title: Mycobacterium tuberculosis transcriptional response to Pretomanid

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug pretomanid. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing pretomanid at the predetermined amounts (0, 0.7, 3.5 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Persistent inflammation and nitric oxide dysregulation are transcriptomic blueprints of subglottic stenosis

status: Public on Dec 14 2021

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

country: USA

institute: University of Pennsylvania Perelman School of Medicine

type: Expression profiling by high throughput sequencing

summary: Subglottic stenosis (SGS) is a recurrent, obstructive, fibroinflammatory disease of the upper airway resulting in severe dyspnea, dysphonia, as well as other potentially fatal complications. Although aberrant inflammation and wound-healing are commonly associated with pathogenesis, the mechanism through which such processes occur and recur in affected patients remains poorly studied. Here we report that transcriptomic profiling of laryngotracheal regions from minimally-invasive mucosal swabs of SGS patients reveals a distinctively pro-inflammatory gene signature. Surprisingly, comparative genomics between SGS patients and mice with direct laryngotracheal injury suggest that SGS patients bear more resemblance to the acute than chronic phase of injury. Furthermore, functional and regulatory network analyses identify neutrophilic involvement through hyper-activation of NF-κB and its downstream inflammasome as a potential master regulator. Interestingly, nitric oxide synthesis was found to be downregulated in SGS patients compared to healthy controls. Thus, SGS represents a state of immunodeficiency whereby defective immune clearance triggers recurrent, long-lasting production of pro-inflammatory cytokines.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptomic profiling (RNA-seq) of human laryngotracheal swabs and murine tracheas. NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® and sequenced by Novogene.

middle: C

first: Natasha

last: Mirza


title: CRISPR/Cas9 editing of directly reprogrammed myogenic progenitors restores dystrophin expression in a dystrophic mouse model

status: Public on Dec 15 2021

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Genetic mutations in dystrophin manifest in Duchenne muscular dystrophy (DMD), the most prevalent form of a genetically inherited muscle disease. Dystrophin is expressed in skeletal muscle stem cells and fibers, playing a critical role in maintaining skeletal muscle structure, regeneration and function. Here, we report on direct reprogramming of fibroblasts from the Dmdmdx mouse model into induced myogenic progenitor cells (Dmdmdx iMPCs) utilizing transient MyoD overexpression in concert with small molecule treatment. Dmdmdx iMPCs proliferate extensively in vitro and express canonical skeletal muscle stem and progenitor cell markers including Pax7, Sox8 and Myf5. Furthermore, Dmdmdx iMPCs readily give rise to highly contractile and multinucleated myofibers that express a suite of mature skeletal muscle genes however lack dystrophin expression. Utilizing an exon-skipping based approach with CRISPR/Cas9 we report on a genetic correction of the dystrophin mutation in Dmdmdx-iMPCs and subsequent restoration of dystrophin protein expression in vitro. Furthermore, engraftment of genetically-corrected Dmdmdx iMPCs into dystrophic limb muscles of Dmdmdx mice restored dystrophin expression in vivo. Collectively, our findings report on a novel in vitro stem cell-based model for DMD and further establish a new approach to treat this disease via a combination of direct cellular reprogramming, genome engineering and stem cell transplantation methods.

overall_design: Reprogramming of Dmdmdx fibroblasts into myogenic progenitor cells using ectopic MyoD overexpression in combination with small molecule (F/R/C) treatment

first: Seraina

middle: A

last: Domenig

first: Adhideb

last: Ghosh


title: Mycobacterium tuberculosis transcriptional response to linezolid

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug linezolid. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing linezolid at the predetermined amounts (0, 0.84, 4.2 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.

middle: J

first: Nitin

middle: S

last: Baliga


title: Mycobacterium tuberculosis transcriptional response to Isoniazid

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug isoniazid. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing isoniazid at the predetermined amounts (0, 0.18, 1.8 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Transcription regulation and genome rewiring governing sensitivity and resistance to FOXM1 inhibition in breast cancer I

city: Urbana

first: Yvonne

last: Ziegler

state: IL

address: 407 S Goodwin Ave.

department: MIP

institute: University of Illinois

summary: Forkhead box M1 (FOXM1) is an oncogenic transcription factor overexpressed in many cancers and associated with aggressiveness. Using 1,1-diarylethylene-diammonium compounds that suppress FOXM1 activity, we utilized genome-wide transcriptomic, protein analyses, and functional approaches to identify mechanisms by which these compounds inhibit breast cancer growth and survival. These compounds downregulated FOXM1 gene networks in estrogen receptor (ER)-positive and triple negative breast cancer (TNBC) cells, and RNA-Seq and pathway analyses revealed that cell cycle progression, DNA damage repair, and apoptosis were most greatly affected, in agreement with the cancer promoting functions of FOXM1. TNBC and ER-positive breast cancer cells grown long-term with the inhibitors developed resistance. Notably, resistant cells showed transcriptional alterations and rewiring leading to reversal of the regulation of many genes in the FOXM1 network and marked changes in inflammatory signaling and HER2 and EGFR signature genes and pathways. High expression of a 43-gene Interferon-Related FOXM1 inhibitor resistance Signature (IRFMS) derived from ER-positive inhibitor resistant cells predicted a less good prognosis and poorer survival in patients with ER-positive breast cancer. Resistant cells showed greatly reduced ERα levels and responsiveness to fulvestrant and a 10-fold increased sensitivity to lapatinib, suggesting that targeting rewired processes in the resistant state may provide benefit and enable prolonged anticancer effectiveness.

overall_design: Examine how the development of resistance to FOXM1 inhibitors results in changes in gene expression in both estrogen receptor positive and triple negative cancer cell lines.

first: Valeria

last: Guillen

first: Sung

middle: H

last: Kim

first: John

last: Katzenellenbogen

first: Benita


title: Mycobacterium tuberculosis transcriptional response to Clofazamine

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug clofazamine. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing clofazamine at the predetermined amounts (0, 0.73, 3.65 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Transcription regulation and genome rewiring governing sensitivity and resistance to FOXM1 inhibition in breast cancer II


title: Transcription regulation and genome rewiring governing sensitivity and resistance to FOXM1 inhibition in breast cancer

