title: RNA-seq of wild-type and mfn2-/- activated muscle stem cells (mouse)

first: Prashant

last: Mishra

summary: We report the transcriptome changes in purified mouse activated muscle stem cells in response to deletion of the Mfn2 gene.

overall_design: A floxed Mfn2 allele combined with the Pax7-Cre (ERT2) driver was used to induce Mfn2 deletion in muecle stem cells of adult animals (mice), via administration of tamoxifen. Tibialis anterior muscles were injured with BaCl2 administration, and activated muslce stem cells were purified 2 days post injury from wild-type (control) and mfn2-/- animals.

first: Xun

last: Wang


title: Isolation of an efficient glycosaminoglycans degrading human gut Firmicutes Hungatella hathewayi and the characterization of its Chondroitin ABC exolyase with high activity and broad substrate specificity

status: Public on Aug 14 2022

city: Qingdao

first: Parkash

middle: Singh

last: Rawat

state: Shanding

address: 72 Binhai Road, Jimo

department: State Key Laboratory for Microbial Technology, School of Life Sciences

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: The degradation of glycosaminoglycans (GAGs) by intestinal bacteria is critical for their colonization in the human gut and the health of the host. Both Bacteroides and Firmicutes have been reported to degrade GAGs, while the enzymatic details of the latter remain largely unknown. In this study, we isolated a Firmicutes strain, Hungatella hathewayi N2-326, that can catabolize various GAGs. While H. hathewayi N2-326 was less efficient in utilizing chondroitin sulfate A (CSA) and dermatan sulfate (DS) than Bacteroides thetaiotaomicron, a characterized GAG degrader, it outperformed B. thetaiotaomicron in assimilating hyaluronic acid. Unlike B. thetaiotaomicron, H. hathewayi N2-326 could not utilize heparin. The chondroitin lyase activity of H. hathewayi N2-326 was found to be induced by CSA and displayed both cell-associated and extracellular distributions. We further identified and characterized the first chondroitin ABC lyase from Firmicutes. The recombinant H. hathewayi chondroitin ABC lyase was found to be a predominantly exolyase and exhibited higher specific activity than any other characterized chondroitin ABC lyase. Thus, the HH-chondroitin ABC lyase offers a viable commercial option for the production of chondroitin, dermatan, and hyaluronan oligosaccharides and potential medical applications.

overall_design: Comparative gene expression analysis of RNA-seq data for Hungatella hathewayi N2-326 cells grown to mid-log phase on either 1.5% chondroitin sulfate A (CSA) or 1.5% glucose (Glc). Three replicates for each group, i.e. CSA and glc, were included.

middle: S

first: Xiangfeng

last: Meng

first: Weifeng

last: Liu


title: Mitotic H3K9 acetylation patterns are controlled by phase-specific activity of the histone deacetylases HDAC2, 3 and SIRT1

city: Jerusalem

first: Itamar

last: Simon

state: Israel

address: Hebrew University Medical School

department: Microbiology and Molecular Genetics

country: Israel

institute: The Hebrew University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone acetylation play a fundamental role in many biological processes. H3K9ac is tightly linked to active transcription, and enriched in promoters, enhancers and insulators. During mitosis H3k9ac levels are reduced, and the mechanism of this reduction is not clear. Here, we used small molecules inhibitors of histone deacetylases and evaluated by immunofluorescence and western blots the involvement of each of the targeted enzymes in regulating H3K9ac during prophase, metaphase, anaphase, telophase and cytokinesis. We identified three histone deacetylases, HDAC2, HDAC3 and SIRT1, as modulators of H3K9ac mitotic levels. HDAC2 inhibition, increased global H3K9ac in prophase, whereas HDAC3 or SIRT1 inhibition, increased H3K9ac levels in metaphase. Next, we performed ChIP-seq in mitotic cells following specific inhibition of each of these histone deacetylases. While we observed a high concordance between the genomic areas impacted by HDAC2 and HDAC3, we detected a small set of loci that were unique to each condition, with HDAC3-specific targets being enriched for genes involved in mitosis regulation.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: Examination of 4 different HDACs inhibitors in STC arrested mitotic Hela S3 cells. each experiment was done in duplicates and we also checked untreated mitotic cells and untreated unsynchronized cells

first: Raizy

last: Mitterhoff

first: Rachel

last: Rapoport


title: mRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

status: Public on Aug 13 2022

city: Columbus

first: William

middle: E.

last: Carson III

state: OH

country: USA

institute: The Ohio State University

summary: mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

overall_design: In this study microRNA and mRNA expression was assessed in formalin fixed, paraffin embedded melanoma tissue from primary, cutaneous lesions with (n=6) and without (n=5) histologically confirmed tumor ulceration using the Nanostring human miRNA assay and Nanostring human tumor signaling 360 mRNA assay, respectively.

first: Mallory

middle: J

last: DiVincenzo

first: Emily

last: Schwarz


title: microRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

summary: microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma (n=6) compared to non-ulcerated primary cutaneous melanoma (n=6)

overall_design: In this study microRNA and mRNA expression was assessed in formalin fixed, paraffin embedded melanoma tissue from primary, cutaneous lesions with and without histologically confirmed tumor ulceration using the Nanostring human miRNA assay and Nanostring human tumor signaling 360 mRNA assay, respectively.


title: Expression patterns of microRNAs and associated target genes in ulcerated primary cutaneous melanoma

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

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

overall_design: Refer to individual Series


title: mRNA expression in ulcerated primary cutaneous melanoma

overall_design: In this study microRNA and mRNA expression was assessed in formalin fixed, paraffin embedded melanoma tissue from primary, cutaneous lesions with (n=14) and without (n=8) histologically confirmed tumor ulceration using the Nanostring human miRNA assay and Nanostring human tumor signaling 360 mRNA assay, respectively.


title: microRNA expression in ulcerated primary cutaneous melanoma

summary: microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

overall_design: In this study microRNA and mRNA expression was assessed in formalin fixed, paraffin embedded melanoma tissue from primary, cutaneous lesions with (n=19) and without (n=16) histologically confirmed tumor ulceration using the Nanostring human miRNA assay and Nanostring human tumor signaling 360 mRNA assay, respectively.


title: Molecular identification of spatially distinct anabolic responses to mechanical loading in murine cortical bone

status: Public on Aug 12 2022

city: Ithaca

first: Carolyn

last: Chlebek

state: NY

address: 110 Hoy Road

department: Biomedical Engineering

institute: Cornell University

summary: Osteoporosis affects over 200 million women worldwide, one third of whom are predicted to suffer from an osteoporotic fracture in their lifetime. The most promising anabolic drugs involve administration of expensive antibodies. Because mechanical loading stimulates bone formation, our current data, using a mouse model, replicates the anabolic effects of loading in humans and may identify novel pathways amenable to oral treatment. Murine tibial compression produces axially-varying deformations along the cortical bone, inducing highest strains at the mid-diaphysis and lowest at the metaphyseal shell. To test the hypothesis that load-induced transcriptomic responses at different axial locations of cortical bone would vary as a function of strain magnitude, we loaded the left tibiae of 10wk female C57Bl/6 mice in vivo in compression, with contralateral limbs as controls. Animals were euthanized at 1, 3 or 24 h post-loading or loaded for 1 wk (n=4-5/group). Bone marrow and cancellous bone were removed, cortical bone was segmented into the metaphyseal shell, proximal diaphysis and mid-diaphysis, and load-induced differential gene expression and enriched biological processes were examined for the three segments. At each time point, the mid-diaphysis (highest strain) had the greatest transcriptomic response. Similarly, biological processes regulating bone formation and turnover increased earlier and to the greatest extent at the mid-diaphysis. Higher strain induced greater levels of osteoblast and osteocyte genes, whereas expression was lower in osteoclasts. Among the top differentially-expressed genes at 24-hours post-loading, seventeen had known functions in bone biology, of which twelve were present only in osteoblasts, three exclusively in osteoclasts, and two were present in both cell types. Based on these results, we conclude that murine tibial loading induces spatially-unique transcriptomic responses correlating with strain magnitude in cortical bone.

overall_design: Comparative gene expression profiling of RNA-seq data for bone samples from loaded limbs and contralateral control limbs of 10wk old female C57Bl6 mice. At various time points following tibial loading, the cortical bone was segmented into 3 sections: metaphyseal cortical shell, proximal diaphysis and mid-diaphysis. Cancellous bone was removed prior to processing. Differential expression was assessed at each cortical location at 1-h, 3-h, and 24-h following a single loading session. To evaluate long term time points, mice received daily cyclic compressive loading for 7 consecutive days. To replicate standard loading protocols, a final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session

first: Jacob

last: Moore

first: Patrick

middle: F

last: Ross

first: Marjolein

last: van der Meulen


title: Potential Role of HTLV-1 Tax-Specific Cytotoxic T Lymphocytes expressing a Unique T-cell Receptor to Promote Inflammation of the Central Nervous System in Myelopathy Associated with HTLV-1

city: Tokyo

first: Yukie

last: Tanaka

address: 1-5-45 Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

summary: We performed immunoprofiling of HTLV-1 Tax301-309 (SFHSLHLLF) specific CD8+ T cells in PB of HAM patients associated with T cell activation by single cell RNA sequencing (scRNA-seq).

overall_design: Live HTLV-1 Tax301-309-specific CD8+ T cells in PB of three HAM patients (-1, -7, -8) were isolated by fluorescence-activated cell sorting (FACS). We performed scRNA-seq of 259 targeted gene expressions associated with T cell activation and TCR VDJ sequences of these cells using the BD Rhapsody Single-Cell Analysis System.

first: Tomoo

last: Sato

first: Naoko

last: Yagishita

first: Junji

last: Yamauchi

first: Natsumi

last: Araya

first: Satoko

last: Aratani

first: Katsunori

last: Takahashi

first: Yasuo

last: Kunitomo

first: Misako

last: Nagasaka

first: Yoshinobu

last: Kanda

first: Kaoru

last: Uchimaru

first: Tomohiro

last: Morio

first: Yoshihisa

last: Yamano


title: Evaluation of the impact of chromosomal inversions on replication origin usage in fission yeast

