title: HIV latency reversal via combined non-canonical NF- B agonism and targeted BET family bromodomain inhibition

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

summary: Latency reversal and clearance strategies for HIV cure are beginning to employ IAP antagonists (IAPi) to induce unprecedented levels of latent reservoir expression without immunotoxicity during suppressive antiretroviral therapy (ART). However, full targeting of the reservoir may require combinatorial approaches. A Jurkat latency model screen for IAPi combination partners demonstrated synergistic latency reversal with Bromodomain and Extra-Terminal domain protein inhibitors (BETi). Mechanistic investigations using CRISPR-CAS9 and single cell-RNAseq informed comprehensive ex vivo evaluations of IAPi plus pan-BET, bromodomain (BD)-selective BET, or selective BET isoform targeting in CD4 T cells from ART-suppressed donors. IAPi+BETi treatment resulted in striking induction of cell-associated HIV gag RNA but lesser induction of fully elongated and tat-rev RNA, especially compared to T cell activation positive controls. IAPi/BETi resulted in HIV protein induction in bulk cultures of CD4 T cells using an ultrasensitive p24 assay, but did not translate to enhanced viral outgrowth frequency using a standard quantitative viral outgrowth assay. Overall, this study defines HIV transcriptional elongation and splicing as key barriers to latent HIV protein expression following latency reversal, delineates the roles of BET proteins and their bromodomains in HIV latency, and provides rationale for testing of IAPi+BETi in animal models of HIV latency.

overall_design: N6 cells were treated with the indicated inhibitors for 24 hours and processed for scRNA seq using the 10x Genomics 3' v3 platform.

first: Jackson

last: Peterson

first: Shane

last: Falcinelli

first: David

last: Margolis


title: miR-4730 suppresses progression of hepatocellular carcinoma by targeting high mobility group A1 pathway

status: Public on Feb 09 2022

city: Kyoto

first: Hirotaka

last: Furuke

state: Japan

address: 465 Kajii-cho, Kamigyo-ku, Kyoto, 60285

department: Division of digestive surgery

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: Expression of miR-4730 in hepatocellular carcinoma suppresses tumor progression, and might be a prognostic marker or a therapeutic target of miRNA-based therapies.

overall_design: Total RNA of Li-7 and HEP-G2 cells were extracted using an miRNeasy Mini Kit (Qiagen; Hamburg, GErmany). Real-time quantitative PCR (The Step One plus Real-Time PCR System; Applied Biosystems, Foster City, CA) and TaqMan Gene Expression Assays (Applied Biosystems) were employed. We compared the differences in gene expression between negative control and miR-4730 mimic transfection in Li-7 and HEP-G2 cells using Microarray assay.

last: Konishi

first: Tomohiro

last: Arita

first: Satoshi

last: Kataoka

first: Jun

last: Shibamoto

first: Kazuya

last: Takabatake

first: Wataru

last: Takaki

first: Hiroki

last: Shimizu

first: Yusuke

last: Yamamoto

first: Ryo

last: Morimura

first: Shuhei

last: Komatsu

first: Atsushi

last: Shiozaki

first: Hisashi

last: Ikoma

first: Eigo

last: Otsuji


title: Next Generation Sequencing analysis of KSHV lytic replication in TREx-BCBL1-RTA cells

city: Leeds

first: Adrian

last: Whitehouse

address: Leeds

department: 1School of Molecular and Cellular Biology

country: United Kingdom

institute: University of Leeds

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: miR-Seq was utilised to identify miRNAs which are altered during the course of KSHV lytic replication at  0, 16 and 24 hours post reactivation in TREx-BCBL1-RTA cells.
Methods: Virus lytic replication was induced via addition of 2 µg/mL doxycycline hyclate (Sigma-Aldrich). Total RNA was extracted from TREx-BCBL-1s at 0, 16 and 24 hours post lytic induction. Small RNA libraries were prepared using the TruSeq Small RNA Library Prep Kit (Illumina). Quality filtered (Q < 20), and adapter trimmed reads (Trimmomatic v0.39) [59] were aligned to the GRCh38/hg38 assembly of the human genome using Bowtie2 (V 2.4.2).

overall_design: miRNA profiles during the course of KSHV lytic replication at  0, 16 and 24 hours post reactivation in TREx-BCBL1-RTA cells in triplicates.

first: Chinedu

middle: A

last: Anene


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency (ATAC-seq)

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we report that chemical-based external stimulation reprograms human somatic cells to generate human induced pluripotent stem cells. Using transcriptome, chromatin accessibility and DNA methylome profiling, we identified the cells exhibited key features of embryonic stem cells in transcriptomic profiles, epigenetic status. In addition, we also analyzed the reprogramming process.

overall_design: The induced PSCs were analyzed and compared to human somatic cells and human embryonic stem cells (hES) by ATAC-seq.

first: Jingyang

last: Guan

first: Guan

last: Wang

first: Jinlin

first: Zhengyuan

last: Zhang

first: Yao

last: Fu

first: Lin

last: Cheng

first: Gaofan

last: Meng

first: Hongkui

last: Deng


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency (single cell RNA-seq)

type: Expression profiling by high throughput sequencing

overall_design: To dissect the molecular mechanism, the reprogramming process were analyzed by single cell RNA-seq.


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency

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

overall_design: Refer to individual Series


title: BRD2 regulates accessible genome organization

city: Berkeley

first: Robert

last: Tjian

state: CA

address: LKS

country: USA

institute: UC Berkeley/HHMI

summary: To dissect Cohesin-independent mechanisms that compartmentalize the mammalian genome, we combined super-resolution imaging and high-resolution chromatin interactome, chromatin binding and accessibility and RNA sequencing analysis. We found that the bromodomain and extra-terminal domain (BET) family protein BRD2 is one key regulator to promote compartmental interactions in the absence of Cohesin. We also identified competitive, rather than cooperative relationship between BET family proteins in shaping the 3D genome organization. This study uncovers new mechanisitc insights on the 3D organization of the mammalian genome.

overall_design: We generated inducible protein degradation system for Cohesin subunit RAD21, BET family proteins in mouse embryonic stem cells (ESCs). We performed Micro-C, ChIP-seq, ATAC-seq and RNA-seq experiments and analysis after acute depleting individual protein or in combination.

first: Liangqi

last: Xie


title: A novel paracrine induction of RNA granules by feline calicivirus

city: Guildford

first: Nicolas

last: Locker

state: Surrey

address: Faculty of Health and Medical Sciences

department: School of Biosciences and Medicine

institute: University of Surrey

summary: In this study we are examining the paracrine effect induced by feline calicivirus (FCV) infection on stress granule (SG) accumulation. We provided an understanding of paracrine granules function and specificity through their affinity purification followed RNAseq to systematically analyse their RNA content.

overall_design: We purified in triplicate a granule enriched fraction from GFP-G3BP1 U2OS cells treated (and not) with the virus free supernatant. The RNA was then purified, sequenced and compared to the total RNA.

first: Valentina

last: Iadevaia

first: Carla

last: Moller-Levet

first: James

last: Burke

first: Roy

last: Parker


title: ZNF117 target ChIP-seq

status: Public on Feb 08 2022

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

summary: Glioblastoma (GBM) is a deadly disease without effective treatment. Because glioblastoma stem cells (GSCs) contribute to tumor resistance and recurrence, improved treatment of GBM can be achieved by eliminating GSCs through inducing their differentiation. Prior efforts have been focused on studying GSC differentiation towards the astroglial lineage.

overall_design: GS5 cells were used for ZNF117 ChIP using anti-ZNF117 antibody

last: Zhou

first: Jun

last: Liu

first: Jianhui

first: Xingchun

last: Gao


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency (RNA-seq)

first: Yulin

last: Lyu

overall_design: Cells at the end of each reprogramming stage were analyzed by RNA-seq.

first: Jingyang

last: Guan

first: Guan

last: Wang

first: Jinlin


title: Transcriptomic analysis of AML bone marrow biopsies in a Phase II trial of cytarabine and mitoxantrone with devimistat

city: Winston-Salem

first: Jeff

last: Chou

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary: Devimistat is a novel TCA cycle inhibitor. A previously completed phase I study of devimistat in combination with cytarabine and mitoxantrone in patients with relapsed or refractory acute myeloid leukemia (AML) showed promising response rates. A single arm phase II study (NCT02484391) of AML patients to assess the feasibility of maintenance devimistat, response, survival and safety is now complete. A dose response was observed in older patients, but not younger patients. RNAseq analysis of pre-treatment bone marrow biopsies revealed an age-related decline in mitochondrial gene sets. Devimistat impairs ATP synthesis, and there is a direct correlation between mitochondrial membrane potential and chemotherapy sensitization. Devimistat induces mitochondrial reactive oxygen species and turnover consistent with mitophagy. Pharmacological or genetic inhibition of mitochondrial fission or autophagy sensitizes cells to devimistat. These data support a model where devimistat may benefit older patients as a consequence of age related decline in mitochondrial quality and autophagy.

overall_design: Bone marrow biopsies of 25 AML patients were profiled by bulk RNAseq using Illumina library preparation kits and the Illumina NextSeq 500 sequencing platform.

first: Timothy

middle: S

last: Pardee

first: Lance

middle: D

last: Miller

middle: W


title: Fetal toll-like receptor 3 signalling contributes to the induction of autism-like behaviors in a mouse model of maternal immune activation

city: Seattle

first: Eva

middle: Kristine

last: Nichols

state: Washington

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: A mouse model of maternal immune activation (MIA) is commonly used to study neurodevelopmental disorders. Gene expression analysis has suggested that fetal brain macrophages may be activated by MIA, but it is unclear whether these transcriptional changes connect to behavioral phenotypes in offspring. Here, we have shown that the induction of autism spectrum disorder (ASD)-like behavioral phenotypes by MIA in male offspring is dependent upon fetal activation of the toll-like receptor 3 (TLR3) signaling molecule TRIF. Using single-cell RNA sequencing, we identified a cluster of border-associated macrophages (BAMs) that was significantly enriched in wild-type fetal brains following TLR3-MIA but not diminished in Trif -/- fetal brains. Moreover, after TLR3-MIA, the number of fetal BAMs in the choroid plexus, but not in the meninges, was increased, and these cells were characterized by increased S100a8/9 expression. Finally, we proposed that activation of fetal TLR3-TRIF signaling was induced by transplacental viral infection. Overall, our data suggest that fetal TLR3 signaling contributes to MIA-induced ASD-like behavioral phenotypes in mice.