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

overall_design: Refer to individual Series


title: Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation [ChIP,CutRun]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulatory T (Treg) cells play crucial roles in suppressing deleterious immune response. Here, we investigate how mechanistically Treg cells are induced and stabilized via transcriptional regulation of Treg lineage–specifying factor Foxp3. Acetylation of histone tails in the Foxp3 locus is induced during Treg cell development and required in cis for the initiation of Foxp3 transcription. Upon induction, histone acetylation signal largely acts in trans to sustain Foxp3 transcription via multiple factors. Subsequently, Tet-mediated DNA demethylation of Foxp3 cis-regulatory elements particularly enhancer CNS2 increases chromatin accessibility and protein binding, drastically stabilizing Foxp3 transcription, although histone acetylation still regulates global gene expression. These processes transform stochastic Treg cell induction into a stable cell fate, with the former sensitive and latter resistant to genetic and environmental perturbations. Thus, our study reveals distinct roles of histone acetylation in Foxp3 induction and maintenance, reflecting sequential mechanical switches governing Treg cell lineage specification.

overall_design: Examination of chromatin accessibility, Stat5 binding, histone modifications, DNA methylation, RNA Polymerase II occupation, and nascent RNA expression in naive CD4 T cells, effector CD4 T cells, regulatory T cells, and in vitro induced regulatory T cells with or without ascorbic acid treatment, or in combination with JQ1 treatment.

first: Jun

last: Li

first: Minghong

last: He

first: Yiping

last: Fan

first: Yongqiang

last: Feng


title: CLIP1 and DMD are two novel RNA-binding proteins through computational prediction and experimental validation

city: Wuhan

first: Shiyong

last: Liu

country: China

institute: Huazhong University of Science and Technology

summary: Since RBPs play important roles in the cell, it’s particularly important to find new RBPs. We performed iRIP-seq and CLIP-seq to verify two proteins, CLIP1 and DMD, predicted by RBPPred whether are RBPs or not. The experimental results confirm that these two proteins have RNA-binding activity. We identified significantly enriched binding motifs UGGGGAGG, CUUCCG and CCCGU for CLIP1 (iRIP-seq), DMD (iRIP-seq) and DMD (CLIP-seq), respectively. The computational KEGG and GO analysis show that the CLIP1 and DMD share some biological processes and functions. Besides, we found that the SNPs between DMD and its RNA partners may associate with Becker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy 3B and Cardiovascular phenotype. Among the thirteen cancers data, CLIP1 and another 300 genes always co-occur, and 123 of these 300 genes interact with CLIP1. These cancers may be associated with the mutations in both CLIP1 and the genes it interacts with.

overall_design: iRIP-seq and CLIP-seq was performed in biological replicate for CLIP1 and DMD in HeLa cell. Each sample has a input control for analysis.

first: Juan

last: Xie

first: Xiaoli

last: Zhang

first: Jinfang

last: Zheng

first: Xu

last: Hong

first: Xiaoxue

last: Tong

first: Xudong

first: Yaqiang

last: Xue

first: Xuelian

last: Wang

first: Yi


title: Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation [SLAM-Seq]


title: Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation

type: Methylation profiling by high throughput sequencing


title: Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation [WGBS]

first: Richard

last: Cross


title: Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation [ATAC-Seq]

overall_design: Examination of chromatin accessibility, Stat5 binding, histone modifications, DNA methylation, RNA Polymerase II occupation, and RNA expression in naive CD4 T cells, effector CD4 T cells, regulatory T cells, and in vitro induced regulatory T cells with or without ascorbic acid treatment, or in combination with JQ1 treatment.


title: Emergence and patterning dynamics of mouse definitive endoderm

status: Public on Dec 13 2021

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: The segregation of definitive endoderm (DE) from bi-potent mesendoderm progenitors leads to the formation of two distinct germ layers. Dissecting DE commitment and onset has been challenging as it occurs within a narrow spatio-temporal window in the embryo. Here we employ a novel dual Bra/Sox17 reporter cell line to study DE onset dynamics. We find Sox17 expression initiates in a few isolated cells in vivo within a temporally restricted window. Using 2D and 3D in vitro models, we show that DE cells emerge from mesendoderm progenitors at a temporally regular, but spatially stochastic pattern, which is subsequently arranged by self-sorting of Sox17+ cells. A subpopulation of Bra-high cells commits to a Sox17+ fate independent of external Wnt signal. Self-sorting coincides with up-regulation of E-cadherin but is not necessary for DE differentiation or proliferation. Our in vivo and in vitro results highlight basic rules governing DE onset and patterning through the commonalities and differences between these systems.

overall_design: In this study, we analyzed the dynamics of Sox17 (marker of definitive endoderm) dynamics in vitro and in vivo. We show that majority of these cells originate from T+ population, and that the disperse pattern of Sox17+ cells is a cell-autonomous choice which is free of spatial feedback.

first: Maayan

last: Pour

first: Abhishek

last: Kumar

first: Naama

last: Farag

first: Adriano

last: Bolondi

first: Maria

last: Walther

first: Lars

last: Wittler

first: Alexander

last: Meissner

first: Iftach

last: Nachman


title: Insulin receptors in tanycytes gate hypothalamic insulin uptake and regulate AgRP neuronal activity

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: We reveal a critical role of tanycyte insulin receptors in gating feeding state-dependent regulation of AgRP neurons and systemic insulin sensitivity, and show that insulin resistance in tanycytes contributes to the pleiotropic manifestations of obesity-associated insulin resistance

overall_design: Bac-TRAP based RNA sequencing. 12 week old mice injected with AAV-Dio2-CreTW in lateral ventricle to express fluorescent L10-EGFP fusion protein in NCD-fed  insulin receptor (IR) KO,  WT or HFD-fed (for 8w) WT mice  (NCD:IR fl/fl Rosa26-L10-EGFP tg/wt , IR wt/wt Rosa26-L10-EGFP tg/wt; HFD: IR wt/wt Rosa26-L10-EGFP tg/wt)  in Cre dependent manner in tanycytes. 4 weeks later mediobasal hypothalamus was dissected. 5-7 mice (M&F) were pooled for replicate. Translating mRNA was pulled down via immunoprecipitation. Isolated RNA was subjected for RNA sequencing using Illumina platform. See full protocol below.

first: Marta

last: Porniece Kumar

first: Paul

last: Klemm


title: Transcriptome profiling of Mycobacterium tuberculosis H37Rv to primary drugs

first: Eliza

last: Peterson

sample_organism:
Mycobacterium tuberculosis
Mycobacterium tuberculosis H37Rv


title: Antitumor effects of DOT1L inhibition in retinoblastoma

city: Guangzhou

first: Chunsik

last: Lee

state: Guangdong

address: NO.7 Jinsui Rd.