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

summary:
Eukaryotic DNA replication is regulated by conserved mechanisms that bring about a spatial and temporal organization in which distinct genomic domains are copied at characteristic times during S phase. Although this replication program has been closely linked with genome architecture, we still do not understand key aspects of how chromosomal context modulates the activity of replication origins. To address this question, we have exploited models that combine engineered genomic rearrangements with the unique replication programs of post-quiescence and pre-meiotic S phases. Our results demonstrate that large-scale inversions surprisingly do not affect cell proliferation and meiotic progression, despite inducing a restructuring of replication domains on each rearranged chromosome. Remarkably, these alterations in the organization of DNA replication are entirely due to changes in the positions of existing origins along the chromosome, as their efficiencies remain virtually unaffected genome wide. However, we identified striking alterations in origin firing proximal to the fusion points of each inversion, suggesting that the immediate chromosomal neighborhood of an origin is a crucial determinant of its activity. Interestingly, the impact of genome reorganization on replication initiation is highly comparable in the post-quiescent and pre-meiotic S phases, despite the differences in DNA metabolism in these two physiological states. Our findings therefore shed new light on how origin selection and the replication program are governed by chromosomal architecture.
Genes 2022, 13(7), 1244; https://doi.org/10.3390/genes13071244

overall_design: Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase. Two distinct chromosomal inversions were analyzed, each compared to an accompanying control (pre-arrangement) strain. Two biological repeats were performed and averaged for each experiment; dye-swaps  were performed and averaged for each biological repeat. Each chromosomal inversion and its control were analyzed for origin usage in post-quiescence and pre-meiotic S phase. A total of 16 experiments were performed, giving rise to 32 datasets.

first: Pei-Yun


title: Transcriptome sequencing analysis of satellite cells by RNA-seq

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: Regulation of chromatin accessibility is critical for cell fate decisions. Chromatin architecture responds to extrinsic environments rapidly. The traditional adult stem cell isolation approach requires tissue dissociation, and adult stem cells respond to the stimulation and adapt a different chromatin conformation. Here, we characterized the DNA regulatory landscape and transcriptomic profile of muscle stem cell quiescence exit and self-renewal by time-course profiling of the in situ fixed SCs upon injury-induced activation and during aging. Detailed analysis of the chromatin accessibility profiles leads to the identification of enhancer elements for SC quiescence. Constant activation of the enhancer elements promotes stemness and prevents SCs from differentiation, whereas loss of them causes cell-cycle arrest and essentially leads to defects in SC activation. Interestingly, we also showed that aged SCs display a more open chromatin environment than young SCs.  Our compre  hensive characterization of the chromatin accessibility and transcriptomic landscapes during SC quiescence exit and self-renewal broadens our understanding of this process and identifies functional distal regulatory elements for SC function.

overall_design:
To understand the transcriptomic changes of  satellite cells during quiescence exit and regeneration, we performed time-course RNA-seq of satellite cells injured for different time points from mouse hindlimb using PFA perfusion-based sorting scheme.
The polyA+ RNA from fix-sort satellite cells were sequenced using DNBSEQ-G400 sequencer (BGI)

first: Anqi

last: Dong

first: Wai-Kin

last: So

first: Wenshu

last: Zeng

first: Jing

last: Liu

middle: H


title: Histone modifications in activated and freshly isolated mouse muscle stem cells by ChIP-seq

overall_design:
We report the application of ChIPmentation on examination of H3K27ac histone marks in freshly isolated satellite cells (FISC) and activated satellite cells isolated after 2.5 days post-injury (ASC). We observed increase of H3K27ac marks around transcription start sites (TSS) and distinct peak patterns in distal intergenic regions during satellite cell activation.
Examination of H3K27ac marks in FISC and ASC.

first: Shenyuan

last: Hu


title: Gene expression in glioblastoma cell with sh-lncEPAT

city: Richmond

first: LINLIN

last: LI

state: Virginia

address: 401 college street

institute: Massey Cancer Center, VCU Health

summary:
Depleting lncEPAT in GBM cells leads to altered gene expression profile
lncRNAs are aberrantly expressed in different cancers; recent discoveries showed that lncRNAs participate in cancer signaling pathways via interacting with proteins, nucleotides, and lipids. Our goal is to characterize the role of an oncogenic lncRNA (lncEPAT) that mediates the integration of the dysregulated EGFR pathway with H2A deubiquitination in glioblastoma tumorigenesis.

overall_design: GSC23 cells were transduced with sh-Control and sh-lncEPAT lentivirus and selected with puromycin. The RNAs of tumor cells were obtained and Affymetrix microarrays was performed to explore consequent gene expression pattern change.

first: Suyun

last: Huang

first: Aidong

last: Zhou

first: Linlin

last: Li


title: Transcriptomic and topological analyses of human lung tumors identify cancer-associated fibroblast subsets associated with T cell exclusion

city: New York

first: John

last: Grout

address: 50 east 98th, apt. 11a4

institute: Mount Sinai School of Medicine

summary: We report on the application of focused stromal cell single cell sequencing on paired adjacent and NSCLC tissue from 15 patients.

overall_design:
Stromal cells were sorted from single cell suspensions of NSCLC and adjacent lung tissue samples then sequenced using the 10X genomics platform. 15 tumor and 12 adjacent tissue samples were analyzed.
The adjacent lung and tumor tissue were weighed and cut into sections of 0.1-0.2 grams then placed into 5 mL microtube (Argos Technologies). Sections were minced with scissors and enzymatically digested in CO2-independent media (Fisher Scientific, 18045088) with Collagenase IV 0.25mg/ml (Sigma-Aldrich, C5138-1G), Collagenase D 200 U/ml (Sigma-Aldrich, 11088882001), and DNAse 0.1 mg/ml (Sigma-Aldrich, DN25-1G) for 40 minutes at 37°C under 80 rpm agitation. Cell suspensions were passed through a syringe with an 18-gauge needle 8-10 times, filtered through a 70µm cell strainer, then lysed in red blood cell (RBC) buffer (Fisher Scientific, NC9067514). The cells were resuspended in buffer comprising of DPBS (Corning, D8537-6X500ML) with 5% BSA (Equitech-Bio, BAH62-0500) and 1mM EDTA (Sigma-Aldrich, 46-034-CI) then counted using hemocytometer and Trypan blue (Fisher Scientific, MT25900CI).
Raw FASTQ files and processed feature-barcode matrices, containing UMI counts in Market Exchange Format.

middle: A

first: Philemon

last: Sirven

first: Andrew

middle: M

last: Leader

first: Shrisha

last: Maskey

first: Eglantine

last: Hector

first: Isabelle

last: Puisieux

first: Evan

last: Cheng

first: Navpreet

last: Tung

first: Mathieu

last: Maurin

first: Romain

last: Vaineau

first: Léa

last: Karpf

first: Martin

last: Plaud

first: Maria

last: Casanova-Acebes

first: Alexandra

last: Tabachnikova

first: Shilpa

last: Keerthivasan

first: Jessica

last: LeBérichel

first: Laura

last: Walker

first: Adeeb

last: Rahman

first: Sacha

last: Gnjatic

first: Julien

last: Adam

first: Jerome

middle: C

last: Martin

first: Andrea

last: Wolf

first: Raja

last: Flores

first: Mary

middle: B

last: Beasley

first: Rachana

last: Pradhan

first: Sören

last: Müller

first: Thomas

middle: U

last: Marron

first: Shannon

last: Turley

first: Miriam

last: Merad

first: Ephraim

last: Kenigsberg

first: Helene

last: Salmon


title: Chromatin structure profiling of mouse muscle stem cells by ATAC-seq

first: Tom

last: Cheung

overall_design:
By comparing ATAC-seq from satellite cells (SCs) activated for different time points, we showed the trajectory of chromatin accessibility changes during SCs quiescence exit, activation and regeneration. Our data showed that QSCs have a relatively closed chromatin environment. Upon activation, scs have a dramatic increase in chromatin accessibility and re-establish the closed chromatin environment during regeneration.
Examination of chromatin accessibility using ATAC-seq in quiescent SCs, activated and regenerating SCs across different injury time course.

first: Anqi

last: Dong

first: Wai-Kin

last: So

first: Jing

last: Liu


title: IL-4-induced quiescence of resting naïve B cells is disrupted in systemic lupus erythematosus

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: Activated naïve (aNAV) B cells have been shown to be the precursor of the CD11c+T-bet+ IgD−CD27− double negative (DN)2 or atypical memory (aMEM) B cells in systemic lupus erythematosus (SLE).  To determine factors that maintain resting naïve (rNAV) B cells, the transcriptomics program in naïve (IGHD+IGHM+) B cells in human healthy controls (HC) and SLE was analyzed by single cell RNA-sequencing analysis. In HC, naive B cells expressed IL-4 pathway genes whereas in SLE, naive B cells expressed type I interferon stimulated genes (ISGs).  In HC, aNAV B cells exhibited upregulation of gene signature of germinal center (GC) and classical memory (cMEM) B cells.  In contrast, in SLE, aNAV B cells expressed signature genes of aMEM.  In vitro exposure of SLE B cells to IL-4 promoted B cell development into CD27+CD38+ plasmablasts/plasma and IgD−CD27+ cMEM B cells. The same treatment blocked the development of CD11c+Tbet+ aNAV and DN2 B cells and preserved DN B cells as CD11c−Tbet− DN1 B cells.  Lower expression of IL-4R and increased intracellular IFN-β in naïve B cells was correlated with the accumulation of CD21−IgD− B cells and the development of anti-Smith and anti-DNA autoantibodies in SLE patients (n=47).  Our results show that IL-4R and type I IFN signaling in naïve B cells induce the development of distinct lineages of cMEM versus aMEM B cells, respectively.  Further, a diminished IL-4R signaling shifted activated B-cell development from the DN1 to the DN2 trajectory in SLE patients.   Therapies that enhance IL-4R signaling may be beneficial for ISGhi SLE.

