title: b2 integrins inhibit suppressor of cytokine signaling but also inflammation-associated gene expression in dendritic cells (DC), in line with attenuated T cell activation in autoimmune encephalomyelitis

city: Mainz

first: Christoph

last: Hieber

department: Dermatology

country: Germany

institute: University Medical Center Mainz

summary: Heterodimeric b2 integrin surface receptors (CD11a-d/CD18) are specifically expressed by leukocytes that contribute to pathogen uptake, cell migration, immunological synapse formation and cell signaling. In human, loss of CD18 expression results in leukocyte adhesion deficiency syndrome (LAD-)1, largely characterized by recurrent severe infections.. All available mouse models display a constitutive and ubiquitous knockout of either a or the common b2 (CD18) subunit, which hampers analysis of the cell type-specific role of b2 integrins in vivo. To overcome this limitation, we generated a CD18 gene floxed mouse strain. Offspring generated from crossing with CD11c-Cre mice displayed efficient knockdown of b2 integrins specifically in dendritic cells (DC). Stimulated b2 integrin-deficient splenic DC showed enhanced cytokine production, and concomitantly elevated activity of signal transducers and activators of transcription (STAT) 1, 3 and 5, as well as impaired expression of suppressor of cytokine signaling (SOCS) 2-6 as assessed in bone marrow-derived (BM)DC. Paradoxically,, these BMDC also showed attenuated expression of genes involved in inflammatory signaling. In line, in experimental autoimmune encephalomyelitis mice with a conditional DC-specific b2 integrin knockdown presented with a delayed onset and milder course of disease, associated with lower frequencies of T helper cell (Th)1/Th17 in the inflamed spinal cord. Altogether, our mouse model may prove a valuable tool to study leukocyte-specific functions of b2 integrins in vivo.

overall_design: We isolated bone marrow cells of CD18fl/fl and CD18ΔCD11c mice and cultured them for 10 days in GM-CSF containing medium to induce differentiation to dendritic cells (BMDC). BMDC were either treated with 100 ng/mL LPS for 24 h or left untreated. > 10^6 cells of each samples were lysed and total RNA was purified for sequencing.

first: Matthias

last: Bros


title: Understanding the development of oral epithelial organs through single cell transcriptomic analysis

status: Public on May 27 2022

city: LOS ANGELES

first: Jimmy

last: Hu

state: CA

address: 650 Charles E Young DR S, CHS 73-041

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: During vertebrate craniofacial development, the oral epithelium begins as a simple and morphologically homogeneous tissue. It then gives rise to locally complex structures, including the developing teeth, salivary glands, and taste buds. While there is significant knowledge about the molecular mechanisms regulating the morphogenesis of these organs at later stages, how the epithelium is initially patterned and specified to generate diverse cell types and organs remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations, we conducted single cell RNA-sequencing using mandibular epithelia from embryonic day (E) 12.0 mouse embryos and whole mandibles from E9.5 mouse embryos. The goal of this study is therefore to generate a detailed transcriptional atlas of the developing mandibular epithelium.

overall_design: For the E12.0 epithelial dataset, mandibular epithelial cells from six K14Cre;R26mT/mG mouse embryos from the same litter were separated from the mesenchyme, dissociated and sorted using fluorescence-activated cell sorting (FACS) to isolate GFP+ single epithelial cells. The single pooled population was analyzed using 10X scRNA-seq. For the E9.5 dataset, mandibular arches including both the epithelium and mesenchyme were dissected from eight embryos and dissociated. The single pooled population was analyzed using 10X scRNA-seq.

middle: K

first: Qianlin

last: Ye


title: Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in Staphylococcus aureus

status: Public on May 30 2022

city: Omaha

first: MARAT

last: SADYKOV

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1.

overall_design: Comparative gene expression profiling analysis if RNA-seq data for UAMS-1 WT, codY, ccpA, and CodYCcpA

first: Logan

last: Bulock

first: Jongsam

last: Ahn

first: Dhananjay

last: Shinde

first: Sanjit

last: Pandey

first: Cleofes

last: Sarmiento

first: Vinai

middle: C

last: Thomas

first: Kenneth

middle: W

last: Bayles

first: Marat

middle: R

last: Sadykov


title: MET∆14 promotes a ligand-dependent, AKT-driven invasive growth

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: MET is an oncogene encoding the tyrosine kinase receptor for hepatocyte growth factor (HGF). Upon ligand binding, MET activates multiple signal transducers, including PI3K/AKT (survival/migration), STAT3 (differentiation), and MAPK (proliferation). When mutated or amplified, MET becomes a "driver" for the onset and progression of cancer. The most frequent mutations in the MET gene affect the splicing sites of exon 14, leading to its "skipping" from mRNA and consequent deletion of the receptor's juxtamembrane domain (MET∆14). It is currently believed that, as in gene amplification, MET∆14 kinase is constitutively active.  Analysis of MET in carcinoma cell lines showed that MET∆14 strictly depends on HGF for kinase activation. Compared to WT MET, ∆14 is sensitive to lower HGF concentrations, with more sustained kinase response, ultimately leading to a robust phosphorylation of AKT, without affecting MAPK or STAT3. This altered kinase response leads to a distinctive transcriptomic signature. Functional studies revealed that ∆14 activation is predominantly responsible for enhanced protection from apoptosis and cellular migration. Thus, the unique HGF-dependent ∆14 oncogenic activity suggests consideration of HGF in the tumour microenvironment to select patients for clinical trials.

overall_design: A549 and NCI-H596 cells linew were treated with HGF for  0, 3, 6 and 12 hours

first: Marina

last: Cerqua

first: Orsola

last: Botti

first: Maddalena

last: Arigoni

first: Noemi

last: Gioelli

first: Guido

last: Serini

first: Carla

last: Boccaccio

first: Paolo

middle: M

last: Comoglio

first: Dogus

last: Altintas


title: Mouse slurry colons 2 weeks

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary:
Defining the complex role of the microbiome in colorectal cancer (CRC) and the discovery of novel, pro-tumorigenic microbes are areas of active investigation. In the present study, culturing and reassociation experiments revealed that toxigenic strains of Clostridioides difficile drove the tumorigenic phenotype of a subset of CRC patient-derived mucosal slurries in germ-free ApcMin/+ mice. Tumorigenesis was dependent on the C. difficile toxin TcdB and was associated with induction of Wnt signaling, reactive oxygen species, and pro-tumorigenic mucosal immune responses marked by infiltration of activated myeloid cells and interleukin-17 (IL-17)-producing lymphoid and innate lymphoid cell subsets. In vitro, purified TcdB directly induced DNA strand breaks at low picomolar concentrations. These findings suggest that chronic colonization with toxigenic C. difficile is a potential driver of CRC in patients.
Comparing scRNA-seq from mouse colon tissue 2 weeks after inoculation with different bacterial slurries

overall_design: 2 groups of mice, each given 1 slurry gavage. 3 samples from each group. Samples '9' and '15' are technical replicates.

middle: S

first: Nicholas

middle: O

last: Markham

first: Julia

middle: L

last: Drewes


title: Transcriptome of Aged and Unaged E. coli populations

city: Carson

first: Karin

middle: E.

last: Kram

state: California

address: 1000 E. Victoria St.

department: Biology

institute: California State University Dominguez Hills

summary: Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogenous environment. During this incubation, E. coli acquires mutations that are selected for in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogenous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10-days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified putative mutations in the regulatory gene sspA, as well as other genes, that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation, while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive.

overall_design: Analysis of 2 replicates of the transcriptome of E. coli in populations that are unaged (grown overnight) and aged (incubated for 10 days, then frozen and regrown).

middle: E

first: Autumn

last: Henderson


title: Absent in Melanoma 2 (AIM2) Regulates the Stability of Regulatory T Cells

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Absent in melanoma 2 (AIM2) is a cytosolic dsDNA sensor that has been broadly studied for its role in inflammasome assembly. However, little is known about the function of AIM2 in adaptive immune cells. The purpose of this study was to investigate whether AIM2 has a cell-intrinsic role in CD4+ T cell differentiation or function. We found that AIM2 is expressed in both human and mouse CD4+ T cells and that its expression is affected by T cell receptor (TCR) activation. Naïve CD4+ T cells from AIM2-deficient (Aim2-/-) mice showed higher ability to maintain forkhead box P3 (FOXP3) expression in vitro, while their capacity to differentiate into T helper (Th)1, Th2 or Th17 cells remained unaltered. Transcriptional profiling by RNA sequencing showed that AIM2 might affect regulatory T cell (Treg) stability not by controlling the expression of Treg signature genes, but through the regulation of the cell's metabolism. In addition, in a T cell transfer model of colitis, Aim2-/--naïve T cells induced less severe body weight loss and displayed a higher ability to differentiate into FOXP3+ cells in vivo. In conclusion, we show that AIM2 function is not confined to innate immune cells but is also important in CD4+ T cells. Our data identify AIM2 as a regulator of FOXP3+ Treg cell differentiation and as a potential intervention target for restoring T cell homeostasis.

overall_design: Sequencing of mRNA libraries from WT and AIM2 KO splenic naïve CD4+ T cells and from WT and AIM2 KO CD4+ T cells cultured in Treg conditions for 2 days

first: Beatriz

last: Lozano-Ruiz

first: Claudia

last: Martínez-Cardona

first: David

last: Moreno

last: Cortazar

first: Amalia

last: Tzoumpa

first: Joanna

last: Picó

first: Gloria

last: Peiró

first: Juanjo

last: Lozano

first: Pedro

last: Zapater

first: Rubén

last: Francés

first: José

last: González-Navajas


title: Gene expression in different culture conditions in breast cancer cell lines

status: Public on May 26 2022

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

summary: Breast cancer has a high risk of recurrence and distant metastasis after remission. Controlling distant metastasis is important for reducing breast cancer mortality, but accomplishing this goal remains elusive. In this study, we aimed to find a way to control distant metastasis using a model that mimics the various forms of tumor cells present during distant metastasis. Breast cancer cells were cultured under two-dimensional (2D) adherent, tumor sphere (TS), and reattached (ReA) culture conditions to mimic primary tumors, circulating tumor cells, and metastasized tumors, respectively. ReA cells demonstrated increased TS formation, enhanced invasion capacity, and a higher frequency of ESA⁺CD44⁺CD24⁻ cells compared to the original 2D-cultured parental cells. In addition, RNA sequencing identified the cholesterol synthesis pathway as one of the most significantly increased pathways in TS and ReA cells compared to parental cells, which was verified by measuring intracellular cholesterol levels. Furthermore, the pharmacological inhibition of the cholesterol synthesis pathway decreased the ability of cancer cells to form TSs and invade. Our results suggest that the cholesterol synthesis pathway plays an important role in the distant metastasis of breast cancer cells by augmenting TS formation and invasion capacity.

