sedentary mice versus 14 days exercised (voluntary running) mice.

first: Zheng

last: Fan

first: Gillian

last: Fitzgerald


title: Epigenetic profiling of young and aged spermatogonial stem cells (ChIP-Seq)

summary: Spermatogonial stem cells (SSC), the foundation of spermatogenesis and male fertility, possess lifelong self-renewal activity. Aging leads to the decline in stem cell function and increased risk of paternal age-related genetic diseases. Epigenetic profiling revealed reduced H3K27me3 deposition at numerous pro-differentiation genes during SSC differentiation as well as aberrant H3K27me3 distribution at genes in Wnt and TGF-β signaling upon aging.

overall_design: We separated stem cells (Oct4-GFP+/KIT-) and their immediate proliferating daughter cells (Oct4-GFP+/KIT+) using FACS from adult (6-8 months) and aged mice (15-18 months), which were subjected to ChIP-Seq analysis of H3k4me3 and H3k27me3 modification.


title: Single-cell analysis of limbal niche heterogeneity and crosstalk with corneal epithelial stem/progenitor cells

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: Compared to stem cells in other tissues, relatively little is known about the limbal niche, which is believed to play a pivotal role in regulating self-renewal and fate decision of limbal epithelial stem cells. Here we comprehensively investigated the human limbal niche with single-cell RNA sequencing. On analysis, all 47,627 cells located at human Limbus was classified into 14 clusters, and 8 types of cells were annotated. Specifically, we depicted the heterogeneity and hierarchy of limbal epithelial cells, and revealed a consecutive differentiation trajectory from limbal stem/progenitor cells by RNA velocity and pseudotime analyses. Besides, representative signaling pathway components and cell-cell communications engaged in limbal niche regulation were deciphered, suggesting a tightly regulation of the microenvironment around limbal stem/progenitor cells. Finally, comparative analysis revealed conservational and divergent transcriptional signals across species. Overall, this study provides an unbiased and systematic view of transcriptional organization of human Limbus, and dissected cell-contact-dependent regulations of limbal niche, providing foundations for investigating the cellular and molecular mechanisms, pathogenesis of related disease and potential interventions.

overall_design: Single-cell RNA-seq analysis of human corneal limbal tissues

first: Shengqian

last: Dou

first: Qingjun

last: Zhou

first: Weiyun

last: Shi


title: Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening

first: Thorold

last: Theunissen


title: CD16+ CD163+ monocytes traffic to sites of inflammation in NEC

city: NEW HAVEN

first: Oluwabunmi

last: Olaloye

state: CT

address: 1435 STATE ST, APT 301

department: Pediatrics

institute: Yale University

summary: Using suspension (CyTOF) and imaging (IMC) mass cytometry coupled with single cell RNA sequencing (scRNAseq) on intestinal mucosa, we demonstrated severe inflammation in patients with NEC. scRNAseq revealed that  the CD163+CD16+ monocytes/Mf transcribe a large number of inflammatory genes including TREM1, IL1a and IL1b, IL8 and calprotectin. Gene set enrichment analysis identified pathways involved in chemotaxis and migration to be enriched in the clusters containing CD163+CD16+ monocytes/Mf, confirming our observations that they traffic from the periphery.

overall_design: 3' Single cell RNA sequencing of viably cryoprserved human small intestinal tissue samples after live/dead selection. 3' GEM libraries from 10X Medgenome kit sequenced on HIgSeq lane with a target of 5000 cells/sample.

first: Peng

last: Liu

first: Xiaojing

last: An

first: Fujing

last: Wan

first: George

last: Tseng

first: Liza

last: Konnikova

first: Kong

last: Chen


title: Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [WGBS]

overall_design: Whole genome bisulfite sequencing analysis of primed and naïve hESCs induced and maintained under alternative conditions

first: Shafqat

last: Khan

first: Sabine

last: Dietmann


title: MYC-deficiency impairs the development of effector/memory T lymphocytes

city: Marseille

first: Mathis

last: Nozais

address: 27bd Lei Roure

country: France

institute: CRCM

summary: Using scRNA-seq we investigate the impact of the absence of MYC on physio-pathological development of PTEN-proficient or PTEN-deficient T lymphocytes.  We demonstrate that MYC-deficient effector/memory T cells is drastically reduced. MYC is then essential for effector/memory differentiation

overall_design: Single cell RNA-seq study of T lymphocyte differentiation in Pten and/or Myc deleted mice

first: Marie

last: Loosveld

first: Saran

last: Pankaew

first: Clémence

last: Grosjean

first: Noémie

last: Gentil

first: Julie

last: Quessada

first: Cyrille

last: Mionnet

first: Delphine

last: Potier

first: Dominique

last: Payet-Bornet


title: Differential usage of Zeb2 enhancer distinguishes adult and embryonic hematopoiesis [bulkATAC-seq]

city: Stanford

first: Julia

last: Belk

address: 450 Serra Mall

institute: Stanford University

summary: ATAC-seq of Zeb2 WT and Zeb2 enhancer KO B cells

overall_design: Epigenetic differences induced by KO of an enhancer of Zeb2 in mouse B cells

first: Xiao

last: Huang

first: Quanming

last: Shi

first: Nghi

last: Ly


title: Virtual memory T-cells orchestrate extra-lymphoid responses conducive to resident memory

city: BEIJING

first: SHIYUE

last: HOU

state: China Mainland

address: ROOM A104, MEDICAL SCIENCE BUILDING, TSINGHUA UNIVERSITY

institute: TSINGHUA UNIVERSITY

summary: A primary immune response is typically initiated in secondary lymphoid organs. Virtual memory CD8+ T (TVM) cells are antigen-inexperienced T cells of a central-memory phenotype, acquired through self antigen-driven homeostatic proliferation. Unexpectedly, here we find that, TVM cells are composed of CCR2+ and CCR2- subsets that differentially elaborate a spectrum of effector- and memory-poised functions directly in the tissue. During a primary flu infection, TVM cells rapidly infiltrate the lung in the first day and execute early viral control. TVM cells that recognize viral antigen are retained in the tissue, clonally expand independent of secondary lymphoid organs, and preferentially give rise to tissue-resident memory cells. By orchestrating an extra-lymphoid primary response, heterogenous TVM cells bridge innate reaction and adaptive memory directly in the infected tissue.

overall_design: Differential expression analysis between CCR2+ and CCR2- virtual memory CD8+ T cells

first: Hai

last: Qi

first: Shiyue

last: Hou

first: Tiange

last: Shao

first: Tianyang

last: Mao

first: Jingwen

first: Jiahui

last: Sun

first: Miao

last: Mei

first: Xu

last: Tan


title: Differential usage of Zeb2 enhancer distinguishes adult and embryonic hematopoiesis [scATAC-seq]

summary: scATAC-seq of myeloid cells

overall_design: Profiling of epigenetic differences at different stages of hematopoiesis

first: Yanyan


title: The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct from its DNA-binding function in Ewing sarcoma [RNA-seq]

first: Megann

last: Boone

summary: The purpose of this study was to determine the roles of the flanking regions of the FLI ETS DNA-binding domain in gene regulation of Ewing sarcoma cells. EWS/FLI cDNA constructs including various deletions of the FLI portion were virally transduced into cells and we sought to determine the transcriptional profile of each.

overall_design: Endogenous EWS/FLI was knocked-down in the Ewing sarcoma A673 cell line and EWS/FLI cDNA constructs were expressed in these cells. 3 biological replicates of A673 cells containing the cDNA constructs were collected after 8 days and total RNA was extracted to study the transcriptomic profiles of each EWS/FLI construct. Data used for analysis and creation of Figure 4.