overall_design: We carried out single cell RNAseq and single-cell V(D)J seq for three autoantibody-positive (autoAb+) SLE subjects (SLEs) and Three healthy controls (HCs)

first: Shanrun

first: John

middle: D

last: Mountz

first: Hui-Chen

last: Hsu


title: Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways

status: Public on Aug 11 2022

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: To investigate the role of PRPF39 in the regulation of alternative splicing, we performed RNAseq and splicing analysis on PRPF39 knockdown and control HEK293 cells

overall_design: Comparative gene expression and alternative splicing analysis on cells treated with PRPF39 shRNA and control, scrambled shRNA

first: Rui

last: Zhao


title: Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways [Dataset 2]

summary:
Leptin plays a critical role in the regulation of metabolic homeostasis. However, the molecular mechanism and cross talks between leptin and metabolic pathways leading to metabolic homeostasis across different species is not clear. This study aims to explore the effects of leptin in mice and zebrafish larvae by integration of metabolomics and transcriptomics.
We performed gene expression profiling analysis using data obtained from RNA-seq. . Deep sequencing showed that many genes involved in proteolysis and arachidonic acid metabolism were dysregulated in ob/ob mice heads and lepb mutant zebrafish larvae compared to their wild type counterparts, respectively.

overall_design: Male ob/ob mice and lean C57BL/6 wild type mice were obtained from Charles River Laboratories at 6 weeks of age (n=8 per group) and maintained for 8 weeks under specific pathogen-free conditions in the animal facility of the Leiden University Medical Center (LUMC). Heads were used to exctract RNA for RNAseq.

middle: P

first: Yi

last: Ding


title: Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways [Dataset 1]

summary:
Leptin plays a critical role in the regulation of metabolic homeostasis. However, the molecular mechanism and cross talks between leptin and metabolic pathways leading to metabolic homeostasis across different species is not clear. This study aims to explore the effects of leptin in mice and zebrafish larvae by integration of metabolomics and transcriptomics.
We performed gene expression profiling analysis using data obtained from RNA-seq. Deep sequencing showed that many genes involved in proteolysis and arachidonic acid metabolism were dysregulated in ob/ob mice heads and lepb mutant zebrafish larvae compared to their wild type counterparts, respectively.

overall_design: Zebrafish larvae at 5 dpf from lepb-/- and lepb+/+ groups were collected for RNAseq


title: Effect of Arid5b overexpression on the B cell development

city: Memphis

first: Xujie

state: TN

address: 246 Danny Thomas Place, MS 313

institute: St. Jude Children's Research Hospital

summary: To investigate the role of Arid5b in B cell development, we established a mouse model with overexpression of Arid5b driven by Vav1

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of B220+ B cells from Arid5b overexpression vs wildtype mice.

first: Charnise

last: Harris-Goodings

first: Jun

last: Yang


title: CARM1-mediated methylation of ASXL2 impairs tumor suppressor gene activation by MLL3/COMPASS

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: An imbalance in the activities of the Polycomb and Trithorax complexes underlies numerous human pathologies, including cancer. The BAP1 deubiquitinase (DUB) complex negatively regulates Polycomb activity and also recruits the Trithorax histone H3K4 methyltransferase, MLL3/COMPASS, to the enhancers of tumor suppressor genes. We and others have demonstrated that the BAP1-MLL3 pathway is mutated in several differ cancers. Yet, how BAP1 recruits MLL3 to these loci remains a fundamentally important unanswered question.  Here we demonstrate that ASXL2 directly mediates the interaction between the BAP1 complex and MLL3/COMPASS. ASXL2 loss abolishes the MLL3-BAP1 interaction, leading to decreased MLL3 occupancy at enhancers and reduced expression of BAP1-MLL3 target genes.  The interaction between ASXL2 and MLL3 is negatively regulated by protein arginine methyltransferase 4 (PRMT4, also known as CARM1), which methylates ASXL2 on R639/R641. Methylation of ASXL2 by CARM1 blocks binding to MLL3 binding and impairs the expression of MLL3 dependent genes. This finding uncovers a novel transcription repression function for CARM1 and provides a unique insight into the BAP1/ASXL2/MLL3 axis, which is controlled by arginine methylation and could serve as a target for potential cancer therapeutics.

overall_design: We evaluted how ASXL2 mediates the interaction between BAP1 and MLL3/COMPASS, and how methylation of ASXL2 by CARM1 blocks binding to MLL3 binding and impairs the expression of MLL3 dependent genes.

first: Lu

last: Wang

first: Zibo


title: A Quantitative Epistasis Framework For Interrogating the Network of Enhancers

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

summary: The mammalian genome possesses a network of non-coding regulatory elements with key genes regulated by many enhancers. It remains unknown why these genes require multiple enhancers for regulation and what is the functional role of each enhancer contributing to a coordinated enhancer network. Here we develop a novel framework, named SEER (Systematic Enhancer Epistasis Regulatory network analysis), which leverages a suite of perturbative, mapping, and imaging approaches, combined with machine learning and Genome-Wide Association Study (GWAS) analysis to systematically and quantitatively anatomize the enhancer epistasis network. Applying the framework to the MYC locus, we revealed a hierarchical two-layer epistasis model and defined a class of synergistic regulatory elements (SREs) which can maintain both high expression and robustness upon perturbation. Via machine learning, we identified and validated that two features, spatial contacts and BRD4 coactivator condensation, are major factors in maintaining the synergistic interactions of SREs. We used SEER to predict the synergistic functions of non-coding variants in SREs for their clinical risks in cancer and autoimmune disorders. The SEER framework provides a novel approach and theory for delineating roles of the massive enhancer network in gene regulation and interpreting non-coding variants for clinical risks in complex diseases.

overall_design:
To explore the ultralong-distance enhancer network, we examined the regulatory landscape of MYC, a key oncogene governing cellular proliferation and cancer pathogenesis. The MYC locus encompasses 7 enhancers (e1-e7) spanning a 1.8 Mb region. We conducted a multiplexed CRISPR interference (CRISPRi) screen using a pooled library consisting of 87,025 pairs of single guide RNAs (sgRNAs) targeting all single and pairwise combinations of 7 enhancers . We then transduced the pooled sgRNA library into K562 erythroleukemia cells stably expressing the nuclease-dead dCas9-KRAB fusion and cultured cells for 30 doublings (more than 1 month).

Trac-looping experiment was used to exam the changes of enhancer-enhancer spatial contacts upon CRISPR individual and pairwise perturbation.

H3K9me3 ChIP-seq experiment was used to exam the KRAB effect on chromatin status upon CRISPR individual and pairwise perturbation

ATAC-seq experiment was used to exam the KRAB effect on chromatin status upon CRISPR individual and pairwise perturbation

H3K27ac ChIP-seq experiment was used to exam the KRAB effect on chromatin status upon CRISPR individual and pairwise perturbation

first: Liu

last: Yanxia

first: Lin

last: Xueqiu

first: Wu

last: Linlin

first: Qi

last: Lei


title: Stem cell factor (SCF) effect on mouse bone marrow derived dendritic cells (BMdDCs) under hypoxia

city: Rome

first: Francesca

last: Di Rosa

address: viale Regina Elena 291

country: Italy

institute: Italian National Research Council (CNR)

summary: BMdDCs were cultured under hypoxic conditions for 2 days and then for additional 6 hours either in the presence or absence of SCF at 100 ng/ml. Differentially expressed genes were evaluated by Affymetrix microarray (Affymetrix Mouse Gene 2.1 ST Array).

overall_design: Four identical experiments were performed (experiments were named as follows: BC; D2; E; I). Each time BMdDCs were generated under normoxia from mouse bone marrow cells by in vitro culture with GM-CSF for 7 days and subsequent CD11c+ cell-purification by CD11c-microbeads  (4 biological replicates of BMdDCs). Then highly purified CD11c+ (>98% pure) BMdDCs were cultured under hypoxia (2% O2, ~14 mmHg) in the following conditions: with GM-CSF at 20 ng/ml for 2 days, and finally either in the presence or absence of SCF at 100 ng/ml for further 6 hours (medium and SCF conditions, respectively).

first: Amairelys

last: Barroeta Seijas

first: Sonia

last: Simonetti

first: Irene

last: Filippi

first: Antonella

last: Naldini

first: Gabriele

last: Favaretto

first: Teresa

last: Colombo

first: Ambra

last: Natalini

first: Fabrizio

last: Antonangeli

first: Mattia

last: Laffranchi

first: Silvano

last: Sozzani

first: Angela

last: Santoni


title: Molecular mechanisms of ARID5B-mediated genetic susceptibility to acute lymphoblastic leukemia

first: Xujie

last: Zhao

summary: There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-ALL leukemogenesis remain largely unknown. In this study, by targeted sequencing in germline DNA of 5,008 children with ALL, we identified 31 common variants in ARID5B significantly associated with leukemia risk, all of which were non-coding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P=1.82×10-10) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The rs7090445 variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n=349,861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P=8.6×10-22 and 2.1×10-18, respectively). Taken together, our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.

overall_design: Characterize the molecular mechanisms by which non-coding variants contribute to genetic susceptibility to ALL.

first: Jun

last: Yang

first: Wenjian


title: Polyvinyl alcohol/gelatin hydrogels regulate cell adhesion and chromatin accessibility

city: Hefei

first: Ran

last: Zhang

address: No.96 Jinzhai road

institute: University of Science and Technology of China

summary: Cell adhesion is known to heavily influence cell migration and wound healing. A number of cell adhesion molecules and their roles has been extensively studied. However, the changes of global chromatin accessibility and gene expressions correlated with cell adhesion is still unclear. Here we prepared a series of PVA/Gelatin hydrogels to handily regulate cell adhesion by adjusting gelatin concentration and found that cell adhesion area and the ratio of non-circular cells were increased with the increasement of gelatin concentration while cell circularity was decreased. Our results showed that widespread chromatin accessibility was increased with increasing expression level of histone deacetylase 11 (Hdc11) under poor cell adhesion. Meanwhile, one branch of MAPK pathway -  ERK 1/2 which involved in mechanotransduction signaling was also found in the enrichment analysis of downregulated genes. This work provided a handy method to regulate cell adhesion and these findings deepen our understanding of the cell adhesion process and its associated chromatin accessibility.