overall_design: mRNA expression profiles of the breast cancer of Homo sapiens with different culture conditions were examined by Illumina Nova-seq 6000

first: Kim

middle: H

last: Yeon


title: Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence

city: Stanford

last: Belk

address: 450 Serra Mall

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: Refer to individual Series


title: Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence [Perturb-seq]

summary: T cell exhaustion limits anti-tumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic antigen stimulation assay, we performed genome-wide CRISPR/Cas9 screens to systematically discover genetic regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of several epigenetic regulators, including members of the INO80 and BAF chromatin remodeling complexes, improved T cell persistence in tumors. In vivo paired CRISPR perturbation and single-cell RNA sequencing revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of terminal exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a-depletion limited the global acquisition of chromatin accessibility associated with T cell exhaustion and led to improved anti-tumor immunity after adoptive cell therapy. In summary, we provide a comprehensive atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of the epigenetic state of T cell exhaustion can improve T cell responses in cancer immunotherapy.

overall_design: Perturb-seq samples from mouse T cells sorted from MC-38 tumors.

first: Winnie

last: Yao

first: Nghi

last: Ly

first: Ansuman

last: Satpathy


title: Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence [ATAC-seq]

first: Julia

overall_design: ATAC-seq samples from mouse and human T cells with either (1) no genetic perturbation, (2) a single-targeting control sgRNA, or (3) an sgRNA targeting ARID1A.

first: Katherine

last: Freitas


title: Stomatin modulates adipogenesis through ERK pathway and regulates fatty acid uptake and lipid droplet growth

status: Public on May 28 2022

city: Taipi

first: Shao-Chin

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary:
Controlling fatty acid uptake, lipid production and storage, and metabolism of lipid droplets (LDs), is closely related to lipid homeostasis, adipocyte hypertrophy and obesity. We report here that stomatin, a major constituent of lipid rafts, participates in adipogenesis and adipocyte maturation by modulating related signaling pathways. In adipocyte-like cells, increased stomatin promotes LD growth or enlargements by facilitating LD-LD fusion, as well as fatty acid uptake from extracellular environment by recruiting effector molecules, such as FAT/CD36 translocase, to lipid rafts to promote internalization of fatty acids. Stomatin transgenic mice fed with high-fat diets exhibit obesity, insulin resistance and hepatic impairments; however, such phenotypes are not seen if feeding the transgenic animals with regular diets. Inhibitions of stomatin by gene knockdown or OB-1 pharmacological treatments inhibit adipogenic differentiation and LD growth through downregulation of PPARγ pathway. Effects of stomatin on PPARγ involve ERK signaling; however, an alternate pathway may also exist.
Differential expression analyses by microarray were performed comparing stomatin-knockdown and control 3T3-L1 adipocyte-like cells.

overall_design: Gene modified 3T3-L1 were differentiated to day7 and harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Chi-hung

last: Lin


title: PU.1 and MYC transcriptional network defines a synergist drug response to combined KIT and LSD1 inhibition in acute myeloid leukemia

status: Public on May 29 2022

city: Portland

first: Theodore

middle: P

last: Braun

state: Oregon

address: 2720 S Moody Ave

institute: Oregon Health and Science University

summary: KIT mutant acute myeloid leukemia (AML) confers a worse prognosis for patients in a subtype of AML that has an otherwise favorable outcome. Here, we demonstrate that lysine specific demethylase 1 (LSD1) inhibition potentiates cytotoxic effect of KIT inhibition in KIT mutant AML. We identified loss of PU.1 binding to be a key feature of LSD1 inhibition, contributing to a decrease in MYC enhancer and promoter activation. This loss of MYC enhancer/promoter activation results in decreased MYC expression and binding at proliferation associated promoters decreasing cell cycle progression. Our results nominate PI3K/AKT pathway inactivation as a key feature of KIT and LSD1 inhibition ultimately leading to decreased MYC and blocking LSD1 from activating its targets. Our findings support a mechanistic model for synergy between dual KIT and LSD1 inhibition and suggest this combination should be investigated in a clinical setting.

overall_design: Kasumi-1 and patient sample cells were analyzed by multi-omic profiling including bulk RNA seq, scRNAseq, CUT&Tag, CUT&RUN, and ATACseq to understand the mechanism of KIT and LSD1 inhibitor synergy.

first: Brittany

last: Smith

first: Jake

last: VanCampen


title: Mettl3-mediated m6A modification controls postnatal liver development by modulating Hnf4a-centred regulatory network [Primary hepatocyte RNA-seq]

city: Guangzhou

first: Yan

last: Xu

state: Guangdong

address: No. 600 Tianhe Road

country: China

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: RNA sequencing of primary hepatocytes from Control and and hepatocyte-specific Mettl3 knockout with ALB-Cre (Mettl3 cKO) mice after Actinomycin D treatment.

overall_design: Primary hepatocytes were treated with 5 μM Actinomycin D for 0 hour, 2 hours, and 6 hours. Differentially expressed genes were compared between WT and Mettl3 cKO mouse primary hepatocytes at each time points after Actinomycin D treatment.

first: Xinmei

last: Kang

first: Zhuowei

last: Zhou

first: Qi

last: Zhang


title: Identification of a LncRNA EPR—>METTL7A1 pathway modulating  translation of select genes (Polysomes)

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

summary: EPR is a long non-coding RNA (lncRNA) that controls cell proliferation in mammary gland cells by regulating gene transcription and, here, we report on Mettl7a1 as a target of EPR. We show that the lncRNA induces Mettl7a1 transcription by remodeling the 3-dimensional chromatin structure at the Mettl7a1 locus. Our data indicate that METTL7A1 participates in the EPR-dependent pathway that antagonizes TGF-β signaling. METTL7A1 is absent in tumorigenic murine mammary gland cells and its human ortholog (METT7A) is downregulated in breast cancers. Importantly, expression of METTL7A1 in 4T1 tumorigenic cells reduces their transformation potential, and the putative methyltransferase activity of METTL7A1 appears dispensable for its biological functions. METTL7A1 is a cytoplasmic protein and, from a mechanistic perspective, interacts with factors implicated in the early steps of mRNA translation, associates with ribosomes, and affects the levels of select proteins without substantial changes in mRNA abundance. Our data suggest the possibility that METTL7A1 conveys the transcriptional regulation operated by EPR into specific changes of mRNA translation.

overall_design: Polysomal and sub-polysomal RNA isolated upon sucrose gradient centrifugation from Mock and Mettl7a1 4T1 transfected cells. RNA was equenced in triplicates 12 samples.

first: Paola

last: Briata

first: Luca

last: Caputo

first: Ettore

last: Zapparoli

first: Gabriele

last: Bucci

first: Roberto

last: Gherzi


title: Mettl3-mediated m6A modification controls postnatal liver development by modulating Hnf4a-centred regulatory network [Liver RNA-seq]

summary: RNA sequencing of livers tissues from control and hepatocyte-specific Mettl3 knockout with ALB-Cre (Mettl3 cKO) mice at different time points after birth.

overall_design: Control and Mettl3 cKO mouse liver tissues were collected separately at day 1, 1 week, 2 weeks, and 4 weeks after birth. Differentially expressed genes and related pathways were analyzed and compared between Control and Mettl3 cKO livers to show how Mettl3 affects postnatal liver development.


title: CRISPRi DSP-kd in iAT2

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: We performed single cell transcriptomic profiling of induced human pluripotent stem cells (iPSCs)-derived type 2 alveolar epithelial cells (iAT2).  iPSCs stably expressed CRISPRi (dCas9-KRAB) under the control of doxycyline.  iAT2s were transduced with a lentivirus expressing gRNA targeting the transcriptional start site of DSP.  Cells were treated with or without doxycyline to intiate CRISPRi-knockdown.  Prior to capture, cells were labelled with hashing antibodies (HTO).  Cells were captured for 10x Genomics Single cell capture (V3 protocol), and GEX and HTO libraries were sequenced.  HTODemux function was used to demultiplex the samples.  Knockdown of DSP caused cells to cluster separately from wild-type cells.

overall_design: Single-cell transcriptomic analysis of iPSC-derived type 2 alveolar epithelial cells (iAT2) comparing wild-type cells with CRISPRi-mediated knockdown of DSP

first: Rhiannon

last: Werder

first: Carlos

last: Villacorta-Martin

first: Andrew

last: Wilson

first: Jonathan

last: Lindstrom-Vautrin


title: Application of Omni-ATAC to Profile Chromatin Accessibility Before and After Ovarian Tissue Cryopreservation

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

summary: We analyzed chromatin accessibility before and after ovarian tissue cryopreservation.

overall_design: Omni-ATAC analysis on follicles derived from human ovarian cortex.

first: Jennifer

last: Shannon

first: Aishwarya

last: Sundaresan


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ATAC-Seq)

first: Peng

last: Huang

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

summary: The switch from fetal to adult hemoglobin production has been studied in great depth in part because of its relevance to the treatment of hemolobinopathies. Transcription factor BCL11A, which is essential for repression of the fetal beta-type globin (γ-globin) genes after birth, is largely controlled at the level of transcription but the mechanism of BCL11A developmental control is unknown. Here, using a CRISPR-Cas9 screen in human erythroblasts, we identify transcription factor HIC2 as a repressor of BCL11A transcription. HIC2 and BCL11A expression are anti-correlated in fetal and adult erythroblasts. Forced expression of HIC2 in adult erythroblasts silences BCL11A transcription and markedly induces γ-globin expression. HIC2 binds selectively to constituent erythroid developmental BCL11A enhancer to reduce chromatin accessibility and impair access by transcription factor GATA1, resulting in loss of enhancer activity and enhancer-promoter contacts. Conversely, loss of HIC2 in fetal erythroblasts increases enhancer accessibility, enables GATA1 binding and induces BCL11A transcription. HIC2 is unveiled as a critical evolutionarily conserved regulator of globin gene switching by imposing developmental control on the BCL11A gene.