institute: Sun Yat-Sen University

summary: Epigenetic dysregulation is one of the molecular mechanisms contributing to retinoblastoma (RB) development. Consistent with this notion, human RB tumors show an aberrant expression of many chromatin regulators whereas normal retina or nontumoral retinal tissues do not have any detectable expression of such proteins. Among the chromatin regulators found to be misregulated in RB, this study focuses on a histone methyltransferase DOT1L to assess the therapeutic potential of its targeting for RB treatment. We found that pharmacological inhibition of DOT1L has growth-inhibitory effects on RB cells by itself and also can sensitize RB cells to standard chemotherapeutic drugs by inducing more robust apoptotic cell death when cells are subjected to combination treatments. To understand the molecular mechanisms underlying the growth inhibition and chemosensitization of RB cells upon DOT1L inhibition, we performed the gene expression profiling in Y79 cells treated with a DOT1L inhibitor EPZ5676 in comparison with a vehicle control by RNA-sequencing to identify differentially expressed genes. Our RNA-seq results revealed that DOT1L inhibition downregulates several genes which are known to be misregulated in cancers, including HMGA2.

overall_design: Gene expression profiling of Y79 retinoblastoma cell line treated with 10 µM EPZ5676 for 6 days in comparison with a vehicle control (DMSO); Identification of differentially expressed genes between the DMSO and EPZ5676 groups using three independent biological replicates

first: JongKyong

last: Kim


title: Placental Immune alterations in early-onset preeclampsia and late-onset preeclampsia

city: Rotterdam

first: Michelle

last: Broekhuizen

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: Preeclampsia is a severe placenta-related pregnancy disorder that is generally divided into  two subtypes named early-onset preeclampsia (onset <34 weeks of gestation), and lateonset  preeclampsia (onset ≥34 weeks of gestation), with distinct pathophysiological  origins. Both forms of preeclampsia have been associated with maternal systemic  inflammation. However, alterations in the placental immune system have been less well  characterized. Here, we studied immunological alterations in early- and late-onset  preeclampsia placentas using a targeted expression profile approach. RNA was  extracted from snap-frozen placenta samples (healthy n=13, early-onset preeclampsia  n=13, and late-onset preeclampsia n=6). The expression of 730 immune-related genes  from the Pan Cancer Immune Profiling Panel was measured, and the data were analyzed Q10  in the advanced analysis module of nSolver software (NanoString Technology). The results  showed that early-onset preeclampsia placentas displayed reduced expression of  complement, and toll-like receptor (TLR) associated genes, specifically TLR1 and TLR4.  Mast cells and M2 macrophages were also decreased in early-onset preeclampsia  compared to healthy pl acentas. The findings were confirmed by an  immunohistochemistry approach using 20 healthy, 19 early-onset preeclampsia, and  10 late-onset preeclampsia placentas. We conclude that the placental innate immune  system is altered in early-onset preeclampsia compared to uncomplicated pregnancies.  The absence of these alterations in late-onset preeclampsia placentas indicates dissimilar  immunological profiles. The study revealed distinct pathophysiological processes in earlyonset  and late-onset preeclampsia placentas and imply that a tailored treatment to each  subtype is desirable.

first: Emilie

last: Hitzerd

first: Thierry

middle: P

last: van den Bosch

first: Jasper

last: Dumas

first: Robert

middle: M

last: Verdijk

first: Bas

last: van Rijn

first: A

last: Jan Danser

first: Casper

last: van Eijck

first: Irwin

middle: K

last: Reiss

first: Dana

last: Mustafa


title: Loss of Nucleoporin Nup210 Results in Muscle Repair Delays and Age-Associated Alterations in Skeletal Muscle Integrity

city: La Jolla

first: Maximiliano

last: D'Angelo

state: CA

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: This study describes how absence of a member of the nuclear pore complex is important for skeletal muscle maintenance and function but is not required for mammalian muscle development.

overall_design: Transcriptomics comparison of the muscles of Nup210 knockout and wild-type animals by RNA-seq on Quadriceps muscles

first: Stephen

last: Sakuma


title: Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

summary: T cell activation induces rapid proliferative expansion and the acquisitions of specialized effector functions that enable protection against invading pathogens.  While a multitude of transcription factors (TFs) have been implicated in the regulation of T cell activation, it remains largely unclear how their functions are organized and integrated at the genomic level. Here, we leveraged naturally occurring TF binding site polymorphisms in wild derived inbred mice to identify the most critical “heavy lifters” that shape the epigenetic landscape of naïve and activated antiviral CD4 and CD8 T cells. We found that representative members of Ets, Runx, and TCF/Lef families occupied the vast majority of accessible chromatin regions and that interactions between them were associated with distinct epigenetic responses to T cell activation. We define prevalent genomic functions of Ets1, Runx1, and TCF1 as “housekeeper”, “universal amplifier”, and “placeholder”, respectively. Interestingly, regulatory elements associated with some of the most strongly induced and well-characterized immune response genes showed a non-canonical pattern of TF recruitment.

overall_design: The project studied the chromatin accessibility and multiple transcription factors binding profiles of CD8/CD4 T cell in response to virial infection. 84 samples were analysed in total, including 12 ATAC-Seq, 12 RNA-Seq, 60 CUT&RUN samples.

first: Christina

last: Leslie

first: Joris

last: van der Veeken

first: Alexander

last: Rudensky


title: Long-term caffeine treatment of Alzheimer mouse models ameliorates behavioural deficits and neuron loss and promotes cellular and molecular markers of neurogenesis

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Epidemiological studies suggest that consumption of caffeine, the most commonly consumed psychoactive substances found in coffee, tea or soft drinks reduces the risk of developing Alzheimer’s disease (AD). While previous studies employing transgenic AD mouse models reported on reduced amyloid plaque load or an amelioration of behavioral deficits, there is only limited information on its potential effects on neurodegeneration. In the current study, we assessed whether long-term caffeine consumption affects hippocampal neuron loss and associated behavioral deficits in the Tg4-42 mouse model of AD. Treatment over a 4 months period reduced hippocampal neuron loss, rescued learning and memory deficits and ameliorates impaired neurogenesis. Neuron-specific hippocampal transcriptome analysis revealed an altered expression profile with an up-regulation of genes linked to synaptic function and processes, as well as neural progenitor proliferation. Treatment of 5xFAD mice with the same paradigm also rescued behavioral deficits, however, without affecting extracellular amyloid-beta (Abeta) levels or altered APP processing.