overall_design: Inverstigation the  difference of chromatin accessbility and RNA expression in NIH3T3 cells under different adhesion condition

first: Duo

first: Haiyi

last: Liang


title: Structure, function and microbial ecology of diverse MarR bacterial regulators of auxin catabolism

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

summary: Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.

overall_design: We performed RNA-Seq on triplicate cultures of CL14 wild type, IAA degradation deficient strain CL14 ΔiadDE, and MarR mutants CL14 ΔMarR_73 and CL14 ΔMarR_50. Standardized gene expression of the IAA degradation locus in these strains with and without IAA supplementation


title: Comprehensive Analysis of Chromatin Accessibility Changes during Muscle Stem Cell Quiescence Exit and Self-renewal

first: Tom

last: Cheung

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

overall_design: Refer to individual Series


title: Rho stimulates both Rho-dependent and intrinsic termination in Bacillus subtilis

city: State College

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

institute: Pennsylvania State University

summary: In this work we conducted Term-seq on Wild Type B. subtilis, and strains compromosing all logical mutations in all combinations of the genes that encode for NusA, NusG, and Rho, where we developed the first transcription termination atlas. We used this atlas to find that Rho can stimulate intrinsic termination in B. subtilis and we recapitulated this finding in vitro to dissect the mechanism.

overall_design: Term-seq on Wild Type B. subtilis, and strains compromosing all logical mutations in all combinations of the genes that encode for NusA, NusG, and Rho, as well as a KOW domain deletion strain of NusG +/- a rho deletion allele, followed by in vitro follow-up

first: Zachary

last: Mandell

first: Rishi

middle: K

last: Vishwakarma

first: Helen

last: Yakhnin

first: Katsuhiko

last: Murakami

first: Mikhail

last: Kashlev


title: Efficacious anti-CTLA-4 antibodies drive myeloid activation and TME reprograming through FcγR engagement and Type-I interferon signaling

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Despite the clinical success of checkpoints inhibitors, a significant gap still exists in our understanding of their in vivo mechanism of action, thus limiting the rational development of next generation agents. Amongst these, anti-CTLA-4 antibodies were originally developed to block inhibitory signals into activated effector T cells. However, several recent studies have demonstrated that depletion of regulatory T cells expressing high levels of CTLA-4 is critical to anti-CTLA-4 anti-tumor activity. Whereas the mechanism of action remains controversial, the emerging data support clinical development of new antibodies with enhanced killing activity. Here, using single-cell RNA sequencing in in vivo and in vitro mouse models, we sought to dissect the impact of anti-CTLA-4 blocking, Treg depleting, and FcR engaging activity on the immune responses within tumors. We observed a rapid remodeling of the innate immune landscape as early as 24-hours post-treatment. Immune remodeling was driven mainly by FcγR-engagement, and not by Treg depletion or CTLA-4 blockade, and included reduction of suppressive macrophages and activation of type-I interferon signaling. Our findings indicate that FcγR engagement and innate immune remodeling are involved in successful anti-CTLA-4 treatment, supporting further development of optimized immunotherapy agents with these features.

overall_design: Dissecting the effect of blocking vs depleting anti-CTLA4 mAb on tumor immune microenvironment using single-cell RNA sequencing. Mice were inoculated with MCA-205 cells and treated with either Anti-CTLA-4 mIgG1 or Anti-CTLA-4 mIgG2a or untreated. Immune cells were harvested from tumors in 2 different time-points and underwent scRNAseq. We also utilized FOXP3-DTR, IFNAR KO and FCGR KO mice in different settings. Ex vivo incubation of iTregs with bone-marrow derived myeloid cells was performed.

last: Yofe

first: Tomer

last: Landsberger

first: Adam

last: Yalin

first: Isabelle

last: Solomon

first: Cristobal

last: Costoya

first: Dafne

last: Franz-Demane

first: Eyal

last: David

first: Chamutal

last: Borenstein

first: Ignacio

last: Garcia

first: Karl

last: Peggs

first: Sergio

last: Quezada


title: Sex differences in statin response in hypercholesterolemic (Apoe knockout) Four Core Genotypes mice.

city: Los Angeles

first: Karen

last: Reue

state: CA

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: RNA-sequening of livers from Apoe knockout Four Core Genotypes mice (XX ovaries, XX testes, XY ovaries, XY testes) fed either chow diet or chow diet + simvastatin (0.1g/kg) for 8 weeks.

overall_design: Apoe knockout Four Core Genotypes mice were fed either chow diet (Research Diets D1001) or chow diet + simvastatin (0.1g/kg) for 8 weeks. RNA was isolated from liver tissue and prepared for total RNA sequencing.

first: Carrie

last: Wiese


title: Drosophila E93 promotes adult development and suppresses larval responses to ecdysone during metamorphosis

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

summary: Pulses of the steroid hormone ecdysone act through transcriptional cascades to direct the major developmental transitions during the Drosophila life cycle. These include the prepupal ecdysone pulse, which occurs 10 hours after pupariation and triggers the onset of adult morphogenesis and larval tissue destruction. E93 encodes a transcription factor that is specifically induced by the prepupal pulse of ecdysone, supporting a model proposed by earlier work that it specifies the onset of adult development. Although a number of studies have addressed these functions for E93, little is known about its roles in the salivary gland where the E93 locus was originally identified. Here we show that E93 is required for development through late pupal stages, with mutants displaying defects in adult differentiation and no detectable effect on the destruction of salivary glands. RNA-seq analysis demonstrates that E93 regulates genes involved in development and morphogenesis in the salivary glands, but has little effect on cell death gene expression. We also show that E93 is required to direct the proper timing of ecdysone-regulated gene expression in salivary glands, and that it suppresses earlier transcriptional programs that occur during larval and prepupal stages. These studies support the model that the stage-specific induction of E93 in late prepupae provides a critical signal that defines the end of larval development and the onset of adult differentiation.

overall_design: Examination of the effects of an E93 null mutation on ecdysone regulated gene expression in late prepupal salivary glands

first: Geanette

last: Lam

first: Hyuck-Jin

last: Nam

first: Panagiotis

last: Velentzas

first: Eric

last: Baehrecke


title: Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [RNA-seq]

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

institute: Erasmus University Medical Center Rotterdam

summary: Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. Our studies describe fundamental principles of how the architectural proteins contribute to genome folding at multiple genomic scales and transcriptional regulation.

overall_design: Acute depletion of CTCF WAPL and RAD21 using AID-mediated protein depletion, followed by RNA-seq using Illumina TruSeq Stranded RNA LT Kit.

first: Ning

middle: Q

first: Tom

last: van Schaik

first: Elzo

last: de Wit

first: Bas

last: van Steensel


title: Mechanisms Underlying Asthma Exacerbations Prevented and Persistent with Immune Based Therapy: A Systems Approach Phase 2 (MUPPITS-2)

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

summary: A Trial of Mepolizumab Adjunctive Therapy for the Prevention of Asthma Exacerbations in Urban Children (MUPPITS-2). ClinicalTrials.gov Identifier: NCT03292588

overall_design: The MUPPITS-2 study was a randomized, double-blind, placebo-controlled, parallel group trial conducted at 9 study sites in the U.S. between November 2017 and April 2021. Eligible participants were randomized in a 1:1 ratio to receive blinded adjunctive therapy with either mepolizumab or matching placebo by subcutaneous injection every 4 weeks for 52 weeks.

first: Matthew

last: Altman

last: Jayavelu

first: Kim

last: Dill-McFarland

first: Daniel

last: Jackson


title: Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [ATAC-seq]

overall_design: Acute depletion of CTCF WAPL and RAD21 using AID-mediated protein depletion, followed by ATAC-seq as described (Liu et al., 2017).


title: ROLE OF ENDOPLASMIC RETICULUM STRESS IN  IMPAIRED NEONATAL LUNG GROWTH AND BRONCHOPULMONARY DYSPLASIA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Myeloperoxidase (MPO), oxidative stress (OS), and endoplasmic reticulum (ER) stress are all increased in the lungs of neonatal rat pups raised in hyperoxia (HOX, >90% O2), an established model of bronchopulmonary dysplasia (BPD). However, the relationship between OS, MPO, and ER stress has not been examined in HOX rat pups. To determine the relationship between OS, MPO, and ER stress in BPD we treated Sprague-Dawley neonatal rat pups with Tunicamycin (Tun) or with HOX. Tun directly induces ER stress and simplifies neonatal lung alveolarization. Previously, we showed that HOX induces a cycle of destruction that we hypothesize through increased OS, MPO, and ER stress to induce BPD. To inhibit ER stress specifically, we used tauroursodeoxycholic acid (TUDCA), a molecular chaperone. To break the cycle of destruction and reduce OS and MPO we used N-acetyl-lysyltyrosylcysteine-amide (KYC), a systems pharmacology agent. Lung structure was studied morphometrically. ER stress was detected using immunofluorescence (IF), transcriptomic, proteomic, and electron microscopic analyses. Increased ER stress was observed in the lungs of HOX rat pups and also in human BPD lungs by IF. Morphometric and proteomic studies of rat lungs showed that Tun treatment decreased lung complexity and increased ER stress and BPD severity. The fact that TUDCA improved lung complexity in Tun-treated neonatal rat pups, and decreased BPD induced by HOX provides strong support for the idea that ER stress plays a causal role in BPD. Additional support comes from data showing TUDCA decreased lung myeloid cells and MPO levels in the lungs of both Tun- and HOX-treated neonatal rat pups. These data link OS and MPO to ER stress in the mechanisms mediating BPD. KYC's effective inhibition of ER stress in the lungs of Tun-treated rat pups provides additional support for the idea that MPO-induced ER stress plays a direct causal role in BPD. Thus, ER stress appears to expand our proposed cycle of destruction. Our results suggest ER stress evolves from OS and MPO to increase neonatal lung injury and impaired neonatal lung growth and development. The encouraging effect of TUDCA indicates chemical chaperone has the potential in treating BPD.
Using multiomic data to investigate the role of endoplasmic reticulum stress in the development of BPD in rat model.