overall_design: HIC2 overexpression and knockout


title: Expression data of Arabidopsis leaves (WT and PIF5) during extended darkening of an individual leaf

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

summary: Loss-of-function allele of the PIF5 transcription factor reveals a molecular feedback loop, in which specific metabolites modulate the energy status and hormone-dependent signalling cascades that regulates leaf senescence

overall_design: Samples of leaf blades were harvested at noon, at 0 days (light/T0) and after 1, 3 and 6 days of individual darkening treatment for both WT and mutant. For pif5-621, samples for an additional time point after darkening were collected at 12 days of IDL (T12).

first: Daniela

last: Liebsch

first: Marta

last: Juvany

first: Zhonghai

last: Li

first: Hou-ling

first: Agnieszka

last: Ziolkowska

first: Daria

last: Chrobok

first: Xing

last: Wen

first: Helena

last: Janečková

first: Bastiaan

last: Brouwer

first: Pernilla

last: Lindén

first: Nicolas

last: Delhomme

first: Hans

last: Stendlund

first: Thomas

last: Moritz

first: Per

last: Gardeström

first: Hongwei

last: Guo

first: Olivier

last: Keech


title: Isha is a su(Hw) mRNA-binding protein required for insulator function [RIP-seq]

city: Bethesda

first: Elissa

last: Lei

state: MD

address: 50 South Drive

department: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics

institute: NIDDK/NIH

summary: Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here we utilized RNA-affinity pull down coupled with mass spectrometry to identify a novel RNA-binding protein, Isha, that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif (RRM) and RNA Polymerase II CTD-interacting domain (CID). We found that Isha physically interacts with total and elongating RNA Pol II and associates with chromatin at the 5’ end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with gypsy factor CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.

overall_design: Examining the enriched su(Hw) and other transcripts with Isha in vivo.

first: Indira

last: Bag

first: Yang

last: Chen


title: Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection

city: New York

first: Roham

last: Parsa

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary: The intestinal epithelium comprises the body’s largest surface exposed to viruses. Additionally, the gut epithelium hosts a large population of intraepithelial T lymphocytes, or IELs, although their role in resistance against viral infections remain elusive. By fate-mapping T cells recruited to the murine intestine, we observed accumulation of newly recruited CD4+ T cells after infection with murine norovirus CR6 and adenovirus type-2 (AdV), but not reovirus. CR6 and AdV-recruited intraepithelial CD4+ T cells co-express Ly6A and CCR9, exhibit T helper 1 and cytotoxic profiles and confer protection against AdV in vivo and in an organoid model in an IFN-g-dependent manner. Ablation of the T cell receptor (TCR) or the transcription factor ThPOK in CD4+ T cells prior to AdV infection prevented viral control, while TCR ablation during infection did not impact viral clearance. These results uncover a protective role for intraepithelial Ly6A+CCR9+CD4+ T cells against enteric adenovirus.

overall_design: RNAseq analysis of recently recruited small intestinal intraepithelial CD4+CD62L-Tomato+ T cells 10 days post murine Adenovirus-2 infected or PBS treated mice.

first: Mariya

last: London

first: Tiago

middle: B

last: Rezende de Castro

first: Bernardo

last: Reis

first: Julian

last: Buissant des Amorie

first: Jason

middle: G

last: Smith

first: Daniel

last: Mucida


title: Comparison of the Inflammatory Circuits in Psoriasis Vulgaris, Non-Pustular Palmoplantar Psoriasis, and Palmo-Plantar Pustular Psoriasis

status: Public on May 25 2022

first: James

last: Krueger

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: In this study, our aim was to investigate the potential inflammatory pathways underlining PV, PPPP, and NPPP, through histologic and immunohistochemical characterization of the inflammation and gene expression profiling in skin samples of participants with PPPP, NPPP, PV (without palmo-plantar involvement), and healthy controls.

overall_design:
40 participants were enrolled, comprising 10 healthy participants, and 10 participants each with PPPP, NPPP, and PV.

**Please note that raw data is not included to protect patient privacy.  Innovaderm is the Sponsor of the Study and they do not approve the release of individual level patient data**

first: Sandra

last: Garcet

first: Claire

middle: Q

last: Wang

first: Robert

last: Bissonnette


title: Sema3d restrained Hepatocellular carcinoma progression through inactivating Pi3k/Akt signaling via interact with FLNA

city: Changsha

first: Yiming

last: Li

state: Hunan

address: 78 Xiangya road

department: Department of Surgery

institute: Xiangya Hospital, Central South University

summary: Purpose: High throughput RNA-seq has provided an efficient and convenient access to screening substantial differentially expressed genes (DEGs). The goals of this study are to screen out Sema3d-regulated DEGs of HCC cells by utilizing RNA-sequencing and to furtherly identify specific biological function-related gene subset from Sema3d-regulated DEGs. Method: Firstly, HCCLM3 cells were seperated into two groups and respectively transfected with lentivirus-delivered Sema3d and control. We cultured these cells with DMEM containing 10% FBS serum. 48 hours later, cells of two groups were harvested by Trizol RNA isolater and examined expression difference of Sema3d, and then analyzed by High througput RNA-sequencing. Conclusion: Using next generation high throughput RNA-sequencing technology and using |log2(FoldChange)|>1 and Qvalue<0.05 as a cutoff for statistic analysis, we identified 75 positive-regulated DEGs and 282 negative-regulated DEGs were identified. Finally, pathway and process enrichment analysis identified a series of Sema3d regulated DEGs.

overall_design: HCCLM3 cells were seperated into two groups and respectively transfected with lentivirus-delivered Sema3d and control. We cultured these cells with DMEM containing 10% FBS serum. 48 hours later, cells of two groups(3 Samples of each group) were harvested by Trizol RNA isolater and examined expression difference of Sema3d, and then analyzed by High througput RNA-sequencing. Using next generation high throughput RNA-sequencing technology and using |log2(FoldChange)|>1 and Qvalue<0.05 as a cutoff for statistic analysis.

first: Cong

last: Xu

first: Bo

last: Sun

first: Fangjing

last: Zhong

first: Momo

last: Cao

first: Lianyue

last: Yang


title: Isha is a su(Hw) mRNA-binding protein required for insulator function [ChIP-seq]

first: Elissa

last: Lei

overall_design: Examination of overlapping of Isha with insulator proteins Su(Hw), CP190 and Mod(mdg4) genome wide in Kc167 embryonic cell lines and also to investigate whether association of these insulator factors are dependent on Isha.

first: Indira

last: Bag

first: Yang

last: Chen


title: Isha is a su(Hw) mRNA-binding protein required for insulator function

overall_design: Refer to individual Series


title: Telomeric 8-Oxoguanine Drives Rapid Premature Senescence in the Absence of Telomere Shortening

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

summary: Oxidative stress is a primary cause of cellular senescence and contributes to the pathogenesis of numerous human diseases. Oxidative damage to telomeric DNA is proposed to trigger premature senescence by accelerating telomere shortening. Here we tested this model directly using a precision tool to produce the common base lesion 8-oxoguanine (8oxoG) exclusively at telomeres in human fibroblast and epithelial cells. A single induction of telomeric 8oxoG is sufficient to trigger multiple hallmarks of p53-dependent senescence. Telomeric 8oxoG activates ATM and ATR signaling, and enriches for markers of telomere dysfunction in replicating, but not quiescent cells.  Acute 8oxoG production fails to shorten telomeres, but rather generates fragile sites and delayed mitotic DNA synthesis at telomeres, indicative of impaired replication. Based on our results we propose that oxidative stress promotes rapid senescence by producing oxidative base lesions which drive replication-dependent telomere fragility and dysfunction in the absence of shortening and shelterin loss.

overall_design: RNA-seq on 3 cells lines. Untreated and 24 hours following induction of 8oxoG at telomeres.

first: Ryan

last: Barnes

first: Patricia

last: Opresko


title: Induction of mouse totipotent stem cells by a defined chemical cocktail [scRNA-seq]

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

summary: We demonstrate induction and long-term maintenance of totipotent stem cells (TotiSCs) from mouse pluripotent stem cells (PSCs) by a combination of three small molecules, TTNPB, 1-Azakenpaullone, and WS6. These cells, which we designated as ciTotiSCs (chemically induced totipotent stem cells), resembled mouse totipotent 2C-embryo stage cells at both transcriptome and epigenome level.

overall_design: ciTotiSC single-cell RNA-seq and single-cell RNA-seq of tdTomato+ cells from placenta and yolk sac of E13.5 chimera

first: Yanyan

last: Hu

first: Yuanyuan

first: Yuxia

last: Zhang

first: Jiawei

last: Yu

first: Xin

first: Zeran

last: Jia

first: Dan

first: Yinqing

first: Tianhua

last: Ma

first: Kang

last: Liu

first: Sheng

last: Ding


title: Induction of mouse totipotent stem cells by a defined chemical cocktail [bulk RNA-seq]

overall_design: Bulk RNA-seq of P1, P2, P4, P8 ciTotiSC and OG2 mESC. Each has two replicates.

last: Wang

last: Li


title: Genome-wide analysis of Wild Type and Relb-/- MEFs

city: Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Road

department: Immunology

country: India

institute: National Institute of Immunology

summary: Recent studies indicated that the NF-kB RelB subunit may play roles beyond immune modulations. The molecular mechanism that may allow RelB to engage in such diverse physiological activities remains unclear. To better understand the RelB-driven transcriptome, therefore, we subjected wild type and Relb-/- mouse embryonic fibroblast (MEF) to microarray analyses using Illumina MouseRef-8 v2.0 Expression BeadChip. We propose that our transcroptomic analyses will help linking RelB to other important cellular pathways.

overall_design: Total RNA was isolated from mouse embryonic fibroblast(MEFs) of Wild Type and Relb-/- genetic background  and microarray was performed.