first: Cenny

last: Taslim

first: Stephen

middle: L

last: Lessnick


title: NFAT signalling in human mesenchymal stromal cells affects extracellular matrix metabolism and anti-fungal immune responses

city: Brno

first: Marco

last: De Zuani

address: Pekarska, 53

department: CTM

country: Czech Republic

institute: FNUSA - ICRC

summary: Mesenchymal stromal cells (MSCs) combined with calcineurin-NFAT (CN-NFAT) inhibitors are being tested as a treatment for graft versus host disease (GvHD). The immunosuppressive properties of MSCs seem beneficial; however, their response during fungal infection, which is an important cause of mortality in GvHD patients, is unknown. We report that MSCs phagocytose the fungal component zymosan, resulting in phosphorylation of Syk kinase, increase in cytosolic calcium levels and ultimately, in NFAT1 nuclear translocation. RNA-sequencing analysis of zymosan-treated MSCs showed that CN-NFAT inhibition affects extracellular matrix (ECM) genes, but not cytokine expression that is under the control of the NF-κB pathway. When co-culturing MSCs or decellularized MSC-ECM with human peripheral blood mononuclear cells (PBMCs), selective NFAT inhibition in MSCs decreased cytokine expression by PBMCs. These findings reveal a dual mechanism underlying the MSC response to zymosan: while NF-κB directly controls inflammatory cytokine expression, NFAT impacts immune-cell functions by regulating ECM remodelling.

overall_design: mRNA transcriptome of human adipose derived mesenchymal stromal cells (AT-MSCs) treated with zymosan in presence or absence of CN-NFAT inhibitor FK506

first: Federico

last: Tidu

first: Shyam

middle: S

last: Jose

first: Kamila

last: Bendickova

first: Lukas

last: Kubala

first: Frank

last: Caruso

first: Francesca

last: Cavalieri

first: Giancarlo

last: Forte

first: Jan

last: Fric


title: Transcriptional response of wild type and dmr6 mutants of tomato to Xanthomonas gardneri

city: Berkeley

first: Daniela

middle: Paula

last: de Toledo Thomazella

address: 2151 Berkeley Way

department: PMB/IGI

institute: UC Berkeley

summary: This study evaluates the transcriptional response of Solanum lycopersicum cv. Fla. 8000 (wild-type and dmr6 mutants) to the pathogen Xanthomonas gardneri 153.

overall_design: Wild type and mutant (Sldmr6-1.1 and Sldmr6-1.2) plants were grown on soil (Miracle-Gro Supersoil Potting Soil) in a growth chamber at 25°C under a 16h light/8h dark photoperiod. Four individual plants of each genotype (wild type, Sldmr6-1.1 and Sldmr6-1.2 mutants) were used for RNA sequencing. Two leaves from six-week-old plants of each genotype were syringe-infiltrated with a mock solution (10 mM MgCl2) or with a X. gardneri strain 153 suspension (OD600=0.25). Samples were harvested six hours after infiltration.

first: Brian

middle: J

last: Staskawicz


title: Using Endothelial Cells as a Model to Study Trypanosoma cruzi Infection

city: Boston

first: Mercio

last: Perrin

address: 150 Harisson Avenue

country: Canada

institute: Tufts University

summary: Mouse cardiac endothelial cells responses to T. cruzi trypomastigotes

overall_design: Primary mouse cardiac endothelial cells were incubated with T. cruzi trypomastigotes for 3h at an MOI.  The mRNA was isolated using TRIzol reagent and RNA-sequencing was performed using the Illumina NextSeq 500 system.

first: Panagiotidou

last: Smaro

first: Perrin

last: Mercio


title: Astrocytes from mouse NSCs

city: Barcelona

first: Simona

last: Iacobucci

state: Spain

address: Travessera de Gracias

department: Department of Molecular Genomics

country: Spain

institute: IBMB-CSIC

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

overall_design: Refer to individual Series


title: Human induced-Pluripotent Stem Cells-derived Preepicardial Cells

first: Harald

middle: Christian

last: Ott

state: Massachusetts

address: 55 Fruit Street.

department: Surgery

institute: Mass General Hospital

summary: Bulk RNA Sequencing to Characterize Human induced-Pluripotent Stem Cells-derived Pre-epicardial Cells,the extended culture at Passage 1 and the donated H9 ESC-lined derived epicardial cells (Bao et al., 2016)

overall_design:
Bulk RNAseq, 9 samples
This study includes re-analyzed samples from GSE84085.

first: Jun Jie

last: Tan

first: Jacques

last: Guyette

first: King-Hwa

last: Ling

middle: C


title: RNA-seq experiment of shControl and shPHF8 Astrocytes

summary: In this study we analyzed the contribution of PHF8 histone demethylase to astrocytes differentiation from mouse neural stem cells. We found that PHF8 depletion affects astocytes differentiation. Moreover, PHF8 is crucial for synaptogenesis in neurons/astrocytes cocultures. Genome wide analysis demonstrated that PHF8 controls the expression of critical astrogenic and synaptogenic genes by keeping low levels of H4K20me1 at promoters. PHF8 depletion induces aberrant astrocytes phenotype and caused a significant decrease in miniature excitatory postsynaptic currents (mEPSC) frequency and amplitude in neurons/astrocytes coclutures. These data reveal a new role of PHF8 in astrocyte differentiation and function, modulating neuronal synapse. Thus, lack of histone demethylase activity associated to PHF8 mutations might led to synapse disfunction that could directly impact into X-linked intellectual disabilities.

overall_design: RNA-seq of shPHF8 in Astrocytes was performed using two biological replicates of control (shctr rep1, shctr rep2) and shPHF8 (shPHF8 rep1, shPHF8 rep2).

first: Natalia

last: Padilla

first: Martina

last: Gabrielli

first: Claudia

last: Navarro

last: Verderio

first: DelaCruz

last: Xavier

first: Martínez-Balbás

last: Marian


title: Transcriptional changes by PARP7 inhibitor in cancer cell lines

status: Public on Jun 13 2021

city: Cambridge

first: Mario

last: Niepel

state: MA

address: 35 Cambridgepark Dr Suite 300

institute: Ribon Therapeutics, Inc.

summary: PARP7 is a monoPARP that catalyzes the transfer of single units of ADP-ribose onto substrates to change their function.  PARP7 expression is increased by aromatic hydrocarbons and cellular stress, and the PARP7 gene is amplified in cancers, especially in those of the upper aerodigestive tract.  PARP7 is a negative regulator of nucleic acid sensing in tumor cells.  Inhibition of PARP7 restores Type I IFN signaling responses to nucleic acids in tumor models.  Restored signaling can directly inhibit cell proliferation and activate the immune system, both of which contribute to tumor regression.  RBN-2397 is a potent and selective inhibitor of PARP7.  To further investigate the mechanism of action of RBN-2397 and identify potential biomarkers we investigated transcriptional changes after RBN-2397 treatment in two PARP7 inhibitor sensitive cell lines, NCI-H1373 and NCI-H647, by RNA sequencing.

overall_design: NCI-H1373 and NCI-H647 were treated with 2 different PARP7 inhibitors (RBN-2397 and RBN012337) at 3 concentrations around the IC25, IC50 and IC90 (RBN-2397: 10, 30, 300 nM and RBN012337 3, 10, 100 nM) for 6 or 24 hours.  RNA was isolated from triplicate experiments using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher Scientific, #AM1839) per manufacturer’s instructions.  RNA concentration was determined using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA).  Paired-end sample libraries consisting of 60 bp with 6 nucleotide indices were prepared for measuring high-throughput 3’ digital gene expression based on a previously published protocol (Massachusetts Institute of Technology, Cambridge, MA) (Soumillon, 2014).  Vehicle (DMSO) treated cells were used as control.

