title: Cell landscape of Xenopus laevis at single-cell resolution

status: Public on Jun 22 2022

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

summary: Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for Xenopus laevis is still lacking. Here, we construct the Xenopus cell landscape with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of Xenopus laevis, and studying difference between vertebrates at single cell level.

overall_design:
Over 500,000 cells derived from adult Xenopus (one year old) dissociated tissues, including stomach (2 replicates), bladder (1 replicate), eye (1 replicate), intestine (2 replicates), kidney (2 replicates), lung (1 replicate), pancreas (1 replicate), spleen (1 replicate) and testis (2 replicates).
Over 300,000 cells derived from adult Xenopus (one year old) dissociated tissues, including bone marrow (1 replicate), bladder (1 replicate), brain (2 replicates), eye (1 replicate), heart (1 replicates), liver (1 replicates), lung (2 replicates), muscle (1 replicate), ovary (1 replicate), oviduct (1 replicate), pancreas (1 replicate), skin (1 replicate) and spleen (1 replicate). Over 190,000 cells derived from Xenopus whole-body single-cell dissociation and profiling at the larval stage (NF48, NF54, NF59 and NF66 for each replicate).

first: Xiaoping

last: Han

first: Guoji

last: Guo

first: Wanhua

last: Shen

first: Yuan

last: Liao

first: Lifeng

last: Ma

first: Ewei

last: Gao

first: Lei

last: Yang


title: Expression data from 2 month old mouse dorsal root ganglia(DRG) - various mutant conditions

city: Beijing

first: Zijing

last: Liu

address: Fengtai District, #20 East St.

country: China

institute: Beijing Institute of Biotechnology

summary:
Transcription factor Meis1 regulates DRG development. We study Meis1 function through assessing whole genome transcriptional profiling of mouse DRG.
We used microarrays to examine gene expression in control and Meis1 mutant DRGs.

overall_design: 2 month old contol and Meis1 mutant DRGs were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Chengcheng

last: Huang


title: Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease

status: Public on Jun 23 2022

city: Neuherberg

first: Sebastian

last: Schmidt

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München

type: Expression profiling by high throughput sequencing

summary: Parkinson’s disease (PD) as a progressive neurodegenerative disorder arises from multiple genetic and environmental factors. However, underlying pathological mechanisms remain poorly understood. Using multiplexed single-cell transcriptomics, we analyze human neural precursor cells (hNPCs) from sporadic PD (sPD) patients. Alterations in gene expression appear in pathways related to primary cilia (PC). Accordingly, in these hiPSC-derived hNPCs and neurons, we observe a shortening of PC. Additionally, we detect a shortening of PC in PINK1-deficient human cellular and mouse models of familial PD. Furthermore, in sPD models, the shortening of PC is accompanied by an increased SHH signal transduction. Inhibition of this pathway rescues the alterations in PC morphology and mitochondrial dysfunction. Thus, increased SHH activity due to ciliary dysfunction is needed for the development of pathoetiological phenotypes observed in sPD, like mitochondrial dysfunction. In sum, altered PC function is part of early PD pathoetiology and inhibiting the overactive SHH signaling is a potential neuroprotective therapy.

overall_design: Single-cell transcriptome analysis of human neural precursor cells derived from 6 healthy individuals, 7 late-onset sporadic PD patients and 1 cell line with a familial PD mutation.

first: Malte

middle: D

last: Luecken

first: Dietrich

last: Trümbach

first: Sina

last: Hembach

first: Kristina

middle: M

last: Niedermeier

first: Nicole

last: Wenck

first: Klaus

last: Pflügler

first: Constantin

last: Stautner

first: Anika

last: Böttcher

first: Heiko

last: Lickert

first: Ciro

last: Ramirez-Suastegui

first: Ruhel

last: Ahmad

first: Michael

middle: J

last: Ziller

first: Julia

middle: C

last: Fitzgerald

first: Viktoria

last: Ruf

first: Wilma

last: van de Berg

first: Allert

last: Jonker

first: Thomas

last: Gasser

first: Beate

last: Winner

first: Jürgen

last: Winkler

first: Daniela

last: Vogt Weisenhorn

first: Florian

last: Giesert

first: Fabian

last: Theis

first: Wolfgang

last: Wurst


title: RNA-seq in chondrocyte differentiation of human spinal ligament cells

status: Public on Jun 24 2022

city: HONGO, BUNKYO-KU

first: Taku

last: Saito

state: TOKYO

department: Orthopaedic Surgery, Faculty of Medicine

country: Japan

institute: The University of Tokyo

summary: Ectopic endochondral ossification in the tendon/ligament is caused by repetitive mechanical overload or inflammation. Tendon stem/progenitor cells (TSPCs) contribute to tissue repair and lubrication by producing proteoglycan 4 (Prg4). However, the mechanisms of ectopic ossification and association of TSPCs are not yet known. Here, we investigated the characteristics of Prg4-positive (+) cells and identified that R-spondin 2 (RSPO2), a WNT activator, is specifically expressed in a distinct Prg4+ TSPC cluster. The Rspo2+ cluster was characterized as mostly undifferentiated, and RSPO2 overexpression suppressed ectopic ossification in a mouse Achilles tendon puncture model via chondrogenic differentiation suppression. RSPO2 expression levels in patients with ossification of the posterior longitudinal ligament were lower than those in spondylosis patients, and RSPO2 protein suppressed chondrogenic differentiation of human ligament cells. RSPO2 was induced by inflammatory stimulation and mechanical loading via nuclear factor-kappa B (NF-κB). Rspo2+ cells may contribute to tendon/ligament homeostasis by suppressing chondrogenic differentiation.

overall_design: Samples of human spinal ligament cells induced with chondrogenic differentiation were compared to control samples.

first: Naohiro

last: Tachibana


title: A study on the radiosensitivity of radiation-induced lung injury at the acute phase based on single-cell transcriptomics

status: Public on Jun 21 2022

first: Gangqiao

last: Zhou

address: 27 Taiping Road, Haidian District, Beijing

institute: Beijing Institute of Radiation Medicine

summary: Radiation-induced lung injury (RILI) is the most common complication associated with chest tumors, such as lung and breast cancers, after radiotherapy; however, the pathogenic mechanisms are unclear.Here, a single-cell transcriptome map was established in a mouse model of acute RILI. In total, 18,500 single-cell transcripts were generated, and 10 major cell types were identified. The heterogeneity and radiosensitivity of each cell type or subtype in the lung tissues during the acute stage were revealed. It was found that immune cells had higher radiosensitivity than stromal cells. Immune cells were highly heterogeneous in terms of radiosensitivity, while some immune cells had the characteristics of radiation resistance. Two groups of radiation-induced Cd8+Mki67+ T cells and Cd4+Cxcr6+ helper T cells were identified. In summary, This study investigated the dynamic changes in the cellular microenvironment during acute lung injury.

overall_design: Four male C57BL/6N and C3H/HeN mice (two for each strain) were split into control and radiation groups, with one mouse in each group for each strain. For the radiation group, mice were exposed to a single dose of 20 gray (Gy) at a dose rate of 153.56 cGy/min on the thoraces to induce lung injury in vivo. The mice were sacrificed 1 day after irradiation, and the lungs were collected for experiments.

first: Luyu

last: Ma

first: Yumeng

last: Ye

first: Hao

last: Lu

first: Yuan

last: Xing

first: Zhen

last: Zhao

first: Cheng

last: Quan

first: Zhaoqian

last: Jia

first: Yiming

first: Yang

last: Li


title: Genome-wide identification of transcribed enhancer candidates during pattern triggered immunity in Arabidopsis

city: Wuhan

first: Ying

last: Zhang

address: Shizishan

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Proper transcriptional reprogramming is central for hosts to launch an effective defense response upon pathogen attack. Relatively short DNA sequences known as enhancers play a key role in gene regulation by increasing the amount of transcription from associated genes. Here, we investigate the Arabidopsis thaliana distal enhancers involved in early innate immunity. Using an integrated computational pipeline, a class of low abundant transcripts that are transcribed uni- or bidirectionally from putative distal enhancers are identified based on intergenic open chromatin. Most of them may be non-polyadenylated, which are in concert with the enhancer RNAs (eRNAs) found in mammalian cells. The production of eRNAs at distal enhancers is strongly correlated with open chromatin architecture, low DNA methylation, as well as the enrichment of RNA poly II and acetylated histone marks. Immune transcription factors are enriched in the PTI-induced enhancers, such as WRKYs and SARD1, and up-regulated enhancers significantly associated with early immune gene regulation. Moreover, a subset of core patterns induced-enhancers was defined which up-regulated by multiple patterns from diverse pathogens.

overall_design: Genome-wide dynamic correlation of transcribed enhancer activity to gene transcription.


title: Synaptotagmin 2 is ectopically overexpressed in a widely used CaMK2a-Cre mouse line [T29-1 dataset]

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

institute: Okinawa Institute of Science and Technology

summary: The Cre-loxP system is one of the most powerful and commonly used techniques in neurogenetics, as well as in broad biomedical studies. The CaMKIIa-Cre mouse line, one of the earliest established Cre driver lines, has resulted in over 800 papers to date. While Cre driver lines are well characterized for Cre expression patterns, many are not well characterized for phenotypes. Here, we show the results of differential expression analyses in the hippocampi of Cre+/- mice and wild-type littermates from the most widely used CaMKIIa-Cre line, Tg(Camk2a-cre)T29-1Stl (or T29-1). Results show differential expression of many genes including significant upregulation of St6gal2, a gene encoding beta-galactoside alpha-2,6-sialyltransferase 2, in the Cre+/- hippocampi. The physiological role of St6gal2 is not well studied, but it is implicated in schizophrenia and autism. These unexpected results may affect the interpretation of the results from studies using the T29-1 line and raise awareness of potential pitfalls in the use of Cre driver lines in general.

overall_design: HIppocampal RNA profiles of 9-week-old wild type (WT) and Tg(Camk2a-cre)T29-1Stl (T29-1) Cre+/- mice

first: Ken

last: Matsuura

first: Haytham

last: Mohamed

first: Tadashi

last: Yamamoto


title: Mesenchymal stem cells exert renoprotection via extracellular vesicle-mediated modulation of M2 macrophages and spleen-kidney network.