overall_design: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. Two or four pregnant rats were used for each experiment, according to the study design. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity.

first: Kirkwood

last: Pritchard  Jr

first: Xigang

last: Jing

first: Michelle

last: Teng

first: Clive

last: Wells

first: Shuang

last: Jia

first: Jason

last: Jarzembowski

first: Billy

middle: W

last: Day

first: Stephen

last: Naylor

first: Marty

first: G

middle: G

last: Konduri

first: Ru-Jeng


title: Expression data from DP cells in the thymus of SRSF1-null and wild type mice

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: iNKT cells are highly conserved innate-like T lymphocytes that develop from CD4+CD8+ DP cells. It remains largely unknown whether post-transcriptional regulation has critical roles in iNKT cells. Here we show conditional deactivation of SRSF1 in DP thymocytes impaired iNKT cell development and survival in a cell-intrinsic manner.

overall_design: WT and SRSF1-null CD4+CD8+ DP cells (2 samples per group) were sorted. Then the total RNAs were extracted and subjected to RNA sequencing.

first: S


title: Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes

first: Yueqi

last: Wang

state: Utah

address: 20 South 2030 East


title: Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes [scRNA-seq]

summary: Human telencephalon is an evolutionary advanced brain structure associated with many uniquely human behaviors and disorders. However, cell lineages and molecular pathways implicated in human telencephalic development remains largely unknown. We generated human telencephalic organoids from stem cell-derived single neural rosettes (SNRs) and investigated telencephalic development under normal and pathological conditions. SNR-derived organoids contained pallial and subpallial neural progenitors (NPs), excitatory and inhibitory neurons, as well as macroglial and periendothelial cells, and demonstrated predictable organization and cytoarchitecture. We comprehensively characterized the properties of neurons in SNR-derived organoids and identified transcriptional programs associated with the specification of+B50:B51 excitatory and inhibitory lineages from a common pool of NPs early in telencephalic development. We also demonstrated that neurons in organoids with a hemizygous deletion of an autism- and intellectual disability associated gene SHANK3 exhibit intrinsic and excitatory synaptic deficits associated with impaired expression of clustered protocadherins. Collectively, this study  validates SNR-derived organoids as a reliable new model for studying human telencephalic development and identifies novel molecular pathways disrupted by SHANK3 hemizygosity in human telencephalic tissue.

overall_design: Gene expression profiling of 1-month-old and 5-month-old cortical organoids using the 10X Genomics Chromium single-cell platform.

first: Simone

last: Chiola

first: Guang

last: Yang

first: Chad

last: Russell

first: Celeste

last: Armstrong

first: Yuanyuan

last: Wu

first: Jay

last: Spampanato

first: Paisley

last: Tarboton

first: H

last: Arif Ullah

first: Nicolas

last: Edgar

first: Amelia

middle: N

last: Chang

first: David

last: Harmin

first: Vittoria

last: Dickinson Bocchi

first: Elena

last: Vezzoli

first: Dario

last: Besusso

first: Jun

last: Cui

last: Cattaneo

first: Jan

last: Kubanek

first: Alex

last: Shcheglovitov


title: Human pluripotent stem cell-derived macrophages host Mycobacterium abscessus infection

status: Public on Aug 10 2022

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

summary: Human macrophages are a natural host of many mycobacterium species, including Mycobacterium abscessus (M. abscessus), an emerging pathogen affecting patients with lung diseases and immunocompromised individuals. There are few available treatments and the search for effective antibiotics against M. abscessus has been hindered by the lack of a tractable in vitro intracellular model of infection. Here, we established a reliable model for M. abscessus infection using human pluripotent stem cell-derived macrophages (hPSC-macrophages). hPSC differentiation permitted a reproducible generation of functional human macrophages that were highly susceptible to M. abscessus infection. Electron microscopy demonstrated that M. abscessus was present in the vacuoles of hPSC-macrophages. RNA-sequencing analysis revealed a time dependent host cell response to M. abscessus, with differing gene and protein expression patterns observed at 3-hours, 24-hours and 48-hours post-infection. Culture of engineered tdTOMATO-expressing hPSC-macrophages with GFP-expressing M. abscessus enabled rapid and image-based high-throughput analysis of intracellular infection and quantitative assessment of antibiotic resistance and efficacy. Our study describes the first hPSC-based model for M. abscessus infection, which represents a novel platform for studying M. abscessus-host interaction and an accessible tool for drug discovery.

overall_design: The hPSC line PB1 (PB001) (Vlahos et al., 2019) was differentiated into macrophages, which were inoculated with M. abscessus-GFP. RNA-sequencing were performed at 3 hours, 24 hours and 48 hours post-infection, with uninfected samples used as controls collected at 3 hours post-infection (3h_un).

first: S

last: Sun

first: M

first: E

last: Stanley

middle: T

last: Nim


title: Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [ChIP-seq]

first: Ning Qing

last: Liu

overall_design: Acute depletion of WAPL and CTCF/WAPL using AID-mediated protein depletion, followed by a calibrated ChIP-seq as described (Liu et al., 2021).

first: Ning

first: Tom

last: van Schaik

first: Elzo

last: de Wit

first: Bas

last: van Steensel


title: Complement factor B is critical for sub-RPE deposit accumulation in a model of Doyne honeycomb retinal dystrophy with features of age-related macular degeneration

city: Cambridge

first: Angela

middle: Mae

last: Banks

state: MA

address: 22 Windsor St.

department: Ophthalmology

institute: Novartis Institutes for Biomedical Research

summary:
To characterize female aged Efemp1 R345W knock-in (Efemp1ki/ki) mice, a model for Doyne honeycomb retinal dystrophy/malattia leventinese by bulk RNA sequencing
We performed differential expression and gene set enrichment analysis analysis using data obtained from RNA-seq of the neural retina and posterior eyecups (whole eye without lens and retina) from 3- to 17-month-old Efemp1+/+ and Efemp1ki/ki mice

overall_design: Gene expression profiling analysis of RNA-seq data of of the neural retina and posterior eyecups (whole eye without lens and retina) from 3- to 17-month-old Efemp1+/+ and Efemp1ki/ki mice

first: Sha-Mei

last: Liao


title: Differential gene expression analysis of RNAseq data comparing control and srGAP1 knockdown MDA-MB-231 primary tumors.

city: New York

first: Jose Javier

last: Bravo-Cordero

address: 1468 Madison Avenue

institute: Icahn School of Medicine

summary: To investigate the differential expression of genes in human tumor xenografts of control MDA-MB-231 primary tumors (Ctrl) and srGAP1 knockdown MDA-MB-231 primary tumors.

overall_design: We performed differential gene expression analysis using bulk RNAseq data obtained from 3 Ctrl MDA-MB-231 primary tumors (biological replicates) and 3 srGAP1 knockdown MDA-MB-231 primary tumors (biological replicates).

first: Jose

middle: J


title: MicroRNA-375 repression of Kruppel-like Factor 5 Improves Angiogenesis in Diabetic Critical Limb Ischemia

city: Boston

first: Mark

last: Feinberg

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's

summary: Screening of dysregulated microRNAs identified miR-375 as a potential biomarker and therapeutic target which may improve outcomes in diabetic critical limb ischemia.

overall_design: RNA-Seq analysis was performed on HUVECs treated with 50 nM of either non-specific or miR-375 mimics for 48 hours using standard library construction and Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).

last: McCoy

first: Anurag

last: Jamaiyar

first: Grasiele

last: Sausen

first: Henry

middle: S

last: Cheng

first: Daniel

last: Pérez-Cremades

first: Rulin

last: Zhuang

first: Jingshu

last: Chen

first: Philip

last: Goodney

last: Creager

first: Marc

last: Sabatine

last: Bonaca


title: Nociceptor neurons affect cancer immunosurveillance [RNA-seq 1]

city: montreal

first: sebastien

last: Talbot

state: quebec

address: 2900 Boulevard Edouard-Montpetit,

department: pharmacology

country: Canada

institute: university of Montreal

summary: Neuron, melanoma and CD8 co-cultures

overall_design: Naive splenocyte CD8+ T-cells were FACS-purified from RAMP1wt (CD45.1+) or RAMP1-/- (CD45.2+) mice, cultured and amplified. 8-week-old female RAG1-/- mice were transplanted (i.v., 2.5x106 cells) with either of RAMP1-/- or RAMP1wt CD8+ T-cells or 1:1 mix of 5x106 RAMP1-/- and RAMP1wt CD8+ T-cells. One week post transplantation, the mice were inoculated with B16F10-mCherry-OVA cells (5x105 cells; i.d.). On day 14, tumor and draining lymph node were harvested, and RAMP1-/- (CD45.2+) and RAMP1wt (CD45.1+) CD8+ T-cells were FACS-purified and RNA sequenced.

first: Sebastien


title: Differential expressed genes regulated by FXI in the heart and white adipose tissue

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the heart and white adipose tissue whose expression is regulated by F11 overexpression in the context of HFpEF.

overall_design: RNA-Seq of heart and white adipose tissue in C57BL/6J male mice injected with AAV8-GFP or AAV8-F11 and fed with HFD + l-NAME for 7 weeks.

first: Aldons

last: Lusis

first: Yang

last: Cao


title: Identification of Potential Models for Predicting Progestin Insensitivity in Patients with Endometrial Atypical Hyperplasia and Endometrial Cancer Based on Integration of ATAC-Seq and RNA-Seq Analysis [ATAC-seq]

city: Shanghai

first: Jiali

last: Hu

address: No.419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: To establish predictive models based on molecular profiles of endometrial lesions that might help to identify progestin insensitive endometrial atypical hyperplasia (EAH) or endometrioid endometrial cancer (EEC) patients before progestin-based fertility preserving treatment. Endometrial lesions from progestin sensitive or progestin insensitive patients were prospectively collected before progestin treatment and analyzed by ATAC-Seq and RNA-Seq. Potential chromatin accessibility and expression profile were compared between PS and PIS groups. Candidate genes were identified by bioinformatic analysis and literature review. Expanded samples (n = 35) were used for verification and model construction.