first: Joseph

last: Gozgit


title: Brown adipose tissue monocytes support tissue expansion

city: Saint-Petersburg

first: Maria

last: Firulyova

address: Kronverksky Pr. 49

department: Department of Computer Technologies

country: Russia

institute: Information Technologies, Mechanics, and Optics University

summary: We report that monocytes contribute to the maintenance of BAT macrophages in a dynamic manner at steady state, and allow tissue remodelling during BAT expansion. Using scRNA-Seq, we explored monocyte and macrophage diversity in BAT at steady state and during BAT expansion.

overall_design: Brown adipose tissue CD45+ cells from AdipoQcre-ERT2 ATGLfl/fl and control mice were cell sorted and analyzed by single-cell RNA sequencing.

first: Alexandre

last: Gallerand

first: Marion

middle: I

last: Stunault

first: Johanna

last: Merlin

first: Hannah

last: Luehmann

first: Deborah

last: Sultan

first: Virginie

last: Magnone

first: Narges

last: Khedher

first: Antoine

last: Jalil

first: Bastien

last: Dolf

first: Alexia

last: Castiglione

first: Adelie

last: Dumont

last: Ayrault

first: Nathalie

last: Vaillant

first: Jérôme

last: Gilleron

first: Pascal

last: Barbry

first: David

last: Dombrowicz

first: Matthias

last: Mack

last: Masson

first: Thomas

last: Bertero

first: Burkhard

last: Becher

first: Jesse

last: Williams

first: Konstantin

last: Zaitsev

first: Yongjian

last: Liu

first: Rodolphe

last: Guinamard

first: Laurent

last: Yvan-Charvet

first: Stoyan

last: Ivanov


title: Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

summary: PU.1 (encoded by Spi1), an ETS-family transcription factor with many hematopoietic roles, is highly expressed in the earliest intrathymic T cell progenitors but must be downregulated during T-lineage commitment.  Transcription factors Runx1 and GATA3 have been implicated in this Spi1 repression, but the basis of the timing was unknown.  We show that increasing Runx1 and/or GATA3 downregulates Spi1 expression in pro-T cells, while deletion of these factors after Spi1 downregulation reactivates its expression.  Leveraging the stage-specificities of repression and transcription factor binding revealed an unconventional but functional site in Spi1 intron 2. Acute Cas9-mediated deletion or disruption of the Runx and GATA motifs in this element reactivates silenced Spi1 expression in a pro-T cell line, substantially more than disruption of other candidate elements, and counteracts the repression of Spi1 in primary pro-T cells during commitment.  Thus, Runx1 and GATA3 work stage-specifically through an intronic silencing element in mouse Spi1 to control strength and maintenance of Spi1 repression during T-lineage commitment.

overall_design: ChIP-seq; 5-10M cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by an additional 10 min with addition of formaldehyde up to 1%, or with 1% FA formaldehyde for 10 min.  Five ug of anti-GATA3 mAbs (a mixture of 2.5 ug of sc-268, Santa Cruz and, 2.5 ug of MAB26051, R&D systems) were pre-bound to Dynabeads anti-Mouse Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots.  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

first: Maria

last: Koizumi

first: Kaori

last: Masuhara

first: Maile

last: Romero-Wolf

first: Toshinori

last: Nakayama

first: Ellen

middle: V

last: Rothenberg

first: Tomoaki

last: Tanaka


title: The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder

city: Salt Lake City

first: Jeff

last: Morgan

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

summary: Peroxisomal Biogenesis Disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs—Zellweger Spectrum Disorder (ZSD)—is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.

overall_design: 4 total S. cerevisiae samples with 1 RNA-seq and 1 Ribosome-footprint profiling entry for each sample

first: Esther

last: Neubel

first: Jeffrey

first: Jared

last: Rutter


title: ChIP-seq experiment of PHF8 in Astrocytes differentiated from mouse NSCs

first: Simona

last: Iacobucci

overall_design: ChIP-seq of PHF8 was performed in Astrocytes. Input of PHF8 is included.

first: Natalia

last: Padilla

first: Martina

last: Gabrielli

first: Claudia

last: Navarro

last: Verderio

first: DelaCruz

last: Xavier

first: Martínez-Balbás

last: Marian


title: USP12-repressed genes in lung adenocarcinoma cells

city: Shanghai

first: Zhaojuan

last: Yang

address: Wenxuan medical building, Jiaotong University, 800 Dongchuan Road, Shanghai, China

institute: Shanghai Cancer Institute

summary: The study aims at elucidating the effects of the deubiquitinase USP12 on lung tumorigenesis and malignant progression. To obtain molecular details of how USP12 functions in lung tumor cells, we profiled the genes transcriptionally affected by USP12 knockdown.

overall_design: The transcriptional profiles of the control and USP12-knockdown H1944 cells were measured by RNA-seq and compared with each other. The alterations of gene expression were then analyzed by pathway enrichment calculation.

first: Yongzhong

last: Liu


title: Transcriptome of mouse splenic NK cells with MYC deficiency

city: Cincinnati

first: Yuting

last: Tang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: To understand the mechanism of the defective NK cell functions with MYC deficiency, we isolated splenic NK cells (CD3-NK1.1+CD49b+) from Mycf/f and MycΔ/Δ/Ncr1Cre mice and performed RNA-seq analysis. It revealed that ribosome and natural killer cell-mediated cytotoxicity were the two most enriched pathways in the differentially down-regulated genes. Functional studies showed reduced synthesis of NK cell effector molecules in the NK Cells with MYC deficiency. Collectively, these data suggest impaired ribosomal biogenesis and reduced synthesis of cytotoxic molecule in the NK cells with MYC deficiency.

overall_design: Flow sorted splenic NK cell mRNA profiles of 8-week old Mycf/f (control) and MycΔ/Δ/Ncr1Cre mice were generated by sequencing, in triplicate and replicate, respectively, using HiSeq 1000 (Illumina, San Diego, CA)

first: Gang

last: Huang


title: Kras mutation-induced gene expression in mouse MEF

summary: The oncogenic activations of KRAS, or its surrogates, occur frequently in human cancers. The alterations in the transcriptional profiles of genes in response to KRAS activation were examined using mouse embryonic fibroblasts.

overall_design: Mouse embryonic fibroblasts (MEFs) with or without the Loxp-Stop-Loxp-KrasG12D/+ allele were immortalized with the SV40 large T antigen and subsequently modified by Cre-recombinase-induced activation of oncogenic KrasG12D. The gene expression profiling in the tumorigenic KrasG12D MEFs and non-tumorigenic Kraswt MEFs were analyzed by RNA-seq.


title: FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [ChIP-seq]

status: Public on Jun 12 2021

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: DNA methylation can be established by RNA-directed DNA methylation (RdDM) in plants. The association of RNA polymerase V (Pol V) with chromatin is a critical step for RdDM. While the SRA-domain-containing proteins SUVH2 and SUVH9 and the DDR complex are known to be required for the association of Pol V with chromatin, it is unknown whether the association of Pol V with chromatin requires other unidentified regulators. Here we found that SUVH9 is able to interact with a conserved histone-interaction protein, FVE, and a previously uncharacterized RRM domain-containing protein, which we named RRM1. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci, while RRM1 is only slightly involved in RdDM. FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than FVE-independent RdDM target loci. FVE was previously shown to be a shared subunit of the RPD3-type histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex, both of which are involved in transcriptional repression. This study reveals a previously uncharacterized role of FVE in RdDM and suggests that FVE may coordinate RdDM, histone deacetylation, and H3K27 trimethylation, thus ensuring transcriptional silencing of TEs in gene-rich chromosome arms to protect genes from harmful effects of potentially transcribed TEs.