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: Adipose-derived mesenchymal stem cells (ASCs) have shown therapeutic potentials against refractory diseases. However, the detailed therapeutic mechanisms remain unclear. Here, we report the therapeutic actions of human ASCs in nephritis, focusing on cellular dynamics and multi-organ networks. Intravenously-administered ASCs accumulated in spleen but not kidneys. Nevertheless, ASCs increased M2 macrophages and Tregs in kidneys and drove strong renoprotection. Splenectomy abolished these therapeutic effects. ASC-derived extracellular vesicles (EVs) were transferred to M2 macrophages, which entered the bloodstream from spleen. EVs induced the transcriptomic signatures of hyperpolarization and PGE2 stimulation in M2 macrophages and ameliorated glomerulonephritis. ASCs, ASC-derived EVs, and EV-transferred M2 macrophages enhanced Treg induction. These findings suggest that EV transfer from spleen-accumulated ASCs to M2 macrophages and subsequent modulation of renal immune-environment underlie the renoprotective effects of ASCs. Our results provide new insights into the therapeutic actions of ASCs, focusing on EV-mediated modulation of macrophages and the spleen-kidney immune network.

overall_design: RNA sequencing (RNA-seq) to study the impacts of ASCs-derived EVs on M2 macrophages in a rat nephritis model.

middle: I

first: Yuko

last: Shimamura

first: Kazuhiro

last: Furuhashi

first: Shoichi

last: Maruyama


title: Effect of small molecule DMGV on gene expression, prolilferation and fuction of activated T cells

city: Guangzhou

first: Jongdae

last: Lee

state: Guangdong

address: No.195, Dongfengxi Road,

department: School of Basic Medicines

institute: Guangzhou Medical University

summary: Activated effector T cells (Teff) and/or compromised regulatory T cells (Treg) underlie chronic inflammatory diseases. We discovered a novel pathway to inhibit survival and expansion of Teff without compromising Treg survival and a potential therapeutic to treat these diseases. We found dimethylguanidino valeric acid (DMGV) is a rheostat for Teff: while cell-intrinsic DMGV generated by Alanine-Glyoxylate Aminotransferase 2 (AGXT2) is essential for survival and expansion by inducing mitochondrial ROS, an excessive (or exogenous) DMGV level inhibits effector T cell survival, thereby the AGXT2-DMGV-ROS axis functioning as a switch to turn on and off Teff expansion via regulation of glycolysis. DMGV-induced ROS is essential for glycolysis, and paradoxically DMGV induces ROS only in cells utilizing glycolysis as the major source of energy. Mechanistically, DMGV rapidly activates mitochondrial calcium uniporter (MCU), causing a surge in mitochondrial Ca2+ without provoking calcium influx to the cytosol. The mitochondrial Ca2+ surge in turn triggers the mitochondrial Na+/Ca2+ exchanger (NCLX) and the subsequent mitochondrial Na+ import induces ROS by uncoupling the Coenzyme Q cycle in Complex III of the electron transport chain. In preclinical trials, DMGV administration significantly diminished the number of inflammatory T cells, effectively suppressing chronic inflammation in mouse models of colitis and rheumatoid arthritis. DMGV also suppressed expansion of various cancer cells in vitro and in a mouse T cell leukemic model by the same mechanism. Our data provide a new pathway regulating cell survival and a novel mode to treat autoimmune diseases and cancers.

overall_design: To investigate DMGV's effect on T cell gene expression and phenotypes, mouse splenic CD3+ T cells were activated with or without DMGV for 24h and the gene expression profiles were analyzed by RNAseq.The RNAseq was performed on triplicates of anti-CD3/CD28 activated mouse splenic CD3+ T cells with or without DMGV added.


title: RNA-seq analysis on human T cells cultured in normoxia or hypoxia condiition

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: To interrogate the molecule changes induced by hypoxia in differentiated T cells, T cells from three donors cultured in normoxia and hypoxia conditions were subject to RNA-seq analysis

first: Shijun

last: Ma

last: Oguz

first: Adaikalavan

last: Ramasamy

first: Zhitong

last: Niu

first: Wenyu

last: Wang

first: Qiang

last: Yu


title: PHF20 Activates Autophagy Genes through Enhancer Activation via H3K36me2 Binding Activity

city: Seoul

first: Se Won

last: Park

state: Gwanak-Gu

address: Gwanak-ro 1, Gwanak-gu, Seoul, Seoul Nat'l Univ Bldg504 Rm607

country: South Korea

institute: Seoul national university

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

overall_design: Refer to individual Series


title: Gene-regulatory potential of 25-hydroxyvitamin D3 and D2

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: In this study, we compared the modulation of the transcriptome of human PBMCs by the vitamin D metabolites 25-hydroxyvitamin D3 (25(OH)D3), 25(OH)D2 and 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3).

overall_design: PBMCs of a healthy male donor were isolated within one hour after peripheral blood collection and treated for 4, 8 or 24 h either with 1,25(OH)2D3 (0.1, 1 and 10 nM), 25(OH)2D3 (100, 250, 500, 750 and 1000 nM), 25(OH)D2 (100, 250, 500, 750 and 1000 nM) or solvent (0.1% EtOH).

first: Carsten

last: Carlberg


title: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ATAC-Seq]

status: Public on Jun 20 2022

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk partially rely on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CREs’ sequence, an observation supported by a genome-wide comparative approach.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: ATAC-seq experiments were performed as described in (Bolt et al., 2022)

first: Aurélie

first: Isabel

last: Guerreiro

first: Christopher

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Denis

last: Duboule

first: Leonardo

last: Beccari


title: Different transcriptomic response to T. cruzi infection in hiPSC-derived cardiomyocytes from Chagas disease patients with and without chronic cardiomyopathy

city: São Paulo

first: Theo

last: Oliveira

state: State/Province Not Applicable

address: Av Dr Eneas de Carvalho 44

department: Heart Institute

country: Brazil

institute: University of São Paulo

summary: Investigate transcriptional responses of T. cruzi infected hiPSC-derived cardiomyocytes from chagasic patients with and without cardiomyopathy.

overall_design: We generated hiPSC-derived cardiomyocytes from 3 cardiac and 2 asymptomatic patients and reinfected them with T. cruzi Y strain for 24 hours. Non-infected replicates were also generated.


title: Transcriptomic analysis of human fallopian tube secretory epithelium

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

country: USA

institute: Cedars Sinai Medical Center

summary:
Transcriptomic data of human fallopian tube secretory epithelial cells.
Main correspondance: Kate.Lawrenson@cshs.org

overall_design: Total RNA was extracted from primary human fallopian secretory epithelium and RNA-sequenced as described in Corona et al. 2020 (PUBMED ID 33852846)

first: Robbin

last: Nameki

first: Xianzhi

last: Lin


title: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [4C-seq]

overall_design: 4C-seq on mouse and chicken forebrain and posterior trunk at different development stages


title: Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI


title: Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice II

summary: We have used a conditional mouse model to investigate the role of Smchd1 specifically in hematopoiesis. We found that Smchd1-deleted mice have an altered hematopoietic stem and progenitor cell (HSPC) compartment with reduced repopulating capacity in competitive bone marrow transplantation assays and the gradual loss of adult hematopoietic stem cells (HSCs) with age, suggesting a role for Smchd1 in the maintenance of long-term adult HSCs. The phenotype was more pronounced in female Smchd1-deleted mice, which showed a more severe reduction in HSCs with age, as well as depleted numbers of B cell lymphocytes. Gene expression profiling of Smchd1 deficient HSCs and B cells revealed several known and novel Smchd1-sensitive genes, a significant disruption to X-linked gene expression, although this was not widespread upregulation of X-linked genes in female cells. These data show Smchd1 as a new regulator of long-term HSCs whose effects are more profound in females.

overall_design: We have compared Smchd1 deleted B cells with controls that are heterozygous for the same Smchd1 deletion. Here we have compared n=5 female Smchd1 null bone marrow-derived B cells with n=5 female control cells of the same type, and n=4 Smchd1 null male and n=4 control male samples of the same cell type.

first: Sarah

last: Kinkel

first: Marnie

last: Blewitt

middle: F


title: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [Hi-C]

overall_design: We used Capture Hi-C enriching the Hoxd locus and its flanking TADs to using mouse E9.5 and chicken HH18 posterior trunks to evaluate the conservation of chromatin architecture in amniotes.


title: Transcriptome changes after curcumin analog treatment in human glioblastoma cells

status: Public on Jun 19 2022

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

summary: Glioblastoma cells were treated with curcumin analog CCA-1.1 and analyzed mRNA expression through mRNA sequencing

overall_design: We performed mRNA sequencing to undertand differentially expressed genes in CCA-1.1 treated glioblastoma cells.

first: Febri

last: Wulandari

first: Naufa

last: Hanif

first: Rohmad

middle: Y

last: Utomo

first: Riris

last: Jenie

first: Muthi

last: Ikawati

first: Ahmad

middle: S

last: Tafrihani


title: Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice I

overall_design: We have compared Smchd1-deleted LT-HSCs with controls that are heterozygous for the same Smchd1 deletion. Here was have sorted duplicate or triplicate wells of 50-100 Lin-ckit+ Sca1+ Flt3- CD48- CD150+ LT-HSCs from the bone marrow of n = 3 Smchd1-het (control) females, n = 3 Smchd1-del (test) females, n= 3 Smchd1-het males and n = 2 Smchd1-del males.