overall_design: Single-cell RNA-sequencing data of fetal brain myeloid cells derived from embryonic-day (E)13.5 wildtype and Trif-KO mice that were exposed to Vehicle control or immunogenic double-stranded RNA (TLR3 agonist), Poly(I:C), in utero.

middle: K

first: Hsiu

middle: C

last: Chuang

first: Matthew

middle: T

last: Davis

first: Kristina

middle: M

last: Geiger

first: Madeline

middle: L

last: Arnold

first: Rick

middle: Z

last: Li

first: Patrick

last: Lin

first: Rhea

last: Misra

first: Laurent

last: Coscoy

first: Kaoru

last: Saijo


title: Single cell profiling of lung carcinoid tumors

city: Berlin

first: Philip

last: Bischoff

address: Charitéplatz 1

department: Institute of Pathology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Tumor tissue of lung carcinoid tumors (pulmonary neuroendocrine tumors) and adjacent normal lung tissue was profiled using scRNA-seq

overall_design:
Pairs of tumor and normal lung tissue samples of 3 lung carcinoid patients were collected after surgical removal of the tumor. In addition, 7 normal lung tissue samples were collected from lung adenocarcinoma patients. Normal tissue samples of patients 2 and 4-10 have already been part of a previous study (patient 2 = P028, patient 4 = P018, patient 5 = P019, patient 6 = P027, patient 7 = P029, patient 8 = P030, patient 9 = P031 and patient 10 = P033) (Bischoff et al., Oncogene 2021). Tissue was dissociated into single cell suspensions. Single cells were loaded into a comercial drop-seq device (Chromium controller, 10x Genomics) and scRNA-seq libraries were generated using single cell 3' v3 kits from 10x Genomics.
***Raw data not available due to patient privacy concerns***

first: Alexandra

last: Trinks

first: Benedikt

last: Obermayer

first: Jan

middle: P

last: Pett

first: Dieter

last: Beule

first: Markus

last: Morkel

first: Christine

last: Sers

first: Frederick

last: Klauschen

first: Nils

last: Blüthgen


title: Altered small non-coding RNA expression profiles of extracellular vesicles in prostatic fluid of patients with chronic pelvic pain syndrome

city: Guangzhou

first: Bin

last: Ouyang

state: Guangdong

address: No. 1, Panfu Rd

department: Department of Andrology

institute: Guangzhou First People's Hospital,School of Medicine,South China University of Technology

summary: Chronic pelvic pain syndrome (CPPS) and chronic prostatitis (CP) is difficult to distinguish from each other, herein termed CP/CPPS. This study aimed at gaining further insight into the change of extracellular vesicles (EVs) in prostatic fluid of male CPPS. From December 2019 to November 2020, after clinical screening, 24 patients with CPPS without obvious urinary symptoms and 13 healthy male participants were included. EVs were isolated from expressed prostatic secretion (EPS) of all subjects. The small non-coding ribonucleic acid (sncRNA) expression of EVs was sequenced, analysed, and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assays. The results showed that plenty of sncRNAs were differentially expressed between the patients and healthy participants. Further qRT–PCR assays validated that several chronic pain-related miRNAs, including miR-204-5p, let-7d-3p, let-7b-3p, let-7c-3p, miR-146a-5p, and miR-320a-5p, were differentially expressed. Series sncRNAs including several chronic pain-related miRNAs were altered in EVs in prostatic fluid of patients with CPPS, which may serve as diagnostic markers for CPPS.

overall_design: Extracellular vesicles were isolated from expressed prostatic secretion of CPPS patients and healthy men. The small non-coding ribonucleic acid (sncRNA) expression of EVs was sequenced.

first: Dayu

last: Han

first: Zexin

last: Guo

first: Junhong

last: Deng


title: Dissecting the mechanism of action of spiperone, a candidate of drug repurposing for colorectal cancer

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

summary: We evaluated the modulation of mRNA upon spiperone treatment in colorectal cancer epithelial cell line (HCT116) and colorectal cancer stem cells (CRC-SC#1)

overall_design: Gene expression profile study of HCT116 and CRC-SC#1 treated with 10 µmol/L spiperone for 20 hours

first: Annamaria

last: Antona

first: Miriam

last: Zuccalà

first: Davide

last: Corà

first: Sandra

last: D’Alfonso

first: Daniela

last: Capello


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency (single cell ATAC-seq)

first: Yulin

last: Lyu

overall_design: To dissect the molecular mechanism of human cell reprogramming, stage II samples were analyzed by single cell ATAC-seq.

first: Jingyang

last: Guan

first: Guan

last: Wang

first: Jinlin

first: Zhengyuan

last: Zhang

first: Yao

last: Fu

first: Lin

last: Cheng

first: Gaofan

last: Meng

first: Hongkui


title: Transcriptional profiling of murine small intestine in conventional or SPF housing conditions

city: Amsterdam

first: Hein

middle: te

last: Riele

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

summary: We studied the influence of the microbiota on intestinal homeostasis and tumor development after loss of the intestinal tumor phenotype in Msh2-Lynch mice upon rederivation of the mouse line in an SPF facility. We generated RNA seq data from total RNA of small intestine (jejunum) derived from either conventional or SPF mice.

overall_design: We performed differential gene expression analysis comparing SPF mice with conventional mice. Mice were of comparable age and received comparable treatments. Four biological replicats were analysed for each condition.

first: Wietske

last: Pieters

last: te Riele


title: Human Tubular Epithelial Cells Activate a Coordinated Stress Response after Serum Exposure [RNAseq-pid2019]

first: Shreeram

last: Akilesh

address: 1959 NE Pacific St, Box 356100

summary: Proteinuria, the spillage of serum proteins into the urine, is a feature of glomerulonephritides, podocyte disorders and diabetic nephropathy. However, the response of tubular epithelial cells to serum protein exposure has not been systematically characterized. Using transcriptomic profiling we studied serum-induced changes in primary human tubular epithelial cells cultured in 3D microphysiological devices. Serum proteins induced cellular proliferation, secretion of cytokines and activated a coordinated stress response. We orthogonally confirmed our findings by comparing the transcriptomic and epigenomic landscapes of. Importantly, key transcriptomic programs in response to serum exposure remained consistent when comparing intact renal cortex to primary human tubules cultured in 10% fetal bovine serum and to an established mouse model of kidney injury. This serum-induced transcriptional response was dominated by AP-1 and NFkB signatures in the tubular epigenomic landscape with features of active regulation at canonical kidney injury genes (HAVCR1) and genes associated with COVID-19 (ACE2, IL6). Our data provide a reference map for dissecting the regulatory and transcriptional response of tubular epithelial cells to serum-induced injury.

overall_design: Cells from three donors were seeded into a total of 47 kidney chips. Kidney MPS were exposed to maintenance media or maintenance media spiked with 2% normal human serum or 720 ug/mL albumin for either 8 hours or 7 days.

first: Kevin

last: Lidberg

first: Selvaraj

last: Muthusamy

first: Mohamad

last: Adil

first: Ranita

last: Patel

first: Lu

first: Theo

last: Bammler

first: Jonathan

last: Reichel

first: Catherine

last: Yeung

last: Himmelfarb

first: Edward

middle: J

last: Kelly


title: Migratory and anti-fibrotic programmes define the regenerative potential of human cardiac progenitors

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary:
In the present study, scRNAseq was carried out to establish a molecular roadmap for HVP specification and maturation during heart repair as well as HVP properties in response to acute cardiac injury.
Transcriptional profiling by scRNAseq was performed at various timepoints during Human ventricular progenitor-differentiation at D0 and D3 towards cardiomyocytes at D21 that were co-cultured on chimeric human- NHP heart slices. scRNAseq was also performed for HVPs and NHP cells at 24h and 48 h after RFA- induced injury.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: Chimeric heart slices were dissociated and single-cell RNA was isolated from eGFP+ cells at D0, D3 and D21 without RFA, and from eGFP+ and eGFP- cells 24h and 48h after RFA- injury and subsequently subjected to scRNA sequencing.

first: Alessandra

last: Moretti


title: RNA-seq of human kidney cortex and medulla

summary: We report gene expression (RNA-seq) from macro-dissected human kidney cortex and medulla from 3 individuals. The samples were from patients undergoing kidney removal for tumors, but the tissues used in the study itself were normal tissue/cultured cells not involved by tumor.

overall_design: RNA-seq on macro-dissected kidney cortex and medulla from 3 individuals


title: Chromatin accessibility maps and RNA-seq of human kidney cortex and medulla


title: Role of BEND3 in transcription repression

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: We have uncovered that BEND3 is a heterochromatin-associated protein that functions as a transcription repressor. Expression of BEND3 correlates with the state of pluripotency, with a significant decline in BEND3 levels in differentiated cells. Cells lacking BEND3 show defects in cell cycle progression with failure to enter S-phase. BEND3 affects the transcription of cellular genes that modulate chromatin organization and cellular differentiation and that downregulation of BEND3 is critical for cellular differentiation.

overall_design: Chromatin immunoprecipitation was performed using chromatin isolated from NTera2 cell line as explained in Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8338-43. doi: 10.1073/pnas.1424705112. Anti-BEND3 (S3242-2) and rabbit IgG antibodies were used to pull the chromatin. The ChIPseq libraries were prepared with the Hyper Library Construction Kit from Kapa Biosystems with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 10 cycles. The libraries were quantitated by PCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fasta files were generated and demultiplexed with the bcl2fast v2.17.1.14 Conversion Software (Illumina). Adaptors have been trimmed from the 3'-end of the reads. Construction of ChIP-Seq libraries and sequencing on the HiSeq 4000 was carried out at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign (UIUC).


title: Human Tubular Epithelial Cells Activate a Coordinated Stress Response after Serum Exposure [RNAseq-pid1830]

overall_design: Kidney MPS were exposed to maintenance media or maintenance media spiked with 2% normal human serum (~720 ug/mL albumin equivalent) for 48 hours.