overall_design: Examination of H3Ac levels in wild type and two mutants grown under long day condition.

first: Xin


title: Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN downregulation

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

type: Non-coding RNA profiling by high throughput sequencing

summary: The transcription factor Pax5 is known to control B-cell development, but its role in mature B- cells is largely enigmatic. Here, we demonstrate by conditional mutagenesis in peripheral B- lymphocytes that B-1a, marginal zone (MZ) and germinal center B-cells as well as plasma cells are not generated upon loss of Pax5. Follicular (FO) B-cells tolerate the loss of Pax5 but have a shortened half-life. The Pax5-deficient FO B-cells fail to proliferate upon B-cell receptor or Toll- like receptor stimulation due to impaired PI3K-AKT signaling, which is caused by increased expression of PTEN, a negative regulator of the PI3K pathway. Pax5 restrains PTEN protein expression at the posttranscriptional level, likely involving Pten-targeting microRNAs. Additional PTEN loss in Pten,Pax5 double-mutant mice rescues FO B-cell numbers and the development of MZ B-cells. Hence, the posttranscriptional downregulation of PTEN expression is a dominant function of Pax5 that facilitates the differentiation and survival of mature B cells, thereby promoting humoral immunity.

overall_design: 25 samples in total: A) 3 ChIP-seq in 1 cell type: stimulated B cell (H3K4me2, 2 genotypes, 1 replicate each; Pax5 Bio-ChIP, 1 genotype, 1 replicate) B) 12 RNA-seq samples in 2 cell types: lymph node mature B cells (2 genotypes, 2 replicates each) stimulated B cells (2 genotypes, 2 stimulations, 2 replicates each) C) 8 miRNA-seq samples (2 genotypes, 2 cell types, 2 replicates each) D) 2 DHS-seq samples in 1 cell type: stimulated B cell (2 genotypes, 1 stimulation, 1 replicate each)

first: Karina

last: Schindler

first: Stephen

last: Malin

first: Alexandra

last: Schebesta

first: Qiong

last: Sun

first: Hiromi

last: Tagoh

first: Markus

last: Jaritz

first: Lesly

last: Calderon

first: Anja

last: Ebert

last: Minnich

first: Maria

last: Fischer

first: Meinrad

last: Busslinger

first: Tanja

last: Schwickert

first: Chiara

last: Alberti

first: Adrian

last: Liston

first: Louisa

last: Cochella


title: USP12-induced gene expression in lung adenocarcinoma cells

first: Zhaojuan

last: Yang

summary: The study aims at exploring the function of the deubiquitinase USP12 in lung tumorigenesis and malignant progression. To obtain molecular insights into how USP12 acts in lung tumor cells, we profiled the genes transcriptionally affected by enforced USP12 expression.

overall_design: The gene expression profiling in the control and USP12-overexpressed A549 cells were measured by RNA-seq and compared between groups. The alterations of gene expression were then subjected to pathway enrichment analysis.

first: Yongzhong

last: Liu


title: FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [RNA-seq]

first: xinjian

last: He

overall_design: Examination of the mRNA expression of wild type and five mutants grown under long day condition.

first: Xin


title: Gene expression profile of U87 cells depleted from ZNF768

status: Public on Jun 11 2021

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

institute: Université Laval

summary:
ZNF768 is a protein that plays key roles in regulating proliferation. ZNF768 depletion was found to repress proliferation and to cause cellular senescence.

We used microarrays to define the transcriptional impact of ZNF768 deletion in cancer cells.

overall_design: U87 cells were transduced with lentiviruses to knockdown ZNF768 and were selected with puromycin. 96 hours post infection, RNA was isolated and microarrays were performed.

first: Romain

last: Villot


title: LONA lncRNA overexpression delays myeloid differentiation of OCI-AML3 cell line

city: Toulouse

first: Marina

last: Bousquet

address: 2 av H Curien

department: CRCT

institute: INSERM

summary: Here, we report the identification of one long noncoding RNA (lncRNA) overexpressed in NPM1-mutated AML patients (named LONA) and whose intracellular localization inversely reflects that of NPM1. LONA overexpression in mutant NPM1 cells inhibits in vitro myeloid differentiation and enhances in vivo tumor growth. LONA overexpression combined with a genome-wide RNA-seq search followed by RT-qPCR validations identified a set of mRNA targets encoding proteins involved in myeloid differentiation (including THSB1, MAFB and ASB2) and in tumor cell apoptosis and interaction with its microenvironment.

overall_design: We cloned the entire sequence of LONA lncRNA in the retroviral pMSCV-PIG vector. The vector contains a RNA polymerase II promoter driving the lncRNA expression and the PGK promoter driving the puromycin followed by an internal ribosome entry site and GFP . OCI-AML3 (NPM1c+) cell line was transduced with either the PIG-LONA or the PIG EMPTY vector viruses and sorted for GFP+ cells. RNA-sequencing was performed on two independent transductions.

first: Morgane

last: Gourvest


title: Mice deficient in Zfp871 are prone to early death and steatohepatitis in part through the p53-Mdm2 axis

city: Davis

first: Xinbin

last: Chen

state: CA

address: One Shields Avenue

institute: University of California Davis

summary: p53 transcription factor is activated upon exposure to various cellular stresses, leading to growth suppression.  However, aberrant activation of p53 can lead to defects in embryonic development and other abnormalities.  Here, we identified zinc finger protein Zfp871 as a p53 target gene.  We showed that as an RNA-binding protein, Zfp871 binds to Mdm2 3’UTR and stabilizes Mdm2 mRNA, which in turn suppresses p53 expression through increased expression of Mdm2 E3 ubiquitin ligase.  Consistently, Zfp871 deficiency increases p53 expression, leading to growth suppression in a p53-dependent manner.  To determine the role of Zfp871 in the p53 pathway, we utilized Zfp871-deficient mouse model and found that Zfp871-null mice were prone to embryonic/pre-weaning lethality, which can be partially rescued by simultaneous deletion of Trp53.  We also found that mice heterozygous for Zfp871 had a short lifespan and were susceptible to steatohepatitis but not to spontaneous tumors.  To determine the underlying mechanism, RNA-seq analysis was performed and showed that an array of genes involved in development, lipid metabolism and inflammation are regulated by Zfp871 in conjunction with p53.  Taken together, we conclude that the Zfp871-Mdm2-p53 pathway plays a critical role in tumor-free survival and development.

overall_design: Mouse embryonic fibroblasts (MEFs) were isolated from 12.5–13.5 days post-coitum mouse embryos. To generate WT, Trp53-/- and Zfp871-/-; Trp53-/- MEFs, Zfp871+/−; Trp53+/- mice were inter-crossed. To generate WT, Zfp871+/- and Zfp871-/- MEFs, Zfp871+/- mice were interbred. Exponentially growing primary MEFs at passage 4 were used for RNA extraction and RNA-sequencing.

first: Shakur

last: Mohibi

first: Jin

last: Zhang


title: FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [Bisulfite-seq]

overall_design: Examination of the DNA methylation of wild type and six mutants grown under long day condition.


title: A prion accelerates proliferation at the expense of lifespan [samples with spike-in controls]

city: Eugene

first: David

last: Garcia

state: OR

address: 1318 Franklin Blvd.,, Room 273 Onyx Bridge

department: Biology

institute: University of Oregon, Institute of Molecular Biology

summary: Manuscript abstract: In fluctuating environments, the ability to switch between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Tradeoffs arise, however. Mechanisms that aberrantly increase cell size or proliferation— such as mutations, or chemicals that interfere with growth regulatory pathways—can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.

overall_design:
RNA-sequencing of naive (non-prion) and prion-containing, or [BIG+], budding yeast cells

These samples include spike-in control. A related dataset without spike-in controls is available at GSE153930.

first: Edgar

middle: A

last: Campbell

first: Christopher

last: Jakobson

first: Mitsuhiro

last: Tsuchiya

first: Ethan

last: Shaw

first: Acadia

last: DiNardo

first: Matt

last: Kaeberlein

first: Daniel

middle: F

last: Jarosz


title: Molecular basis for substrate recruitment to the PRMT5 methylosome

first: Sellers

last: Lab

address: 415 Main St

institute: Broad Institute

summary: PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP null cancers. PRMT5 utilizes adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1 and COPR5) and show it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable to other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosome assembly complexes. Further, disruption of this site affects Sm spliceosome stability and activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface leads to a hypomorphic decrease in growth of MTAP null tumor cells in vitro and in vivo, and is thus a novel site for development of therapeutic inhibitors of PRMT5.

overall_design:
2 experimental conditions (WT or ADA treatment), in triplicate, of human HCT116 tumor cells.