first: Balaji

last: Banoth

first: Manti

middle: K

last: Saha


title: RNA-seq of induced pluripotent stem cell or somatic stem cell-derived corneal epithelial cell sheet

city: Suita

first: Yu

last: Yoshinaga

state: Osaka

address: 2-2 Yamadaoka

department: Ophthalmology

country: Japan

institute: Osaka University Graduate School of Medicine

summary: Our previous study indicate that corneal epithelial cell sheet (CEPS) derived from stem cells, including induced pluripotent stem cells (iPSCs), has low immunogenicity. Therefore, we hypothesized that CEPS express immunosuppressive molecules. To address this hypothesis, we performed RNA-seq of human iPSC-derived CEPS (iCEPS) and somatic stem cell-derived CEPS (sCEPS) with or without human recombinant IFN-g (rIFN-g) treatment.

overall_design: Examination of 4 samples; iCEPS and sCEPS with or without rIFN-g treatment.

first: Takeshi

last: Soma

first: Shohei

last: Azuma

first: Kazuichi

last: Maruyama

first: Tomohiko

last: Katayama

first: Daisuke

last: Okuzaki

first: Ryuhei

last: Hayashi

first: Kohji

last: Nishida


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (RNA-Seq)

first: Peng

last: Huang

overall_design: Overexpression


title: miRNA Expression Pattern in Papillary Thyroid Cancer

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

summary:
The aim of this study was to conduct a comparison of tissue miRNA in thyroid cancer (papillary (PTC), follicular (FTC), and microcancer (PTMC)) and  healthy thyroid tissue (Control). The expression level of 798 miRNAs using NanoString technology was examined. ROC curve analysis, and logistic regression modeling were performed. Gene ontology (GO), canonical pathways analysis were used to explore the biological functions of the miRNA target genes.
The study revealed that 10 miRNAs were deregulated in samples of patients with PTC. Pathway analysis showed that miRNA target genes were mainly significantly enriched in endocrine resistance, EGFR tyrosine kinase inhibitor resistance, and pathways in cancer. ROC analysis demonstrated that miR-146-5p, miR-551b-3p, and miR-222-3p can be introduced as a diagnostic tool for PTC (AUC=0.770; 0.740; 0.720; respectively). Validation by qRT-PCR confirmed our findings. The results suggest that tissue miRNAs can potentially be used as predictive biomarkers of PTC in patients.

overall_design: A total of 111 FFFPE samples were included in the study. miRNA profile in 49 PTCs, 7 FTCs, 5 PTMCs and matched 50 normal thyroid samples was analyzed.

first: Magdalena

last: Niemira

first: Mariusz

last: Rogucki


title: Induction of mouse totipotent stem cells by a defined chemical cocktail

first: Pengcheng

last: Tan

type: Methylation profiling by high throughput sequencing

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


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development [CUT&RUN]

overall_design: CD34+ cells derived from human fetal liver and peripheral blood were cultured and differentiated to erythroblasts. H3K27ac and GATA1 CUT&RUN were performed.


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (Capture-C)

overall_design: HIC2 overexpression


title: Genome-wide gene expression Haloferax volcanii under oxidative stress

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 H. volcanii upon treatment of NaOCl.

overall_design:
mRNA from H. volcanii wt and oxsR deletion strains incubated with/without 1.5 mM of NaOCl.

Grant ID: NSF-1642283
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Remodelling Replication Roadblocks: Regulatory Systems that Integrate DNA Replication, Recombination and Protein Modification
Name of the funding source: National Science Foundation

Grant ID: DE-FG02-05ER15650
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Ubiquitin-like Proteins in Protein-conjugation and Sulfur-transfer in Archaea
Name of the funding source: US Department of Energy

Grant ID: NIH-5R01GM057498
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Ubiquitin-like Proteins and Proteasomes of Archaea
Name of the funding source: National Institutes of Health

Grant ID: NSF-1651117
Grantee First Name: Amy
Grantee Last Name: Schmid
Grant title: Elucidating cell cycle regulatory networks across the tree of life.
Name of the funding source: National Science Foundation

Grant ID: NSF-1936024
Grantee First Name: Amy
Grantee Last Name: Schmid
Grant title:  Causes and consequences of regulatory network rewiring under extreme environmental selection
Name of the funding source: National Science Foundation

first: Paula

last: Mondragon

first: Amy

last: Schmid

first: Julie

last: Maupin-Furlow


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (ChIP-Seq)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HIC2 overexpression and knockout


title: RNA-Seq and ChIP-seq analysis of SCC2 in Saccharomyces cerevisiae

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute


title: The HES1 effects on TCL cells

status: Public on May 24 2022

city: Philadelphia

first: Wasik

last: Mariusz

state: Pennsylvania

address: 422 Curie Blvd

institute: University of Pennsylvania

summary: This study investigated the effects of HES1 depletion on TCL cells with RNA expression profile of two ALK+ TCL cells by Highthrough sequencing

overall_design: RNAseq on SUDHL-1 and SUP-M2 cells with wildtype and HES1 depletion

first: Qian

last: Zhang

first: Hong

middle: Y

last: Wang

first: Xiaobin

last: Liu

last: Wasik


title: RNA Seq analysis of SCC2 mutations R787G and G1242V at 9 hours following SCC2 depletion in Saccharomyces cerevisiae

summary: The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 function as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate localization of the Scc2-Scc4 cohesin loader. Here we identify a broad range of Scc2- chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in recruitment of the cohesin loader.  We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and decreased binding of Scc2 at RNA Pol II transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in direct recruitment of Scc2 to RNA pol II transcribed genes. We identified two mutations in the evolutionarily conserved HEAT domain of SCC2 that result in significantly reduced growth, scc2R787G and scc2G1242V. This experiment uses RNA-Seq analysis to study the effect of these mutations on gene expression.

overall_design: RNA Seq analysis of SCC2 WT, R787G, G1242V, and null mutants, at 9 hours following auxin-induced degradation of endgenous SCC2 in Saccharomcyes cerevisiae in triplicate.

first: Mark

last: Mattingly

first: Sofia

last: Munoz

first: Yan

last: Hao

first: Ying

first: Zhihui

last: Wen

first: Laurence

last: Florens

first: Frank

last: Uhlmann

first: Jennifer

last: Gerton


title: The Essential Rhodobacter sphaeroides RSP1056-RSP0847 (CenKR) Two-Component System Regulated Tol-Pal and Cell Envelope Biosynthesis

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: To determine the regulon of RSP1056-RSP0847 TCS (response regulator with DNA-binding domains) we used ChIP-seq to determine the genomic occupancy of RSP0847 in strains with a hyperactive (RSP0847(D56E)), WT, and low activity (ΔRSP1056, RSP0847(D56A)) TCS. We then correlated cenR binding sites with changes in global gene expression between WT and strains with a hyperactive (RSP1056(D56E)) or low activity (ΔRSP1056, RSP0847(D56A)) TCS in RNA-seq experiments.

overall_design: Use ChIP-seq to identify CenR binding sites and RNA-seq to determine how CenR binding affects transcription and define the CenR regulon in Rhodobacter sphaeroides.

first: Bryan

middle: D

last: Lakey

first: François

last: Alberge

first: Daniel

middle: R

last: Noguera

first: Timothy

middle: J

last: Donohue


title: ChIP Seq Analysis of SCC2 in the Presence or Absence of MED14 in Saccharomyces cerevisiae

first: Chris

last: Seidel

summary: The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 function as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate localization of the Scc2-Scc4 cohesin loader. Here we identify a broad range of Scc2- chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in recruitment of the cohesin loader.  We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and decreased binding of Scc2 at RNA Pol II transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in direct recruitment of Scc2 to RNA pol II transcribed genes. We identified two mutations in the evolutionarily conserved HEAT domain of SCC2 that result in significantly reduced growth, scc2R787G and scc2G1242V. This experiment uses ChIP Seq to examine global localization of Scc2 in the presence or absence of MED14.

overall_design: ChIP Seq analysis of SCC2 following auxin-induced degradation of MED14 in Saccharomcyes cerevisiae in triplicate. Saccharomyces pombe cells expressing Myc-tagged Mis4 were added at 1:4 ratio for calibration.


title: Single cell RNA-seq of CDH5+; Rela fl/fl murine hepatic CD4+ T-cells

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Single-cell sequencing of CD4+ T-cells from mouse livers containing RAS-senescent hepatocytes, with or without endothelial-specific knockout of Rela.

overall_design:
multiplexed single cell RNA-seq experiment:
Eight Cdh5:Cre-ERT2;Rela fl / fl mice were used. All eight received a hydrodynamic tail-vein (HDTV) injection of NRAS^G12V-containing transposons, leading to mosaic RAS-senescent hepatocytes. Subsequently, 4 were injected with vehicle control and 4 injected with tamoxifen, leading to endothelial-specific deletion of Rela. CD4+ T cells were flow-sorted from the harvested livers at day 9 post-HDTV injection, labelled with Hashtag oligos, before multiplexing and single cell RNA sequencing.

first: Matthew

last: Hoare


title: Nuclear condensation of CDYL links histone crotonylation and cystogenesis in autosomal dominant polycystic kidney disease

city: Tianjin

first: Xinyi

last: Cao

state: State...

address: Qi Xiangtai Road, HePing District, Tianjin, P.R. China

institute: Tianjin Medical University

overall_design: Refer to individual Series


title: RNA Seq analysis of SCC2 mutations R787G and G1242V at 3 hours following SCC2 depletion in Saccharomyces cerevisiae

overall_design: RNA Seq analysis of SCC2 WT, R787G, G1242V, and null mutants, at 3 hours following auxin-induced degradation of endgenous SCC2 in Saccharomcyes cerevisiae in triplicate.

first: Mark

last: Zhang


title: Nuclear condensation of CDYL links histone crotonylation and cystogenesis in autosomal dominant polycystic kidney disease [RNA-Seq]

summary:
Background:molecular mechanisms coupling cellular metabolisms with the epigenome in cystic cells remains largely unknown
Methods:To investigate the molecular mechanisms underlying the suppression of cyst growth by CDYL overexpression, we generated an engineered ADPKD cell line by stably expressing CDYL with TY1 tag in WT 9-12 human ADPKD cells (CDYL OE). We profiled genome-wide distribution of CDYL through chromatin immunoprecipitation coupled with sequencing (ChIP-seq) analysis in both parental WT 9-12 cells (control) and CDYL OE cells. Genetic overexpression of CDYL reduces histone Kcr. We examined histone Kcr on CDYL-target genes by performing ChIP-seq analyses using antibody recognizing PanKcr and H3K18cr in control and CDYL OE cells.
Results: Using integrative cistromic and transcriptomic analyses, CDYL-regulated cyst-associated genes are identified, whose downregulation depends on CDYL-mediated suppression of histone Kcr.
Conclusions: Thus, through establishing a metabolic niche via nuclear condensation, CDYL connects metabolic changes to transcriptional response via histone Kcr in ADPKD.