last: Wang


title: Human Tubular Epithelial Cells Activate a Coordinated Stress Response after Serum Exposure

overall_design: Refer to individual Series


title: Effect of liposome on gene expression of splenic macrophages

city: Asahikawa

first: Hiroshi

last: Azuma

state: Hokkaido

address: Higashi 2-1-1-1, Midorigaoka

department: Pediatrics

institute: Asahikawa Medical University

summary: Myeloid-derived suppressor cells (MDSC) are induced in various situations. Generation of MDSC has been investigated extensively. Several cytokines are involved in regulating MDSC. Cellular microvesicles, which comprise cellular membrane (single lipid bilayer) are involved in the induction of MDSC. Especially, proteins or nucleic acids encapsulated in them or expressed on their surface are thought to play a role in the induction of MDSC. Nevertheless, the role of lipid components remains to be investigated. Our earlier study using WKAH rat revealed that MDSC-like cells can be induced in the rat spleen by intravenous injection of liposomal microparticles. They comprise a single lipid bilayer of approximately 250 nm diameter, with no cellular component. Therefore, they resemble cellular microvesicles, Cells capable of suppressing T cell proliferation were liposome-internalized cells. The cell surface phenotype was class II low/-, CD11b/c+. Nitric oxide was responsible for their suppression. In this study, we showed that they express B7-H3 molecule on their surface, removal of B7-H3 positive cells restored T cell proliferation. Western blot analysis confirmed that they are positive for iNOS and NFkB was activated 4 hr after liposomal injection. These results indicate that these cells in question belongs to a subset of MDSCs. Furthermore, we elucidated that vesicular form of lipid is important for the induction of T cell suppressive function. Based on these data, we concluded that liposomal microparticles can induce B7-H3 positive MDSC in vivo and the vesicular formation of lipid is essential for the induction of MDSC.

overall_design: Spleens were excised from liposome-loaded or control rats 24 hr after liposome or saline injection. Enrichment of MHC-class II-/CD11b/c+ cell was performed using magnetic beads according to the manufacturer’s protocol. Cells were applied to anti-MHC class II(OX-6) microbeads (Miltenyi Biotec) for negative selection of MHC-class II positive cells. Subsequently they were mixed with PE conjugated anti CD11b/c(OX-42), then stained with anti-PE microbeads and applied for the MACS column for positive selection of CD11b/c positive cells. Total RNA extracted from MHC-class II negative and CD11b/c positive cell enriched fractions of both liposome-loaded and saline-loaded rat were applied to a microarray system

first: Mitsuhiro

last: Fujihara


title: Chromatin accessibility maps in human kidney cortex and medulla

summary: We report chromatin accessibility (ATAC-seq) maps from macro-dissected human kidney cortex and medulla from 3 individuals. The samples were from patients undergoing kidney removal for tumors, but the tissues used in the study itself were normal tissue/cultured cells not involved by tumor.

overall_design: ATAC-seq on macro-dissected kidney cortex and medulla from 3 individuals


title: The effects of PBRM1 loss on the ccRCC transcriptome

status: Public on Feb 07 2022

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

summary: Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the tumor suppressor protein PBRM1 (BAF180), as well as ARID2 (BAF200), that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). In this study, we integrate RNA-seq, histone modification ChIP-seq, and ATAC-seq data to show that loss of PBRM1 results in de novo gains in H3K4me3 peaks throughout the epigenome including activation of a retinoic acid biosynthesis and signaling gene signature. We show that one such target gene, ALDH1A1, which regulates a key step in retinoic acid biosynthesis, is consistently upregulated with PBRM1 loss in ccRCC cell lines and primary tumors, as well as non-transformed cells. We further find that ALDH1A1 increases the tumorigenic potential of ccRCC cells. Using biochemical methods, we show that ARID2 remains bound to other PBAF subunits after loss of PBRM1 and is essential for increased ALDH1A1 after loss of PBRM1, whereas other core SWI/SNF components are dispensable, including the ATPase subunit BRG1.  In total, this study uses global epigenomic approaches to uncover novel mechanisms of PBRM1 tumor suppression in ccRCC.

overall_design: 786O cells infected with either two independent shRNAs against PBRM1 or an off-target control were grown in full RPMI media with either 10% or 1% fetal bovine serum. RNA was extracted when cells were at 70% confluency , poly-A tail captured, and subject to the Illumina TruSeq V2 library prep kit and single end sequenced on an Illumina NextSeq.

first: Ramon

last: Parsons

first: Royce

last: Zhou


title: Sex specific role of KDM5 demethylases in Alcohol-associated Liver Disease

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

summary: Alcohol-associated liver disease (ALD) is a major cause of alcohol related mortality. The specific mechanisms responsible for ALD development and progression are not fully understood, and there is limited therapy for any stage of ALD. Sex differences are often disregarded in in genetic and mechanistic studies. We aimed to take an unbiased approach to define sex specific pathways in livers exposed to alcohol.  METHODS: Mice were fed LieberDeCarli alcohol liquid diet for 3 weeks. To identify the role of Kdm5b and Kdm5c we injected mice with AAV-shControl at 2x10^11 gc per mouse or AAV-shKdm5b and AAV-Kdm5c vectors at 10^11 gc per mouse. To assess the role of AhR we injected mice with AAV-shControl or AAV-shAhR vectors at 10^11 gc per mouse.  RESULTS: We found several pathways affected by alcohol in sex specific way and identified KDM5 demethylases as contributors to that specificity.

overall_design: Whole liver mRNA analysis in alcohol fed mice treated with different AAV vectors

first: Michal

last: Schonfeld


title: Inflammation phenotype of conjunctiva from mice subjected to desiccating stress with or without tributyrin treatment

city: Houston

first: Cintia

last: de Paiva

state: TX

address: 6565 Fannin Street, Room NC 505G

department: Ophthalmology

institute: Baylor College of Medicine

summary: Dry eye is a common ocular inflammatory disorder characterized by tear film instability and reduced tear production. There is increasing evidence that homeostasis of the ocular surface is impacted by the intestinal microbiome. We are interested in investigating the potential role of microbially produced small molecules in mediating the interaction between the intestinal microbiota and the ocular surface.  One such molecule is butyrate, a short-chain fatty acid (SCFA) produced by certain members of the gut microbiota through fermentation of dietary fiber. We have shown that oral administration of tributyrin, a prodrug form of butyrate, is protective of the ocular surface in mice undergoing desiccating stress.  To gain insight into the mechanism, we analyzed gene expression in conjunctival tissue from mice treated with either tributyrgn or vehicle control.

overall_design: Female C57BL/6J mice were subjected to 5 days of desiccating stress to induce dry eye and treated with a daily oral gavage of either tributyrin or vehicle control. Conjunctival tissue was collected from the mice, placed in Qiagen RLT buffer with beta-mercaptoethanol and flash-frozen in liquid nitrogen. For RNA isolation, tissue was chopped with surgical scissors then sonicated, and RNA was extracted using Qiagen RNeasy Plus for NanoString analysis with the Mouse Inflammation Panel v2.

first: Laura

last: Schaefer

first: Humberto

last: Hernandez

first: Rosalind

last: Coats

first: Zhiyuan

last: Yu

first: Stephen

last: Pflugfelder

first: Robert

last: Britton


title: Intermittent glucocorticoid treatment enhances skeletal muscle performance through sexually dimorphic mechanisms [ChIP-seq]

city: Chicago

first: Isabella

last: Salamone

state: IL

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

summary: Glucocorticoid steroids are commonly prescribed for inflammatory conditions such as rheumatoid arthritis and acute respiratory distress, but chronic daily use produces an array of adverse effects including muscle wasting and weakness.  In contrast, shorter and lower dose glucocorticoid pulses may improve athletic performance, although the mechanisms by which this occurs remain unclear.  Muscle is sexually dimorphic and comparatively little is known about how male and female muscle respond to glucocorticoid steroids.  In this work, we investigated the impact of a once-weekly glucocorticoid exposure on body mass and skeletal muscle performance, comparing male and female mice. We performed RNA sequencing of isolated myofibers from quadriceps of C57BL/6 male and female mice given vehicle, weekly, or daily prednisone for one month.

overall_design: H3K27ac ChIP sequencing of one control (vehicle) and three treatment (four, six, and eight days after fifth injection of weekly prednisone) groups, n=2 males and 2 females per treatment

first: Mattia

last: Quattrocelli

middle: Y

last: Barefield

first: Patrick

middle: G

last: Page

first: Ibrahim

last: Tahtah

first: Michele

last: Hadhazy

first: Garima

last: Tomar

first: Elizabeth

last: McNally


title: Comparison of Transcriptomes of Wild Type and aan1∆ cells by Next Generation RNA Sequencing

city: NEW YORK

first: Cierra

last: Sing

state: NY

department: Pathology and Cell Biology

institute: Columbia University

summary: We use RNAseq to compare the transcriptomes of wild type and aan1∆ cells to determine the mechanism behind AAN1 function in the actin cytoskeleton and lifespan. We find deleting AAN1 results in changes in expression of genes involved in branched-chain amino acid synthesis.

overall_design: mRNA profiles of mid-log wild type (WT) yeast cells and aan1∆ cells were generated by deep sequencing

middle: N

first: Liza

middle: A

last: Pon


title: Chemical-based external stimulation reprograms human somatic cells into pluripotency (WGBS)

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: Here, we report that chemical-based external stimulation reprograms human somatic cells to generate human induced pluripotent stem cells. Using transcriptome, chromatin accessibility and DNA methylome profiling, we identified the cells exhibited key features of embryonic stem cells in transcriptomic profiles, epigenetic status. In addition, we also analyzed the reprogramming process.

overall_design: To dissect the molecular mechanism of human cell reprogramming, cells at different time points were analyzed by WGBS.

first: Jingyang

last: Guan

first: Guan

last: Wang

first: Jinlin

first: Zhengyuan

last: Zhang

first: Yao

last: Fu

first: Lin

last: Cheng

first: Gaofan

last: Meng

first: Hongkui

last: Deng


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [Ascl1 KD RNA-seq]

city: Stanford

first: Julien

last: Sage

state: California

address: 265 Campus Drive

institute: Stanford

summary: The Notch pathway is a conserved cell-cell communication pathway that controls cell fate decisions. Here we sought to determine how Notch pathway activation inhibits the neuroendocrine cell fate in the lungs, an archetypal process for cell fate decisions orchestrated by Notch signaling that has remained poorly understood at the molecular level. Using heterogeneity in small cell lung cancer as a model system, we uncovered a role for the transcriptional regulators REST and YAP as promoters of the neuroendocrine to non-neuroendocrine transition. We further identified the specific neuroendocrine gene programs repressed by REST downstream of Notch in this process. Importantly, we validated the importance of REST and YAP in neuroendocrine to non-neuroendocrine cell fate switches in both developmental and tissue repair processes in the lungs. Altogether, these experiments identify conserved roles for REST and YAP in Notch-driven inhibition of the neuroendocrine cell fate in embryonic lungs, adult lungs, and lung cancer.

overall_design: To determine transcriptomic changes when Ascl1 is knocked down in mouse SCLC cell lines for 3days.