Please note that the published GSM2462895-GSM2462900 (in GSE93813) data has been re-analyzed as below and the re-analyzed 'prev_publish_*txt' data (is linked as Series supplementary files:
The fastq files from the above mentioned previously published data was processed using rMATS turbo v4.1.1 with read length as 75 and gencode.v19.chr_patch_hapl_scaff.annotation.gtf gtf file to create tab delimited files recording events observed for each of the different alternate splicing events among the replicates and comparing them across the DMSO and EPZ015666 scenarios. The generated JC files for the 5 splicing events were used for further analysis.

first: Kathleen

last: Mulvaney


title: Transcriptomic analysis of biofilm formation in persistent and transient Listeria monocytogenes from the retail deli environment

city: Burlington

first: Andrea

last: Etter

state: VT

address: 109 Carrigan Drive

department: Nutrition and Food Science

institute: University of Vermont

summary: Persistence of Listeria monocytogenes in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of L. monocytogenes persistence in delis across multiple states. We hypothesized that this was correlated with isolates’ innate characteristics, such as biofilm-forming capacity or gene differences.We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome to their global planktonic transcriptome. Analysis of biofilm vs planktonic gene expression did not show the expected differences in gene expression patterns. Overall, L. monocytogenes persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates’ biofilm-forming capacity, sanitizer tolerance, or genomic content

sample_organism:
Listeria monocytogenes
Listeria innocua

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: 4 isolates were chosen for transcriptional analysis. For each isolate RNA was extracted in biological triplicate from 3-day old biofilms grown on stainless steel and from early stationary phase planktonic cultures as a control.

first: Etter

last: Andrea J.

first: Oliver

last: Haley F.

first: Assisi

last: Clara


title: SNP rs4971059 Predisposes to Breast Carcinogenesis and Chemoresistance by Powering DNA Replication.

first: Zihan

address: No. 38 Xuyuan Stress

institute: Peking University

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

overall_design: Refer to individual Series


title: Rejuvenating Age-impaired Fracture Healing

city: Sacramento

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

summary: Skeletal aging and disease are associated with a misbalance in the opposing actions of osteoblasts and osteoclasts that are responsible for maintaining the integrity of bone tissues. Here, we show through detailed functional and single-cell genomic studies that intrinsic aging of bona fide mouse skeletal stem cells (SSCs) alters bone marrow niche signaling and skews bone and blood lineage differentiation leading to fragile bones that regenerate poorly. Aged SSCs have diminished bone and cartilage forming potential but produce higher frequencies of stromal lineages that express high levels of pro-inflammatory and pro-resorptive cytokines. Single-cell transcriptomic studies reveal a distinct population of SSCs in aged mice that gradually outcompete their younger counterparts in the bone marrow niche. While systemic exposure to a youthful circulation through heterochronic parabiosis reduced local expression of inflammatory cytokines, it did not reverse the diminished osteochondrogenic activity of aged SSCs and was insufficient to improve bone mass and skeletal-healing parameters in aged mice. Hematopoietic reconstitution of aged mice with young hematopoietic stem cells (HSC) also did not improve bone integrity and repair. We find that deficient bone regeneration in aged mice could only be reversed by the local application of a combinatorial treatment that re-activates aged SSCs and simultaneously abates crosstalk to hematopoietic cells favoring an inflammatory milieu. This treatment expanded aged SSC pools, reduced osteoclast activity, and enhanced bone healing to youthful levels. Our findings provide mechanistic insight into the complex, multifactorial mechanisms underlying skeletal aging and offer new prospects for rejuvenating the aged skeletal system.

overall_design: 10X Genomics single cell RNA-sequencing of fracture calluses from 24-months old mice at day-10 after stabilized bi-cortical fracture induction. Fracture callus tissue was harvested from 24-mo mice at day-10 after injury. Three fracture calluses treated with hydrogels containing PBS at day of injury and three fractures with hydrogels containing anti-Csf1/BMP2  were processed, digested, and prepared for FACS as described above. Single cell solutions of each treatment group were then pooled (n=3 per group) and 2x105 PI-Ter119- cells were sorted into collection tubes containing FACS buffer. Cells were then processed with 10X Chromium Next GEM Single Cell 3ʹ GEM kit (10X Genomics Inc, v3.1) according to manufacturer’s instruction.

first: Owen

last: Marecic

first: Adrian

last: McArdle

first: Rahul

last: Sinha

first: Gunsagar

last: Gulati

first: Xinming

last: Tong

first: Yuting

last: Wang

first: Holly

last: Steininger

first: Malachia

last: Hoover

first: Lauren

last: Koepke

first: Matthew

last: Murphy

first: Jan

last: Sokol

first: Elly

last: Seo

first: Ruth

last: Tevlin

first: Michael

last: Lopez

first: Stephanie

middle: D

last: Conley

first: Rachel

middle: E

last: Brewer

first: Shamik

last: Mascharak

first: Laura

last: Lu

first: Oyinkansola

last: Ajanaku

first: Maurizio

last: Morri

first: Jun

last: Seita

first: Norma

last: Neff

first: Fan

last: Yang

first: Debashis

last: Sahoo

first: Irving

last: Weissman

last: Longaker

first: Charles

middle: K

last: Chan


title: SNP rs4971059 Predisposes to Breast Carcinogenesis and Chemoresistance by Powering DNA Replication [ChIP-seq]

first: Zihan

last: Zhang

summary: Identification of the driving force behind malignant transformation holds the promise to combat the relapse and therapeutic resistance of cancer. We report here that the single-nucleotide polymorphism (SNP) rs4971059, one of the 65 new breast cancer risk loci identified in a recent genome-wide association analysis, locates at the 6th intron of TRIM46 that functions as an active enhancer. We find that G to A polymorphic switch of the rs4971059 allele augments its chromosomal interaction with the promoter and boosts its enhancer activity. Accordingly, cells carry SNP[A] rs4971059 display an elevated TRIM46 expression. We find that TRIM46 is a ubiquitin ligase that targets HDAC1 for ubiquitination and degradation. Integrative genomic and transcriptomic studies reveal that the TRIM46-HDAC1 axis regulates a panel of genes including ones that are critically involved in DNA replication and repair. Consistently, depletion of TRIM46 impedes S phase progression and sensitizes cells to DNA-damaging reagents. We demonstrate that TRIM46 promotes breast cancer cell proliferation and chemoresistance in vitro and accelerates breast cancer growth in vivo. Importantly, TRIM46 is frequently overexpressed in breast carcinomas, and its level of expression is negatively correlated with that of HDAC1 as well as with higher histological grades and worse prognosis of breast cancer patients. Together, our study links SNP rs4971059 to replication and to breast carcinogenesis and chemoresistance, supporting the pursuit of TRIM46 as a potential target for breast cancer intervention.