overall_design: RNA-sequencing of different conditions: control and CDYL overexpression WT 9-12 cell lines

first: Lin

last: Dang

first: Yupeng

last: Chen


title: Rabies-Infected Neurons Can Be Transcriptomically Characterized Despite Changes in Gene Expression

city: LA JOLLA

first: Edward

middle: M.

last: Callaway

state: CA

address: 10010 N Torrey Pines Rd

department: SNL-C

institute: Salk Institute

summary: Cortical circuit tracing using modified rabies virus can identify input neurons making direct monosynaptic connections onto neurons of interest. However, challenges remain in our ability to establish the cell type identity of rabies-labeled input neurons. While transcriptomics may offer an avenue to characterize inputs, the extent of rabies-induced transcriptional changes in distinct neuronal cell types remains unclear and whether these changes preclude characterization of rabies-infected neurons according to established transcriptomic cell types is unknown. We used single-nucleus RNA sequencing to survey the gene expression profiles of rabies-infected neurons and assessed their correspondence with established transcriptomic cell types. We demonstrated that when using transcriptome-wide RNA profiles, rabies-infected cortical neurons can be transcriptomically characterized despite global and cell-type-specific rabies-induced transcriptional changes. Notably, we found differential modulation of neuronal marker gene expression, suggesting that caution should be taken when attempting to characterize rabies-infected cells with single genes or small gene sets.

overall_design: Rabies-infected nuclei were collected from V1 of wild-type C57BL/6 mice (n=3, 2 females and 1 male) injected with unpseudotyped SAD-B19 G-deleted rabies virus expressing nuclear-localized mCherry (G+RVdG.H2B.mCherry). To enrich for rabies-infected inhibitory neurons, Gad2-Cre mice were crossed to R26-LSL-TVA-LacZ mice to express TVA in inhibitory neurons. These transgenic mice (n=8, 5 females and 3 males) were then injected with EnvA-pseudotyped G-deleted rabies virus expressing nuclear-localized mCherry (EnvA+RVdG.H2BmCherry), which resulted in direct and selective rabies infection of the targeted inhibitory cell class. 10 days after injection, V1 containing mCherry+ rabies-labeled nuclei was dissected and single-nucleus suspensions were prepared from dissected tissue for fluorescence-activated nuclei sorting (FANS) to collect mCherry+ nuclei. snRNA-seq of FANS sorted rabies-infected nuclei was performed using the 10X Genomics 3’ Kit v3.1.

first: Maribel

last: Patiño

middle: M

first: Hongkui

last: Zeng

first: Bosiljka

last: Tasic


title: Thy1 Marks a Distinct Population of Slow-Cycling Stem Cells in the Mouse Epidermis

city: Haifa

first: Marianna

last: Yusupova

address: Technion City

country: Israel

institute: Technion- Israel Institute of Technology

summary:
Here, we report a discrete population of keratinocytes, marked by Thy1, in the basal layer of the IFE. We find that basal keratinocytes expressing differential levels of Thy1 display distinct transcriptional signatures. Thy1+ keratinocytes do not express T cell markers, express a unique transcriptional profile, cycle significantly slower than epidermal progenitors and display significant expansion potential in vitro.
Collectively, these results reveal a distinct stem cell population that plays a critical role in epidermal homeostasis and repair.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of dorsal epidermal skin of 8-week old mice. 5 different cell populations were isolated using fluorescence-activated cell sorting (FACS). RNA-seq samples were prepared and run in two separate batches, and 3 or more biological replicates were obtained for each sample in total.

first: Yaron

last: Fuchs

first: Alona

last: Feldman

first: Stefanie

last: Gerstberger


title: Expression data that humanized anti-RGMa antibody treatment effect on blood-spinal cord barrier in mouse model of locally induced autoimmune encephalomyelitis

city: Yokohama

first: Takeshi

last: Hirata

state: Kanagawa

address: 1000, Kamoshida-cho, Aoba-ku

institute: Mitsubishi Tanabe Pharma Corporation

summary: The aim of this study was to longitudinally evaluate the effect of anti-RGMa antibody on spinal cord pathology in a mouse model of experimental autoimmune encephalomyelitis. The effect of anti-RGMa antibody on accelerated blood-spinal cord barrier repair was revealed by high-field MRI. Immunohistochemical analysis and gene expression analysis were also used to confirm the effects.

overall_design: C57BL/6 mice were divided into three experimental groups: Naive, anti-RGMa antibody-treated, and isotype control antibody-treated. total RNA was isolated from the thoracic spinal cord of the three experimental groups (3 experimental groups x 5-6 mice = 17 mice in total).

first: Atsushi

last: Sasaki

first: Takahide

last: Itokazu

first: Toshihide

last: Yamashita


title: HIC2 represses BCL11A transcription to regulate hemoglobin switching during development

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

institute: Guangzhou Medical University


title: The Evening Complex integrates photoperiod signals to control flowering in rice [ChIP-Seq]

city: Großbeeren

first: Philip

last: Wigge

address: Theodor-Echtermeyer-Weg 1

institute: Leibniz-Institut für Gemüse- und Zierpflanzenbau (IGZ) e.V.

summary: This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.

overall_design: ChIP-seq in WT and elf3-1 lines grown in SD condition.

first: Luis

last: Andrade

first: Katja

last: Jaeger

first: Yunlong

last: Lu


title: Deciphering protective mechanism against human type 2 diabetes through in vitro β cell differentiation

city: Stockholm

first: Menghan

last: Wang

state: please select...

address: Karolinska Vägen 6

institute: Karolinska Institute

summary: To systemically investigate the role of ZnT8 in β cell maturation, we performed single cell RNA-seq in both WT and KO β cells at both S6 (immature) and S7 (mature) stages.  Both WT and KO β cells were obtained from FACS as positive for both INS and NKX6.1. Single cell RNA-seq results revealed that SLC30A8 is mainly involved in β cell maturation process, and further showed that SLC30A8 LOF accelerates β cell maturation and upregulates insulin secretion pathway in mature β cells.

overall_design: In total, 1543 cells with four types of β cell were utilized.

first: Qing

last: Ma

first: Yini

last: Xiao


title: The effect of the SASP upon liver sinusoidal endothelial cells

first: Ioana

last: Olan

summary: Primary human liver sinusoidal endothelial cells from 7 explanted livers were incubated in conditioned media from IMR90 cells undergoing several forms of senescence

overall_design: Conditioned media was generated from IMR90 cells transduced with ER:RAS (4OHT-inducible HRAS^G12V) and XIH-N1ICD (Doxycyline-inducible NOTCH1 intracellular domain) treated with 4OHT or doxycycline or both, leading to RAS-induced senescence (RIS) or NOTCH-induced senescence (NIS) or NOTCH/RAS-induced senescence (N+RIS). Primary human liver sinusoidal endothelial cells (LSECs) were obtained from 7 explanted human livers at liver transplantation, purified and lines established. The LSECs were incubated in the senescence conditioned  media before extraction and isolation of RNA.

first: Matthew

last: Hoare


title: ATAC-seq of immature B cells in presence or absence of γδ T cells

city: Heidelberg

first: Elisa

last: Donato

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: Deutsches Krebsforschungszentrum  (DKFZ) - German Cancer Research Center

summary:
Purpose: compare immature B cells in presence or not of γδ T cells in vivo and in vitro.
Methods: immature B cells were sorted from spleen of control Tcrd-GDL mice and Tcrd-GDL mice treated with Diphteria toxin (DTx) for depletrion of γδ T cells after eight days and were sequenced for transcriptional (RNA-seq) and epigenetic profile (ATAC-seq). Further, immature B cells were sorted from spleen of Tcdr-H2B mice, cultured alone or in presence of γδ T cells and sequenced for transcriptional profile (RNA-seq).
Results/Conclusions: In presence of γδ T cells, immature B cells upregulated genes related to unfolded protein response and mTORC1 signaling

overall_design: Transcriptional and epigenetic profile of splenic immaure B cells isolated from control mice and mice depleted for eight days of γδ T cells; transcriptional profile of immature B cells cultured alone or in presence of γδ T cells

first: Francesca

last: Rampoldi


title: TRIM28-dependent SUMOylation protects the adult ovary from the male pathway

city: Montpellier

first: Francis

last: Poulat

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: IGH CNRS-UM UMR9002


title: The Evening Complex integrates photoperiod signals to control flowering in rice [RNA-Seq]

overall_design: Transcriptome in WT, phyb-1 and elf3-1 elf3-2 lines at multiple points in the day under SD or LD conditions.


title: Alphaherpesviruses remodel the cellular transcriptome to deplete m6A-containing transcripts

city: Merelbeke

first: Robert

last: Jansens

address: Salisburylaan 133

department: Department of Translational Physiology, Infectiology and Public Health

country: Belgium

institute: Ghent University

summary:
Virus infections are accompanied by major transcriptional changes in the host cell.
We systematically investigated whether infection with viruses from different virus families specifically affects transcripts containing m6A, the most common internal modification of mRNA.
Alphaherpesviruses were found to extensively alter m6A processing of infected cells.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design:
To investigate the effect of alphaherpesviruses on m6A methylated transcripts, we infected Swine Testicle cells (ST) with Pseudorabies virus (PRV) for 16 hours or HEK-T cells with Herpes simplex virus type I (HSV-1) for 16 hours.
In addition, ST cells that were depleted of different m6A readers (YTHDF1, YTHDF2 and YTHDF3, YTHDC1 or YTHDC2) were infected with PRV for 16 hours.
We then performed RNA-seq to determine gene expression differences to determine the impact alphaherpesvirus infection has on m6A methylated transcripts.