first: Yan

last: Shue

first: Alexandros

last: Drainas


title: A transcriptional roadblock protects yeast centromeres

first: Glennis

middle: Amelia

last: Logsdon

state: WA

summary: Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. Overall, cenRNAs are derived from transcription readthrough of pericentromeric regions but rarely span the entire centromere and are a complex mixture of molecules that are heterogeneous in abundance, orientation, and sequence. While most pericentromeres are transcribed throughout the cell cycle, centromere accessibility to the transcription machinery is restricted to S-phase. This temporal restriction is dependent on Cbf1, a centromere-binding transcription factor, that we demonstrate acts locally as a transcriptional roadblock. Cbf1 deletion leads to an accumulation of cenRNAs at all phases of the cell cycle which correlates with increased chromosome mis-segregation that is partially rescued when the roadblock activity is restored. We propose that a Cbf1-mediated transcriptional roadblock protects yeast centromeres from untimely transcription to ensure genomic stability.

overall_design: We performed long-read isoform sequencing (Iso-Seq) combined with transcriptional enrichment to identify the full reportoire of centromeric RNAs (cenRNAs) in S. cerevisiae. We found that transcription at and around centromeres is complex and heterogenous between chromosomes and highly regulated during the cell cycle. Transcription initiates in the pericentromeric domain and usually terminates before entering the centromere, making cenRNAs a small subset of the surrounding RNA repertoire. While most pericentromeres are transcribed throughout the cell cycle, centromeres only become accessible to the transcription machinery in S phase.  We found that centromere accessibility is regulated via a transcription roadblock mechanism mediated by Cbf1. Restoring transcription roadblock activity at CDEI partially rescues chromosome segregation defects, suggesting that one activity of Cbf1 at centromeres is to safeguard this domain from surrounding transcription. Overall, our findings highlight the importance of shielding centromeres from transcription during most cell cycle phases, in order to protect kinetochore function and ensure genomic stability.

first: Sabrine

last: Hedouin

first: Jason

last: Underwood

first: Sue

last: Biggins


title: Intermittent glucocorticoid treatment enhances skeletal muscle performance through sexually dimorphic mechanisms

first: Isabella

last: Salamone

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


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [REST & YAP1 RNA-seq]

overall_design: To determine transcriptomic changes when REST or YAP1 is overexpressed in mouse SCLC cell lines for 48hrs or 5days.


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [REST TKO RNA-seq]

overall_design: To determine transcriptiomic differences between NE and non-NE cells in the tumors when REST is deleted from the onset of tumor initiation.


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [ATAC-seq]

overall_design: To determine chromatin accessibility differences between Hes1-GFP- NE cells and Hes1-GFP+ non-NE cells in mouse small cell lung cancer tumors by bulk ATAC-seq. 4 pairs of Hes1-GFP- and Hes1-GFP+ cells sorted from 3 mice (1 technical replicate).


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [ChIP-seq]

overall_design: ChIP-seq using Rest antibody in Hes1-GFP positive cell lines derived from mouse tumors.


title: Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP:RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency, and scalability.

overall_design: Identification of PRPF39 targets using transcriptome-wide seCLIP-seq in HepG2 cells.

first: Steven

last: Blue

first: Brian

last: Yee

first: Gabriel

last: Pratt

first: Jasmine

middle: R

last: Meuller

first: Samuel

middle: S

last: Park

first: Eric

last: Van Nostrand

first: Eugene

middle: W


title: TBX5 G125R induces profound transcriptional deregulation and atrial dysfunction in vivo [Tbx5_p.G125R]

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: snRNA-seq of Tbx5_p.G125R and control atrial nuclei

overall_design: snRNA-seq of Tbx5-p.G125R atria

first: Antoinette

middle: F

last: van Ouwerkerk

first: Karel

last: van Duijvenboden

first: Jan

last: Koster


title: Intermittent glucocorticoid treatment enhances skeletal muscle performance through sexually dimorphic mechanisms [RNA-seq]

middle: M

overall_design: RNA sequencing of one control (vehicle) and two treatment (weekly, daily prednisone) groups, n=3 males and 3 females per treatment

first: Mattia

last: Quattrocelli

first: David

last: Barefield

first: Patrick

last: Page

first: Ibrahim

last: Tahtah

first: Michele

last: Hadhazy

first: Garima

last: Tomar

first: Elizabeth

last: McNally


title: TBX5 G125R induces profound transcriptional deregulation and atrial dysfunction in vivo [ATAC-seq]

summary:
Rationale: Pathogenic variants in the gene for T-box transcription factor (TF) 5 (TBX5) cause Holt-Oram syndrome (HOS), characterized by congenital heart defects and limb abnormalities. A particular missense variant in TBX5 (G125R) in a Dutch family causes atypical HOS as well as early onset atrial fibrillation (AF). Understanding the effects of such an altered key cardiac TF on the transcription regulatory network and cardiac physiology provides a unique opportunity to gain insight into the mechanisms underlying diseases such as AF.
Objective: To determine the in vivo TBX5-G125R-induced changes in the transcriptional regulatory network and epigenetic state underlying the atypical HOS with early onset AF found in an extended pedigree.
Methods and Results: We modeled the TBX5-G125R pathogenic variant in vivo in the mouse and found severe cardiac defects and fetal lethality in Tbx5G125R/G125R mice, whereas Tbx5G125R/+ mice were viable and morphologically unaffected. Electrophysiological analysis of adult Tbx5G125R/+ mice revealed variable RR interval, atrial extra systole and susceptibility to AF upon pacing. These characteristics were also observed in the patient family. Additionally, calcium homeostasis as well as conduction were changed in the mutant atrial cardiomyocytes. Single-nucleus transcriptional profiling of right atria revealed the most profound changes in expression in the cardiomyocytes of Tbx5G125R/+ mice. Transcriptional profiling of atrial tissue identified differential expression of over a thousand genes, whereas expression levels of several genes known to respond to Tbx5 insufficiency did not change. Epigenetic profiling revealed shifts in sites associated with acetylated H3K27 as well as in chrom  atin accessibility in Tbx5G125R/+ atrial cardiomyocytes indicating Tbx5-G125R has altered DNA binding and TF interaction properties.

overall_design: Cardiomyocyte nucleus ATAC-seq of atria of Tbx5G125R/+ and control adult mice (n=4)


title: TBX5 G125R induces profound transcriptional deregulation and atrial dysfunction in vivo [CUT&RUN]

overall_design: Cardiomyocyte nucleus H3K27Ac CUT&RUN of atria of Tbx5G125R/+ (n=6) and control adult mice (n=5)


title: A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs [Hes1 RNA-seq]

first: Julien

last: Sage

overall_design: To determine transcriptomic differences between Hes1-GFP- NE cells and Hes1-GFP+ non-NE cells in mouse small cell lung cancer tumors by bulk RNA-seq. 4 pairs of Hes1-GFP- and Hes1-GFP+ cells sorted from 4 mice.

first: Yan

middle: T

last: Shue

first: Alexandros

last: Drainas


title: TBX5 G125R induces profound transcriptional deregulation and atrial dysfunction in vivo

overall_design: Refer to individual Series


title: Developmental Venous Anomalies are a Genetic Primer for Cerebral Cavernous Malformations

status: Public on Feb 06 2022

first: Issam

last: Awad

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

summary:
Purpose: Cerebral cavernous malformations (CCMs) are hemorrhagic neurovascular malformations that may lead to stroke, seizures and other clinical sequelae. Recent studies have shown that somatic mutations in MAP3K3 and PIK3CA also contribute to CCM pathogenesis; however, it remains unclear how these mutations contribute to sporadic versus familial cases. In our previous research, we’ve shown that co-occurring MAP3K3 and PIK3CA mutations are present within the same clonal population of cells. The overall goal of this study was to identify PIK3CA mutations in CCM-associated developmental venous anomalies (DVA). We also analyzed the plasma miRNome of patients with (1) DVA without associated CCM, as well as (2) DVA with an associated CCM) to identify circulating miRNAs that might serve as biomarkers reflecting PIK3CA activity.
Methods: We collected and sequenced the plasma miRNome of 12 individuals with a sporadic CCM associated with a DVA (CCM + DVA), 6 individuals with a DVA without a CCM (DVA only), and 7 healthy controls.
Results: We found that the identical PIK3CA mutation is found in endothelial cells of both the DVA and its associated CCM, but that an activating MAP3K3 mutation appears only in the CCM. The analyses miR-134-5p was downregulated in the groups of patients with only a DVA only group (when compared to healthy controls). This miRNA has been shown to target PIK3CA. In addition, miR-182-5p, was upregulated and targets MAP3K3; while let-7c-5p was downregulated and targets both PIK3CA and MAP3K3 in the group of patients with CCM and an associated DVA (when compared to DVA only).
Conclusions: These results support a mechanism where DVA develop as the result of a PIK3CA mutation, creating a region of the brain vasculature that functions as a genetic primer for CCM development following acquisition of an additional somatic mutation.

overall_design: Sequencing and analyses of the differential of the human plasma miRNome in 3 cohort of patients with (1) a DVA with an associated CCM, (2) only a DVA, and (3) healthy controls.

first: Girard

last: Romuald

first: Chen

last: Chang

first: Awad

last: Issam

first: Marchuk

last: Douglas


title: scRNA sequencing of skeletal repair cells at 4 days post injury

city: Los Angeles

first: Maxwell

last: Serowoky

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

summary: We isolated cells from the repair callus of rib bones 4 days after large-scale rib resection injury. The purpose is to characterize the transcriptional landscape of repair cells in control mice, and compare them to the repair cells of Sox9CreER;Smo fx/fx mice, which do not heal.

overall_design: repair cells isolated from 3 mice of each genotype were pooled together to create one control and one KO sample for scRNA library prep using 10x genomics chromium platform.

first: Serowoky

last: Maxwell

first: Mariani

last: Francesca


title: MVV vector integration

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

institute: The Francis Crick Institute

sample_organism:
Homo sapiens
Ovis aries

platform_organism:
Homo sapiens
Ovis aries


title: pH-Degradable, Bisphosphonate-Loaded Nanogels Repolarize Immunosuppressive Macrophages Towards Antifibrotic Liver Therapy

status: Public on Feb 05 2022

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

summary:
Liver fibrosis is a hard-to-treat disease with liver transplantation as only effective curation to this date. During disease progression, immune suppressive macrophages dominate and support fibrosis formation by replacement of functional parenchyma with collagen-dominating scare tissue. To alter the macrophage behavior, a pH-degradable, nanogel-based delivery system was developed for the covalent conjugation of the clinically approved bisphosphonate alendronate. The nanocarrier mediates the drugs’ delivery into hepatic nonparenchymal cells after intravenous administration and, thereby, triggers a macrophage repolarization against fibrosis progression. This approach may provide a significant contribution to establish further nanotherapeutic delivery strategies to effectively treat liver fibrosis.
Immune suppressive macrophages contribute to the progression of several diseases including cancer and fibrosis. Especially in chronically damaged liver tissues they trigger the replacement of functional parenchyma by collagen-dominating scare tissue. In this study, we aimed to intervene into this cascade by repolarizing the macrophage phenotype via a pH-degradable, squaric ester-based nanogel carrier system. This nanotechnology platform enables a selective covalent conjugation of the highly water-soluble bisphosphonate alendronate and, thus, its safe and efficient delivery to hepatic nonparenchymal cells of fibrotic livers after intravenous administration. The bisphosphonate triggers a reprogramming of profibrotic M2- towards antifibrotic M1-phenotype macrophages affording an fibrolytic outcome, as verified both on mRNA and protein level. Further insights by genomic and proteomic studies confirm the macrophages’ repolarization and thus corroborate the virtue of the nanogels as biocompatible nanocarrier platform for hepatotropic bisphosphonate delivery. Beyond preventing liver fibrosis progression, these nanogels may therefore represent an attractive device for further nanotherapeutic interventions in M2-type macrophage dominating diseases.