title: Temporal dynamics of macrophage heterogeneity after myocardial infarction

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

summary: In this study, we attempted to identify the heterogeneity and temporal dynamics of leukocytes at single-cell level in mouse heart after inducing MI using the longitudinal single-cell RNA sequencing and spatial transcriptome sequencing.

overall_design: To obtain a comprehensive landscape of immune cell profiling after ischemic injury of heart, we performed single-cell RNA sequencing on flow cytometry sorted CD45+ leukocytes from infarcted area of the heart at 1, 3, 5, and 7 days after inducing MI in mice. CD45+ cells from the steady state (no MI) mice were also used for single-cell RNA sequencing as a control.

first: Seung-Hyun

first: Kiyuk

last: Chang

first: Yeun-Jun

last: Chung


title: The application of quantitative ChIP-seq to study the impact of EZH2 inhibition on the facultative and constitutive heterochromatin landscape

status: Public on Jun 17 2022

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

summary: We conducted quantitative ChIP-seq following inhibition of EZH2 to better understand the influence of H3K27me3 on facultative and consitutive heterochromatin.

overall_design: Quantitative ChIP-seq was performed in duplicate for H3K27me3 and H3K9me3 following 72 hours of EZH2 inhibitor or vehicle treatment with doxycycline added for the final 24 hours of the drug treatment.

middle: B

first: Allison

middle: P

last: Siegenfeld

first: Shelby

middle: A

last: Roseman

first: Heejin

last: Roh


title: SaptioTemporal dynamics of macrophage heterogeneity after myocardial infarction

overall_design: To obtain a comprehensive landscape of immune cell profiling after ischemic injury of heart, we performed spatial transcriptome sequencing on mouse heart at 1, 3, 5, and 7 days after inducing MI.


title: MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakawa Oiwakecho, Sakyo-ku

institute: Division of Integrated Life Sciences, Graduate School of Biostudies

summary: Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)+ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)+ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates, and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of multiple alternative complexes rather than the prevailing one.

overall_design: Nuclear poly(A)+ RNA profiles of HeLa cells transfected with either siControl, siRRP6, siDIS3, siMPP6, siRRP6/siDIS3, siRRP6/siMPP6 or siMTR4. Samples were prepared in two biological replicates.

first: Naoko

last: Fujiwara

first: Maki

last: Shigemoto

first: Mizuki

last: Hirayama

first: Ken-ich

last: Fujita

first: Shigeto

last: Seno

first: Hideo

last: Matsuda

first: Masami

last: Nagahama


title: Epithelial HVEM maintains intraepithelial T cell survival and contributes to host protection

city: San Diego

first: Gooyoung

last: Seo

state: CA

address: 9420 Athena Cir, La Jolla

institute: La Jolla Institute for immunology

summary: Intraepithelial T cells (IET) provide surveillance of the intestinal epithelium, but little is known about how epithelial-derived signals regulate IET. Analyzing mice with a deficiency for the herpes virus entry mediator (HVEM), a member of the TNF receptor superfamily (TNFRSF14), we showed HVEM maintains the survival of subsets of small intestine IET through interactions with TNFSF14 (LIGHT).  RNA-seq and analysis of organoids showed that epithelial cell expressed HVEM provided signals that were required for optimal synthesis of collagen IV. Collagen IV supported IET survival in vitro via interactions with IET β1 integrins.  Furthermore, absence of β1 integrin expression in  T lymphocytes decreased TCR αβ+ IET  in vivo.  Intravital microscopy showed that the patrolling movement of all IET was reduced without epithelial HVEM, and we hypothesize that  collagen IV interactions with β1 integrins could have been responsible.  As likely consequences of decreased total IET number and movement, protective responses to Salmonella enterica were reduced in mice lacking either epithelial HVEM, HVEM binding partners CD160 or LIGHT, or β1 integrins. Therefore, these data defined a circuit whereby epithelial HVEM regulated IET indirectly, through basement membrane synthesis that interacts with T cell integrins, with consequences for mucosal immunity.

overall_design: mRNA from sorted proximal SI IEC or from sorted SI TCRab+CD8aa+ IET from Hvemfl/fl or Villin Cre x Hvemfl/fl mice

first: Goo-Young

first: Daisuke

last: Takahashi

first: Qingyang

last: Wang

first: Zbigniew

last: Mikulski

first: Angeline

last: Chen

first: Ting-Fang

last: Chou

first: Paola

last: Marcovecchio

first: Sara

last: McArdle

first: Ashu

last: Sethi

first: Jr-Wen

last: Shui

first: Masumi

first: Charles

last: Surh

first: Hilde

last: Cheroutre

first: Mitchell

last: Kronenberg


title: Reduced representation bisulfite sequencing of cadmium-exposed mouse placentas

status: Public on Jun 18 2022

city: Raleigh

first: Michael

last: Cowley

state: NC

address: Campus Box 7633

institute: North Carolina State University

type: Methylation profiling by high throughput sequencing

summary: The goal of the study was to identify regions of differential methylation between e18.5 mouse placentas exposed to cadmium and control placentas.

overall_design: Animal work was approved by the North Carolina State University Institutional Animal Care and Use Committee, under protocols 16-045-B and 19-049-B. All mice were on a 14-hour/10-hour light/dark cycle at 30-70 % humidity, 22°C ± 4°C. 5-week-old C57Bl/6J (B) female mice were exposed for 5 weeks to 0, 1, or 50 ppm CdCl2 through drinking water (Sigma-Aldrich, 202908). At 10 weeks B mice were mated with unexposed CAST/EiJ (C) males. Cd exposure continued throughout mating and gestation. Embryos and placentae were dissected at e18.5; collected tissues were weighed, snap-frozen immediately upon dissection and stored at -80°C. Genomic DNA was isolated from four female 0 ppm and four female 50 ppm exposed placentae using the AllPrep DNA/RNA/miRNA kit (Qiagen). 100 ng of gDNA was digested with TaqaI (NEB) at 65⁰C for 2 hours followed by MspI (NEB) at 37⁰C overnight. Following enzymatic digestion, samples were used for library generation using the Ovation RRBS Methyl-Seq System (Tecan) following the manufacturer’s instructions. In brief, digested DNA was randomly ligated, and, following fragment end repair, bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen) following the Qiagen protocol. After conversion and clean-up, samples were amplified resuming the Ovation RRBS Methyl-Seq System protocol for library amplification and purification. Libraries were measured using the Agilent 2200 TapeStation System and quantified using the KAPA Library Quant Kit ABI Prism qPCR Mix (Roche). Libraries were sequenced on a NextSeq 550 using single end 75 bp sequencing.

first: Mark

last: Simmers

first: Kathleen

last: Hudson

first: Marine

last: Baptissart


title: Gene expression in fra-2 transgenic mice

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Microarray analysis of Fra-2 tg female and male mice at 8 weeks of their disease development give an indication of possible differentially regulated genes. Wildtype mice serve as a healthy control.The mRNA was obtained from lung homogenate of the mice (n=4/group for all). There was no treatment applied, we investigate the baseline differences.

overall_design: 4 groups, each with 4 biological replicates

first: Valentina

last: Biasin

first: Grazyna

last: Kwapiszewska


title: The application of LIMe-ID to study the impact of PRC2 perturbations on lamina assoication.

first: Brian

last: Liau

summary: We developed and performed LIMe-ID to simultaneously measure lamina association and DNA methylation in one experimental workflow. We then conducted LIMe-ID following perturbations of PRC2 to better understand the influence of H3K27me3 on lamina association.

overall_design: LIMe-ID experiments were performed in duplicate for either the M.CviPI-Lamin-B1 K562 cell line following inhibitor/vehicle treatments or the FLAG-NLS-M.CviPI-Lamin-B1 K562 EZH2 knock-in cell line following dTAG-13/vehicle treatment. EZH2 inihibtion, EED inhibition and vehicle (DMSO) treatment were each performed in duplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment for the inhibitor LIMe-ID. For the degradation LIMe-ID experiment, dTAG-13 and vehicle (DMSO) treatment were each performed in duplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment.

first: Allison

last: Siegenfeld

first: Shelby

last: Roseman

first: Heejin

last: Roh


title: Analysis of the repressive activity of RBPJ in a mature T cell line

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: The Notch signaling pathway regulates gene expression via the transcription factor RBPJ. Here we investigated the the repressive role of RBPJ in a mature T cell line by combining RNA-Seq, ChIP-Seq and ATAC-Seq data under several different conditions.

overall_design: Mouse mature T cells were analyzed by ChIP-Seq using an RBPJ-specific antibody upon RBPJ depletion or Notch activation. In addition, histone modifications such as H3K27ac, H3K4me1 and H3K4me3 were analyzed together with chromatin accessibility (ATAC-Seq) upon RBPJ depletion. Finally, gene expression was analyzed upon RBPJ depletion, Notch induction, gamma-secretase inhibitor (GSI) DAPT treatment, by overexpressing the active Notch intracellular domain (NICD) in the RBPJ depleted background or overexpression the RBPJ interactor KYOT2.

first: Marek

last: Bartkuhn

first: Benedetto

last: Giaimo

first: Francesca

last: Ferrante


title: Single-nucleus chromatin accessibility and RNA-seq reveal impaired brain development in prenatal e-cigarette exposed neonatal rats

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

summary: We studied the influence of maternal vaping on rat neonates' brain development, using single nucleus -ATAC-seq (snATAC-seq) and -RNA-seq (snRNA-seq) technologies. We found that maternal vaping distorted neuronal lineage differentiation by promoting excitatory neuron and inhibiting lateral ganglionic eminence derived inhibitory neuron differentiation. Maternal vaping also diminished microglia population in rat developing brain. Functional enrichment revealed that the distorted neuronal differentiation and reduced microglia population were associated with disrupted brain calcium homeostasis and signaling. Our findings raise the concern that maternal vaping may cause adverse long-term brain damage to the offsprings. In addition, we proposed a set of brain cell specific chromatin accessibility markers for identifying rat brain cells directly from snATAC-seq data.