overall_design: Examination of the targetgenes regulated by TRIM46-HDAC1 axis

first: Xiaoping

last: Liu

first: Lei

last: Li

first: Yang

first: Jianguo

first: Yue

last: Wang

first: Jiajing

last: Wu

first: Xiaodi

first: Lin

last: Shan

first: Fei

last: Pei

first: Shu

first: Wei

first: Luyang

last: Sun

first: Jing

last: Liang

first: Yongfeng

last: Shang


title: mSWI/SNF promotes polycomb repression both directly and through genome-wide redistribution [ChIP-seq]

city: Stanford

first: Christopher

middle: Michael

last: Weber

address: B209 Beckman Center

department: Pathology

institute: Stanford University

summary: The mammalian SWI/SNF, or BAF complex, has a conserved and direct role in antagonizing polycomb-mediated repression. Yet, BAF also promotes repression by polycomb in stem cells and cancer. How BAF both antagonizes and promotes polycomb-mediated repression remains unknown. Here, we utilize targeted protein degradation to dissect the BAF-polycomb axis in embryonic stem cells on short timescales. We report that rapid BAF depletion redistributes PRC1 and PRC2 complexes from highly occupied domains, like Hox clusters, to weakly occupied sites normally opposed by BAF. Polycomb redistribution from highly repressed domains results in their decompaction, gain of active epigenomic features, and transcriptional derepression. Surprisingly, through dose-dependent degradation of PRC1 & PRC2 we identify a conventional role for BAF in polycomb-mediated repression, in addition to global polycomb redistribution. These findings provide new mechanistic insight into the highly dynamic state of the Polycomb-Trithorax axis.

overall_design: We conducted ChIPseq with mES cell lines where Smarca4 (Brg1) can be targeted for degradation with auxin or Ring1A-/-;Ring1Bfl/fl; Rosa26::CreERT2 ES cells . Ring1b and Suz12 binding were assayed in quadruplicate. Histone marks and BAF155 were analyzed in duplicate.


title: Aged skeletal stem cells during fracture healing

first: Thomas

last: Ambrosi

overall_design: Bulk RNA-sequencing gene expression profiling of mSSCs from fracture callus tissue of adult  (2-months), middle-aged (12 months), and aged (24-months) mice at ten days post injury.

first: Owen

last: Marecic

first: Adrian

last: McArdle

first: Rahul

last: Sinha

first: Gunsagar

last: Gulati

first: Xinming

last: Tong

first: Yuting

first: Holly

last: Steininger

first: Malachia

middle: Y

last: Hoover

first: Lauren

last: Koepke

first: Matthew

middle: P

last: Murphy

first: Jan

last: Sokol

first: Elly

last: Seo

first: Ruth

last: Tevlin

first: Michael

last: Lopez

first: Stephanie

last: Conley

first: Rachel

last: Brewer

first: Shamik

last: Mascharak

first: Laura

last: Lu

first: Oyinkansola

last: Ajanaku

first: Maurizio

last: Morri

first: Jun

last: Seita

first: Norma

last: Neff

first: Debashis

first: Fan

first: Irving

middle: T

first: Charles


title: Transcriptional milestones in Dictyostelium development

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis,. These strains exhibit developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1,371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1,099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly co-regulated with cell division genes, so they are expressed in mid-development even though chromosomal DNA is not replicated. Our dataset includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We demonstrate its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The dataset is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.

overall_design: In this study 486 developmental samples were used, consisting of 21 strains, 5-19 time points, and 2-7 replicates. Using 486 transcriptomes, including existing GEO data (from GSE61914, GSE131209, GSE144892) transcriptional comparisons between strains, phenotype groups, and morphological stages and clustering analyses were performed.

first: Mariko

last: Katoh-Kurasawa

first: Karin

last: Hrovatin

first: Blaz

last: Zupan

first: Shigenori

last: Hirose

first: Amanda

last: Webb

first: Hsing-I

last: Ho


title: Maternal folic acid mild over consumption in mice leads to sex-specific transcriptional alterations in embryonic placenta

city: Montreal

first: Rima

last: Rozen

state: Quebec

address: 1001 Decarie Blvd

department: Departments of Human Genetics and Pediatrics

institute: McGill University

summary:
Food fortification and increased use of multivitamins have led to concerns over high folate intake periconceptionally.  We reported that diets containing 5-fold higher FA than recommended for mice (5xFASD) during pregnancy, resulted in deficiency of methylenetetrahydrofolate reductase (MTHFR) and altered choline/methyl metabolism, with neurobehavioral abnormalities in newborns. Our goal was to determine whether these changes had their origins in the placenta during embryonic development.
We used microarrays to compare the placental gene expression changes by 5xFASD and indentified different gene expression profiles due to diet or sex.

overall_design: At weaning, wild-type C57BL/6 female mice were placed for a month on control diet (CD) or 5xFASD, then mated, and were maintained on the same diets until embryonic day 17.5 (E17.5). Placentas of both sexes from both diets were used for RNA extraction and were conducted gene expression analysis by microarray using Affymetrix Clariom S array_Mouse Chip.

first: Yan

last: Luan

first: Daniel

last: Leclerc

first: Marta

last: Cosín-Tomás

first: Olga

last: Malysheva

first: Brandi

last: Wasek

first: Teodoro

last: Bottiglieri

first: Marie

last: Caudill


title: SNP rs4971059 Predisposes to Breast Carcinogenesis and Chemoresistance by Powering DNA Replication [RNA-seq]

first: Zihan

last: Zhang

overall_design: MCF-7 cells were treated with control siRNA or siRNA of TRIM46. Total RNA was isolated and used for RNA-seq analysis. Repeat twice for each group

first: Xiaoping

last: Liu

first: Lei

last: Li

first: Yang

last: Yang

first: Jianguo

first: Yue

last: Wang

first: Jiajing

last: Wu

first: Xiaodi

first: Lin

last: Shan

first: Fei

last: Pei

first: Shu

first: Wei

first: Luyang

last: Sun

first: Jing

last: Liang

first: Yongfeng

last: Shang


title: mSWI/SNF promotes polycomb repression both directly and through genome-wide redistribution [RNA-seq]

first: Christopher

last: Weber

overall_design: We conducted Brg1 degron RNA-seq time-courses (0, 0.5h, 1h, 2h, 4h, and 8h) and Ring1b/EED double degron dose dependent degradation experiments at 8h. All experiments were done with n = 4 biological replicates in mouse ESCs.


title: RNA-seq of postnatal day 0 (P0) wild-type, Fezf2-/- cortices, and Fezf2-/-;Fezf2-EnR cortices

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

summary: The goal of the study was to compare gene expression of P0 wild-type, P0 Fezf2-/- cortices, and Fezf2-/-; Fezf2-EnR cortices. Total RNAs were isolated from P0 cortices dissected from wild-type (n=3),  Fezf2-/- mice (n=4), and Fezf2-/-; Fezf2-EnR cortices (n=2), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA PolyA library preparation guide.The libaries were pair-end sequenced (150nt per end). Differentially expressed genes were identified by DESEQ.

overall_design: Total RNAs were isolated from P0 cortices, and sequenced on Illumina Novaseq4

first: David

last: Tastad

first: Jeremiah

last: Tsyporin

first: Sol

last: Katzman


title: Molecular Characterization and Cell Type Composition Deconvolution of Fibrosis in NAFLD

city: Boston

first: Zhu

last: Zhuo

address: 401 Park Dr

department: Department of Biostatistics

institute: Harvard TH Chan School of Public Health

summary: Using RNA-sequencing, we conducted a cross-sectional study of 143 NASH patients to identify  differentially expressed genes, significantly enriched pathways, cell composition changes, and predictive gene signatures related to fibrosis severity.