overall_design: AL/NP treatment versus control (samples alnp_R1-alnp_R3, ctrlfib_R1-ctrlfib_R3)

first: Leonard

last: Kaps

first: Barbara

last: Schrörs

first: Lutz

last: Nuhn


title: YAP regulates an SGK1/mTORC1/SREBP-dependent lipogenic program to support proliferation and tissue growth

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

summary: We report the role of YAP in promoting de novo lipogenesis through the SREBP transcriptional program. By using paired-end RNA sequencing, we show that transgenic zebrafish livers expressing activted YAP exhibit an increase in SREBP target genes associated with lipogenesis. The paired-end RNA sequencing was performed in larval zebrafish livers at 7 days post fertilization (7 dpf)

overall_design: Examination of differentially expressed genes in larval livers isolated from WT and transgenic lf:YAP zebrafish.

first: Talhah

last: Salmi

first: Kristin

middle: K

last: Brown


title: MVV vector integration in sheep cells

summary: To test if LEDGF/p75 influences distribution of Maedi-visna virus (MVV) integration sites, we infected sheep CPT3, LKO1 (PSIP1-null), LHKO1 and LHKO2 (PSIP1/HDGFL2-null) cells with MVV-derived vector. Genomic DNA was isolated from infected cells, and chromosomal junctions at integrated U5 vDNA ends were amplified using linker-mediated PCR, sequenced using Illumina technology and mapped to sheep genome.

overall_design: Genomic DNA isolated from cells 5 days post-infection with MVV vector was processed for linker-mediated PCR, and the amplified viral LTR-chromosome junctions were sequenced. To this end, genomic DNA, digested with MseI overnight at 37°C, was ligated to a double-stranded DNA linker containing 5'-TA overhang overnight at 12°C. Customized DNA linkers were used in conjunction with barcoded primers to aid in multiplexing and prevent crosstalk between samples. The first round and the nested MVV U5 primers were 5'-CTAATTCCGTGCAACACCG and 5'-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNN NCA ACA CCG GAG CGG ATC, respectively (including the 6-nucleotide barcode for multiplexing). The nested PCR primers contained Illumina adaptor sequences appended at the 5' ends. The PCR products, multiplexed on a single lane of a flow cell, were subjected to 150-bp paired-end sequencing on a HiSeq-4000 Illumina instrument.

first: Parmit

last: Singh

first: Vidya

last: Chivukula

first: Alan

last: Engelman


title: Single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae

status: Public on Feb 04 2022

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

summary: In this study, we determined the expression of V. cholerae strain A1552 and its SNP45-converted derivative as well as the expression of strain ATCC25872 and its SNP45-converted derivative.

overall_design: mRNA profiles of the indicated V. cholerae strains; the strains were grown in vitro in LB medium for 3 h post dilution at 30°C with agitation

first: Natalia

middle: C

last: Drebes Dörr


title: Selective chemical tracking of Dnmt1 catalytic activity in live cells

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

summary: Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved in mammalian development and disease. DNA methylation is brought about by collective action of three AdoMet-dependent DNA methyltransferases (DNMTs), whose catalytic interactions and temporal interplay are poorly understood. We used structure-guided engineering of the Dnmt1 methyltransferase to enable catalytic transfer of azide tags onto DNA from a synthetic cofactor analog, Ado-6-azide, in vitro . We then CRISPR-edited the Dnmt1 locus in mouse embryonic stem cells to install the engineered codon, which, following pulse- internalization of the Ado-6-azide cofactor by electroporation, permitted selective azide-tagging of Dnmt1-specific genomic targets in cellula . The deposited covalent tags were exploited as ‘click’ handles for reading adjoining sequences and precise genomic mapping of the methylation sites. The proposed approach, Dnmt-TOP-seq, enables high-resolution temporal tracking of the Dnmt1 catalysis in mammalian cells paving the way to selective studies of other methylation pathways in eukaryotic systems.

overall_design: Genome-wide tracking of DNA methyltransferase Dnmt1 action in mouse embryonic stem cells. Mouse Dnmt1-directed DNA modifications were analyzed in E14TG2a cells bearing the homozygous Dnmt1N1580A knock-in substitution following the delivery of Ado-6-azide by electroporation. Wild-type Dnmt1 cells were used as a control. All experiments were carried out in triplicates and included two technical replicates for each input.

first: Vaidotas

last: Stankevičius

first: Povilas

last: Gibas

first: Bernadeta

last: Masiulionytė

first: Liepa

last: Gasiulė

first: Viktoras

last: Masevičius

first: Saulius

last: Klimašauskas


title: Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (HDLBP PAR-CLIP)

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

summary: The biological role of RNA-binding proteins (RBPs) in the secretory pathway and their contribution to the recognition and co-translational targeting of ER-localized mRNAs is not well established. In this work we used biochemical, transcriptomic and proteomic approaches to delineate the role of human HDLBP/vigilin. PAR-CLIP analysis revealed that HDLBP directly and specifically interacted with more than 80% of all expressed ER-localized mRNAs. Interestingly, the binding to the coding sequence was most prominent for ER-localized mRNAs, while cytosolic mRNAs showed higher binding in the 3’UTR. HDLBP crosslinked strongly to long CU-rich motifs that resided more frequently in coding sequences of ER-localized but not in cytosolic mRNAs. This indicated that the primary sequence composition determines the basis for HDLBP binding specificity and its multivalent interactions with ER-bound mRNAs. PAR-CLIP analysis also revealed direct interactions of HDLBP with the RNA components of the translational apparatus, while in vivo proximity proteomics detected proteins involved in translation and components of the signal recognition particle (SRP). Functional studies using CRISPR-Cas9 HDLBP knockout cell lines in combination with ribosome profiling, pSILAC, and luciferase assays showed decreased translation efficiency of HDLBP target mRNAs, impaired protein synthesis and secretion in the knockout conditions. Finally, HDLBP absence resulted in decrease of in vivo lung tumor formation. These results highlight a general function for HDLBP in the translation of ER -localized mRNAs via the secretory pathway and discover its relevance for cell proliferation and tumor progression.

overall_design: HDLBP RNA targets were analyzed by PAR-CLIP.

first: Ulrike

last: Zinnall

first: Miha

last: Milek

first: Carlos

middle: H

last: Vieira e Vieira

first: Simon

last: Müller

first: Orsalia

last: Hazapis

first: Stefan

last: Hüttelmaier

first: Matthias

last: Selbach


title: Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (Cell fractionation RNA-seq)

overall_design: Cell fractionation experiments were carried out in WT vs HDLBP KO HEK293T cells and fractions were analyzed by RNA-seq.


title: RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation.

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: RNase H2 is a specialized enzyme that degrades RNA in RNA/DNA hybrids and deficiency of this enzyme causes a severe neuroinflammatory disease, Aicardi Goutières syndrome (AGS). However, the molecular mechanism underlying AGS is still unclear. Here, we show that RNase H2 is associated with a subset of genes, in a transcription-dependent manner where it interacts with RNA Polymerase II. RNase H2 depletion impairs transcription leading to accumulation of R-loops, structures that comprise RNA/DNA hybrids and a displaced DNA strand, mainly associated with short and intronless genes. Importantly, accumulated R-loops are processed by XPG and XPF endonucleases which leads to DNA damage and activation of the immune response, features associated with AGS. Consequently, we uncover a key role for RNase H2 in the transcription of human genes by maintaining R-loop homeostasis. Our results provide insight into the mechanistic contribution of R-loops to AGS pathogenesis.

overall_design: In Hela cells: ChIP-seq of RNaseH2A and RNA polymerase II, DRIP-seq -/+ RNaseH after siLuc or siRNaseH2A, and chromatin RNA-seq after siLuc or siRNAseH2A.

first: Agnese

last: Cristini

first: Flavia

last: Constantinescu

first: Clelia

last: Accalai

first: Laura

middle: O

last: Albulescu

first: Robin

last: Heiringhoff

first: Nicolas

last: Bery

first: Olivier

last: Sordet

first: Shona

last: Murphy

last: Gromak


title: Anti-microRNA-21 therapy on top of ACE-inhibition delays renal failure in Alport syndrome mouse models

city: Framingham

first: herve

last: husson

state: ma

address: 49 New York Avenue

department: genomics medicine unit

institute: Sanofi

summary: The goal of this study was to compare Next Generation mRNA (RNA-seq) data obtained from whole kidney tissue from WT and untreated, Lademirsen treated and Ramipril treated Col4a3-/- mice in the mixed 129/SvJ and B57BL/6J background

overall_design: Comparison in WT vs Col4a3-/- Vehicle, Col4a3-/- Vehicle vs Ramipril, and Col4a3-/- Vehicle vs Lademirsen kidneys of RNA expression of 10 most altered canonical pathways and more specifically "Renal Tubulointerstitial Injury in Lupus Nephritis" and "Mitochondrial Dysfunction in Neurodegenerative Diseases" .