first: Anthony

last: Olarerin-George

first: Herman

last: Favoreel


title: Single cell RNA-seq from Trim28 ovary knockout and wildtype mice ovaries and testis

city: Geneva

first: Chris

last: Rands

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

summary: Single cell RNA-seq (scRNA-seq) from Trim28 ovary knockout and wildtype mice ovaries and testis to help elucidate the function of Trim28 in the adult mouse ovaries. The analysis revealed that loss of Trim28 in the adult mouse ovaries lead to a transcriptional repogramming of the Granulosa cells towards the Sertoli cell fate. Therefore, Trim28 has a function to maintain the adult ovarian cell identity

overall_design: 10X scRNA-seq from Trim KO 8 week mouse ovaries, wildtype 8 week mice ovaries and testis

first: Yasmine

last: Neirijnck

first: Serge

last: Nef


title: The Evening Complex integrates photoperiod signals to control flowering in rice

first: Philip

last: Wigge

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


title: The Transcription Factor ThPOK Regulates ILC3 Lineage Homeostasis and Function during Intestinal Infection

status: Public on May 23 2022

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

summary: To investigate the role of ThPOK in the regulation of ILC3 development and function, we established conventional ThPOK knockout mice.

overall_design: All samples were sorted from siLP of wild-type and ThPOK-deficient mice. Comparative gene expression profiling analysis of RNA-seq data for wild-type and ThPOK-deficient.

first: Xianzhi

last: Gao

first: Lie


title: Identification of transcripts directly bound to U1A (iCLIP data) and the cell transcriptome after U1A knockdown (3´end sequencing) [RNA-seq]

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

institute: Biogipuzkoa Health Research Institute

summary: Investigate the role of U1A (SNRPA) in gene expression regulation

overall_design: Flag iCLIP performed in HeLa cells stably expressing 3xFlag-U1A transgene. 3´end sequencing in HeLa cells after siControl and siU1A treatment


title: TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 2)

summary: We study the role of the protein Trim28 in the maintenance of sexual identity of the adult ovary. With the help of conditional knock out (cKO) of Trim28 using the Nr5a1:Cre, we observed that deletion of the Trim28 gene in granulosa cells of the adult ovary induces their transdifferentiation into Sertoli cells, the supporting cell lineage of the testicular seminiferous tubules. FOXL2 expression has disappeared and follicles were completely remodeled into tubular structures with cells that expressed the Sertoli cell markers SOX8, SOX9 and DMRT1. Histological analysis confirmed the progressive reorganization of ovarian follicles into tubular structures and the and the transdifferentiation of granulosa cells by cells with a Sertoli cell morphology. TRIM28 acts as a SUMO-E3 ligase by interacting with the SUMO-E2 conjugating enzyme UBC9 (encoded by the Ube2i gene) via the Plant homeodomain (PHD), and can self-SUMOylate. To study in vivo the role of TRIM28-dependent SUMOylation, we generated a point mutation in exon 13 of mouse Trim28 within the PHD domain of the TRIM28 protein (C651F) that abrogates its SUMO-E3 ligase activity. We generated Trim28Phd/cKO mice (termed PHD mutant). Like in cKO ovaries, FOXL2 expression was undetectable, whereas we observed expression of the Sertoli cell markers SOX9, SOX8 and DMRT1 within structures organized in pseudo-tubules in PHD ovaries. Our results indicate that maintenance of the female pathway in the adult ovary depends on the E3-SUMO ligase activity of TRIM28.

overall_design: To determine whether in PHD mice, SUMOylation was modified genome-wide, we performed quantitative SUMO1 and SUMO2 ChIP-seq analyses with adult 8-weeks-old ovaries from control, cKO and PHD.

first: Moïra

last: Rossitto


title: Identification of transcripts directly bound to U1A (iCLIP data) and the cell transcriptome after U1A knockdown (3´end sequencing) [iCLIP]


title: TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 1)

summary: We study the role of the protein Trim28 in the maintenance of sexual identity of the adult ovary. With the help of conditional knock out (cKO) of Trim28 using the Nr5a1:Cre, we observed that deletion of the Trim28 gene in granulosa cells of the adult ovary induces their transdifferentiation into Sertoli cells, the supporting cell lineage of the testicular seminiferous tubules. FOXL2 expression has disappeared and follicles were completely remodeled into tubular structures with cells that expressed the Sertoli cell markers SOX8, SOX9 and DMRT1. Histological analysis confirmed the progressive reorganization of ovarian follicles into tubular structures and the and the transdifferentiation of granulosa cells by cells with a Sertoli cell morphology.

overall_design: As the Trim28 cKO phenotype was similar to that of mice after Foxl2 deletion in adult ovarian follicles (Uhlenhaut et al, Cell 2009,139, 1130-42), we asked whether these two proteins co-regulated common target genes in the ovary. We performed TRIM28 and FOXL2 chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-seq) in 8-weeks ovaries to gain a global view of TRIM28 and FOXL2 co-localization genome-wide.


title: RNA-seq of immature B cells in presence or absence of γδ T cells


title: Nuclear condensation of CDYL links histone crotonylation and cystogenesis in autosomal dominant polycystic kidney disease [ChIP-Seq]

first: Xinyi

last: Cao

overall_design: ChIP sequencing with different antibodies: PanKcr, H3K18cr, and TY1 Tag in control and CDYL OE WT 9-12 cell lines.

first: Lin

last: Dang

first: Yupeng

last: Chen


title: TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (RNA-Seq)

overall_design: We performed bulk RNA-seq experiments using 7-month-old Trim28 cKO ovaries, when transdifferentiation was completed.


title: Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

summary: Pseudomonas aeruginosa is a Gram-negative bacterium able to survive and adapt in a multitude of niches as well as thriving within many different hosts. This versatility lies within a large genome of ca 6Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widely spread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. It is made by diguanylate cyclases and broken by phosphodiesterases while the intracellular level of this molecule drives phenotypic responses. The signaling involve modification of enzymes or proteins function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca 40 genes encoding putative DGC or PDE. The combined activity of those enzymes should reflect the c-di-GMP concentration while specific phenotypic output could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool, with essentially an impact on biofilm phenotypes including initial attachment and maturation, while very little is observed on motility which differs from previous studies. We observe that minor changes in c-di-GMP level have a drastic phenotypic impact thus supporting the idea of local vs global c-di-GMP pool. Our RNA-seq analysis indicates that all PAO1 dgc/pde genes are expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks owe to be reconstructed in one single strain and cannot be built by cross-comparison with studies in other strains.

overall_design: We engineered a mutant library of 41 diguanylate cyclases (dgc) and phosphodiesterases (pde) genes in P. aeruginosa PAO1. We tested the impact of these mutants on biofilm formation, motility and intracellular c-di-GMP contents. We performed transcriptomic analysis on wild-type P. aeruginosa PAO1 to reveal the regulation of deg/pde genes in planktonic and biofilm growth conditions.

first: Kira

last: Eiler

first: Joey

last: Yam

first: Richard

last: Morton

first: Adeline

last: Yong

first: Jaime

last: Brizuela

first: Corina

last: Hadjicharalambous

first: Michael

last: Givskov

first: Scott

last: Rice

first: Alain

last: Filloux


title: Single-cell RNA sequencing unravel distinct tumor microenvironment of different components of lung adenocarcinoma featured as mixed ground glass opacity

city: changsha

first: Xiaofeng

address: No.139 Renmin road, Furong district

institute: second xiangya hospital, central south university

summary: Single cell RNA seqencing data of six paired samples from three chinese females with early stage lung adenicarcinomas featured as mixed ground glass opacity (mGGO). Each paired samples contain one sample from solid component and one from ground-glass like component within each mGGO. The result reveiled the intratumoral heterogeneity of mGGO.

overall_design: tissue samples of solid components and ground-glass like components were macrodissected from three patients who underwent surgical resections of mGGOs. GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) was used to barcode single cells, capture mRNA and generate cDNA libraries for scRNA-seq. Then pooled for sequencing on a HiSeq X platform (Illumina, San Diego, USA) with 150 bp paired-end reads

first: Yu

last: He

first: Muyun

last: Peng


title: Group 3 innate lymphoid cell pyroptosis represents a host defense mechanism against Salmonella infection

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

summary: Group 3 innate lymphoid cells (ILC3s) produce interleukin (IL)-22 and, together with other cells in the gut, orchestrate to mount productive host immunity against bacterial infection. However, the role of ILC3s in Salmonella enterica serovar Typhimurium (S. Typhimurium) infection, which causes foodborne enteritis in humans, remains elusive. Here, we show that S. Typhimurium exploit ILC3-produced IL-22 to promote its infection. Specifically, S. Typhimurium secrete flagellin through activation of the TLR5-Myd88-IL-23 signaling pathway in antigen presenting cells (APCs) to selectively enhance IL-22 production by ILC3s, but not T cells. Deletion of ILC3s but not T cells in mice led to better control of S. Typhimurium infection. We also show that S. Typhimurium can invade ILC3s directly and cause caspase-1-mediated ILC3 pyroptosis independently of flagellin. Genetic ablation of Casp1 in mice leads to increased ILC3 survival and IL-22 production, and enhanced S. Typhimurium infection. Collectively, our data suggest a key host defense mechanism against S. Typhimurium infection via induction of ILC3 death to limit intracellular bacteria and reduce IL-22 production.

overall_design: RNA-seq (3 replicates) analysis of ILC3 isolated from large intestine of S. Typhimurium infected (SL1344) mice vs uninfected (control) mice.

first: Lifeng

last: Xiong

first: Joseph

last: Dean


title: Runx3 drives a tissue residency program that is absent in CD4+ T cells [ATAC-seq]

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Tissue-resident memory T (TRM) cells provide rapid and superior control of localized infections. The transcription factor Runx3 was recently identified as a master regulator of CD8+ T cell tissue residency. However, Runx3 also drives CD8+ T cell lineage commitment and is repressed in CD4+ T cells, raising the possibility that this transcription factor defines a form of tissue residency unique to the CD8+ T cell subset. Here, we show that as a direct consequence of Runx3-deficiency, CD4+ TRM cells in epithelia lack the TGFb-responsive transcriptional network that underpins CD8+ TRM cell residency. Ectopic Runx3 expression in CD4+ T cells rescued this transcriptional program to promote prolonged survival, decreased tissue egress and a microanatomical redistribution towards epithelial layers that combined, resulted in superior local immune protection. Our results thus reveal a mechanistic discordance between CD4+ and CD8+ TRM cell formation in barrier tissues that is controlled by Runx3. Consequently, CD4+ TRM cells are unable to adopt a type of tissue residency that is intrinsically accessible to the CD8+ TRM cell subset.