overall_design: Examination of sorted neuronal gene expression in hippocampal CA neurons of caffeine-treated APP mice.

first: M

last: Sakib

first: Tonatiuh

last: Pena Centeno


title: Single-cell sequencing analysis and weighted co-expression network analysis based on public databases identified that TNC is a novel biomarker for keloid

status: Public on Dec 12 2021

city: Nanjing

first: Jiaheng

last: Xie

address: 300 Guangzhou Rd

department: Burn and Plastic Surgery

institute: Jiangsu Province Hospital

summary: Background: The pathophysiology of keloid formation is not yet understood, so the identification of biomarkers for kelod can be one step towards designing new targeting therapies which will improve outcomes for patients with keloids or at risk of developing keloids.   Methods: In this study, we performed single-cell RNA sequencing analysis, weighted co-expression network analysis, and differential expression analysis of keloids based on public databases. And 3 RNA sequencing data from keloid patients in our center were used for validation. Besides, we performed QRT-PCR on keloid tissue and adjacent normal tissues from 16 patients for further verification.  Results: We identified the sensitive biomarker of keloid: Tenascin-C (TNC). Then, Pseudotime analysis found that the expression level of TNC decreased first, then stabilized and finally increased with fibroblast differentiation, suggesting that TNC may play an potential role in fibroblast differentiation. In addition, there were differences in the infiltration level of macrophages M0 between the TNC-high group and the TNC-low group. Macrophages M0 had a higher infiltration level in low TNC- group (P<0.05).  Conclusion: Our results can provide a new idea for the diagnosis and treatment of keloid.

overall_design: mRNA profiles of keloids

first: Liang

last: Chen

first: Ming

last: Wang


title: Comparative analysis of transcriptomic points-of-departure (tPODs) and adverse apical responses in embryo-larval fathead minnows exposed to fluoxetine

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

summary: Current methods to support chemical hazard assessment face significant challenges given the rapidly growing number of compounds of emerging concern (CEC) requiring assessment.   Standard testing strategies rely upon live animal testing, which are time-consuming, expensive, and ethically questionable.  These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests.  This study explored the application of the molecular benchmark dose (BMD) approach in a 7-day embryo-larval fathead minnow (FHM) assay to derive determine transcriptomic points-of-departure (tPODs) which can be useds to predict apical BMDs  of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters.  Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at <LOD, 0.19, 0.74, 3.38, 10.2, 47.5 µg/L) for 32 days.  Subsets of fish were subjected to omics and locomotor analyses  at 7 days post-fertilization (dpf) and to histological and biometric measurements  at 32 dpf.  Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions.  BMD analysis resulted in tPOD values of 0.56 µg/L (median of the 20 most sensitive gene-level BMDs), 5.0 µg/L (tenth percentile of all gene-level BMDs), 7.51 µg/L (mode of the first peak of all gene-level BMDs) , and 5.66 µg/L (pathway-level BMD).  These tPODs are protective of apical locomotor and reduced weight effects (LOEC of 10.2 µg/L) observed in this study and are well within the range of chronic apical BMDs of FLX reported in the literature.  Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations.  This is one of the first studies to derive tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations.

overall_design: mRNA profiles of whole fathead minnow larvae (Pimephales promelas; 7 days post-fertilization, pools of 20 larvae per sample) exposed to water control (as reference sample), 0.19, 0.74, 3.38, 10.2, 47.2 µg/L fluoxetine (FLX; measured concentrations)  from 6hr post-fertilization to 7 days post-fertilization. Water control, 0.74, 3.38, and 10.2 treatment groups have 5 replicates each while 0.19 and 47.5 treatment groups have 3 replicates each.

first: Alper James

last: Alcaraz

first: Kamil

last: Mikulášek

first: Bradley

last: Park

first: Taylor

last: Lane

first: Connor

last: Burbridge

first: Jessica

last: Ewald

first: Potěšil

last: David

first: Jiangou

last: Xia

first: Zbyněk

last: Zdráhal

first: David

last: Schneider

first: Doug

last: Crump

first: Niladri

last: Basu

first: Natacha

last: Hogan

last: Brinkmann


title: Characterization of novel whole body Poldip2 knockout mice generated by [Precisely "flox"ing Poldip2 gene] and crossing with Cre deleter mice

status: Public on Dec 20 2021

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

summary: Poldip2 is a multifunctional protein whose roles are only partially understood. The previous Poldip2 knockout mouse generated by the gene trap model suffers from two limitations: perinatal lethality in homozygotes and constitutive Poldip2 inactivation. To overcome these limitations, we developed a new conditional floxed Poldip2 mouse. Here, we correctly targeted floxed Poldip2 mice to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no Poldip2 expression. To characterize the effect of Poldip2 ablation in the vasculature, we performed a RNA-seq study using the carotid arteries of these mice.

overall_design: The carotid arteries were harvested from the Poldip2 knockout mice (n=4) as well as from the littermate controls (n=4). The lumen of these areries were quickly flushed with Qiazol to extract the endothelial-enriched RNAs. Also, RNAs were extracted from the leftover arteries (containing the media and adventitia, consisting of smooth muscle cells and other adventiatial cells). These RNAs were subjected to RNAseq to determine the effect of Poldip2 knockdown in endothelium and in the vascular smooth muscle fraction of the carotid arteries.

first: Bernard

last: Lassègue

first: Kathy

last: Griendling


title: CircZNF609 regulates microtubule dynamics ad tumorigenicity by sustaining CKAP5 protein levels.