first: Herve

last: Husson

first: Ethan

last: Xu

first: Joseph

last: Boulanger


title: A Snapshot of RNA Expression in a Single Segment of the Kidney Reveals Stimulus Specific Responses

city: New York

first: Jacob

last: Stauber

address: 1150 Saint Nicholas Ave., Russ Berrie Bldg. Rm.408A

summary: The identification of acute kidney disease at the time of patient encounter remains a central problem in clinical medicine. A single analyte, the serum creatinine (sCr) is currently in use as a surrogate for tubular, vascular, or interstitial cellular damage. Nonetheless the sCr test is not specific to kidney injury, but rather might reflect physiological responses to a the primary disease in a distant organ. In addition, while cellular events occur over minutes or hours, sCr requires 24 hours or more to reach a worrisome clinical threshold or demonstrate further deterioration of tissue function and architecture. Here we have adapted the method of Gay et al, Genes Dev. 2013 27(1):98-115. doi: 10.1101/gad.205278.112. to allow cell specific labelling of RNA at the time of our choosing after an injury. The technique involves the cell specific expression of a uracil phosphoribosyltransferase (Uprt) and the subsequent purification of 4-thio-uracil labelled nascent RNAs. Using this technique focused on the collecting duct, we found that a model of volume depletion and a model of ischemic damage, both of which raise the sCr do not activate the same cohort of genes nor the same pathways of gene expression. Hence, a snapshot of newly synthesized RNA reveals the complexity subsumed by diagnostic classifications dependent on sCr (called 'AKI'). We suggest that the Uprt technique will allow characterization of each cell type in the nephron at multiple time points after the onset of injury. These data will replace our current diagnostic strategies with Precision Medicine.

overall_design: Examining transcriptional profiles of two models of "acute kidney injury" (iAKI and vAKI), compared to controls, in a single segment of the kidney using cre mediated 4-thio-Uracil tagging of RNA.

first: Tian

last: Shen

first: Katherine

first: Jonathan

last: Barasch


title: Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (tRNA ncRNA-seq)

first: Markus

last: Landthaler

overall_design: Total RNA was sequenced to quantify tRNA abundance in HEK293T cells

first: Ulrike

last: Zinnall

first: Miha

last: Milek

first: Carlos

last: Vieira e Vieira

first: Simon

last: Müller

first: Orsalia

last: Hazapis

first: Stefan

last: Hüttelmaier

first: Matthias

last: Selbach


title: HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins


title: A study of how homozygous ALS-linked FUS P525L mutations perturb transcriptome profile in human iPSC-derived microglia

status: Public on Feb 03 2022

city: Tarrytown

first: Yu

last: Bai

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary:
Purpose: The FUS P525L mutation is highly penetrant and causes ALS cases with earlier disease onset and more aggressive progression.  This study aims to understand the impact of P525L mutations in microglia during ALS pathogenesis. We compare the transcriptome (RNA-seq) of P525L mutations to the wildtype and isogenic controls to derive the differentially perturbed genes.
Methods: Transcriptome profiles of human iPSC-derived microglia with gentoype of wild-type (WT), isogenic control (eCtrl), P525L homozygous (P525LHom), P525L heterozygous (P252LHet) and null deletion (KO) were generated using Illumina HiSeq2000 by multiplexed paired-read run with 100 cycles. Pass-QC sequencing reads were mapped to the human genome (hg19) using the OmicSoft ArrayStudio software followed by differential gene expression analysis via DESeq2 package.
Results: Homozygous P525L mutations perturb the transcriptome profile where many differentially expressed genes are associated with microglial functions. Specifically, dysregulation of several chemoreceptor genes leads to altered chemoreceptor-activated calcium signaling.
Conclusions: Our study underscores the cell- autonomous effects of the ALS-linked FUS P525L mutation in a human microglia model.

overall_design: mRNA profiles of human iPSC-derived microglia with gentoype of wild-type (WT), isogenic control (eCtrl), P525L homozygous (P525LHom), P525L heterozygous (P252LHet) and null deletion (KO)

first: Sze

middle: Y

last: Kerk


title: VPA-treatment of Panc-1-cells to study epigenetic impact mediated by histone acetylation on epithelial-mesenchymal transmission

city: bad nauheim

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Non-mesenchymal pancreatic cells are a potential source for cell replacement therapies aiming to restore the endocrine capacity lost during diabetes mellitus. Although a highly complex network of transcription factors underlies the differentiation, growth, and specification of pancreatic precursors, several studies indicated that the transdifferentiation of non-mesenchymal cells can be achieved by epigenetic regulation. The induction of this epithelial-mesenchymal transition through the post-translational modification of histones, exerting control over both dynamic and long-term gene expression, is a promising approach for reprogramming them into mesenchymal cells. The small molecule and histone deacetylase inhibitor valproic acid was linked to the expression of key transcription factors of pancreatic lineage in epithelial cells and insulin transcription. However, the underlying mechanisms are not fully understood. To shed further light on the potential use of valproic acid for cellular reprogramming strategies, we studied its effects on human ductal Panc-1-cells employing next generation RNA sequencing, real-time PCR and protein analysis by ELISA and western blot. Our data indicate a significant regulation of cell cycle, cell adhesion, histone acetyltransferase and metabolism-related genes, and an epithelial–mesenchymal transition through acetylation of histone H3, resulting in the phenotype of a-cells, supporting the prospect of a therapeutic usage of epithelial pancreatic cells for the purpose of reprogramming into hormonesecreting endocrine cells.

overall_design: Panc-1-cells were incubated with VPA at 1 or 6 mM for 5 days with 2 replicates for each conditions. Treatment without VPA was employed as control.

first: Naga

middle: D

last: Kandula

first: Sebastian

last: Petry

last: Guenther

first: Cristian

last: Helker

first: Thomas

last: Linn


title: TBX5 G125R induces profound transcriptional deregulation and atrial dysfunction in vivo [RNA-seq]

city: Amsterdam

first: Vincent

last: Christoffels

overall_design: Whole tissue RNA-seq of left and right atria of Tbx5G125R/+ and control adult female mice (n=5)

first: Antoinette

last: van Ouwerkerk

first: Karel

last: van Duijvenboden


title: MVV vector integration in human cells

first: Peter

last: Cherepanov

summary: To test if LEDGF/p75 influences distribution of Maedi-visna virus (MVV) integration sites, we infected human HEK293T, LKO (PSIP1-null), and LHKO (PSIP1/HDGFL2-null) cells with MVV-derived vector. Genomic DNA was isolated from infected cells, and chromosomal junctions at integrated U5 vDNA ends were amplified using linker-mediated PCR, sequenced using Illumina technology and mapped to human genome.

first: Parmit

last: Singh

first: Vidya

last: Chivukula

first: Alan

last: Engelman


title: MeRIP Sequencing of Tumor Livers Induced by ALV-J Infection in Chickens

city: Guangzhou

first: Qiqi

last: Zhao

address: 483 WUSHAN ROAD

institute: South China Agricultural University

summary: MeRIP sequencing for 6 samples.

overall_design: Examing 2 conditions, each with 3 replicates

first: Qingmei

last: Xie

first: Xinheng

last: Zhang


title: Differential Regulation of Transcription Factor T-bet Induction during NK Cell Development and Th1 Cell Differentiation

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Adaptive CD4 T helper cells and their innate counterparts, innate lymphoid cells, utilize an identical set of lineage-determining transcription factors (LDTFs) for their differentiation and functions. However, the similarities and differences in the induction of the LDTFs in these lymphocytes are still elusive. Here we show that type 1 T helper (Th1) cells and natural killer (NK) cells displayed distinct epigenomes at the Tbx21 locus, which encodes T-bet, the LDTF for type 1 lymphocytes. The initial induction of T-bet in NK precursors was partially dependent on the NK-specific DNase I hypersensitive site Tbx21-CNS-3 and the expression of IL-18 receptor; IL-18 induced T-bet expression through RUNX3, which binds to Tbx21-CNS-3. By contrast, Tbx21-CNS-12 containing STAT binding motifs was critical for IL-12-induced T-bet expression during Th1 cell differentiation both in vitro and in vivo. Thus, innate and adaptive lymphocytes of same class may utilize distinct enhancer elements for their development and differentiation.

overall_design: Naïve CD4 T cells were isolated from lymph node and cultured under Th1, Th2, or Th17 condition for DNase-seq or ChIP-seq using anti-T-bet antibodies. cNK cells and ILC1s were isolated from liver for DNase-seq. cNK cells were isolated from spleen for ChIP-seq using anti-T-bet antibodies. ILC2s and LTi cells were isolated from small intestine for DNase-seq.

first: Difeng

last: Fang

first: Kairong

last: Cui

first: Mingzhu

last: Zheng

first: Takeshi

last: Kawabe

first: Gangqing

last: Hu

first: Jaspal

last: Khillan

first: Dan

last: Li

first: Chao

last: Zhong

first: Dragana

last: Jankovic

last: Sher

first: Keji

first: Jinfang

last: Zhu


title: Multi-omics approaches for comprehensive analysis and understanding to immune response in miniature pig breed

city: Jeonju

first: Devender

last: Arora

address: 1500, Kongjwipatjwi-Ro, Iseo-Myeon, Wanju-gun

country: South Korea

institute: NIAS

type: Genome variation profiling by high throughput sequencing

summary: Size distribution of Korean minipig is an important feature that made this breed ideal for biomedical research and safe post clinical trials. The extremely tiny (ET) minipig served as an excellent model for various biomedical research but due to prone immune system to surrounding it requires extra after born care over its large (L) size minipig breed. To overcome this pitfall, comparative analysis to the genomic region under selection in L type breed could provide us better understanding at molecular level and able us to develop enhance variety of ET type minipig breeds with advance molecular breeding program. We reports significant selective sweep genes using WGS and RNAseq data and identified a total of 35 common genes amongst 7 were highly expressed and selectively sweep in L type over ET type.

overall_design: Examination of blood sample for immune related understanding was performed.

first: Woncheoul

last: Park


title: Ovarian cancers with low CIP2A tumor expression constitute an APR-246 sensitive disease subtype

status: Public on Feb 02 2022

city: Turku

first: Teemu

middle: Daniel

last: Laajala

address: Turun yliopisto

country: Finland

institute: University of Turku

summary: Identification of ovarian cancer (OvCa) patient subpopulations with increased sensitivity to targeted therapies could offer significant clinical benefit. We report that 22 % of the high grade OvCa tumors at diagnosis express CIP2A oncoprotein at low levels. Further, regardless of their significantly lower likelihood of disease relapse after standard chemotherapy, a portion of relapsed tumors retain their CIP2A-deficient phenotype. Through a screen for therapeutics that would preferentially kill CIP2A-deficient OvCa cells, we identified reactive oxygen species inducer APR-246, tested previously in OvCa clinical trials. Consistent with CIP2A-deficient OvCa subtype in humans, CIP2A is dispensable for development of MISIIR-Tag-driven mouse OvCa tumors. Nevertheless, CIP2A null OvCa tumor cells from MISIIR-Tag mice displayed APR-246 hypersensitivity both in vitro and in vivo. Mechanistically, the lack of CIP2A expression hypersensitizes the OvCa cells to APR-246 by inhibition of NF-kB activity. Accordingly, combination of APR-246 and NF-kB inhibitor compounds strongly synergized in killing of CIP2A positive OvCa cells. Collectively, the results warrant consideration of clinical testing of APR-246 for CIP2A-deficient OvCa tumor subtype patients. Results also reveal CIP2A as a candidate APR-246 combination therapy target for ovarian cancer.