overall_design: Bulk ATAC-seq was performed on mouse CD4 and CD8 T cells with and without Runx3 over expression and with or without TGFB Expression

first: Raíssa

last: Fonseca

first: Laura

last: Mackay


title: RNA-seq and ATAC-seq of immature B cells in presence or absence of γδ T cells

first: Elisa

last: Donato

country: Germany

overall_design: Refer to individual Series


title: Molecular signature of anastasis for reversal of apoptosis

city: Baltimore

first: Ho Lam

last: Tang

state: MD

address: 615 N. Wolfe Street

department: Neurosurgery

country: USA

institute: The Johns Hopkins University School of Medicine

summary: We recently discovered an unexpected reversibility of execution-stage apoptosis in vitro and in vivo, and coined the term anastasis (Greek for “rising to life”) for this cell recovery phenomenon. Promoting anastasis could in principle preserve injured cells that are difficult to replace such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To harness the discovery of anastasis to develop revolutionary new therapies, it is essential to identify the key regulators of anastasis – the therapeutic targets. Therefore, we performed microarray analysis to study the molecular mechanism of anastasis using reversal of ethanol-induced apoptosis in mouse primary liver cells as a model. Our data reveal active transcription involved in multiple pathways during anastasis, including early activation of pro-survival genes, cell cycle arrest, anti-p53-mediated DNA damage response, and at delayed times, stress-inducible responses such as cell migration. Here, we present a dataset containing the time-course gene expression profiles during apoptosis reversal, which has implications for the physiological, pathological, and therapeutic implications of anastasis.

overall_design: Mouse primary liver cells were treated with 4.5% ethanol for 5 hours (0 hour timepoint) and then washed and cultured in fresh medium for 3, 6, 24, and 48 hours. Three biological replicates were analyzed for each of 6 timepoints: pre-ethanol treament (Ctrl), 0 hours (R0), 3 hours (R3), 6 hours (R6), 24 hours (R24), and 48 hours (R48).

first: Ho-Lam

first: Ho-Man

first: Ming-Chiu

last: Fung


title: Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration

city: Los Angeles

first: Yuyan

last: Cheng

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

summary: The goal of this study is to use RNA-seq to investigate the molecular mechanisms by which REST inhibition regulates corticalspinal axon regeneration. To achieve this goal, cortical motor neurons from adult wild-type (WT) and REST conditional knockout (cKO) were purified at 1, 3, 7 days following spinal cord injury (SCI) or sham operation. RNA-seq libraries for cortical motor neurons were prepared with the QuantSeq mRNA-Seq library prep kit FWD for Illumina (Lexogen) and sequenced using HiSeq4000 (Illumina). Sequenced reads were mapped to reference genome (mm10) using STAR, and count level data were quantifed using Salmon. Differential gene expression analysis was performed using limma voom.

overall_design: mRNA profiles were performed in cortical motor neurons from wild-type or REST cKO mice that were recovered 1, 3, 7 days following SCI or sham operation. Each group has 3-4 replicates with ~1000 cells in each replicate.

first: Daniel

last: Geschwind


title: Network Dynamics of the Immune System decodes Asthma Endotypes

status: Public on May 21 2022

city: Boston

first: Vrushali

middle: Dipak

last: Fangal

state: MA

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary: The ‘Genetic Epidemiology of Asthma in Costa Rica’ is a family-based cross-sectional cohort ascertained between February 2001 and August 2008 on a Hispanic population isolate from the Central Valley of Costa Rica. The study recruited children between 6 to 14 years of age with moderate persistent asthma.

overall_design: GACR subjects were recruited by identifying an asthma proband from the records of the Children's Hospital of San Juan, Costa Rica. A total of 1,165 children with asthma were enrolled in the original study with written parental and participant consent. All children completed a protocol at enrollment, including questionnaires, assessment of airway responsiveness to methacholine, spirometry conducted with Survey Tach Spirometer, and collection of blood when children were not exacerbated.

first: Scott

middle: T

last: Weiss

first: Kimberly

last: Glass

first: Jessica

last: Lasky-Su

first: Sofina

last: Begum

first: Julian

last: Hecker

first: Abhijeet

last: Sonawane


title: Systemic blockade of Clever-1 in patients with solid tumours elicits lymphocyte activation alongside checkpoint molecule downregulation

status: Public on May 22 2022

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Macrophages are critical in driving an immunosuppressive tumour microenvironment that counteracts the efficacy of T-cell targeting therapies1. Thus agents, which can re-programme macrophages towards a pro-inflammatory state hold promise as novel immunotherapies for solid cancers2. Here we report that therapeutic targeting of a macrophage scavenger receptor, Clever-13, in heavily pre-treated metastatic cancer patients was able to induce a significant increase and activation of peripheral T-cells including downregulation of several immune checkpoint molecules. Transcriptional and mass cytometry analyses revealed treatment induced inflammatory conversion of blood monocytes, which was partly driven by impaired Clever-1 mediated scavenging. Identification of relevant peripheral signatures indicative of anti-tumour activity showed induction of an effector CD8 T-cell population that resulted from clonal expansion of cytotoxic CD8 T-cells. In some patients this was accompanied by features of increased accumulation of CD8 T-cells in post-treatment tumour biopsies. Our results reveal a non-redundant role played by the receptor Clever-1 in suppressing adaptive immune cell activation in humans. We provide evidence that targeting macrophage scavenging activity can promote an immune switch leading to peripheral activation and potentially intra tumoural proinflammatory responses in metastatic cancer patients. Anti-Clever-1 treatment may therefore provide an attractive immunotherapeutic strategy in cancer.

overall_design: Droplet-based single-cell RNA sequencing (scRNA-seq) with TCR sequencing of peripheral blood T and B cells from cycles 1 and 4 of the responder patient. scRNA-seq and TCRab-libraries was prepared using 10X Genomics Chromium Next GEM Single Cell 5' Library & Gel Bead Kit according to manufacture's instructions. Libraries were sequenced on NovaSeq.

first: Tapio

last: Lönnberg

first: Maija

last: Hollmén


title: Gene expression and muscle contractile physiology in anoles

city: Vermillion

first: Andrea

middle: Lyn

last: Liebl

state: SD

address: 414 E Clark Street

department: Biology

institute: University of South Dakota

summary: Here, we use a transcriptomic apprach to identify genes associated with variation in muscle contractile physiology differences among different muscles of the same individual.

sample_organism:
Anolis cybotes
Anolis sagrei
Anolis chlorocyanus
Anolis osa

overall_design: We used RNAseq to measure gene expression differences between 12 leg muscles and 12 jaw muscles of anolis lizards

first: Luke

last: Smith

first: Christopher

middle: V

last: Anderson

first: Muyuraj

last: Hikkaduwa Withangage

first: Andrew

last: Koch

first: Thomas

last: Roberts

middle: L


title: Methylation data from biological replicates of imatinib and nilotinib resistant K-562 cells

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

institute: University Hospital Schleswig-Holstein, Campus Kiel

summary:
Resistant cells were generated by stepwise exposure to increasing concentrations of imatinib or nilotinib to establish 0.5 and 2 µM imatinib and 0.1 µM nilotinib resistant cells. This procedure was performed twice independently to establish biological replicates of TKI resistance.
We analyzed genome-wide methylation to investigate changes in methylation during the development of TKI resistance.

overall_design: DNA from cells was isolated and bisulfite-converted DNA was hybridized to Illumina Infinium 850k Human Methylation Beadchips.


title: Caveolae-mediated endocytosis of VLDL-sized emulsion particles in macrophages requires NPC1 and STARD3 for further lysosomal processing

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Triglyceride-rich lipoproteins and their remnants contribute to atherosclerosis, possibly by carrying remnant cholesterol and/or by exerting a pro-inflammatory effect on macrophages. Nevertheless, little is known about how macrophages process triglyceride-rich lipoproteins. We show that uptake by macrophages of VLDL-sized emulsion particles is dependent on the enzyme lipoprotein lipase via its C-terminal domain. Subsequent internalization of VLDL-triglycerides by macrophages is carried out by caveolae-mediated endocytosis, followed by hydrolysis by lysosomal acid lipase. STARD3 is required for the transfer of lysosomal fatty acids to the ER for lipid storage, while NPC1 likely is involved in promoting the extracellular efflux of fatty acids. Our data provide novel insights into how macrophages process VLDL-derived triglycerides and suggest that macrophages have the remarkable capacity to excrete internalized triglycerides as fatty acids.

overall_design: Mouse RAW 246.7 macrophages were exposed to 1 mM artifical VLDL- (VLDLsep) and chylomicron-sized emulsion particles (CHYLsep) for 6 hrs, whereafter gene expression was profiled by RNA-sequencing.

first: Lei

last: Deng

first: Frank

last: Vrieling

first: Rinke

last: Stienstra

first: Anouk

last: Feitsma

first: Sander

last: Kersten


title: High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails [RNA-seq]

city: San Francisco

first: Vivasvan

last: Vykunta

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Enhancing site-specific transgene insertion efficiency by homology-directed repair (HDR) using high concentrations of double-stranded DNA (dsDNA) with Cas9 target sequences (CTSs) can be toxic to primary cells. Here, we develop single-stranded DNA (ssDNA) HDR templates (HDRTs) incorporating CTSs with reduced toxicity that boost knock-in efficiency and yield by an average of 2–3-fold relative to dsDNA CTSs. Using small-molecule combinations that enhance HDR, we could further increase knock-in efficiencies by an additional 2–3-fold on average. Our method works across a variety of target loci, knock-in constructs, and primary human cell types, reaching HDR efficiencies of >80–90%. We demonstrate application of this approach for both pathogenic gene variant modeling and gene-replacement strategies for IL2RA and CTLA4 mutations associated with Mendelian disorders. Finally, we develop a good manufacturing practice (GMP)-compatible process for non-viral chimeric antigen receptor (CAR)-T cell manufacturing, with knock-in efficiencies (46–62%) and yields (>1.5×109 modified cells) exceeding those of conventional approaches.