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: Circular RNAs (circRNAs) are widely expressed in eukaryotes and highly regulated in a myriad of biological processes. While many studies indicate their activity as miRNA and protein sponges, little is known about their ability to directly control mRNA homeostasis. We show that a widely expressed circRNA, circZNF609, directly interacts with several mRNAs and increases their stability and/or translation by favouring the recruitment of the RNA-binding protein ELAVL1. Specifically, the interaction with Ckap5 mRNA, that interestingly overlaps the back-splicing junction, regulates microtubule homeostasis in several cancer cell lines and sustains cell-cycle progression. Finally, we show that circZNF609 downregulation increases the sensitivity to several microtubule-targeting cancer drugs in the regulation of microtubule metabolism and that LNA protectors against the Ckap5 pairing region on circZNF609 phenocopies such activity. These data set an example of how the small effects tuned by circZNF609/Ckap5 mRNA interaction might have potent output in tumour growth and drug response.

overall_design: High-throughput sequencing of total RNA from circ-ZNF609 pull-down experiments performed using two sets of specific biotynilated antisense probes targeting ZNF609 exon 2 and control biotynilated antisense probes targeting LacZ bacterial mRNA.

first: Irene

last: Bozzoni

first: Manuel

last: Beltran

first: Michela

last: Damizia

first: Chiara

last: Grelloni

first: Alessio

last: Colantoni

first: Adriano

last: Setti

first: Gaia

last: Di Timoteo

first: Dario

last: Dattilo

first: Alvaro

last: Centron Broco

first: Carmine

last: Nicoletti

first: Patrizia

last: Lavia


title: Transcriptome profiling of Atlantic salmon (Salmo salar) parr with higher and lower pathogen loads following Piscirickettsia salmonis infection

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

summary: Piscirickettsiosis or salmonid rickettsial septicemia (SRS) caused by intracellular Gram-negative bacterial pathogen, Piscirickettsia salmonis, constitutes one of the main infectious diseases in salmonid aquaculture. In the present study, we aimed to explore the transcriptomic responses in the Atlantic salmon kidney following a low dose of EM-90-like P. salmonis infection using the consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent 44K salmonid oligonucleotide microarray. Two infection level phenotypes [low (L-SRS) and high (H-SRS) infection level] were revealed in infected individuals at 21 days post-injection (DPI) based on multivariate analyses of expression of four antibacterial biomarker transcripts (campb, hampa, il8a, tlr5a) and pathogen level measured by qPCR. Five fish from each group (Control, L-SRS, and H-SRS) were selected for transcriptome profiling. We identified 1636 and 3076 differentially expressed probes (DEPs) in the L-SRS and H-SRS groups, respectively (FDR = 0.01).

overall_design: Atlantic salmon parr were anesthetized using Benzocaine (150 µl L-1 BZ-20®, Veterquímica S.A., Maipú, Santiago, Chile) and intraperitoneally (IP) injected with 0.1 mL of a low dose bacterial inoculum with a titer of 10^0.83 TCID50/mL (50% Tissue Culture Infective Dose) or 0.1 mL of a medium that was used to prepare the bacterial inoculum (i.e. minimum essential medium, MEM).  Ten fish per tank [3 tanks from the challenge group (i.e. P. salmonis-injected) and 4 tanks from the control group (CON)] were euthanized using an overdose of Benzocaine (300 µl L-1 BZ-20®) and dissected on the day before injection (PRE) of the remaining fish, as well as 2, 7, 13, 21 and 42 days post-injection (DPI). Head kidney samples were collected and stored in RNAlater (Ambion/Life Technologies, Austin, TX, USA) for 48 h at 4°C and transferred to -80°C until RNA extraction. Two infection level phenotypes [low (L-SRS) and high (H-SRS) infection level] were revealed in infected individuals at 21 days post-injection (DPI) based on multivariate analyses of expression of four antibacterial biomarker transcripts (campb, hampa, il8a, tlr5a) and pathogen level measured by qPCR. Five fish from each group (Control, L-SRS, and H-SRS) were selected for transcriptome profiling with a common reference design. Test samples were labeled with Cy5, whereas the common reference (i.e. a RNA pool of all 15 samples included in microarray experiment) was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array (i.e. 15 arrays in total).

first: Albert

last: Caballero-Solares

first: Jennifer

middle: R

last: Hall

first: Navaneethaiyer

last: Umasuthan

first: Surendra

first: Eva

last: Jakob

first: Christopher

last: Hawes

first: Javier

last: Santander

first: Richard

middle: G

last: Taylor

first: Matthew

middle: L

last: Rise

first: Stanko

last: Skugor


title: DNA demethylase ALKBH1 promotes adipogenic differentiation via regulation of HIF-1 signaling

city: Chengdu

first: yuting

last: Liu

address: people's south road 14

institute: Sichuan University

summary: DNA 6-adenine methylation (6mA), as a novel adenine modification existing in eukaryotes, shows essential functions in embryogenesis and mitochondrial transcriptions. ALKBH1 is a demethylase of 6mA and plays critical roles in osteogenesis, tumorigenesis, and adaptation to stress. However, the integrated biological functions of ALKBH1 still require further exploration. Here, we demonstrate that knockdown of ALKBH1 inhibits adipogenic differentiation in both human mesenchymal stem cells (hMSCs) and 3T3-L1 preadipocytes, while overexpression of ALKBH1 leads to increased adipogenesis. Using a combination of RNA-seq and N6-mA-DNA-IP-seq analyses, we identify hypoxia-inducible factor-1 (HIF-1) signaling as a crucial downstream target of ALKBH1 activity. Depletion of ALKBH1 leads to hypermethylation of both HIF-1α and its downstream target GYS1. Simultaneous overexpression of HIF-1α and GYS1 restores the adipogenic commitment of ALKBH1-deficient cells. Taken together, our data indicate that ALKBH1 is indispensable for adipogenic differentiation, revealing a novel epigenetic mechanism that regulates adipogenesis.

overall_design: RNA profiles of ALKBH1 knockdown (siRNA) hMSCs versus the control cells

first: Yuting

first: Yuan

last: Wang

first: Yaqian

last: Chen

first: Quan

last: Yuan


title: PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids

status: Public on Dec 10 2021

city: Suita

first: Nobuhiko

last: Shiraki

state: Osaka

address: 2-2 Yamadaoka,

department: Ophthalmology

country: Japan

institute: Osaka University


title: PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids [RNA-Seq]

summary: PAX6-positive microglia like cell

overall_design: Microglia are the resident immune cells of the central nervous system (CNS). They govern the immunogenicity of the retina, which is considered to be part of the CNS, however it is not known how microglia develop in the eye. Here we studied human induced pluripotent stem cells (hiPSCs) that had been expanded into a self-formed ectodermal autonomous multi-zone (SEAM) of cells that partially mimics human eye development. Our results indicate that microglia-like cells, which have characteristics of yolk sac-like linage cells, naturally develop in two-dimensional eye-like SEAM organoids, which lack any vascular components. These cells are unique in that they are paired box protein 6 (PAX6) positive, yet possess some characteristics of mesoderm. Collectively, the data support the notion of the existence of an isolated, locally developing immune system in the eye, which is independent of the body’s vasculature and general immune system.