overall_design: Endometrial lesions from progestin sensitive (PS, n = 6) or progestin insensitive (PIS, n = 6) endometrial atypical hyperplasia (EAH) or endometrioid endometrial cancer (EEC) patients were prospectively collected before progestin treatment and analyzed by ATAC-Seq and RNA-Seq on BGIseq500 platform (BGI-Shenzhen, China). Potential chromatin accessibility and expression profile were compared between PS and PIS groups. Candidate genes were identified by bioinformatic analysis and literature review. Expanded samples (n = 35) were used for verification and model construction.

first: Gulinazi

last: Yierfulati

first: Qiaoying

last: Lv

first: Xiaojun


title: Identification of Potential Models for Predicting Progestin Insensitivity in Patients with Endometrial Atypical Hyperplasia and Endometrial Cancer Based on Integration of ATAC-Seq and RNA-Seq Analysis [RNA-seq]


title: Circular RNA Profiling in Peripheral Blood Mononuclear Cells from Retinopathy of Prematurity

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

summary: To reveal the altered expression profiles of circular RNAs (circRNAs) in the peripheral blood mononuclear cells (PBMCs) of patients with retinopathy of prematurity (ROP), microarray analysis was conducted in the samples from ROP patients and controls.

overall_design: Arraystar Human circRNA Arrays V2 was used to identify altered circRNAs in PBMCs from 5 ROP patients and 5 controls.

first: Yun

last: Li


title: Human pluripotent stem cell-derived macrophages host Mycobacterium abscessus infection

first: Michael

last: See

summary: Generation and analysis of human macrophages from induced pluripotent stem cells were infected by Mycobacterium abscessus to examine susceptibility and transcriptomic response

overall_design: RNA sequencing of human pluripotent stem cell derived macrophages infected with mycobacterium abscessus

first: Shicheng

last: Sun

first: Sohinee

last: Sarkar

first: Hieu

last: Nim

first: Eric

last: Hanssen

first: Elizabeth

last: Ng

first: Alejandro

last: Hidalgo

first: Mirana

last: Ramialison

last: Sutton

first: Andrew

last: Elefanty

first: Edouard

last: Stanley


title: Mutational analysis of Rap1 reveals specific vulnerability for long telomeres fusions

city: Mainz

first: Peter

last: Baumann

address: Ackermannweg 4

country: Germany

institute: Johannes Gutenberg University of Mainz

summary: The conserved Rap1 protein is part of the shelterin complex that plays critical roles in chromosome end protection and telomere length homeostasis. Previous studies addressed how fission yeast Rap1 contributes to telomere length maintenance, but the mechanism by which the protein inhibits end fusions has remained elusive. Here, we use a genetic screen in combination with high throughput sequencing to identify several amino acid positions in Rap1 that have a key role in end protection.  Interestingly, mutations at these sites render cells susceptible to genome instability in a conditional manner with longer telomeres being prone to undergoing end fusions, while short telomeres are sufficiently protected.  The protection of long telomeres requires their nuclear envelope attachment mediated by the Rap1-Bqt4 interaction. Our data demonstrates that longer telomeres pose an additional challenge for the maintenance of genome integrity and provides an explanation for a species-specific upper limit in telomere length.

sample_organism:
Escherichia coli
Schizosaccharomyces pombe

overall_design: One sample of the mutanesis library from E.coli and prior to transformation to S.pombe;  One sample from S.pombe after recovery from transformation; and 3 biological replicates of the time course for 5 rounds were included. The Rap1 fragment from each sample was amplified and amplicon libraries were generated for illumina sequencing. Changes of non-native nucleotides abundances at each nucelotide position were analyzed to select for amino acid positions that are important for end protection.

first: Lili

last: Pan

first: Duncan

last: Tormey

first: Nadine

last: Bobon


title: Identification of Potential Models for Predicting Progestin Insensitivity in Patients with Endometrial Atypical Hyperplasia and Endometrial Cancer Based on Integration of ATAC-Seq and RNA-Seq Analysis

first: Jiali

last: Hu

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

overall_design: Refer to individual Series


title: Bortezomib suppresses self-renewal and leukemogenesis of leukemia stem cell by NF-ĸB-dependent inhibition of cyclin dependent kinase 6 in MLL-rearranged myeloid leukemia

city: wenzou

first: zhou

last: bin

address: Xuefubei Street, Ouhai District, Wenzhou

institute: The First Afliated Hospital of Wenzhou Medical University

summary: Acute myeloid leukemia (AML) with chromosomal rearrangements involving the H3K4 methyltransferase mixed-lineage leukemia (MLL) is an aggressive subtype with low overall survival. MLL rearrangements rapidly transform hematological stem and progenitor cell (HSPC) to leukemia stem cell (LSC). Bortezomib (Velcade) is used widely in hematological malignancies. However, it is still unknown whether bortezomib possesses anti-self-renewal and anti-leukemogenesis of LSC in AML with MLL rearrangements. Here, we found that bortezomib inhibited cell proliferation, induced apoptosis, and decreased colony formation in leukemic cell lines, primary AML blasts, and MLL-AF9-transformed murine leukemic blasts. Besides, bortezomib reduced the frequency and function of LSC, inhibited the progression, and prolonged

overall_design: Examination of bortezomib-treated leukemia stem cells.

first: Bin

last: Zhou

first: Jinglai

last: Dong

first: Fang

last: Xiong

first: Xingzhou

last: Huang

first: Zhong

last: Chen

last: Liang

first: Jianchao

last: Ying

first: Haige

last: Ye

first: Shenmeng

last: Gao


title: IκBζ-deficient epidermis mediates systemic autoimmune inflammation via skin dysbiosis.

city: Sendai

first: Hitoshi

last: Terui

state: - - - International - - -

address: Seiryomachi 1-1, Aobaku

department: Dermatology

institute: Tohoku University School of Medicine

summary: Skin microbiota affect systemic inflammation through mechanisms that have not been completely elucidated. We previously demonstrated that keratinocyte-specific IκBζ-deficient mice spontaneously develop autoimmune inflammation resembling human Sjögren syndrome. In this study, we examined how IκBζ-deficient epidermis dictates systemic autoimmune inflammation onset. To examine if IκBζ-deficient keratinocytes are susceptible to apoptotic stimuli in a steady state, we performed microarray analysis of untreated murine back epidermis. Data indicate that IκBζ-deficient epidermis is susceptible to environment antigens through apoptosis-related gene upregulation

overall_design: Gene expression in epidermis obtained from Nfkbiz flox/flox mouse and Nfkbiz flox/flox; K5-cre mouse. In Nfkbiz flox/flox; K5-cre mouse, IκBζ is deficient in the epidermis under the control of keratin 5 promoter.

first: Kenshi

last: Yamasaki

first: Moyuka

last: Wada-Irimada

first: Mayuko

last: Onodera-Amagai

first: Naokazu

last: Hatchome

first: Masato

last: Mizuashi

first: Riu

last: Yamashita

first: Takeshi

last: Kawabe

first: Naoto

last: Ishii

first: Takaaki

last: Abe

first: Yoshihide

last: Asano

first: Setsuya

last: Aiba


title: mRNA-seq of Tgfbr2 KO CD8 T cells (d8/d15)

status: Public on Aug 09 2022

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: This experiment was performed to examine transcriptional differences between differentiated (Tim3+) and stem-like (CXCR5+) WT vs. Tgfbr2 KO antigen-specific CD8 cells.

overall_design: Naïve CD8 T cells were sorted from WT and dLck-Cre+ Tgfbr2 flox/flox (Tgfbr2 KO) P14 mice, and equal number (2k each) of naïve WT and Tgfbr2 KO P14 cells were co-transferred into naïve C57BL/6J mice followed by LCMV clone 13 infection with transient CD4 T cell depletion. At day 8 and day 15 post infection, PD-1+ Tim3+ CXCR5- differentiated subset and PD-1+ CXCR5+ Tim3- stem-like subset were sorted from WT and KO P14 cells harvested from the spleen for RNA-Seq.

first: W

middle: H

first: Y

last: Hu


title: mRNA-seq of Tgfbr2 KO CD8 T cells (d30)

summary: This experiment was performed to examine transcriptional differences between differentiated (Tim3+) and stem-like (CXCR5+) WT vs. Tgfbr2 KO antigen-specific CD8 cells at day 30 after LCMV clone 13 infection.

overall_design: Naïve CD8 T cells were sorted from Tgfbr2 flox/flox (WT) and dLck-Cre+ Tgfbr2 flox/flox (Tgfbr2 KO) P14 mice, and equal numbers (2000 each) of naïve WT and Tgfbr2 KO P14 cells were co-transferred into naïve C57BL/6J mice followed by LCMV clone 13 infection with transient CD4 T cell depletion. At day 30 post infection, PD-1+ Tim3+ CXCR5- differentiated subset and PD-1+ CXCR5+ Tim3- stem-like subset were sorted from WT and KO P14 cells harvested from the spleen for RNA-Seq.


title: mRNA-seq of WT and Tgfbr2 KO CD8 T cells transferred into chronically infected mice

summary: This experiment was performed to examine transcriptional differences between WT and Tgfbr2 KO antigen-specific CD8 cells activated in established chronic infection.

overall_design: Naïve CD8 T cells were sorted from Tgfbr2 flox/flox (WT) and dLck-Cre+ Tgfbr2 flox/flox (Tgfbr2 KO) P14 mice, and equal numbers (10,000 each) of naïve WT and Tgfbr2 KO P14 cells were co-transferred into C57BL/6J mice that had an established chronic LCMV clone 13 infection (day 45 post infection, with CD4 T cell depletion). At day 12 after transfer, WT and KO P14 cells were harvested from the spleen for RNA-Seq.