overall_design: mRNA-seqencing of 143 NASH patients of various fibrosis stages

first: Lorena

last: Pantano

first: George

last: Agyapong

first: Yang

last: Shen

first: Francesc

last: Fernandez-Albert

first: Werner

last: Rust

first: Dagmar

last: Knebel

first: Jon

last: Hill

first: Carine

last: Boustany-Kari

first: Julia

last: Doerner

first: Joerg

last: Rippmann

first: Raymond

last: Chung

first: Shannan

middle: H

last: Sui

first: Eric

last: Simon

first: Kathleen

last: Corey


title: Skeletal Stem Cell Aging

first: Thomas

last: Ambrosi

state: California

overall_design: SmartSeq2 single cell RNA sequencing of flow cytometrically purified single skeletal stem cells from adult mouse long bones.

first: Owen

last: Marecic

first: Adrian

last: McArdle

first: Rahul

last: Sinha

first: Gunsagar

middle: S

last: Gulati

first: Xinming

last: Tong

first: Yuting

last: Wang

first: Holly

last: Steininger

first: Malachia

last: Hoover

first: Lauren

last: Koepke

first: Matthew

last: Murphy

first: Jan

last: Sokol

first: Elly

last: Seo

first: Ruth

last: Tevlin

first: Michael

last: Lopez

first: Stephanie

last: Conley

first: Rachel

last: Brewer

first: Shamik

last: Mascharak

first: Laura

last: Lu

first: Oyinkansola

last: Ajanaku

first: Maurizio

last: Morri

first: Jun

last: Seita

first: Norma

last: Neff

first: Debashis

last: Sahoo

first: Fan

last: Yang

first: Irving

middle: L

last: Weissman

last: Longaker

first: Charles

last: Chan


title: Transcriptome landscape of double negative T cells by single-cell RNA sequencing

first: YangLu

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

institute: Beijing Friendship Hospital, Capital Medical University

summary: CD4 and CD8 coreceptor double-negative  TCRαβ+ T  (DNT) cells are increasingly being recognized for their critical and diverse roles in the immune system. However, their molecular and functional signatures remain poorly understood and controversial. We performed single-cell RNA sequencing on 28,835 single immune cells isolated from mixed splenocytes of mice using strict fluorescence-activated cell sorting. In this study, our analysis revealed five transcriptionally distinct naïve DNT clusters, which expressed unique sets of genes and mainly performed T helper, cytotoxic and innate immune functions. Anti-CD3/CD28 activation enhanced their T helper and cytotoxic functions. Moreover, by comparing with CD4+, CD8+ T cells and NK cells, we found Ly6c2 and Ikzf2 were highly expressed by naïve DNT cells. Upon activation, cytotoxic DNT subpopulation, had significantly higher Ikzf2 expression and protein expression of Ly-6C. Our results presented a comprehensive view of the transcriptional states of individual functional subset of DNT cells, highlighting the importance of DNT cells in immune surveillance, defense, and homeostasis.

overall_design:
Single-cell RNA sequencing on five cell types of TCRαβ+ T cells using 10x Genomics. Naive DNT and  activated DNT cells have two biological replicates.

Grant Information:
Funding Agency: National Natural Science Foundation of China
Grant ID: No. 81570510, 81870399 and 82001694


title: Phospholamban Antisense Oligonucleotides Improve Cardiac Function in Murine Cardiomyopathy

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

summary: Heart failure (HF) is a major cause of morbidity and mortality worldwide, but therapeutic intervention remains limited despite recent improvements. Aberrant Ca2+ handling is a key feature of HF pathophysiology. Restoring the Ca2+ regulating machinery is an attractive therapeutic strategy supported by genetic and pharmacological proof of concept studies. Here, we studied antisense oligonucleotides (ASOs) as a novel therapeutic modality, interfering with the PLN/SERCA2a interaction by targeting Pln mRNA for downregulation in the heart of murine HF models. Mice harboring the PLN R14del pathogenic variant recapitulate the human dilated cardiomyopathy (DCM) phenotype; subcutaneously administrated PLN-ASO prevented PLN protein aggregation, cardiac dysfunction, and led to a 3-fold increase in survival rate. In another genetic DCM mouse model, unrelated to PLN (as  a disease driver) (Cspr3/Mlp-/-), PLN-ASO also reversed the HF phenotype. Finally, in rats with myocardial infarction, progression of left ventricular dilatation was prevented by PLN-ASO treatment, which also improved left ventricular contractility. Thus, our data establish PLN-ASO as a possible precision medicine for genetic cardiomyopathy as well as general HF.

overall_design: Left ventricle RNA sequencing profiles of 7 week old homozygous Pln R14del mice treated with PBS vs. PLN-ASO and WT mice as control. Additionally, long-term survival data is available for PLN-ASO treated mice.

first: Niels

last: Grote Beverborg

middle: J


title: mSWI/SNF promotes distal repression by titrating polycomb dosage

first: Christopher

last: Weber


title: Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra Syndrome

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Kleefstra syndrome (KS, also known as 9q.34.3 deletion syndrome) is a rare genetic disorder characterized by a developmental delay, abnormal behaviors and autism-like features. This syndrome is caused by haplo-insufficiency of the euchromatin histone methyltransferase 1 gene (EHMT1/GLP/KDM1D). This gene product, GLP is a methyltransferase responsible for mono- and di-methylation of lysine 9 on histone H3 N-terminal tail, which modulates epigenetic information. Ehmt1 heterozygous mutant (Ehmt1∆/+) mice show KS-like abnormal behavioral phenotypes and utilized as KS model mice. Here, we isolated nuclei from adult Ehmt1∆/+ mice cortex and analysed gene expression precisely by single nucleus RNA-seq analysis. It showed that many genes were up or down regulated in different cell types of Ehmt1∆/+ mice brain. Among them, inflammation associating genes are up-regulated in Ehmt1∆/+ mice neuronal cells. And this up-regulation was reversed by postnatal supply of GLP in post-mitotic neuron of Ehmt1∆/+ mice brain.

overall_design: Single nuclear RNAseq of Ehmt1 heterozygous KO mice cortex

first: Ayumi

last: Yamada

first: Tetsutaro

last: Hayashi

first: Mika

last: Yoshimura

first: Kei

last: Fukuda

last: Nikaido

first: Yoichi

last: Shinkai


title: Endothelium-specific depletion of LRP1 improves glucose homeostasis through the osteocalcin-IGF1R pathway [II]

first: Xinchun

last: Pi

state: Texas

summary: To evaluate gene expression changes in response to low-density-lipoprotein related protein 1 (LRP1) depletion in endothelial cells, we performed mRNA-sequencing analysis with microvascular endothelial cells isolated from the liver LRP1 endothelial knockout mice and their littermate control wild type mice.

overall_design: Microvascular endothelial cells were isolated from the liver of LRP1 endothelial knockout mice and their littermate control wild type mice.

first: Cristian

last: Coarfa


title: Endothelium-specific depletion of LRP1 improves glucose homeostasis through the osteocalcin-IGF1R pathway [I]

summary: To evaluate gene expression changes in response to low-density-lipoprotein related protein 1 (LRP1) depletion in endothelial cells, we performed mRNA-sequencing analysis with microvascular endothelial cells isolated from the lung, heart and liver LRP1 endothelial knockout mice and their littermate control wild type mice.

overall_design: Microvascular endothelial cells were isolated from the lung, heart and liver of LRP1 endothelial knockout mice and their littermate control wild type mice.