overall_design: Three variants of HEY ovarian cancer cell lines were analyzed in triplicates (rep). The variants include the parental cell line (HEY), stable cell line expressing scrambled shRNA (HEY_NS_shRNA_520) and cell line expressing CIP2A targeted shRNA (HEY_shCIP2A_556).


title: Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary: We report the application of Translating Ribosomal Affinity Purification (TRAP) seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP-tagged ribosomal subunit, we were able to identify translating mRNA transcripts in keratinocytes (krt4), neutrophils (lyz) and macrophages (mpeg) during early cancer transformation. In our zebrafish model of HRasG12V -transformed keratinocytes, we identified 56 differentially expressed genes in keratinocytes, 53 genes in neutrophils, and no differentially expressed genes found in macrophages, compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system.

overall_design: Comparison of TRAP-seq gene expression data in a HRasG12V-transformed keratinocyte Zebrafish model in 3 different cells types

first: Korte

last: Ben

first: Giese

last: Morgan

first: Ramakrishnan

last: Gayathri

first: Ma

last: Stella

first: Bennin

last: David

first: Rindy

last: Julie

first: Dewey

last: Colin

first: Huttenlocher

last: Anna


title: A genetic screen in fetal liver-derived alveolar-like macrophages (FLAMs) identifies new regulators of Siglec-F surface expression

city: East Lansing

first: Andrew

last: Olive

state: MI

address: 567 Wilson Rd, BPS 5100

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Alveolar macrophages (AMs) are tissue resident cells in the lungs derived from the fetal liver that maintain lung homeostasis and respond to inhaled stimuli. While the importance of AMs is undisputed, they remain refractory to standard experimental approaches and high-throughput functional genetics as they are challenging to isolate and rapidly lose AM properties in standard culture. This limitation hinders our understanding of key regulatory mechanisms that control AM maintenance and function. Here, we describe the development of a new model, fetal liver-derived alveolar-like macrophages (FLAMs), which maintains cellular morphologies, expression profiles, and functional mechanisms similar to murine AMs. FLAMs combine treatment with two key cytokines for AM maintenance, GM-CSF and TGFβ. We leveraged the long-term stability of FLAMs to develop functional genetic tools using CRISPR-Cas9-mediated gene editing. Targeted editing confirmed the role of AM-specific gene Marco and the IL-1 receptor Il1r1  in modulating the AM response to crystalline silica. Furthermore, a genome-wide knockout library using FLAMs identified novel genes required for surface expression of the AM marker Siglec-F, most notably those related to the peroxisome. Taken together, our results suggest that FLAMs are a stable, self-replicating model of AM function that enables previously impossible global genetic approaches to define the underlying mechanisms of AM maintenance and function.

overall_design: Genome-wide CRISPR knockout screen in murine alveolar-like macrophages for regulators of surface Siglec-F expression

middle: J

first: Sean

last: Thomas

first: Kathryn

last: Wierenga

first: James

last: Pestka


title: Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (A549 HDLBP KO and WT)

first: Markus

last: Landthaler

overall_design: RNA-seq of xenograft tumors from A549 HDLBP KO and WT cells.

first: Ulrike

last: Zinnall

first: Miha

last: Milek

first: Carlos

last: Vieira e Vieira

first: Simon

last: Müller

first: Orsalia

last: Hazapis

first: Stefan

last: Hüttelmaier

first: Matthias

last: Selbach


title: MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles [RNA-seq]

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: MafB (a bZIP transcription factor), ß-catenin (the ultimate target of the Wnt signal transduction pathway that acts as a transcriptional co-activator of LEF/TCF proteins), and WDR77 (a transcriptional co-activator of multiple hormone receptors) are important for breast cellular transformation.  Unexpectedly, these proteins interact directly with each other, and they have similar genomic binding profiles.  Furthermore, while some of these common target sites coincide with those bound by LEF/TCF, the majority are located just downstream of transcription initiation sites at a position near paused RNA polymerase (Pol II) and the +1 nucleosome.  Occupancy levels of these factors at these promoter-proximal sites are strongly correlated with the level of paused Pol II and transcriptional activity.

overall_design: b-catenin, WDR77, and MafB in the MCF-10A-ER-Src breast cell line

first: Zhiping

last: Weng

first: Lizhi

last: He

first: Henry

last: Pratt

first: Mingshi

last: Gao


title: MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles

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

overall_design: Refer to individual Series


title: MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles [ChIP-seq]


title: Vigilin/HDLBP promotes translation of endoplasmic reticulum-targeted mRNAs (WT vs HDLBP Ribo-seq + RNA-seq)

overall_design: Translational efficiency in WT vs HDLBP KO HEK293T cells were analyzed by ribosome profiling (ribo-seq) and matching RNA-seq datasets.


title: Single cell RNA sequencing for dental pulp cells in endothelial Vegfr2 knockout mice

city: Tokyo

first: Yoshiaki

last: Kubota

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Anatomy

institute: Keio University School of Medicine

summary: Single cell RNA sequencing for dental pulp cells of first molars in control and endothelial Vegfr2 knockout mice at P12

overall_design: mRNA profiles of dental pulp cells cells. One experiment for each genotype (control and endothelial Vegfr2 knockout).

first: Sanosaka

last: Tukasa

first: Jun

last: Kohyama


title: Gene expression analysis of U87 cells with nuclear and non nuclear IGF1R localization

city: Ciudad Autónoma de Buenos Aires

first: Patricia

last: Pennisi

address: Gallo 1330

department: División de Endocrinología

country: Argentina

institute: Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) CONICET- FEI

summary: Transcriptional profiling of U87WT 5 in comparison to U87Mut 5 cells. Three different cultured conditions were tested for 24 h: Serum free media, 50nM IGF1 and 50nM IGF1+ 0.5uM 0SI906

overall_design: Two-condition experiment, U87WT 5 vs. U87Mut 5 cells. Biological replicates: 1 for each culture condition.

first: Ayelen

last: Martin

first: María

last: Fernandez


title: Comparative whole-genome transcriptome analysis in renal cell populations reveals high tissue specificity of MAPK/ERK-targets in embryonic kidney

city: Helsinki

first: Satu

last: kUURE

address: Haartmaninkatu 8

institute: University of Helsinki

summary: We report here bulk RNA sequencing results of control and MAPK/ERK-deficient ureteric bud (UB) epithelium and nephron progenitor cells (NP) in the developing mouse kidney. RNA isolated from 4 biological replicates for UB and 3 biological replicates for NP was subjected to the library preparation  done using NuGen Ovation Solo. Sequencing with NextSeq was performed at BIDGEN DNA Sequencing, after data processing produced 1004 (UB) and 5053 (NP) differentially expressed genes with a statistical cutoff of Padj<0.05 and a magnitude threshold of │log2foldchange│≥1 .

overall_design: Examination of differential gene expressions in two different embryonic kidney tissues: wild type and MAPK/ERK-deficient UB and wild type and MAPK/ERK-deficient NP cells

first: Kristen

last: Kurtzeborn

first: Hyuk Naam

last: Kwon

first: Anneliis

last: Ihermann-Hella

first: Jussi

last: Kupari

last: Kuure


title: Partial resistance to HDAC inhibitors in FAPs of dystrophic muscles at late stages of disease is associated to epigenetic and transcriptional features of cellular senescence [ChIP-seq]

status: Public on Feb 01 2022

city: La Jolla

first: Pier Lorenzo

last: Puri

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys

summary: Pharmacological treatment of Duchenne Muscular Dystrophy (DMD) with histone deacetylase inhibitors (HDACi) is currently being tested in clinical trials. Pre-clinical studies performed in mdx mice - the mouse model of DMD - have shown that HDACi promote compensatory muscle regeneration, while inhibiting fibro-adipogenic degeneration, by targeting fibro-adipogenic progenitors (FAPs); however, these beneficial effects are restricted to early stages of disease progression. We show here that FAPs from late stage mdx mice exhibit epigenetic and transcriptional features of senescence that could not be fully reversed by HDACi. In particular, genome-wide increase in H3K9/14 acetylation at gene promoters of Senescence Associated Secretory Phenotype (SASP) genes was associated with their upregulation in late stage mdx FAPs. Treatment with the HDACi Trichostatin A (TSA) could inhibit SASP gene activation in FAPs, by decreasing H3K9/14 acetylation. Conversely, combinatorial decrease of H3K27 and/or H3K9/14 acetylation at promoters of genes required for cycle activation and progression was associated with their downregulation in FAPs from late stage mdx mice. However, these epigenetic and transcriptional alterations could not be reversed by TSA, due to a general resistance exhibited by FAPs from late stage mdx mice to HDACi-induced H3K9/14 hyperacetylation. Overall, this data reveal that disease-associated features of senescence develop in FAPs of DMD muscle through epigenetically distinct and pharmacologically dissociable events, and suggests that HDACi might at least retain anti- fibrotic and inflammatory activity at late stages of DMD, by repressing FAP-derived SASP.

overall_design: Integrative analysis of 2 different histone modifications (H3K9/14ac and H3K27ac ChIP-seq) and expression profiling (RNAseq) in FAPs derived from mdx mice at early and late stages of disease progression in response to TSA treatment. Comparative analysis of FAP transcriptome to other muscle-derived cells (MuSCs and Macrophages) to evaluate cell-specific features.

first: S

last: Consalvi

first: L

last: Tucciarone

first: E

last: Macrì

first: M

last: De Bardi

last: Picozza

first: I

last: Salvatori

first: A

last: Renzini

last: Valente

last: Mai

first: V

last: Moresi

first: P

middle: L


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes and TCR repertoire in vaccinated PBMCs and tumors

city: San Francisco

first: Hideho

last: Okada

address: 1450 3rd Street

department: Department of Neurological Surgery

institute: University of California, San Francisco

summary: In the clinical trial, we evaluated the immunological efficacy of the vaccination of GBM6-AD, a tumor-cell lysate, assisted with poly-ICLC in low grade glioma. To characterize the gene expression, subset proportions, and T-cell receptor (TCR) profile of T-cells in PBMCs, we analyzed pre- and post-neoadjuvant vaccinated PBMCs from four immunological responders (103-018, -26, -29, -51), using droplet-based 5’ single-cell RNA-sequencing (scRNA-seq) and single-cell T-cell receptor-sequencing (scTCR-seq) with 10x GENOMICS platform. Further, we analyzed the gene expression profiles in resected tumor specimens by bulk RNA-seq analyses.