title: DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma

city: Chicago

first: Carole

last: Ober

address: 920 E 58TH ST

institute: The University of Chicago


title: PADI function in trophoblast stem cells

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

type: Methylation profiling by high throughput sequencing

summary: Investigating the impact of Padi2/3 deletion on trophoblast stem cells.

overall_design: Comparative gene expression profiling analysis by RNA-seq analsysis and DNA methylation profiling by meDIP-seq data for Padi2/3 DKO cells and WT trophoblast stem cells.

first: N

last: Ballasy

first: E

middle: A

last: Bering

first: C

last: Kokorudz

first: B

last: Radford

first: X

last: Zhao

last: Dean

first: M


title: Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase

city: Chongqing

first: Binbin

last: Jin

address: NO.2 Rd Tiansheng, Beibei District

department: Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education

institute: Southwest University

summary: tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however, its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells, and their aberration resulted in protein overloading and activated Perk. nfe2l2b, a paralog of mammalian Nfe2l2, which encodes Nrf2, is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2bΔ1/Δ1 mutants did not affect global larval development. However, aars1cq71/cq71;nfe2l2bΔ1/Δ1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop, an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis.

overall_design: Single cell analyses of zebrafish midbrain by 10X Genomics

first: Li

last: Li

first: Liqin

last: Xie

first: Dan

last: Zhan


title: SPT6 functions in transcriptional pause-release via PAF1C recruitment [PRO-seq]

first: Yuki

last: Aoi

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

institute: Northwestern University

summary: In vitro studies identified various factors including P-TEFb, SEC, SPT6, PAF1, DSIF, and NELF functioning at different stages of transcription elongation driven by RNA polymerase II (RNA Pol II). What remains unclear is how these factors cooperatively regulate pause/release and productive elongation in the context of living cells. Using an acute protein-depletion approach, we report that SPT6 depletion results in release of paused RNA Pol II. Short genes demonstrate a prominent release and a subsequent increase in mature transcripts, whereas long genes fail to yield mature transcripts due to a loss of processivity. Unexpectedly, the recruitment of PAF1 complex (PAF1C) to RNA Pol II fails upon SPT6 depletion, leading to the release of NELF-bound RNA Pol II into the gene bodies. Furthermore, SPT6 depletion impairs heat shock-induced pausing, pointing to a role for SPT6 in regulating RNA Pol II pause-release through PAF1C recruitment and NELF removal during the early elongation.

overall_design: Examination of SPT6 functions in human cells using acute and rapid depletion system and high-throughput sequencing (ChIP-seq, RNA-seq, PRO-seq).

first: Ali

last: Shilatifard


title: Nociceptor neurons affect cancer immunosurveillance [RNA-seq 3]

first: sebastien

last: Talbot

summary: Sequecing tumor-innervating neurons

overall_design: Naive DRG neurons (TRPV1cre::QuASR2-eGFPfl/wt) were cultured alone or in combination with B16F10-mCherry-OVA. After 48h, the cells were harvested, FACS-purified, and RNA sequenced. Hierarchical clustering of sorted neuron DEG, show distinct groups of transcripts enriched in TRPV1+ neuron vs cancer-exposed TRPV1+ neuron populations. Pairwise comparison of naive TRPV1+ neuron vs cancer-exposed TRPV1+ neuron populations showing differentially expressed transcripts as a volcano plot.

first: Sebastien


title: SPT6 functions in transcriptional pause-release via PAF1C recruitment [ChIP-seq]


title: Single cell RNA-seq of human ABCB5-positive limbal stem cells

first: Natasha

last: Frank

department: Medicine

institute: Brigham and Women's Hospital

summary: We performed single cell RNA-seq of human ABCB5-positive limbal stem cells (LSCs) to examine their homogeneity.

overall_design: ABCB5-positive LSC mRNA profiles of 3 human donor at single cell level.

first: Yuzuru

last: Sasamoto

first: Catherine

last: Lee

middle: Y


title: Targeted protein degradation reveals Pol II heterogeneity and functional diversity [RNA-Seq]

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: RNA polymerase II (Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that Pol II subunits contribute differently to Pol II cellular localization and transcription process and preferentially regulate RNA processing (such as RNA splicing and 3’ end maturation). Genes sensitive to the depletion of different Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of Pol II and different genes appear to depend on some of the subunits.

overall_design: We performed PRO-seq, ChAR-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours refer to individual Series. For PRO-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-Rx, the ZBTB11-GFP expressing cells were used as the spike-in cells.

first: Yuanjun

first: Jie

last: Huang


title: MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

address: 269 Campus Drive

institute: Stanford University


title: Developmental Dynamics of RNA Translation in the Human Brain

first: Erin

middle: Elizabeth

last: Duffy

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

summary: The precise regulation of gene expression is fundamental to neurodevelopment, plasticity, and cognitive function. While several studies have profiled transcription in the developing human brain, there is a gap in our understanding of accompanying translational regulation. We performed ribosome profiling on 73 human prenatal and adult cortex samples. We characterized the translational regulation of annotated open reading frames (ORFs) and identified thousands of previously unknown translation events, including small ORFs that give rise to human- and/or brain-specific microproteins, many of which we independently verified using proteomics. Ribosome profiling in stem cell-derived human neuronal cultures corroborated these findings and revealed that several neuronal activity-induced non-coding RNAs encode previously undescribed microproteins. Physicochemical analysis of brain microproteins identified a class of proteins that contain arginine-glycine-glycine (RGG) repeats and thus may be regulators of RNA metabolism.  This resource expands the known translational landscape of the human brain and illuminates previously unknown brain-specific protein products.

overall_design: Ribosome profiling of cultured human embryonic stem cell derived neurons

middle: E

first: Brian

last: Kalish

first: Michael

last: Greenberg


title: CRISPR-Cas9 directed modelling of estrogen receptor mutations identified in breast cancer

city: London

first: Simak

last: Ali

address: Du Cane Road

department: Department of Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary: Estrogen receptor (ER) is the major driver of a large proportion of breast cancers, and many therapies have been designed to target it. These include anti-estrogens, which target ER directly, and aromatase inhibitors, which instead prevent the biosynthesis of estrogen in post-menopausal women. These therapies have been largely successful, but unfortunately many patients eventually succumb to resistance. A hotspot of mutations in exon 8 of ESR1, which cause the ER to be constitutively active, have been discovered in advanced breast cancer patients, and are one cause of resistance to aromatase inhibitors as well as a reduced response to anti-estrogen therapies. Since most studies in to these mutations have so far focused on the mostly commonly seen mutations, Y537S and D538G, it is important to extend our understanding to other frequently found mutations to determine whether there are intrinsic differences between them. For this purpose, CRISPR-Cas9 was used in order to model the following mutations found in exon 8 of ESR1 in breast cancer patients, L536R, Y537C, Y537S, Y537N and D538G, in MCF7 cells, with between two to four clones of each mutation generated. Growth in the absence of estrogen and in the presence of various SERDs was tested to investigate differences in sensitivity between mutations. RNA-seq was carried out in the ESR1 mutant MCF7 lines under full medium conditions to look for gene expression changes compared to WT, shared between all mutations, or the possibility of differences between specific mutations, which were not due to the fact that the ESR1 mutant lines can grow in the absence of estrogen. The results of which should provide great insight into potential alternative genes or pathways, which could be targeted in patients harbouring these mutations.

overall_design: 16 samples were analysed (15 ESR1 mutant clones and the WT MCF7-Luc). 6 replicates were analysed for each sample, except for MCF7-Luc, which had 12 replicates to correct for batch processing of RNA extraction (6 replicates in each of the 2 batches)

first: Alison

last: Harrod


title: The bromodomain protein TRIM28 controls the balance between growth and invasiveness in melanoma

status: Public on Aug 08 2022

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

summary: Melanoma tumors are highly metastatic partly due to the ability of melanoma cells to transition between invasive and proliferative states, however, the mechanisms underlying this plasticity are still not fully understood. To identify new epigenetic regulators of melanoma plasticity, we combined data mining, tumor models, proximity proteomics, and CUT&RUN-sequencing. We focused on the druggable family of bromodomain epigenetic readers, and identified TRIM28 as a new regulator of melanoma plasticity. We found that TRIM28 promotes the expression of pro-invasive genes, and that TRIM28 controls the balance between invasiveness and growth of melanoma cells. We demonstrate that TRIM28 acts via the transcription factor JUNB, that directly regulates the expression of pro-invasive and pro-growth genes. Mechanistically, TRIM28 controls the expression of JUNB by negatively regulating its transcriptional elongation by RNA polymerase II. In conclusion, our results demonstrate that a TRIM28-JUNB axis controls the balance between invasiveness and growth in melanoma tumors and suggests that the bromodomain protein TRIM28 could be targeted to reduce tumor spread.

overall_design: A375 melanoma cells were transduced with pBABE empty vector, pBABE-FOSL1 or pBABE-JUNB followed by RNA-seq to determine gene expression levels. To determine the genome binding/occupancy profiles of TRIM28 and RNA polymerase II in A375 cells we used CUT&RUN.

first: William

last: Nyberg

first: Diego

last: Velasquez-Pulgarin

first: Tianlin

last: He

first: Maria

last: Sjöstrand

first: Lucia

last: Pellé

first: Ruxandra

last: Covacu


title: Transcriptomics of IL9 and IL13-treated human colonic epithelial organoids

first: Nick

last: Powell

department: Department of Metabolism, Digestion and Reproduction

summary: Mapping of transcriptional changes elicited by cytokines mediating Th2 and Th9 responses in human colonic organoids

overall_design: Colonic organoids were derived from crypts isolated from biopsies of three healthy individuals. The effects of treatment with IL9 or IL13 for 24 hours was evaluated in comparison with untreated organoids from the same donors.

first: Polychronis

last: Pavlidis

last: Tsakmaki

first: Domenico

last: Cozzetto

first: Gavin

last: Bewick


title: Transcriptomics of cytokine-treated human colonic epithelial organoids

summary: Mapping of transcriptional changes elicited by cytokines mediating canonical immune responses in human colonic organoids

overall_design: Colonic organoids were derived from crypts isolated from biopsies of four healthy individuals. They were then treated with TNF, IFNG, IL17A, IL22 and combination of IL17 and IL22 for 24 hours.