first: Kazuichi

last: Maruyama

first: Ryuhei

last: Hayashi

first: Yasuhiro

last: Murakawa

first: Kohji

last: Nishida


title: Genetic correlates in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia treated with Hyper-CVAD plus dasatinib or ponatinib

city: Houston

first: Yuya

last: Sasaki

state: TX

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

type: Genome variation profiling by high throughput sequencing

summary: Recurring genetic abnormalities have been identified in Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL). Among them, IKZF1 deletion was associated with poor prognosis in patients treated with imatinib-based or dasatinib-based regimens. However, the molecular determinants for clinical outcomes in ponatinib-treated patients remain unknown. We systematically analyzed genetic alterations in adults with Ph-positive ALL uniformly treated in clinical trials with dasatinib-based regimens or a ponatinib-based regimen and investigated the molecular determinants for treatment outcomes using pretreatment specimens collected from adults with Ph-positive ALL treated with Hyper-CVAD plus dasatinib or ponatinib. DNA sequencing and SNP microarray were performed and recurrent genetic abnormalities were found in 84% of the patients, among whom IKZF1 deletion was most frequently detected (60%). IKZF1 deletion frequently co-occurred with other copy-number abnormalities (IKZF1plus, 46%) and was significantly associated with unfavorable overall survival (OS) (false discovery rate < 0.1) and increased cumulative incidence of relapse (p = 0.01). In a multivariate analysis, dasatinib therapy, lack of achievement of 3-month complete molecular response, and the presence of IKZF1plus status were significantly associated with poor OS. The differential impact of IKZF1plus was largely restricted to patients given Hyper-CVAD plus ponatinib; dasatinib-based regimens had unfavorable outcomes regardless of the molecular abnormalities.

overall_design: Samples were either bone marrow samples obtained from previously untreated patients.

first: Koichi

last: Takahashi

first: Hidetaka

last: Uryu


title: Transcriptomes of TILss

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

summary: We analyzed comprehensive gene expression of TILss

overall_design: Examination of TILs extracted from four NSCLCs by RNA-seq.

first: Shogo

last: Kumagai


title: Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL)

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

overall_design: Refer to individual Series


title: Transcriptomes of NSCLCs

summary: We performed RNA-seq using 46 human surgically-resected NSCLCs.

overall_design: Examination of 46 NSCLCs by RNA-seq.


title: Temporal transcriptome analysis of Bacillus subtilis NDmed in the submerged biofilm model

status: Public on Dec 09 2021

city: Jouy en JOsas

first: romain

last: briandet

address: Domaine de Vilvert

country: France

institute: INRAE

summary:
Investigation of the kinetics of whole genome gene expression level changes in Bacillus subtilis NDmed strain during formation of submerged biofilm and pellicle.
The Bacillus subtilis NDmed strain analyzed in this study is able to form thick and highly structured submerged biofilms as described in Bridier et al., (2011) The Spatial Architecture of Bacillus subtilis Biofilms Deciphered Using a Surface-Associated Model and In Situ Imaging. PLoS ONE 6(1):e16177.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A seven chip study using total RNA recovered from static cultures of Bacillus subtilis NDmed growing in TSB medium in 96-well microplates for different times after adhesion to the bottom of the wells. Each chip measures the expression level of 5,737 transcripts from Bacillus subtilis 168.

first: Pilar

last: Sanchez-Vizuete

first: Dominique

last: Le Coq

first: Yasmine

last: Dergham

first: Arnaud

last: Bridier

first: Stephane

last: Aymerich

first: Kassem

last: Hamze

first: Julien

last: Deschamps

first: Etienne

last: Dervyn

first: Romain

last: Briandet

first: Cyprien

last: Guerin


title: The Lrp/AsnC-type regulator PA2577 controls the Eam-like transporter gene PA2576 in Pseudomonas aeruginosa (RNA-seq)

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: Pseudomonas aeruginosa is a facultative human pathogen especially dangerous for immunocompromised patients. It is known from its high adaptability and complex regulatory systems involving huge repertoire of transcriptional regulators (TRs). The Lrp/AsnC family consists of proteins engaged mostly in regulation of processes such as amino acid metabolism but the function of most of them remains unknown. The aim of this study was characterization of the Lrp/AsnC-type regulator PA2577 of P. aeruginosa. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA2577 revealed changes in mRNA level of 171 genes. Among downregulated loci PA2576 gene, encoding an EamA-like membrane transporter transcribed divergently to PA2577, was identified. ChIP-seq analysis together with EMSA analysis revealed binding site of PA2577 in PA2577/PA2576 intergenic region, indicating direct regulation of PA2576 expression by PA2577. PA2576 was shown to interact with PA5006 and PA3694 proteins predicted to be involved in membrane processes, especially LPS biosynthesis. Defects of growth of PA2577 and PA2576 deficient cells in conditions of polymyxin B supplementation was shown. Overall, presented data uncovered the regulatory properties of PA2577 acting as the repressor of divergently transcribed PA2576 gene, being a part of LPS biogenesis process in P. aeruginosa.

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). To determine the impact of an increased PA2577 level on the transcriptome, the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161/pMEB12 carrying araC araBADp-PA2577 as well as from PAO1161/pKGB8 carrying empty vector (hereafter called EV). The cultures were grown under selection in L broth with 0.02% arabinose. The RNA was isolated from exponentially growing cultures (OD600 0.5) and three independent biological replicates of total RNA were isolated for each strain.

first: Magdalena

last: Modrzejewska

last: Kawalek

first: Aneta

last: Bartosik


title: Transcriptome analysis of IPSC and NPC, derived from twins, discordant by PD

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

summary: This submission contains a result of a study of transcriptiomic profiles of the IPSC and NPC, derived from PD discordant monozygous twins.

overall_design:
Examination of transcriptiomic profiles of the IPSC and NPC, derived from PD discordant monozygous twins.
Two pairs of phenotypically and genetically monozygotic twins discordant for PD were enrolled in the study. These individuals (of Russian ethnic origin and residing in European Russia) were diagnosed at the State Public Health Institution Primorsk Regional Clinical Hospital No. 1 and did not have any family history of PD. The participants were assessed according to the International Parkinson and Movement Disorder Society-sponsored Unified Parkinson?s Disease Rating Scale and Hoehn?Yahr scores. The diagnosis of PD was based on the UK Parkinson?s Disease Society Brain Bank criteria. Patients were at stages 2?4 of the Hoehn?Yahr scale and had a mixed form of PD. The disease duration was at least 7 years. The healthy siblings did not have any signs of PD at the time of collection of the biological material. The twins lived in the same area, and their work was not associated with dangerous factors, such as pesticides or heavy metals. There was no information about the presence of head injuries in their history.