overall_design: Pregnant rats were exposed to e-cigarette vapor during E4 to E20. Droplet based snATAC-seq and snRNA-seq were performed to study the influence of maternal vaping on neonates' brain development.

first: Daliao

last: Xiao


title: The development and application of LIMe-Hi-C to simultanteously study lamina association, DNA methylation and chromosome conformation at baseline and upon EZH2 and DNMT1 inhibition

summary: We developed and performed LIMe-Hi-C in order to assess lamina association, DNA methylation, and chromosome conformation in one experimental workflow. We combined LIMe-Hi-C with chemcial inhibition of EZH2 and DNMT1 to better understand the influence of H3K27me3 and DNA methylation on 3D genome organization.

overall_design: LIMe-Hi-C experiments were performed in triplicate for FLAG-NLS-M.CviPI-Lamin-B1 K562 cells. A no doxycycline triplicate condition was included as a control to assess the specificity of the  lamina association signal. EZH2 inihibtion, DNMT1 inhibition and vehicle (DMSO) treatment were each performed in triplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment. The DMSO + doxyxline condition was utilized as a control. An in situ Hi-C experiment in singlicate for the DMSO + doxycyline condition was included as quality control for the bisulfite Hi-C workflow.


title: Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: BET inhibitors have been tested in several clinical trials, and despite encouraging results from preclinical cancer models, substantial clinical benefit in monotherapy has been limited. An important aspect is the proper translation of preclinical observations into clinical evaluation. The clinical BET inhibitor BI 894999 was tested in mechanistic studies, assessing pathway modulation and rational drug combinations at clinically achievable concentrations. We used NUT carcinoma (NC) cell lines with bona fide oncogenic drivers fusions including BRD4-NUT and BRD3-NUT. Proliferation assays, pathway modulation studies, and in vivo xenografts were performed with BI 894999, in monotherapy, and in combination with the clinical p300/CBP inhibitor CCS1477. Detachment of the BET complex from chromatin in vitro was assessed by LSM immunofluorescence, and by immunohistochemistry in tumour sections. Clinical findings on pathway modulation marker such as HEXIM1 and HIST2H2BF as well as human PK data were back translated to the preclinic setting. The clinical phase I scheduling regimen of 1 week-on (with a loading dose on day 1) and one week-off, derived from modelling of preclinical and clinical data, achieved plasma levels of about 20 nM. This concentration led to the full removal of BRD-NUT from chromatin and resulted in sustained and prolonged PD modulation of HEXIM1 and HIST2H2BF, accompanied with better patient tolerability. Rational combination with the p300/CBP inhibitor CCS1477 led to tumour regression in all three NC xenograft models tested. Preclinical mechanistic studies with the BET inhibitor BI 894999, back translation of clinical PK/PD data, and modelling provided guidance for an optimal clinical schedule. BI 894999 holds significant potential as a combination drug and preclinical data identified p300/CBP inhibitors as highly relevant combination partner for NUT carcinoma and beyond, pending clinical trials.

overall_design:
NUT midline carcinoma cell lines were grown in media and treated with either DMSO (control) or compound(s). BI 894999 (WO2014076237) is the clinical compound synthesized by Boehringer Ingelheim. CCS1477 was purchased from Chemie Tek, Indianapolis, USA. The experiment was performed in biological triplicates per condition/cell lines, two samples however had to be excluded from the final analysis as these samples did not meet the quality criteria of sequencing coverage. Information about sampling time points, compounds, compound concentrations, and replicates are detailed out in the respective sample descriptions. All samples were subjected to RNA isolation, followed by library preparation (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen), and messenger RNA sequencing on an Illumina NextSeq 500 system.

Update 2022-08-05: In contrast to the sample titles, the compound BI00894999 was dosed with 10nM in all respective samples, in contrast to the title claiming a dose of 1000nM.

first: Ulrike

last: Tontsch-Grunt

first: Dominik

last: Arnold

first: Paula-Elena

last: Traexler


title: Sex-specific modulation of the host transcriptome in the spleen of Schistosoma mansoni infected mice

status: Public on Jun 16 2022

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

summary: Intestinal Schistosomiasis, caused by the helminth Schistosoma mansoni, results in fibroproliferative disease triggered by liver trapped parasite eggs. Characteristic of the infection is a chronic course of disease with progressive periportal fibrosis, spleno- and hepatomegaly, and portal hypertension. Despite significant progress in understanding the complex immunological processes involved in the host-pathogen relationship, there is currently no effective vaccine against the infection nor antifibrotic drugs, increasing the pressure to find new targets for schistosome drugs and vaccine candidates. We have recently reported that infection with male schistosomes can attenuate reinfections, while female schistosomes appear to weaken the host immune system. To decipher the underlying mechanisms of differential immunogenicity of female and male worms, we performed a comparative transcriptomic analysis of splenic tissue from unisexually and bisexually infected mice. We identified a total of 1293, 512 and 4062 genes, respectively, that were differentially expressed in the group of male-only (M), female-only (F) or bisexually (MF) infected mice compared to naive controls. Bisexual infection and infection with male worms showed the marked effects on host immune response, erythrocyte homeostasis, lipoprotein metabolism and cell cycle processes compared to the infection with female worms. Furthermore, we could show that both worm sexes trigger immune responses in an egg-independent manner, with a non-polarized Th1 and Th2 response, with female worms having a lower regulatory influence than males.

overall_design: Six-week-old female C57BL/6 mice were percutaneously exposed to 100 S. mansoni cercariae, either male only in 3 mice, female only in three mice, or both sexes (50 + 50 cercariae) in 2 mice. Controls were left untreated in 2 mice.

first: Franziska

last: Winkelmann

first: Anne

last: Rabes

first: Cindy

last: Schulz

first: Nicole

last: Koslowski

first: Emil

last: Reisinger

first: Martina

last: Sombetzki


title: Inhibition of EZH2 with GSK343 in the LIMe-Hi-C K562 clone

first: Brian

last: Liau

summary: We characterized the the effect of EZH2 inhibition on gene expression in the LIMe-Hi-C K562 clone

overall_design: For RNA-seq preparation, the M.CviPI-Lamin-B1 inducible K562 clone was treated in triplicate with either with vehicle (DMSO 0.1% v/v) or GSK343 (1µM) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of the drug treatments. Upon completion of the treatments, RNA was isolated and sequenced to assess changes in transcription.

first: Allison

last: Siegenfeld

first: Shelby

last: Roseman

first: Heejin

last: Roh


title: Gene expression profiling of melanoma cell lines with acquired resistance to the BRAF inhibitor PLX4032 and the parental sensitive counterparts and of melanoma cell lines intrinsically resistant.

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Targeted therapy with small molecules inhibiting BRAF and MEK kinase represents a therapeutic option in advanced metastatic melanoma although drug resistance limits the achievement of persistent cures. The genomic analyses of tumors from patients developing treatment resistance indicate that drug tolerance may result from non-mutational events occurring in the tumor microenvironment.  To identify tumor specific transcriptional changes related to resistance to the BRAF-inhibitor PLX4032, cell lines with acquired resistance to PLX4032 were generated from six sensitive melanoma lines by chronic in vitro drug exposure (Vergani E, Oncotarget 2016) and analyzed for gene expression profiles; in addition a set of cell lines with intrinsic resistance was included for comparison. Cell lines were obtained from metastatic surgical specimens and were previously genetically characterized (Daniotti M, Oncogene 2004; Vergani E, JID 2022, accepted).

overall_design: Gene expression profiling of six pairs of Resistant (Ra)/Sensitive (S) melanoma cell lines, and of a set of cell lines with intrinsic resistance (Ri) was performed by Clariom S platform.

first: L

first: E

last: Vergani


title: Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery

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

overall_design: Refer to individual Series


title: Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [scRNA-seq]

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We profiled medullary thymic epithelial cell subsets from a variety of conditions by scRNA-seq to investigate mechanisms of T-cell tolerance.

overall_design: scRNA-seq of mTECs

first: Daniel

last: Michelson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells


title: Virus-induced codon-specific reprogramming to favor viral RNA translation

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

summary: How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in suboptimal codons remains a puzzling question. By integrating subcellular fractionation and transcriptome-wide analyses of translation in CHIKV-infected human cells, we demonstrate an unanticipated virus-induced reprogramming of the host translation machinery to favor translation of viral RNA over cellular genes featuring optimal codon usage. This reprogramming was specifically apparent at the endoplasmic reticulum (ER), the preferred translation compartment of CHIKV RNA, and it is mediated by the wobble uridine 34 tRNA modification enzyme KIAA1456 whose expression is enhanced upon viral infection. Since KIAA1456 itself is encoded by a CHIKV-like codon usage, infection triggers a positive feed-back loop that ensures efficient virus protein production. Our findings demonstrate an unprecedented interplay of viruses with the host tRNA epitranscriptome to favor viral protein expression.

overall_design: HEK 293T cells were subjected to subcellular fractionation after being infected with Chikungunya virus for 12 h (MOI=40), while control cells were mock infected for 12 h. Both subcellular compartments were then subjected to RNA-seq and Ribo-seq to identify differentially translated mRNAs. All experiments were performed at least in triplicates.

first: Jennifer

last: Jungfleisch

first: René

last: Böttcher

first: Marc

last: Talló-Parra

first: Andres

last: Merits

first: Eva

last: Novoa


title: Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [scATAC-seq]

summary: We profiled medullary thymic epithelial cells from AireWT vs AireKO mice by scATAC-seq to investigate mechanisms of T-cell tolerance.

overall_design: scATAC-seq of mTEC


title: Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [RNA-seq]

summary: We profiled medullary thymic epithelial cell subsets and peripheral cell types by bulk RNA-seq to investigate mechanisms of T-cell tolerance.