title: Endothelium-specific depletion of LRP1 improves glucose homeostasis through the osteocalcin-IGF1R pathway

overall_design: Refer to individual Series


title: Chromatin remodeler INO80 mediates trophectoderm permeability barrier to modulate morula-to-blastocyst transition

status: Public on Jun 10 2021

city: Hefei

first: Zubing

last: Cao

state: Anhui

address: 130 changjiang west road

department: Animal Science

institute: Anhui Agricultural University

summary: INO80 promotes blastocyst development through regulating expression of key genes required for lineage specification, tight junction assembly, and fluid accumulation.

overall_design: Examination of 9 different samples about non-injected，control-siRNA injected and INO80-siRNA injected embryos

first: Zu-Bing

first: Di

last: Gao

first: Hui-Qun

last: Yin

first: Hui

last: Li

first: Teng-Teng

last: Xu

first: Meng-Ya

last: Zhang

first: Xin

last: Wang

first: Qiuchen

last: Liu

first: Yelian

last: Yan

first: Yang-Yang

last: Ma

first: Tong

last: Yu

first: Yunsheng

first: Yunhai


title: Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences


title: Specialized Pro-resolving Mediators Regulate Treg Differentiation

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

summary: We aim to demonstrate a central role for omega-3 derived autacoids, termed specialized pro-resolving mediators (SPM), in the differentiation and maturation of Tregs.

overall_design: Naïve CD4+ T lymphocytes were isolated by immunomagnetic negative selection from the spleens of 4 WT and 4  Alox15-/- mices (KO). Tregs were differentiated from naïve CD4+ T lymphocytes for 2 days in the presence of IL-2, TGF-β  and CD3/CD28 activation beads. Using RNA sequencing we assessed the differential gene expression between KO and WT mices.

first: Raquel

last: Marques

first: Mary

last: Walker

last: Gomez

first: Romain

last: Colas

first: Trinidad

last: Montero-Melendez

first: Mauro

last: Perreti

first: Jesmond

last: Dalli


title: Durvalumab with olaparib and paclitaxel for high-risk HER2-negative stage II/III breast cancer: Results from the adaptively randomized I-SPY2 platform trial

city: San Francisco

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: Durvalumab with olaparib was one of the experimental regimens evaluated in I-SPY 2, a neoadjuvant platform trial for high risk, early stage breast cancer, and graduated in the HER2- and HR+HER2- signatures. We hypothesized that (pre-treatment) expression-based immune signatures may predict response to the immune checkpoint inhibitor durvalumab and signatures related to DNA repair deficiency (DRD) may associate with response to olaparib. In this analysis, we assessed 13 expression based signatures related to immune, DRD, proliferation and estrogen signaling as specific predictor of pathologic complete response (pCR) to durvalumab/olaparib.

overall_design: RNA extracted from pretreatment biopsies were profiled using Agilent 44 K expression arrays (GPL20078). I-SPY2 changed biopsy requirements from fresh frozen (FF) tissue to formalin fixed paraffin embedded (FFPE) tissues in May 2018; therefore, patients on the durvalumab/olaparib arm had RNA extracted from FFPE biopsies (N=71). As microarray-based gene expression levels may differ between FF and FFPE tissues, we restricted the control set in the biomarker analysis to patients who received treatment in the control arm and had FFPE-derived gene expression data (N=34).    The sample characteristics and their values represent:  HER2: the status of the HER2 gene.  1 = positive; 0 = negative.  HR: the status of hormone (estrogen and progesterone) receptors  1 = positive; 0 = negative.  pCR: the status of a pathological complete response (pCR)  1 = complete response; 0 = failed complete response  MP: MP status  MammaPrint High 1: 0 ; MammaPrint (ultra)-High2: 1 .  Arm: arm of the trial per patient   ‘durvalumab/olaparib’; control

first: Christina

last: Yau

first: Laura

last: van ‘t Veer


title: Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes (ChIP-Seq)

city: Beijing

summary: Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions.

overall_design: Examination of H3Ac levels in wild type and eight mutants grown under long day  conditions.

first: Xin-Jian


title: Chd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells

first: Hu

last: Jin

address: 10 Shattuck St

department: Biomedical Informatics

institute: Harvard Medical School

summary: Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 binds to genes transcribed by RNA Pol I and II and is required for hypertranscription in embryonic stem (ES) cells in vitro and the early post-implantation epiblast in vivo. Biochemically, Chd1 has been shown to facilitate transcription at least in part by removing nucleosomal barriers to elongation, but its mechanism of action in stem cells remains poorly understood. Here we report a novel role for Chd1 in the repair of promoter-proximal endogenous double-stranded DNA breaks (DSBs) in ES cells. An unbiased proteomics approach revealed that Chd1 interacts with several DNA repair factors including ATM, Parp1, Kap1 and Topoisomerase 2β. We show that wild-type ES cells display high levels of phosphorylated H2AX and Kap1 at chromatin, notably at rDNA in the nucleolus, in a Chd1-dependent manner. Loss of Chd1 leads to an extensive accumulation of DSBs at Chd1-bound Pol II-transcribed genes and rDNA. Genes prone to DNA breaks in Chd1-null ES cells tend to be longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin organization, transcription and signaling. These results reveal a vulnerability of hypertranscribing stem cells to endogenous DNA breaks, with important implications for developmental and cancer biology.

overall_design: We performed double-strand break labeling by terminal transferase followed by affinity purification and deep sequencing (DSB-seq) in Chd1fl/Δ and Chd1Δ/Δ mouse ES cells with 2 biological replicates for each condition. We also performed Chd1 Flag and RNA Pol II ChIP-seq in Chd1fl/Δ mouse ES cells.

first: Aydan

last: Bulut-Karslioglu

first: Marcela

last: Guzman-Ayala

first: Andrew

last: Williamson

first: Miroslav

last: Hejna

first: Anthony

last: Whetton

first: Jun

last: Song

first: Miguel

last: Ramalho-Santos


title: Post-natal supply of GLP/Ehmt1 reverses Histone H3K9 dimethylation in cortical neuron isolated from adult Ehmt1∆/+ mice brain

status: Public on Jun 09 2021

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

summary: EHMT1 haploinsufficiency causes Kleefstra syndrome (KS), a complex disorder of developmental delay and intellectual disability. EHMT1 encodes a lysine methyltransferase GLP and regulates histone H3 lysine 9 dimethylation (H3K9me2). Ehmt1 heterozygous mutant (Ehmt1∆/+) mice show KS-like abnormal behavioral phenotypes. Here, we examined the reversibility of decreased H3K9me2 by postnatal supply of GLP in post-mitotic neuron of Ehmt1∆/+ mice brain. For this purpose, we generated the mice harboring inducible Ehmt1 cDNA with CamKII-creER (Ehmt1 iTG-neuron mice) in Ehmt1∆/+ background. These mice expressed exogenous Ehmt1 in post-mitotic neuron upon Tamoxifen treatment. Using these mice, we sorted out NeuN+ cells from cortical region and performed Histone H3 K9-dimethyation ChIP analysis. Here we showed that Ehmt1 haploinsufficiency induces global reduction of euchromatic H3K9me2 especially in the euchromatic region of brain and that postnatal supply of GLP can reverse the diminished H3K9me2 phenotype, even in a postmitotic situation.

overall_design: H3K9 dimethylation ChIP seq of NeuN+ cells isolated from wild type, Ehmt1∆/+, Ehmt1 Tg; CamKII-CreER and Ehmt1∆/+;Ehmt1 Tg; CamKII-CreER cortex after re-expression of GLP/Ehmt1 in pot-mitotic neuron

first: Ayumi

last: Yamada

first: Yoichi

last: Shinkai