first: Anastasia


title: SPT6 functions in transcriptional pause-release via PAF1C recruitment [RNA-seq]

first: Yuki

last: Aoi

first: Ali

last: Shilatifard


title: The ZFP36 family of RNA-binding proteins regulates homeostatic and autoreactive T cell responses

city: St. Louis

first: Brian

middle: Todd

last: Edelson

state: MO

address: 660 S. Euclid Ave., Box 8118

institute: Washington University School of Medicine

overall_design: Refer to individual Series


title: Human PD-1 agonist treatment alleviates neutrophilic asthma by reprogramming T cells

status: Public on Aug 07 2022

city: Los Angeles

first: Georges Doumet

last: HELOU

state: California

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Neutrophilic asthma is associated with disease severity and corticosteroid insensitivity. Novel therapies are required to manage this life-threatening asthma phenotype. Programmed cell death protein-1 (PD-1) is a key homeostatic modulator of the immune response for T cell effector functions. Our study was conducted to assess the therapeutic potential of a novel human PD-1 agonist in a humanized mouse model in which the PD-1 extracellular domain is entirely humanized. Using single-cell RNA sequencing, we demonstrated that PD-1 agonist treatment alleviates lung inflammation via the reprogramming of pulmonary effector T cells.

overall_design: mRNA profiles of lung CD45+ cells from isotype- and PD-1 agonist treated humanized PD-1 mice were generated by deep sequencing. Three samples from each group were mixed using the cell hashing technique (⁓50,000 cells/group).

first: D

last: Helou

first: O

last: Akbari


title: TRPS1 drives heterochromatic origin refiring and cancer genome evolution [copy number]

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: The molecular etiology underlying TRPS1 loss-of-function in tricho-rhino-phalangeal syndrome (TRPS) remains to be understood. Intriguingly, TRPS1 is also bioinformatically postulated as a breast cancer driver. We report here that TRPS1 is prevalently amplified in breast cancer and promotes breast carcinogenesis. We showed that the tumorigenic potential of TRPS1 is derived from its nucleation of the replication machinery and its enforced replication of H3K9me3-marked heterochromatic regions. During early stage of genome duplication, TRPS1 encourages chromatin loading of the anaphase-promoting complex (APC/C) and subsequent degradation of Geminin, an inhibitor for the assembly of the pre-replication complex, leading to uncontrolled refiring of the heterochromatic replication origins. Overexpression of wild-type but not TRPS-associated loss-of-function mutants of TRPS1 is sufficient to drive genome amplification that mimics the genomic alterations in cancer, and TRPS1-evoked aberrant genome dynamically evolves to confer therapeutic resistance to a broad spectrum of treatment compounds. Together, these results link TRPS1 to heterochromatin replication, highlighting the sufficiency of a single oncogene to drive cancer genome evolution.

overall_design: We established TRPS1-overexpressed cell lines and extracted genomic DNA in control or TRPS1 overexpressed cells, and examined the copy number alterations in control and TRPS1 cells

first: Jianguo

last: Yang


title: Targeted protein degradation reveals Pol II heterogeneity and functional diversity [ChIP-Seq]

first: Xiong

last: Ji

first: Yuanjun

last: Li

first: Jie

last: Huang


title: SPT6 functions in transcriptional pause-release via PAF1C recruitment

state: IL

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


title: Gene expression profiles of control/normoxia and Sox17i∆EC/hypoxia in EC-specific RiboTag mouse

city: Seoul

first: Chan Soon

last: Park

state: Select

address: Department of Internal Medicine Seoul National University Hospital  101 Daehak-ro

country: South Korea

institute: Seoul National University Hospital

summary: To understand molecular changes underlying vascular pathology initiated by endothelial Sox17 deficiency, we performed endothelial-specific transcriptomic profiling using highly endothelial-enriched transcripts from the lung of control and Sox17i∆EC/hypoxic mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells of control mice and Sox17i∆EC/hypoxic mice

first: ChanSoon

first: SooHyun

last: Kim

first: JeeMyung

first: TaeWook

last: Noh

first: YoungSeok

last: Ju

first: Jun-Bean

first: Injune


title: The ZFP36 family of RNA-binding proteins regulates homeostatic and autoreactive T cell responses [RNA-Seq]

first: Brian

overall_design: Subseries 1 consists of Samples 1-32. These are spleen and kidney T cells directly analyzed from the indicated mice by RNA-seq.


title: DMS probing of and sequencing of the EBV infected BJAB-B1 transcriptome

status: Public on Aug 06 2022

city: Ames

first: Walter

middle: N.

last: Moss

state: IA

address: 2437 Pammel Dr

department: BBMB

institute: Iowa State University

summary: To gain in cellulo, experimentally derived RNA structural information within the BJAB-B1 transcriptome

overall_design: DMS probing (and DPBS mock probing control) of BJAB-B1 cells followed by sequencing and computational derivation of RNA per nucleotide structure reactivity values

first: Collin

last: O'Leary

first: Van

last: Tomplkins

first: Warren

middle: B

last: Rouse

first: Gijong

last: Nam


title: Identification and Characterization of a MAPT-targeting Locked Nucleic Acid Antisense Oligonucleotide Therapeutic for Tauopathies III

city: South San Francisco

first: Amy

last: Easton

state: CA

address: 1 DNA Way

department: Department of Neuroscience

institute: Genentech, Inc

summary: Tau is a microtubule-associated protein (MAPT, tau) implicated in the pathogenesis of Tauopathies, a spectrum of neurodegenerative disorders characterized by accumulation of hyperphosphorylated, aggregated tau.  Because tau pathology can be distinct across diseases, a pragmatic therapeutic approach may be to intervene at the level of the tau transcript, as it makes no assumptions to mechanisms of tau toxicity. Here we performed a large library screen of locked-nucleic acid-modified antisense oligonucleotides (LNA-ASOs), where careful tiling of the MAPT locus resulted in the identification of hot spots for activity in the 3’UTR.  Further modifications to the LNA design resulted in the generation of ASO-001933, which selectively and potently reduces tau in primary cultures from hTau mice, monkey, and human neurons.  ASO-001933 was well-tolerated and produced a robust, long lasting reduction in tau protein in both mouse and cynomolgus monkey brain. In monkey, tau protein reduction was maintained in brain for 20 weeks post-injection and corresponded with tau protein reduction in the CSF.  Our results demonstrate that LNA-ASOs exhibit excellent drug-like properties and sustained efficacy likely translating to infrequent, intrathecal dosing in patients. These data further support the development of LNA-ASOs against tau for the treatment of tauopathies.

overall_design: RNA-seq  for hiPSC-derived  neurons  (SA001; NIH Registration Number 0085; Cellectis, Sweden) differentiated for 42 days

first: Marianne

middle: L

last: Jensen

first: Congwei

last: Wang

first: Peter

last: Hagedorn

first: Yuwen

first: Michael

last: Weed

first: Jere

last: Meredith

first: Valerie

last: Guss

first: Kelli

last: Jones

first: Martin

last: Gill

first: Carol

last: Krause

first: Jeffrey

middle: M

last: Brown

first: Lisa

last: Hunihan

first: Alda

last: Fernandes

first: Yifeng

last: Lu

first: Joe

last: Polino

first: Mark

last: Bookbinder

first: Greg

last: Cadelina

first: Yulia

last: Benitex

first: Ramola

last: Sane

first: John

last: Morrison

first: Dieter

last: Drexler

first: Stephen

last: Mercer

first: Charlotte

last: Bon

first: Nikhil

last: Pandya

first: Ravi

last: Jagasia

first: Tai-Hsien

middle: O

first: Tania

last: Distler

first: Fiona

last: Grüninger

last: Meldgaard

first: Marco

last: Terrigno

last: Macor

first: Charles

middle: F

last: Albright

first: James

last: Loy

first: Anja

last: Hoeg

first: Richard

last: Olson

first: Angela

last: Cacace


title: The ZFP36 family of RNA-binding proteins regulates homeostatic and autoreactive T cell responses [mRNA-decaySeq]

first: Brian

last: Edelson

summary: These are CD44hi CD4 T splenic T cells from the indicated mice activated in vitro with anti-CD3/anti-CD28 for 24 hours.  Following activation, cells were treated with Actinomycin D for the indicated time course.

overall_design: mRNA-decay-seq; 24samples


title: Targeted protein degradation reveals Pol II heterogeneity and functional diversity [PRO-Seq]

first: Xiong

last: Ji

overall_design: We performed PRO-seq, ChAR-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours refer to individual Series. For PRO-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the ZBTB11-GFP expressing cells were used as the spike-in cells.

first: Yuanjun

last: Li

first: Jie

last: Huang


title: X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition

city: Toronto

last: Dowling

state: Ontario

address: 686 Bay Street

institute: Hospital for Sick Children

summary: X-linked myotubular myopathy (XLMTM) is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present, there are no directed therapies for XLMTM, and incomplete understanding of disease pathomechanisms. To address these knowledge gaps, we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits, including valproic acid, which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model, and showed that valproic acid ameliorates the murine phenotype.

overall_design: Zebrafish: At 1 dpf, embryos from single-pair in-crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO, sodium valproate (VPA), or trichostatin A. For tissue collection, the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6-10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 day old Mtm1KO and WT mice, either treated with PBS or valproic acid (VPA) starting at 21 days.

first: Jonathan

last: Volpatti

first: Mehdi

last: Ghahramani Seno

first: Melane

last: Mansat

first: Nesrin

last: Sabha

first: Ege

last: Sarikaya

first: Sarah

last: Goodman

first: Eric

last: Chater-Diehl

first: Alper

last: Celik

first: Emanuela

last: Pannia

first: Carine

last: Froment

first: Lucie

last: Combes-Soia

first: Nika

last: Maani

first: Kyoko

last: Yuki

first: Gaetan

last: Chicanne

first: Liis

last: Uusküla-Reimand

first: Simon

last: Monis

first: Sana

last: Alvi

first: Casie

last: Genetti

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