overall_design: Bulk RNA-seq of mTEC subsets


title: RNA-seq analysis of transcriptomes in Wild Type and ANXA2 knockdown HK2 cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We conducted this experiment to study the effects of Annexin A2 (ANXA2) on gene expression in human proximal tubular epithelial (HK2) cells in vitro. Short hairpin RNA targeting ANXA2 was designed and cloned into vector pGFP-B-RS for RNAi to generate the recombinant expression plasmids, which were transfected into HK2 cells. RNA-seq analysis were performed on HK2 cells, with or without ANXA2 knockdown, to reveal the differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). Then the DEGs and RASEs were validated by qRT-PCR. Using criteria of an absolute fold change of ≥2.0 or ≤ 0.5 and false discovery rate (FDR) of < 0.05 with the edgeR package, RNA-seq analysis of the transcriptomes revealed 220 upregulated and 171 downregulated genes related to ANXA2 knockdown.

overall_design: Examination of  transcriptomes in Wild Type and ANXA2 knockdown HK2 cells

first: Jing

first: Ling


title: Long-distance association of topological boundaries through nuclear condensates (Hi-C)

status: Public on Jun 15 2022

city: La Jolla

first: Amir

last: Gamliel

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

summary: Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with  topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally,  and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.

overall_design: Human RUES1 cells were treated with  either 7% 2,5-Hexanediol or 7% 1,6-Hexanediol for 5 minutes, washed with media, and  incubate with fresh media for additoinal time points at 37 deg C as indicated. Cells were subsuqently prccesed for in situ Hi-C, ChIp-seq, GRO-seq and PRO-seq. For transcription inhibition experiments, RUES1 cells were treated with either 5uM flavopiridol hydrochloride (F3055 Sigma) or 1uM triptolide (T3652 Sigma), for 15 minutes, 1 hour and 3 hours. Cells were then washed with PBS, cross-linked with 1% formaldehyde in PBS at room temperature for 10 min and neutralized with 0.125M glycine, and further proccessed for in situ Hi-C.


title: Long-distance association of topological boundaries through nuclear condensates (PRO-Seq)


title: Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [CUT&TAG]

summary: We profiled medullary thymic epithelial cells by CUT&Tag to investigate mechanisms of T-cell tolerance.

overall_design: CUT&Tag of mTECs


title: Embryologic Origin Influences Smooth Muscle Cell Phenotypic Modulation Signatures in Murine Marfan Syndrome Aortic Aneurysm

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

summary: Aortic single-cell RNA sequencing data from second heart field lineage traced mice with Fbn1C1041G/+ and control mice.

overall_design: Aortic tissue from 16-week-old control and Fbn1C1041G/+ (Marfan syndrome) mice with transgenic second heart field lineage tracing cre-lox model (Nkx2-5-cre) was subjected to tissue digestion and single-cell RNA sequencing. Male and female replicate pools from each genotype were used, samples were processed from lineage positive and negative cell pools, yielding 8 total samples.

first: Michael

last: Fischbein


title: Long-distance association of topological boundaries through nuclear condensates (GRO-Seq)


title: Long-distance association of topological boundaries through nuclear condensates (ChIP-Seq)


title: A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer [CRISPRKO]

city: Chapel Hill

middle: Ross

last: Kelly

address: 120 Mason Farm Road

department: Bioinformatics and Genetics

institute: University of North Carolina at Chapel Hill

summary: Ovarian cancer is one of the deadliest cancers among women worldwide and is the leading cause of gynecologic-related cancer deaths in the U.S. Enhancers are often repurposed by the tumor cells for the regulation of genes that allow tumor cells to become more aggressive and resistant to therapy. Recent evidence suggests that exploiting transcriptional dependence by targeting oncogenic super-enhancers may be a viable therapeutic avenue. To this end, we leveraged genomic data such as H3K27ac, BRD4, and copy number information to identify putatively oncogenic super-enhancers. We found that copy number amplification of these super-enhancers is predictive of clinical outcome and that the targets genes associated to the copy number events via chromatin eQTL analysis are involved in numerous oncogenic processes. To systematically probe the functions these super-enhancers we designed a CRISPR interference screen (dCas9-KRAB) so specifically inhibit each super-enhancer and measure the consequences on gene expression via RNA-seq. These results show pervasive gene expression changes that underlie the biology of ovarian cancer. Finally, we select two salient super-enhancers for further analysis. CRISPR-based deletion of these two super-enhancers results in in dramatic changes in gene expression and decreased cell proliferation of ovarian cancer cells. Taken together these analyses highlight the importance of BRD4-bound and copy number amplified super-enhancers in ovarian cancer oncogenic regulation.

overall_design: In this study, two super-enhancers were identified as being oncogenic in ovarian cancer. The genomic coordinates for super-enhancer 60 (SE60) are chr20:52352051-52368920 using the Hg19 human genome reference. The genomic coordinates for super-enhancer 14 (SE14) are chr1:16493671-16516686 using the Hg19 human genome reference.  Each super enhancer was deleted using CRISPR-Cas9 in the ovarian cancer cell line OVCAR3. The guides RNAs used for deletion and the genotyping results are described in the associated publication. For each super enhancer, two independent knockout clones were generated (clone 1 and clone 2). Each clone represents a biological replicate. RNA was purified from asynchronous cells for each clone. Library prep was done using the Illumina TruSeq mRNA Library Kit following the manufacturer's protocol. RNA was sequenced at 150 cycles, paired end, on an Illumina NextSeq. The super-enhancer locations, gRNA locations, and gRNA sequences are located in one of the supplimentary tables from the associated manuscript.

first: Hector

middle: L

last: Franco

first: Kamila

last: Wisniewska

middle: R


title: OASIS overexpression in murine podocyte cell line

city: Suita

first: Masanori

last: Obana

address: Yamadaoka 1-6

institute: Osaka University

summary: Podocyte injury is involved in the onset and progression of various kidney diseases. We previously demonstrated that the transcription factor, old astrocyte specifically induced substance (OASIS) in myofibroblasts, contributes to kidney fibrosis, as a novel role of OASIS in the kidneys. Importantly, we found that OASIS is also expressed in podocytes; however, the pathophysiological significance of OASIS in podocytes remains unknown. Upon lipopolysaccharide (LPS) treatment, there is an increase in OASIS in murine podocytes. Enhanced serum creatinine levels and tubular injury, but not albuminuria and podocyte injury, are attenuated upon podocyte-restricted OASIS knockout in LPS-treated mice, as well as diabetic mice. The protective effects of podocyte-specific OASIS deficiency on tubular injury are mediated by protein kinase C iota (PRKCI/PKCι), which is negatively regulated by OASIS in podocytes. Furthermore, podocyte-restricted OASIS transgenic mice show tubular injury and tubulointerstitial fibrosis, with severe albuminuria and podocyte degeneration. Finally, there is an increase in OASIS-positive podocytes in the glomeruli of patients with minimal change nephrotic syndrome and diabetic nephropathy. Taken together, OASIS in podocytes contributes to podocyte and/or tubular injury, in part through decreased PRKCI. The induction of OASIS in podocytes is a critical event for the disturbance of kidney homeostasis.

overall_design: We searched for genes whose expression is induced by the transcription factor OASIS in podocytes. Murine cultured podocytes were transfected with a lentivirus expressing the active form of Oasis/Creb3l1 or venus for 24 h. Post the lentiviral infection, the medium was changed to RPMI-1640 with 10% FBS. Forty-eight hours after treatment with the lentiviral vectors, total RNA was extracted from the OASIS-overexpressing podocytes, using the RNeasy® mini kit (Qiagen, Venlo, Netherlands). Gene expression was analyzed using the SurePrint G3 Mouse GE v2 8×60K Microarray (Agilent Technologies, Santa Clara, CA, USA).

first: Yoshiaki

last: Miyake


title: Transcriptome sequencing of HUVECs

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

summary: We analyzed the global effect of SOX9 overexpression by sequencing the transcriptomes of HUVECs transduced with SOX9 expression plasmid or an empty vector control.

overall_design: Cells were transduced with plasmids and 4 days after total RNA was extracted. Three individual experiments were performed.  Sample quality control was performed using the Agilent 2100 Bioanalyzer.  Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads

first: Sibyl

last: Drissler

first: Pamela

last: Hoodless


title: Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells

status: Public on Jun 14 2022

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: Doxorubicin resistance remains a major therapeutic challenge leading to treatment failure and poor survival prognosis in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape accompanied by alterations of chromatin accessibility are well known, potential diagnostic or therapeutic targets associated with three-dimensional (3D) genome reorganization in doxorubicin-resistant breast cancer cells have not yet been systematically investigated. Here we performed integrated analyses combining in situ high-throughput chromosome conformation capture (Hi-C), ATAC-seq and mHi-C data on doxorubicin-resistant MCF7 human breast cancer cells compared to parental cells. It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression, and the genome was spatially reorganized into smaller topologically associating domains (TADs) and loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF and BORIS, to gained TAD boundaries and loop anchors. Intriguingly, we observed two condensed genomic regions (~20kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Moreover, we identified a number of gained and lost enhancer-promoter interactions associated with differentially expressed genes, including FA2H, FOXA1, JRKL and EZH, some of which involved in chromatin organization and breast cancer signaling pathways. This study uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription, and provides resources and novel insights into the epigenomic mechanisms with potential therapeutic implications for doxorubicin resistance in breast cancer.

overall_design: Genome-wide landscaps of 3D chromatin architecture in parental and doxorubicin-resistant breast cancer cells. In total, 4 samples were analyzed. Hi-C_MCF7_1 and Hi-C_MCF7_2 were two biological replicates and served as the control group. Hi-C_MCF7-DR_1 and Hi-C_MCF7-DR_2 were two biological replicates and served as the treatment group.