middle: N

first: Anelya

last: Alieva

first: Ekaterina

middle: V

last: Novosadova

first: Elena

last: Arsenyeva

first: Anna

last: Rosinskaya

first: Suzanna

last: Partevian

first: Igor

last: Grivennikov

first: Maria

middle: I

last: Shadrina


title: The Lrp/AsnC-type regulator PA2577 controls the Eam-like transporter gene PA2576 in Pseudomonas aeruginosa (ChIP-seq)

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1, was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis was performed on P. aeruginosa PAO1161 ΔPA2577/pMEB84 (lacIQ-tacp-PA2577-flag) (hereafter referred to as PA2577-F) as well as PAO1161/pABB28.1 (lacIQ-tacp-flag), empty vector control (hereafter called EV-F) strains. Cells were grown under selection in L broth with 0.05 mM IPTG until OD600 = 0.5. For each biological replicate, two independent cultures of each strain were pooled together. The immunoprecipitation was performed with commercially available polyclonal anti-FLAG antibodies (DYKDDDDK Tag polyclonal  antibodies; PA1-985B; Invitrogen).


title: IL-27 induces IFN/STAT1-dependent genes and leads to enhanced function of TIGIT+ HIVGag-specific T cells

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: HIV-specific T cells have diminished effector function and fail to control/eliminate the virus. IL-27, a member of the IL-6/IL-12 cytokine superfamily has been shown to inhibit HIV replication however whether IL-27 can enhance function on HIV-specific T cell is largely unknown. Because of the important implication in cure strategies, in the present manuscript, we investigated the role of IL-27 signaling in human T cells by evaluating the global transcriptional changes and its impact in the function of HIV-specific T cells. We found that T cells from people living with HIV (PLWH), expressed higher levels of STAT1 that leads to enhanced STAT1 activation upon IL-27 stimulation. IL-27 induced transcriptional changes associated with IFN/STAT1-dependent pathways in CD4 and CD8 T cells. More importantly, IL-27 promoted cytokine secretion of TIGIT+HIVGag-specific T cell function by modulating the expression levels of T-bet. This new immunomodulatory property of IL-27 on HIV-specific T cell function suggests its potential therapeutic use in cure strategies.

overall_design: CD4 Naïve, CD4 Memory, CD8 Naïve, CD8 Memory T-cells; from 8 donors (5 HIV infected, 3 healthy); treated with IL-27, IL-6, IFN-alpha, or vehicle

first: Jie

last: Cheng

first: Princy

last: Kumar

first: Jai

first: Bruktawit

last: Goshu

first: Marta

last: Catalfamo


title: MYC assembles and stimulates topoisomerases 1 & 2 in a “topisome” [CAD-seq]

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

summary: High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must somehow manage these high levels of torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with Topoisomerases 1 (TOP1) and 2A (TOP2A) that was confirmed in vitro and in vivo. Beyond recruiting topoisomerases, MYC directly stimulates their activities in vitro and in vivo. We identify a MYC-nucleated “topoisome” complex that unites and increases the levels of both  both TOP1 and TOP2, as well as their activities at promoters and enhancers. Whether TOP2A or TOP2B is included in the topoisome, is dictated by the presence of c-MYC or MYCN, respectively. Thus, in vivo and in vitro, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions.

overall_design:
To probe binding profiles of TOP2A, MYC and RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments were perfromed. ChIP-seq of TOP2A in TOP2A-FLAG HCT116 and MYC in asynchronous wild type HCT116 cells and ChIP-seq of MYC and RNAPII in asynchronous TOP1/TOP2A auxin inducible degron HCT116 cells (-mAID). For mapping of topoisomerase activity we designed CAD-seq method which enables mapping of topoisomerase cleavage complexes. TOP1cc CAD-seq was performed in K562 MYC-mAID cells. To pull down the "topisome" complex we designed cross CAD-seq method which involves trapping of TOP2A by etoposide treatment and then proceeding with a pull down against TOP1. TOP1cc cross-CAD-seq was performed in U2OS cell with and without MYC induction to look at the formation of the topisome.
Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample records.

first: Subhendu

last: Das

first: Donald

last: Cameron

first: Suzanne

last: Sanford

first: Rajiv

last: Jha

first: Zuqin

last: Nie

middle: T

last: Rosello

first: Jan

last: Wisniewski

first: David

last: Price

first: Brian

last: Lewis

first: Fedor

last: Kouzine

last: Levens

first: Laura

last: Baranello


title: PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids [scRNA-Seq]

first: Nobuhiko

last: Shiraki

summary: PAX6-positive microglia like cell

first: Kazuichi

last: Maruyama

first: Ryuhei

last: Hayashi

first: Yasuhiro

last: Murakawa

first: Kohji

last: Nishida


title: The role of Dnj4 in the transcriptional response to hydroxyurea induced DNA damage in Cryptococcus neoformans

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

institute: University of British Columbia

summary: We characterized the impact of the J domain co-chaperone, Dnj4, on the transcriptional response to DNA damage induced by hydroxyurea (an inhibitor of ribonucleotide reductase) in Cryptococcus neoformans. We treated wild type (WT) and mutant dnj4∆ log phase cells with hydroxyurea for one hour and found that the loss of DNJ4 impaired the transcriptional response to HU. In particular, the up-regulation of DNA damage and repair genes as well as iron uptake genes was impaired in these mutants. This study provides the first dataset on the transcriptional response to hydroxyurea in C. neoformans as a resource to the fungal pathogen community.

overall_design: Wild type and mutant (dnj4∆) strains with untreated controls and hydroxyurea treated samples (WT, WTHU, Dnj4, Dnj4HU). For each group 3 replicates were sequenced.

first: Christopher

middle: W

last: Lee

first: Linda

last: Horianopoulos


title: MYC assembles and stimulates topoisomerases 1 & 2 in a “topisome” [cross-CAD-seq]

first: Vladislav

last: Kuzin

first: Subhendu

last: Das

first: Donald

last: Cameron

last: Sanford

last: Jha

first: Marta


title: The METTL3-m6A pathway is a master regulator of muscle maintenance and growth