overall_design: Bulk RNA sequencing for primary human T cells immediately following isolation (pre-stimulation, Day -2), on the day of electroporation (Day 0), and after electroporation (Day 2) with guideRNA/Cas9 ribonucleoprotein complexes in 6 independent healthy human donors.

first: Brian

last: Shy

middle: S

first: Alexander

last: Marson

first: Theodore

last: Roth

first: David

last: Wu


title: microRNA microarray of aortae from 4-week male Fbn1mgR/mgR and wild-type mice [4-week_miRNA]

city: Montreal

first: Rongmo

last: Zhang

state: QC

address: 3640 Rue university

department: Anatomy and Cell Biology

country: Canada

institute: McGill University

summary:
Thoracic aortic aneurysms (TAA) in Marfan syndrome, caused by fibrillin-1 mutations, are characterized by elevated cytokines and fragmentated elastic laminae in the aortic wall. This study explored whether and how specific fibrillin-1-regulated miRNAs mediate inflammatory cytokine expression and elastic laminae degradation in TAA. miRNA expression profiling at early and late TAA stages using a severe Marfan mouse model (Fbn1mgR/mgR) revealed a spectrum of differentially regulated miRNAs. Bioinformatic analyses predicted the involvement of these miRNAs in inflammatory and extracellular matrix related pathways. Complementing mRNA microarray demonstrated the upregulation of multiple pro-inflammatory cytokines and matrix metalloproteases. Correlation analyses between the altered miRNAs and mRNAs present miR-122, the most downregulated miRNAs in the TAA tissue of Fbn1mgR/mgR, to be a core regulatory miRNA to pro-inflammatory cytokines, Ccl2 and Il1b, which were upregulated in the TAA tissues.
3 miRNAs were downregulated and 14 upregulated more than 2-fold

overall_design: Microarray analysis was performed for miRNAs using the GeneChip miRNA 4.0 Array  from Affymetrix. RNA extraction, RNA quality control, cDNA preparation and labeling, and the arrays were conducted as standard procedures at the Genome Quebec Innovation Centre at McGill University. Four ascending aorta samples in each group from 4 -week old wild-type and Fbn1mgR/mgR mice were prepared as described above, and snap-frozen in liquid nitrogen to preserve the integrity of RNA.

first: Rong-Mo

first: Dieter

last: Reinhardt


title: Genomic characterization of nub[1] wing tissue

status: Public on May 20 2022

first: Ryan

last: Loker

state: NY

address: 3227 Broadway

institute: Columbia University

summary: Profiled chromatin accessibility and gene expression in the wing imaginal discs of Drosophila melanogaster, in wild type and nub[1] animals. We demonstrate using RNA-seq that expression of both nub and pdm2 paralogs are reduced in the nub[1] condition, and that this allele contains a previously unannotated deletion within the intergenic region between of nub and pdm2 using ATAC-seq that corresponds to a wing enhancer element.

overall_design: Using ATAC-seq and RNA-seq to profile chromatin accessibility and gene expression in nub/pdm2 mutant wing tissue. ChIP-seq using an rotund-GFP in 3rd instar wing imaginal discs

first: Loker

last: Ryan

first: Mann

last: Richard


title: mRNA microarray of aortae from 10-week male Fbn1mgR/mgR and wild-type mice [10-week_mRNA]

summary:
Thoracic aortic aneurysms (TAA) in Marfan syndrome, caused by fibrillin-1 mutations, are characterized by elevated cytokines and fragmentated elastic laminae in the aortic wall. This study explored whether and how specific fibrillin-1-regulated miRNAs mediate inflammatory cytokine expression and elastic laminae degradation in TAA. miRNA expression profiling at early and late TAA stages using a severe Marfan mouse model (Fbn1mgR/mgR) revealed a spectrum of differentially regulated miRNAs. Bioinformatic analyses predicted the involvement of these miRNAs in inflammatory and extracellular matrix related pathways. Complementing mRNA microarray demonstrated the upregulation of multiple pro-inflammatory cytokines and matrix metalloproteases. Correlation analyses between the altered miRNAs and mRNAs present miR-122, the most downregulated miRNAs in the TAA tissue of Fbn1mgR/mgR, to be a core regulatory miRNA to pro-inflammatory cytokines, Ccl2 and Il1b, which were upregulated in the TAA tissues.
A total of 471 mRNAs were up-regulated (green) and 253 downregulated (red) more than 2-fold (p<0.05) in the aneurysmal versus the wild-type tissues.

overall_design: Microarray analysis was performed for mRNAs using the Affymetrix Clariom D_Mouse. RNA extraction, RNA quality control, cDNA preparation and labeling, and the arrays were conducted as standard procedures at the Genome Quebec Innovation Centre at McGill University. Four ascending aorta samples in each group from 10 -week old wild-type and Fbn1mgR/mgR mice were prepared as described above, and snap-frozen in liquid nitrogen to preserve the integrity of RNA.


title: Gene expression data from biological replicates of imatinib and nilotinib resistant K-562 cells

first: Meike

last: Kaehler

summary:
Resistant cells were generated by stepwise exposure to increasing concentrations of imatinib or nilotinib to establish 0.5 and 2 µM imatinib and 0.1 µM nilotinib resistant cells. This procedure was performed twice independently to establish biological replicates of TKI resistance.
We performed microarrays to analyze the changes in gene expression during the development of TKI resistance.

overall_design: RNA from cells was isolated and microarrays were run using two biological replicates of each resistance as well as four technical replicates. In addition, 8 controls were analyzed.


title: microRNA microarray of aortae from 10-week male Fbn1mgR/mgR and wild-type mice [10-week_miRNA]

summary:
Thoracic aortic aneurysms (TAA) in Marfan syndrome, caused by fibrillin-1 mutations, are characterized by elevated cytokines and fragmentated elastic laminae in the aortic wall. This study explored whether and how specific fibrillin-1-regulated miRNAs mediate inflammatory cytokine expression and elastic laminae degradation in TAA. miRNA expression profiling at early and late TAA stages using a severe Marfan mouse model (Fbn1mgR/mgR) revealed a spectrum of differentially regulated miRNAs. Bioinformatic analyses predicted the involvement of these miRNAs in inflammatory and extracellular matrix related pathways. Complementing mRNA microarray demonstrated the upregulation of multiple pro-inflammatory cytokines and matrix metalloproteases. Correlation analyses between the altered miRNAs and mRNAs present miR-122, the most downregulated miRNAs in the TAA tissue of Fbn1mgR/mgR, to be a core regulatory miRNA to pro-inflammatory cytokines, Ccl2 and Il1b, which were upregulated in the TAA tissues.
At 10 weeks, the number of differentially regulated miRNAs (>2-fold) increased to 129 with 5 down- and 124 upregulated miRNAs

overall_design: Microarray analysis was performed for miRNAs using the GeneChip miRNA 4.0 Array  from Affymetrix. RNA extraction, RNA quality control, cDNA preparation and labeling, and the arrays were conducted as standard procedures at the Genome Quebec Innovation Centre at McGill University. Four ascending aorta samples in each group from 10 -week old wild-type and Fbn1mgR/mgR mice were prepared as described above, and snap-frozen in liquid nitrogen to preserve the integrity of RNA.


title: Sex-related differences in Alzheimer’s disease

city: Dublin

first: Virginia

last: Mela

address: Trinity College Dublin

country: Ireland

institute: Trinity College Institute of Neuroscience

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 779 genes in microglial cells from 36 mice, which had been consecutively operated on within a defined short period of time

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 36 mice from our APP/PS1 colony, followed up more than 1 year and a half for the aged mice (18 months) and only 5/6 months for the young mice, was used to acquire expression profiles of a total of 779 unique genes

first: Marina

middle: A

last: Lynch


title: Small RNA-sequencing of FUS H517Q and healthy iPSC-derived motor neurons

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

institute: Living Systems Institute, University of Exeter

type: Non-coding RNA profiling by high throughput sequencing

summary:
We sought to investigate changes in expression levels of small RNAs including microRNAs in FUS H517Q and healthy motor neurons
Motor neurons were differentiated from patient-derived FUS H517Q and healthy iPSCs, and harvested at day 30. We performed gene expression profiling analysis using data obtained from bulk small RNA-seq.

overall_design: Comparative gene expression profiling using small RNA-seq analysis of FUS H517Q and healthy motor neurons.

first: Sophie

last: Hawkins

first: Seema

last: Namboori


title: RNA seq on primary pancreatic cancer cells growing on collagen 1 homotrimers and heterotrimers

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: RNA seq on primary pancreatic cancer (KPPC;Col1pdxKO cancer-collagen1 knockout) cells growing on collagen 1 homotrimers and heterotrimers. In this study, we identify that pancreatic cancer cells produce a unique Collagen1 homotrimer variant, in contrast to the Collagen1 heterotrimer produced by normal cells (such as fibroblasts). The variant forms of Collagen1 (homotrimer and heterotrimer) have distinct effects on cancer cell behaviors. We culture the pancreatic cancer cells on purified Collagen1 homotrimer and heterotrimer (as well as vehicle control) and examine the global changes of gene expression profile in cancer cells by variant Collagen1 subtypes.

overall_design: Primary pancreatic cancer (KPPC;Col1pdxKO cancer-collagen1 knockout) cells were cultured in the presence of: (1) coated vehicle (2) coated Collagen 1 homotrimers (3) coated Collagen 1 heterotrimers. A total of 9 samples (3 biological replicates per group) were sequenced on Illumina Nextseq 500.


title: Identifying miR-139 targets in motor neurons

summary:
We sought to investigate changes in expression levels of RNAs in response to miR-139 overexpression in human iPSC-derived motor neurons
Motor neurons were differentiated from FUS H517Q iPSCs and transduced with AAVs expressing miR-139 or controls hairpins. RNA was harvested at day 34. We performed gene expression profiling analysis using data obtained from bulk  RNA-seq.

overall_design: Comparative gene expression profiling using RNA-seq analysis of miR-139 overexpression in FUS H517Q motor neurons.


title: FUS H517Q and healthy iPSC-derived motor neurons

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

overall_design: Refer to individual Series