title: Circulating MicroRNA: Myocardium-Derived Prenatal Biomarker of Ventricular Septal Defects

city: Quanzhou

first: Yiru

last: Yang

address: Zhongshan North Road

institute: the Second Affiliated Hospital of Fujian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) regulate transcription factors and relate to ventricular septal defect (VSD) occurrence, progression and outcome. Recently, circulating miRNAs from maternal blood and amniotic fluid have been used as biomarkers for congenital heart defect (CHD) diagnosis. However, whether circulating miRNAs are associated with foetal heart tissue remains unknown. Dimethadione (DMO) induced a VSD rat model and the miRNA expression profiles of the myocardium, amniotic fluid and maternal serum were analysed. MiRNAs were differentially expressed in the myocardium, amniotic fluid or maternal serum of VSD foetal rats and might be involved in cardiomyocyte differentiation and apoptosis.

overall_design: Dimethadione (DMO) induced a VSD rat model. The NC group was given the same dose of distilled water at the same time. In the DMO group, VSD foetuses without malformation of major vessels were selected as the VSD group, and foetuses with intact ventricular septum were selected as the non-VSD group. Seven samples were selected for miRNA sequencing in each group.

first: Hainan

first: Guorong

last: Lyu


title: RNA sequencing analysis of NK cells, T cells and tumor from matched soft tissue sarcoma and peripheral blood

city: Sacramento

first: Robert

last: Canter

address: 4645 2nd Ave, Research III, Room 2200D

department: Surgery

institute: University of California, Davis

summary: Using fluorescence-activated cell sorting, we isolated blood and tumor-infiltrating CD3-CD56+ NK and CD3+ T cells and CD45- viable tumor cells from STS patients undergoing surgery. We then evaluated differential gene expression (DGE) of these purified populations with RNA sequencing analysis

overall_design: The collection of matched whole blood and tumor specimens was approved by the IRB at the University of California, Davis. Human peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a density gradient centrifugation, followed by red blood cell lysis. Tumor tissue from patients undergoing STS resection was collected in sterile RPMI-1640, diluted with PBS and passed through a 70 µm filter, and then subjected to red blood cell lysis. Human cells were washed with PBS and staining buffer, and then incubated with Fc receptor blocking solution for 15 minutes. Cells were stained with the following fluorochrome-conjugated monoclonal antibodies: CD3-FITC, CD56-PE, CD45-BV510 and CD8-BV785. Live/dead staining was performed using Fixable Viability Dye 780. Data were acquired using a BD LSRFortessa flow cytometer and analyzed using FlowJo Software. Fluorescence-associated cell sorting (FACS) was performed using a BD inFlux cell sorter. Cells were sorted for blood and intra-tumoral NK cells (live CD45+CD3-CD56+), blood and intra-tumoral T cells (live CD45+CD3+CD56-), and tumor cells (live CD45-). Following FACS isolation, cells were cryopreserved and stored in liquid nitrogen for subsequent RNA extraction and sequencing. Cells were processed for RNA isolation using the Total RNA Purification Plus Micro Kit. RNAseq libraries were prepared by the University of California, Davis, Bioinformatics Core. Gene expression profiling was carried out using a 3'-Tag-RNA-Seq protocol. Up to forty-eight libraries were sequenced per lane on an Illumina HiSeq 4000 sequencer with single-end 100 base pair reads. Differential gene expression analysis was performed with the DESeq2 package for R. The Benjamini-Hochberg procedure was used to adjust for False Discovery Rate (FDR).

first: Sean

last: Judge


title: Cell free DNA 5-hydroxymethylcytosine as an emerging marker of acute myeloid leukemia

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

summary: Aberrant changes in 5-hydroxymethylcytosine (5hmC) are a unique epigenetic feature in many cancers including acute myeloid leukemia (AML). However, genome-wide analysis of 5hmC in plasma cell-free DNA (cfDNA) remains unexploited in AML patients. We used a highly sensitive and robust nano-5hmC-Seal technology and profiled genome-wide 5hmC distribution in 239 plasma cfDNA samples from 103 AML patients and 81 non-cancer controls. We developed a 5hmC diagnostic model that precisely differentiates AML patients from controls with high sensitivity and specificity. We also developed a 5hmC prognostic model that accurately predicts prognosis in AML patients. High weighted prognostic scores (wp-scores) in AML patients were significantly associated with adverse overall survival (OS) in both training (P = 3.31e-05) and validation (P = .000464) sets. The wp-score was also significantly associated with genetic risk stratification and displayed dynamic changes with varied disease burden. Moreover, we found that high wp-scores in a single gene, BMS1 and GEMIN5 predicted OS in AML patients in both the training set (P =.023 and .031, respectively) and validation set (P = 9.66e-05 and 0.011, respectively). Lastly, our study demonstrated the genome-wide landscape of DNA hydroxymethylation in AML and revealed critical genes and pathways related to AML diagnosis and prognosis. Our data reveal plasma cfDNA 5hmC signatures as sensitive and accurate markers for AML diagnosis and prognosis. Plasma cfDNA 5hmC analysis will be an effective and minimally invasive tool for AML management.

overall_design: Examination of the 5-hydroxymethyl cytosine (5hmC) profiles from cell-free DNA from Acute myeloid leukemia patients in comparison to non-cancer controls

first: Jianming

last: Shao


title: Identification and characterizaton of RBM12 as a novel regulator of fetal hemoglobin expression [eCLIP-Seq]

city: Philadelphia

first: Aoi

last: Wakabayashi

address: 3615 Civic Center Blvd, Abramson Research Center Rm 315A

department: Hematology/Oncology

institute: Children's Hospital of Philadelphia

summary: The fetal-to-adult hemoglobin transition is clinically relevant as reactivation of fetal hemoglobin (HbF) significantly reduces morbidity and mortality associated with sickle cell disease (SCD) and b-thalassemia. Most studies on the developmental regulation of the globin genes, including genome-wide genetics screens, have focused on DNA binding proteins including BCL11A and ZBTB7A/LRF and their cofactors. Our understanding of RNA binding proteins (RBPs) in this process is much more limited. Two RBPs, LIN28B and IGF2BP1 are known post-transcriptional regulators of HbF production but a global view of RBPs is still lacking. Here, we carried out a CRISPR/Cas9-based screen targeting RBPs harboring RNA methyltransferase and/or RRM domains and identified RBM12 as a novel HbF suppressor. Depletion of RBM12 induced HbF expression and attenuated cell sickling in erythroid cells derived from SCD patients with minimal detrimental effects on cell maturation. Transcriptome and proteome profiling revealed that RBM12 functions independently of major known HbF regulators. Enhanced crosslinking and immunoprecipitation followed by high throughput sequencing (eCLIP-Seq) revealed strong preferential binding of RBM12 to 5’UTRs of transcripts, narrowing down the mechanism of RBM12 action. Notably, we pinpointed the first of five RRM domains as essential, and, in conjunction with a linker domain, as sufficient for RBM12-mediated HbF regulation. Our characterization of RBM12 as a negative regulator of HbF points to an additional regulatory layer of the fetal-to-adult hemoglobin switch and broadens the pool of potential therapeutic targets for SCD and b-thalassemia.

overall_design: RBM12 transcriptome binding profile in wild-type primary human CD34+ hematopoietic stem and progenitor cells(HSPCs)

first: Gerd

last: Blobel


title: TCR-Vγδ usage distinguishes pro- and anti-tumor intestinal γδ T cell subsets

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: γδ T cells represent a substantial fraction of intestinal lymphocytes at homeostasis, but also constitute a major lymphocyte population infiltrating colorectal cancers (CRC), albeit their role in CRC remains unclear. Using human CRC samples and murine CRC models, we found that most γδ T cells in pre- or non-tumor colon exhibit cytotoxic markers while tumor-infiltrating γδ T cells express a pro-tumorigenic profile. These contrasting T cell profiles were associated with distinct TCR-Vγδ gene-usage in both mice and humans. Complementary intersectional genetics and antibody-dependent strategies targeting murine γδ T cells enriched in the epithelium at steady state led to heightened tumor development, while targeting γδ subsets that accumulate during CRC resulted in reduced tumor growth. Our results uncover pro- and anti-tumor roles for γδ T cell subsets.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single Cells of Gamma Delta T cells of human patients (p337, p859, p989, p391, p633) sorted from healthy (N) and colon rectal cancer (T) areas; libraries are the antibody derived tags, gene expression and tcr sequencing. Bulk RNA-Seq of sorted CD8a+PD-1- and CD8a-PD-1+ Gamma Delta T cells, extracted from colon tumors of mice in triplicates.

first: Bernardo

last: Reis

first: Patrick

middle: W

last: Darcy

first: Iasha

middle: Z

last: Khan

first: Christine

last: Moon

first: Adam

middle: E

last: Kornberg

first: Vanessa

last: Schneider

first: Yelina

last: Alvarez

first: Olawale

last: Eleso

first: Caixia

last: Zhu

first: Marina

last: Schernthanner

first: Ainsley

last: Lockhart

first: Aubrey

last: Reed

first: Juliana

last: Bortolatto

first: Angelina

last: Bilate

first: Sergei

last: Grivennikov

first: Arnold

last: Han

first: Daniel

last: Mucida


title: Identification and characterizaton of RBM12 as a novel regulator of fetal hemoglobin expression

first: Aoi

last: Wakabayashi

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

overall_design: Refer to individual Series


title: Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [RNA-Seq]

city: Higashi-Hiroshima

first: Yutaka

last: Kikuchi

state: Hiroshima

address: 1-3-1, Kagamiyama

institute: Hiroshima University

summary: CpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription, and hypermethylation of the promoter region is correlated with silencing of gene expression. In contrast to the promoter region, the function of DNA methylation at transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions (including transcription termination sites (TTSs)) during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a-/- mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased transcript counts and chimeric transcripts downstream of TTSs in Dnmt3a-/- Agouti-related protein neurons, but not in Dnmt3a-/- ES cells and MEFs. We experimentally detected increased read-through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal-zygotic Dnmt3aa-/- mutants. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a-/- vertebrates.