overall_design: Pre- and post-neoadjuvant vaccinated PBMCs from four immunological responders (103-018, -26, -29, -51), those were identified by mass cytometric analyses, were analyzed by scRNA-seq analyses. All of the available resected tumor specimens from both Arm 1 (neoadjuvant vaccination) and Arm 2 (control) were analyzed by bulk RNA-seq analyses

first: Hirokazu

last: Ogino

first: Jennie

last: Taylor

first: Takahide

last: Nejo

first: Atsuro

last: Saijo


title: Transcriptome analysis of LT-HSC isolated from WT and CD169DTR/+ mice 5 days after a 2 Gy-Total Body Irradiation

city: Fontenay-aux-roses

first: Stephanie

middle: G.

last: MORENO

address: 18 route du Panorama

department: DRF / iRCM

country: France

institute: CEA

summary:
A 2 Gy-total body irradiation (TBI) of WT mice induces a second wave of ROS and a second wave of apoptosis in hematopoietic stem cells starting from 6 days after irradiation. In CD169DTR/+ mice, which are depleted in CD169+ resident macrophages after a diphtheria toxin injection, these two waves do not occur and a total recovery of the LT-HSC pool is observed, contrarily to the LT-HSC pool from WT mice, which is decreased. Our goal is to understand why these secondary waves of apoptosis and ROS occur in LT-HSC from irradiated WT mice and not in LT-HSC from irradiated mice depleted in resident macrophages, allowing a recovery of the  LT-HSC pool.
We used microarrays to compare the global gene expression in LT-HSC isolated from WT and CD169DTR/+ mice 5 days after irradiation, i.e. just before both secondary waves of ROS and apoptosis occurred in WT mice.

overall_design: Two distinct experiments have been performed to obtain two replicates for each condition (i.e. for both mouse strains, irradiated or not).

first: Stéphanie


title: H3K27me3 localization in UTX deficient Plasma cells by ChIP-seq

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To evalute how deletion of H3K27me3 demethylases, UTX and JMJD3, affect H3K27me3 enrichment in plasma cells. ChIP-seq for H3K27me3 was performed on CreCtrl and dKO (UTX and JMJD3-deficient) PC at day three post in vivo stimulation with LPS.

overall_design: ChIP-seq for H3K27me3 on plamsa cells (PC) from CreCtrl and dKO mice

first: C

first: J

last: Boss


title: Accessible chromatin profiling of H3K27me3 demethylase deficient B cells

summary: To understand the role of the H3K27me3 demethylases, UTX and JMJD3, in regulating chromatin accessibility. ATAC-seq was performed on the following populations from control (CreCtrl) and double knockout (dKO) mice: naïve marginal zone B cells and follicular B cells as well plasma cell generated at three days post in vivo stimulation with LPS.

overall_design: ATAC-seq on margnizal zone B cells, follicular B cells and plamsa cells from CreCtrl and dKO mice


title: H3K27me3 localization in UTX deficient Plasma cells by CUT&Tag

summary: To understand the role of the H3K27me3 demethylases, UTX and JMJD3, in B cell differentiation. CUT&Tag for H3K27me3 was performed on CreCtrl and dKO (UTX and JMJD3-deficient) PC at day three post in vivo stimulation with LPS.

overall_design: CUT&Tag for H3K27me3 or IgG on plamsa cells (PC) from CreCtrl and dKO mice


title: A BRCA1 coiled-coil domain variant disrupting PALB2 interaction predisposes to mammary tumors with a targetable defect in homologous recombination repair.

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

institute: Netherlands Cancer Institute


title: Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing

city: Berkeley

first: Michael

last: Ly

address: 565 Li Ka Shing Center

institute: UC Berkeley

summary: Vaccinia virus (VACV) encodes decapping enzyme D10 that suppresses gene expression by removing the protective 5’ cap off mRNAs, rendering them susceptible to degradation by cellular exonucleases. Here, we use RNA-seq to profile the repertoire of transcripts targeted by D10 in isolation as well as in the context of VACV infection. We found that D10 is a broadly acting decapping enzyme and targets the vast majority of human transcripts. Notably, we found that the splicing architecture of a gene influences how robustly its corresponding transcript is targeted by D10, with transcripts derived from intronless genes being less susceptible to D10 activity. Since all viral genes are intronless, and some viral transcripts are uncapped, D10 preferentially targets host transcripts over viral transcripts. The disproportionate activity of D10 towards host transcripts may help the virus restrict host innate immune response and shift the translational resources towards viral protein synthesis.

overall_design: RNA-seq of HEK293T cells with integrated doxycycline-inducible D10 gene and of HEK293T cells infected with different mutant strains of vaccinia virus. There were three biological replicates per condition, resulting in a total of 42 samples. We included untreated and mock samples as controls for doxycycline-treated cells and vaccinia-infected cells, respectively.

first: Hannah

last: Burgess

first: Sahil

last: Shah

first: Ian

last: Mohr

first: Britt

last: Glaunsinger


title: Placental dysfunction influences fetal monocyte subpopulation gene expression in preterm birth

first: Erika

last: Lin

address: 9500 Gilman Dr,

department: Pediatrics

institute: University of California, San DIego

summary:
Purpose: Identify differences in gene expression profiles in fetal monocytes - cells that persist and differentiate postnatally -  according to distinct placental histologic domains.
Methods: We first isolated classical and intermediate monocyte  subsets via FACS and performed transcriptomic profiling of 140 samples (70 classical and 70  intermediate monocyte samples) using bulk RNA-Seq.
Results: We report that placental lesions are associated with gene expression changes in fetal  monocyte subsets. Specifically,fetal monocytes exposed to acute placental  inflammation upregulate biological processes related to monocyte activation, monocyte  chemotaxis, and platelet function while monocytes exposed to maternal vascular malperfusion  lesions downregulate these processes. Additionally, we show that intermediate monocytes might  be a source of mitogens, such as HBEGF, NRG1, and VEGFA, implicated in different outcomes  related to prematurity.
Conclusions: This is the first study to show that placental lesions are associated with  unique changes in fetal monocytes and monocyte subsets. As fetal monocytes persist and  differentiate into various phagocytic cells following birth, our study may provide insight into  morbidity related to prematurity and ultimately potential therapeutic targets.

overall_design: Gene expression profiles of sorted fetal monoctyes.

first: Abhineet

last: Sharma

first: Rob

last: Birkett

first: Linda

last: Ernst

first: William

last: Grobman

first: Suchitra

last: Swaminathan

first: Hiam

middle: A

last: Valencia

first: Alexander

last: Misharin

first: Elizabeth

last: Bartom

first: Karen

last: Mestan


title: Regulation of gene expression by STIM1 and Ca2+ in human T cells

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

institute: New York University School of Medicine

summary: Human CD4+ T cells were left untreated or stimulated with 5 μg/ml plate-bound anti-CD3 antibody (clone OKT3, 14-0037-82, eBioscience) and 10 μg/ml soluble anti-CD28 antibody (clone CD28.2, 14-0289-82, eBioscience) for 6 h in RPMI1640 medium supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin-streptomycin.

overall_design: RNA Sequencing of human CD4+ T cells from a patient homozygous for a STIM1 c.497+776A>G mutation, heterozygous carriers and a healthy donor

first: Sascha

last: Kahlfuss

first: Ikjot

last: Sidhu

first: Dimitrius

last: Raphael


title: Gene-editing of miR-21 to target glioma

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

institute: Massachusetts General Hospital

summary:
Method: Analysis of the transcriptomal changes in wildtype mouse glioma tumor cells compared to miR-21 knockout glioma tumor cells (GL261)
Result: transcriptional changes are driven through miR-21

overall_design: mRNA expression of GL261 wildtype and miR-21 knockout isoloated from cells were analyzed by RNAseq, using Illumina MiniSeq.

first: Thomas

middle: S

last: van Solinge

first: Pike-See

last: Cheah

first: Liza

last: Morsett

first: Joseph

middle: I

last: Rissman

first: Benjamin

last: Kleinstiver

first: Marike

last: Broekman

first: Xandra

last: Breakefield

first: Erik

middle: R

last: Abels


title: Multi-omics profiling of distinct type I interferon responses in human glioblastoma and osteosarcoma cell lines

city: Moscow

first: Anastasia

last: Nikitina

address: Malaya Pirogovskaya

department: Department of Molecular Biology and Genetics

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia

summary: A potential new line of anticancer therapy is the use of oncolytic viruses. However, there is a heterogenicity among various types of tumors in response to such treatment. This study is aimed at identifying molecular mechanisms that confer sensitivity to viral infection. We investigated type I interferon responses in human glioblastoma cell line DBTRG-05MG (resistant to viral infection) and osteosarcoma cell line HOS (sensitive to viral infection). We applied a multi-omics approach with included transcriptome, proteome and editome analysis of these cell lines before and after interferon treatment.

overall_design: Transcriptomic profiles of DBTRG-05MG and HOS cell lines before and after interferon type I treatment.

first: Anna

last: Kliuchnikova

first: Anton

last: Goncharov

last: Lipatova

first: Petr

last: Chumakov

first: Sergei

last: Moshkovskii


title: A BRCA1 coiled-coil domain variant disrupting PALB2 interaction predisposes to mammary tumors with a targetable defect in homologous recombination repair [CNV-seq]

city: Amsterdam

first: Roebi

last: Bruijn

summary: The BRCA1 tumor suppressor gene encodes a multi-domain protein for which several functions have been described. These include a key role in homologous recombination repair (HRR) of DNA double-strand breaks (DSBs), which is shared with two other high-risk hereditary breast cancer suppressors, BRCA2 and PALB2. Although both BRCA1 and BRCA2 interact with PALB2, BRCA1 missense variants affecting its PALB2-interacting coiled-coil domain are considered sequence variants of uncertain clinical significance (VUS). Using genetically engineered mice, we now show that a BRCA1 coiled-coil domain VUS, Brca1 p.L1363P, disrupting the interaction with PALB2 leads to embryonic lethality and loss of breast cancer suppression. Brca1 p.L1363P mammary tumors develop with a similar latency as Brca1-null tumors, but show different histopathological features and more stable DNA copy number profiles. Nevertheless, Brca1 p.L1363P mammary tumors are HRR-incompetent and responsive to cisplatin and PARP inhibition.

overall_design: RNASeq and CNVSeq of Brca1 p.L1363P mammary tumors from different histology classes were compared to other KP, KB1P, and KB2P breast cancer mouse model mammary tumors

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