overall_design: Analyzing transcriptional profiles by RNA-seq in WT and MZdnmt3aa-/-.

first: Masaki

last: Shirai

first: Yudai

last: Hirose

first: Masashi

last: Fujii

first: Akinori

last: Awazu


title: A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer [CRISPRI_SCREEN]

first: Michael

last: Kelly

overall_design: For this experiment we used dCas9-KRAB expressing ovarian cancer cells (OVCAR3) to systematically inhibit 86 different super-enhancers and 10 controls in a 96-well plate format. We designed two guide RNAs for each super-enahncer and targeted one different super-enhancer per well of the 96-well plate. After 72hrs after guideRNA transfection and epigentic silencing by dCas9-KRAB, RNA was extracted from each well and the changes in gene expression were measured using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD from Lexogen company. The super-enhancer locations, gRNA locations, and gRNA sequences are located in one of the supplimentary tables from the associated manuscript.

first: Hector

last: Franco

first: Kamila

last: Wisniewska


title: Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates


title: Neurons shift translational control to secure proteostatic resilience during ER stress

status: Public on Jun 13 2022

city: Amsterdam

first: Wiep

last: Scheper

address: De Boelelaan 1085

department: Department of Functional Genomics, Center for Neurogenomics and Cognitive Research  (CNCR)

country: Netherlands

institute: Amsterdam University Medical Centers (UMC) Location Vrije Universiteit

summary: Proteostasis is essential for survival and particularly important for highly specialized post mitotic cells like neurons. Transient reduction of protein synthesis by protein kinase R–like endoplasmic reticulum (ER) kinase (PERK)-mediated phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a major proteostatic survival response during ER stress. Paradoxically, neurons are remarkably tolerant to PERK dysfunction, which suggests the existence of cell type-specific mechanisms that secure proteostatic stress resilience. We employed PERK-deficient neuron and astrocyte monocultures to investigate the mechanisms underlying neuron-specific ER stress resilience in the absence of PERK.

overall_design: To study cell type-specific PERK signalling, conditional PERK-deficient (knockout; KO) neurons and astrocytes were cultured from PerkloxP/loxP mice (The Jackson Laboratory (Stock No: 023066)). Perk WT and Perk KO cells were generated by in vitro transduction with lentiviruses expressing inactive ΔCre- or active Cre-recombinase, respectively. ER stress was induced by 20-24 hours treatment with tunicamycin (TM)

first: Kimberly

last: Wolzak


title: RNA sequencing of the interface tissue after mouse anterior-cruciate ligament reconstruction (ACLR)

first: Takayuki

state: NY

address: 515 E 71st St

institute: Hospital for Special Surgery


title: Characterization of N6-methyladenosine in the testis tissue of cattle-yak

status: Public on Jun 12 2022

city: Lanzhou

first: Xingdong

last: Wang

address: The west lake street

institute: CAAS

summary: N6-methyladenosine (m6A) is the most prominent mRNA modification in eukaryotes, and its potential regulatory role has recently been identified in mammals, plants, and yeast. However, how m6A methylation regulates spermatogenesis remains unknown. In this study, cattle-yak testis tissue was used as the experimental material, and the m6A map was generated through preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonia and Sertoli cells were observed in cattle-yak testis tissue. Experiments examining the expression of methylation-related enzymes and the overall methylation level showed that the methylation level in the testis of the cattle-yak was slightly lower than that of the sexually mature yak, but significantly higher than that of the pre-sexually mature yak. Annotation analysis indicated that differentially methylated peaks were most frequently concentrated in exonic regions, followed by 3'UTR and finally 5'UTR regions. Through enrichment analysis of differentially expressed genes and differentially methylated corresponding genes, GO analysis of T-vs-Y group mainly involved spermatogenesis, including cytoskeleton, actin binding, etc. KEGG analysis showed that the differential genes were mainly enriched in actin cytoskeleton regulation and MAPK signaling pathway. GO analysis of the T-vs-M group mainly involved protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism and endocytosis. KEGG analysis mainly involved apoptosis and Fanconi anemia pathways. This study will lay the foundation for elucidating the molecular mechanism of m6A in male sterility of cattle-yak.

overall_design: Detection of m6A in the testis tissue of cattle-yak

first: Jie

last: Pei

first: Xian

last: Guo


title: Sensory neurons display cell-type specific vulnerability to loss of neuron-glia interactions

status: Public on Jun 11 2022

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

summary: PNS injuries initiate transcriptional changes in glial cells and sensory neurons that promote axonal regeneration. While the factors that initiate the transcriptional changes in glial cells are well characterized, the full range of stimuli that initiate the response of sensory neurons remain elusive. Here, using a genetic model of glial cell ablation, we find that glial cell loss results in transient PNS demyelination without overt axonal loss. By profiling sensory ganglia at single-cell resolution we show that glial cell loss induces a transcriptional injury response preferentially in proprioceptive and Aβ RA-LTMR neurons. The transcriptional response of sensory neurons to mechanical injury has been assumed to be a cell autonomous response. By identifying a similar response in non-injured, demyelinated neurons, our study suggests that this represents a non-cell autonomous transcriptional response of sensory neurons to the loss of axon-glial cell interactions.

overall_design: Single-nucleus RNA sequencing were performed on dorsal root ganglia from PLP-CreERT;ROSA26-eGFP-DTA mice, a genetic model of Schwann cell and satellite glial cell ablation.

first: Benayahu

last: Elbaz

first: Maia

last: Vardy

first: Sara

last: Isaac

first: Braesen

last: Rader

first: Riki

last: Kawaguchi

first: Maria

last: Traka

first: Clifford

middle: J

last: Woolf

first: William

last: Renthal

first: Brian

last: Popko


title: Identification and characterizaton of RBM12 as a novel regulator of fetal hemoglobin expression [RNA-seq]

first: Aoi

last: Wakabayashi

overall_design: Expression profiles of RBM12-depleted primary human CD34+ hematopoietic stem and progenitor cells(HSPCs) from 3 donors. CD34+ HSPCs were targetd with an sgRNA against RBM12 versus a non-targeting control at day 0 of differentiation and cultured until day 7 of differentiaiton.

first: Gerd

last: Blobel


title: Dynamic IFNβ signalling underlies treatment response to immune checkpoint therapy in cancer [single-cell RNA-seq]

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

institute: National Centre For Asbestos Related Diseases

summary: The on/off dynamics of IFNβ signalling underlie the therapeutic response to immune checkpoint therapy in cancer, which can be identified in Ly6C+ monocytes

overall_design: 12 samples, 6 across AB1 and 6 across Renca models

first: Rachael

last: Zemek

first: Willem

last: Lesterhuis


title: A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

first: Michael

last: Kelly


title: Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS]

first: Yutaka

last: Kikuchi

overall_design: Analyzing DNA methylation profiles by WGBS in WT and MZdnmt3aa-/-.

first: Masaki

last: Shirai

first: Takuya

last: Nara

first: Yudai

last: Hirose

first: Masashi

last: Fujii

first: Akinori

last: Awazu

first: Nobuyoshi

last: Shimoda


title: Identification of differentially expressed microRNAs as potential biomarkers for carcinoma ex pleomorphic adenoma

city: Hwaseong

first: Heejin

last: Kim

address: Keunjaebonggil 7

department: otorhinolaryngology-head and neck surgery

institute: Hallym university of medicine

summary: We investigated and compared the characteristic miRNA expression patterns across samples of the PA, carcinomatous portions (CA) of CXPA, as well as conventional PA.

overall_design: We selected 13 CXPA and 16 conventional PA FFPE samples, separated the PA and CA portions of CXPA samples and conducted miRNA profiling for each group.

first: Hyojin


title: Type II Alveolar Epithelial Cell Aryl Hydrocarbon Receptor Protects Against  Allergic Airway Inflammation through Controlling Cell Autophagy

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

summary:
Rationale: Aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, has been  considered as an important regulator for immune diseases. We have previously shown that AhR  protects against allergic airway inflammation. The underlying mechanism, however, remains  undetermined. Objectives: We sought to determine whether AhR specifically in Type II alveolar epithelial cells  (AT2) modulates allergic airway inflammation and its underlying mechanisms.
Methods: The role of AhR in AT2 cells in airway inflammation was investigated in a mouse  model of asthma with AhR conditional knock out mice in AT2 cells (Sftpc-Cre;AhRflox/flox). The  effect of AhR on allergen-induced autophagy was examined by both in vivo and in vitro analyses. The involvement of autophagy in airway inflammation was analyzed by using  autophagy inhibitor chloroquine. The AhR-regulated gene profiling in AT2 cells was also  investigated by RNA-seq analysis.
Results: Sftpc-Cre; AhRflox/flox mice showed exacerbation of allergen-induced airway  hyperresponsiveness and airway inflammation with elevated Th2 and airway epithelial-derived  cytokines in bronchoalveolar lavage fluid (BALF). Notably, an increased allergen-induced  autophagy was observed in the lung tissues of Sftpc-Cre; AhRflox/flox mice when compared with  wild-type mice. Further analyses suggested a functional axis of AhR-TGF-β1 that is critical in  driving allergic airway inflammation through regulating allergen-induced cellular autophagy.  Furthermore, inhibition of autophagy suppressed allergic airway inflammation with decreased  Th2 and epithelial cell-derived cytokines in BALFs. Additionally, RNA-seq analysis suggests that autophagy is one of the major pathways and CALCOCO2/NDP52 and S1009 are major  autophagy-associated genes in AT2 cells that contribute to the AhR-mediated allergic airway  inflammation.
Conclusion: These results suggest that AhR in AT2 cells functions as a protective mechanism  against allergic airway inflammation through controlling cell autophagy.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for PBS or CRE treated AT2 cells from AhRfl/fl mice and Sftpc-Cre;AhRfl/fl mice

***Please note that the records have been updated with raw data on June 14, 2022***

first: Ji

last: Wang

first: Yilin

last: Zhao

first: Xin

last: Zhang

first: Wei

last: Tu

first: Rongjun

last: Wan

first: Yingchun

last: Shen

first: Yan


title: Modulation of cAMP levels by a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria

city: London

first: Gerald

last: Larrouy-Maumus

address: Exhibition Road

country: United Kingdom

institute: Imperial College London

summary: The second messenger, cyclic-AMP (cAMP) is conserved across all taxa of life. It is involved in propagating the signal from environmental stimuli and converting it into a response. In bacteria such as M. tuberculosis (Mtb), P. aeruginosa, V. cholerae and B. pertussis, cAMP has been implicated in virulence, regulation of metabolism and gene expression. Cyclic AMP signalling in mycobacteria is especially complex – with 16 enzymes that produce cAMP in Mtb alone. By discovery of a novel, actinobacteria conserved enzyme that degrades cAMP, we have developed a tool to modulate cAMP levels in mycobacteria. By using a combination of metabolomics, bioenergetics and time-to-kill assays, we show that when this enzyme is overexpressed in the model organism M. smegmatis, there is a 3.3 -fold decrease in intracellular cAMP levels. This was concomitant with altered cell envelope permeability, compromised bioenergetics and most importantly, led to a decrease in the tolerance to various frontline antimicrobials. Taken together, this work provides clear evidence that cAMP is involved in antimicrobial tolerance in mycobacteria and that this may represent a promising new target for antimicrobial development.

overall_design: 6 samples, technical triplicates (i.e. 3 samples) of the empty vector control strain of M. smegmatis and technical triplicates (i.e. an additional 3 samples) of M. smegmatis over-expressing the rv1339 gene.

first: Michael

last: Thomson

first: Yi

last: Liu

first: Kanokkan

last: Nunta

first: Ashleigh

last: Cheyne

first: Nadia

last: Fernandes

first: Richard

last: Williams

first: Acely

last: Garza-Garcia


title: Single-cell RNA sequencing of the interface tissue after mouse anterior-cruciate ligament reconstruction (ACLR)

first: Takayuki

last: Fujii

summary: Transcriptomic profile of the cells infiltrated into the interface tissue after mouse ACLR surgery at single-cell resolution

overall_design: ACLR surgery was performed in C57BL/6 WT mice. Cells that infiltrated into the surrounding tissue of the grafted tendon after ACLR surgery were harvested, enzymatically digested, and then non-erythroid cells were obtained by flow cytometry at postoperative day 1, 3, 7, and 14. Control samples were obtained from naïve bone cells in the same area of ACLR surgery.

first: K

middle: H

last: Park-Min

first: Scott

last: Rodeo

first: Lionel

last: Ivashkiv


title: Effect of TGFb on TCR-induced OT-I T cell gene expression

status: Public on Jun 10 2022

city: Leeds

first: Robert

last: Salmond

address: Wellcome Trust Brenner Building, St James's University Hospital Trust

institute: University of Leeds

summary: To investigate the impact of TGFb on CD8 T cell activation and gene expression, we activated TCR transgenic OT-I T cells in the presence or absence of recombinant TGFb in vitro

overall_design: OT-I T cells were stimulated for 24h with SIITFEKL (T4) peptide in the presence or absence of TGFb and gene expression profiling analysis using RNA-Seq was performed


title: ADAR1 mutation causes ZBP1-dependent immunopathology

city: Seattle

first: Andrew

last: Oberst

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

summary: The RNA editing enzyme ADAR1 is essential for suppression of innate immune activation and pathology caused by aberrant recognition of self-RNA, a role it carries out by disrupting the duplex structure of endogenous double-stranded RNA species. A point mutation in the Z-nucleic-acid binding domain (ZBD) of ADAR1 is associated with severe autoinflammatory disease. ZBP1 is the only other ZBD-containing mammalian protein and its activation can trigger both cell death and transcriptional responses via the kinases RIPK1 and RIPK3, and the protease caspase-8. Here, we show that the pathology caused by ADAR1 ZBD mutation is driven by activation of ZBP1. We found that ablation of ZBP1 fully rescued the overt pathology caused by ADAR1 mutation, without reversing the underlying inflammatory program caused by this mutation. While loss of RIPK3 partially phenocopied the protective effects of ZBP1 ablation, combined deletion of caspase-8 and RIPK3, or of caspase-8 and MLKL, unexpectedly exacerbated the pathogenic effects of ADAR1 mutation. These findings indicate that ADAR1 is a negative regulator of sterile ZBP1 activation, and that ZBP1-dependent signaling underlies the autoinflammatory pathology caused by mutation of ADAR1.

overall_design: Comparative gene expression in spleens of 23 day old mice of ADAR P195A/p150- mutants and PKR and ZBP1 knockouts.

first: Nicholas

last: Hubbar

first: Joshua

middle: M

last: Ames

first: Megan

last: Maurano

first: Lan

last: Chu

first: Kim

last: Somfleth

first: Nandan

last: Gokhale

first: Margo

last: Werner

first: Jessica

last: Snyder

first: Katrina

last: Lichauco

first: Ram

last: Savan

first: Daniel

last: Stetson


title: Global transcriptional and circadian regulation in a halotolerant cyanobacterium Halothece sp. PCC7418

status: Public on Jun 09 2022

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

institute: Meijo University

summary: Substantial evidence has been accumulated about the molecular basis underlying halotolerance; however, insights into the regulatory networks for relevant genes and mechanisms of their interplay remain elusive. Here, we present a comprehensive transcriptome investigation, using RNA sequencing, of specific metabolic pathways and networks in a halotolerant cyanobacterium, Halothece sp. PCC7418, including the circadian rhythm profile. Dissecting the transcriptome presented the intracellular regulation of gene expressions, which was linked with ion homeostasis, protein homeostasis, biosynthesis of compatible solutes, and signal transduction, for adaptations to high-salinity environments. The efficient production and distribution of energy were also implicated in this acclimation process. Furthermore, we found that high-salinity environments had a dramatic effect on the global transcriptional expression regulated by the circadian clock. Our findings can provide a comprehensive transcriptome for elucidating the molecular mechanisms underlying halotolerance in cyanobacteria.

overall_design: Halothece sp. PCC7418 cells growing in low salinity (0.5 M NaCl) or high salinity (2.5 M NaCl) were analyzed under continuous light (LL) by RNA-seq analysis. The cells were harvested at LL4, 10, 16, 22, 28, and 34 under LL condition.

first: Rungaroon

last: Waditee-Sirisattha

first: Hiroshi

last: Ito


title: Microenvironmental Sensing by Fibroblasts Controls Macrophage Population Size

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

summary: Animal tissues are comprised of diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF- target genes are both regulated by cell density. We found YAP1, the transcriptional co-activator of the Hippo signaling pathway, directly regulates expression of Csf1, the lineage-specific growth factor for macrophages, through an enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition.

overall_design: For analyzing transcriptional response of MEFs in different stress conditions, 100,000/well (10,000/cm2) MEFs were plated in DMEM. For oxidative stress and osmotic stress, 10 µM sodium arsenite (Sigma Aldrich) or 100 mM NaCl (American Bio) were added to the cells after overnight culture for 3 hours. For ER stress, 1 µM thapsigargin (Cayman) was added for 10 hours after overnight culture. For glucose depletion, glutamine depletion and hypoxia, after overnight culture, cells were incubated in glucose-free DMEM (Gibco) or glutamine-free DMEM (Gibco), or placed in a hypoxia chamber set at 0.1% oxygen for 10 hours.

first: Naomi

last: Philips

first: Ruslan

last: Medzhitov


title: Altered expressions of transfer RNA-derived small RNAs and microRNAs in the vitreous humour of proliferative diabetic retinopathy.

city: Changsha

first: Yedi

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

country: China

institute: The Second Xiangya Hospital, Central South University

summary: To reveal the expression profiles of transfer RNA-derived small RNA (tsRNA)s and microRNA (miRNA)s in the vitreous humour of proliferative diabetic retinopathy (PDR).

overall_design: The vitreous humour samples of PDR patients and the control group were collected for the study. Small RNA sequencing was conducted to assess the expression profiles of tsRNAs and miRNAs in both groups.

first: Yan

last: Yang

first: Chun

last: Ding


title: Long-distance association of topological boundaries through nuclear condensates

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

overall_design: Refer to individual Series


title: Bulk RNA sequencing of the interface tissue after mouse anterior-cruciate ligament reconstruction (ACLR)

first: Takayuki

last: Fujii

summary: Transcriptomic profile of the myeloid cells infiltrated into the interface tissue after mouse ACLR surgery

overall_design: ACLR surgery was performed in C57BL/6 WT mice. Cells that infiltrated into the surrounding tissue of the grafted tendon after ACLR surgery were harvested, enzymatically digested, and then myeloid cell populations were sorted by flow cytometry at postoperative day 1 and 14.

first: K

last: Park-Min

first: Scott

last: Rodeo

first: Lionel

last: Ivashkiv


title: Genome-wide gene expression Oryzias latipes under antibiotics (ampicillin and erythromycin)

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

institute: Korea Institute of Science and Technology

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Oryzias latifes (Korea native ricefish) upon treatment of mock, ampicillin and erythromycin

overall_design: mRNA from three fish of Oryzias latifes incubated with Amp (3.125 μg/ml) and (Ery 3.9 μg/ml) with technical duplicate in each biological replicate

first: Ju

last: Yoon

first: Jun

first: Ki

last: Moon