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

summary: In many members of the animal kingdom, and in particular mammals, skeletal muscle evolved to serve fundamental roles in their health and architectural integrity. While it is clear that dynamic fluctuations of specific gene expression is important for normal muscle function, it is also crucial in the response of skeletal muscle to insults, yet little is known on how such fluctuations are regulated at the post-transcriptional level to impact muscle proteome. Here we report the first genome-wide analysis of mRNA methyladenosine (m6A) dynamics underlying skeletal muscle hypertrophic growth following overload-induced stress. We show that METTL3, the enzyme responsible for m6A formation, orchestrate a previously unrecognized post-transcriptional mechanism controlling skeletal muscle size and function. We found that METTL3 and concomitantly m6A are increased during hypertrophy; manipulating this increase through exogenous delivery of METTL3 is sufficient to induce skeletal muscle growth even in the absence of external triggers. Myofiber-specific conditional genetic deletion of METTL3 abrogated the ability of muscle to undergo overload-induced hypertrophy and led to a spontaneous muscle wasting phenotype over time. In turn, isolation of muscle-specific ribosome-associated transcripts showed that METTL3 affects the translation of specific m6A-modified mRNAs participating in the activin/myostatin pathway, which includes key regulators of muscle size. METTL3 is essential to repress the translation of activin type 2A receptors (ACVR2A), consequently blunting downstream activation of anti-hypertrophic signaling. Notably, the observed hypertrophic growth defect of METTL3-deficient mice can be overcome with co-administration of a myostatin inhibitor. Our findings identify a novel post-transcriptional mechanism of regulating the activin receptor pathway and demonstrate that the N6-adenosine methyltransferase METTL3 is required for and promotes the hypertrophic response of skeletal muscle.

overall_design: High-throughput sequencing of m6A IP and Ribotag IP samples from baseline or muscle overload mouse muscle.

first: J

last: Petrosino

first: S

last: Hinger

first: F


title: Nanostring plasma microRNA profiling in hospitalised patients with COVID-19

city: York

first: Dimitris

last: Lagos

address: YBRI, Wentworth Way,

department: The Hull York Medical School

country: United Kingdom

institute: University of York

summary: Circulating microRNAs (miRNAs) have been shown to be excellent disease diagnostic or prognostic biomarkers in a wide range of chronic and acute inflammatory and infectious diseases including viral respiratory infection. Crucially, circulating miRNA levels are thought to reflect the state of the diseased tissue. Despite their proven value as mechanism-based clinical stratification indicators, miRNAs have only started being explored in the context of COVID-19. here, we aimed to explore whether integrating miRNA with other clinical and biological measurements would reveal more accurate correlates of COVID-19 severity and outcome, and to identify severity-specific correlations of miRNAs with COVID-19-associated inflammatory mediators, clinical parameters, and otucome.

overall_design: We determined 171 microRNA profiles from 58 hospitalised COVID-19 patients using the Nanostring miRNA v3 platform. RNA was from 800μl plasma using the Norgen Plasma/Serum RNA Purification Midi kit (Norgen, Cat #56100). A spike-in non-human miRNA (osa-miR-414) was added to each sample (5μl from a 200 pM per sample) for normalisation.

first: Julie

middle: C

last: Wilson

first: Sally

last: James

first: Katherine

last: Newlin

first: John

last: Grainger

first: Tracy

last: Hussell

first: Nathalie

last: Signoret


title: Unravelling the mechanism of action of Tofacitinib on immune cell trafficking through IBD-associated microvasculature

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: In order to investigate the effect of tofacitinib on leukocyte trafficking through primary HIMEC from patients  with UC, we designed a pilot experiment with the aim to establish the most efficient JAK inhibiting dose. For  this purpose, we performed a dose-dependent experiment on UC-derived HIMEC, assessing Peripheral Blood  Mononuclear Cells (PBMC) transmigration and using a range between 10 and 300 nM (10, 50, 100, 300 nM),  according to the literature. More in detail, in a Transwell system (Figure 1), 500.000 PBMC, in 3 replicates,  have been plated on confluent monolayers of untreated or Tofacitinib pre-treated (24 hours) UC-HIMEC at  the various concentrations. After 18 hours of incubation transmigrated PBMC have been counted and their  phenotype characterized by FACS. In order to avoid any direct effect of Tofacitinib on PBMC, the 18 hour-  long incubation has been performed in the absence of the drug.

overall_design: n=10 Human Lymphatic Endothelial Cells (HLEC) treated with Tofacitinib, and n=10 untreated control cells

first: Silvia

last: D'alessio

last: Ungaro

first: Luigi

middle: A

last: Lamparelli

first: Silvio

last: Danese


title: MYC assembles and stimulates topoisomerases 1 & 2 in a “topisome” [ChIP-seq]

first: Vladislav

last: Kuzin

first: Subhendu

last: Das

first: Donald

last: Cameron

first: Suzanne

last: Sanford

first: Rajiv

first: Zuqin

last: Nie

last: Rosello

first: Jan

last: Wisniewski

first: David

last: Price

first: Brian

last: Lewis

first: Fedor

last: Kouzine

last: Levens

first: Laura

last: Baranello


title: MYC assembles and stimulates topoisomerases 1 & 2 in a “topisome”


title: TRAP seq of the human pluripotent stem cell derived ATOH1 lineage

city: New York

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

department: Bioinformatics

institute: The Rockefeller University

summary: Brain development is regulated by conserved transcriptional programs across species, but little is known about divergent mechanisms that create species-specific characteristics. Among brain regions, the cerebellum is now recognized to contribute to human cognitive evolution having a broad range of non-motor cognitive functions in addition to motor control. Emerging studies highlight the complexity of human cerebellar histogenesis, compared with non-human primates and rodents, making it important to develop methods to generate human cerebellar neurons that closely resemble those in the developing human cerebellum. Here we report a rapid and simple protocol for the directed derivation of the human ATOH1 lineage, the precursor of all excitatory cerebellar neurons, from human pluripotent stem cells (hPSC), and strategies to decrease culture variability; a common limitation in hPSC studies. Upon transplantation into juvenile mice, early postmitotic hPSC-derived cerebellar granule cells migrated along glial fibers and integrated into the cerebellar cortex. By Translational Ribosome Affinity Purification (TRAP)-seq, the ATOH1 lineage most closely resembled human cerebellar tissue in the second trimester. Unexpectedly, TRAP-seq identified a heterochronic shift in the expression of RBFOX3 (NeuN) and NEUROD1, which are classically associated with differentiated neurons, within granule cell progenitors (GCPs) in the human external granule layer. This molecular divergence may provide the mechanism by which the GCP pool persists into year two post birth in humans, but only lasts for two weeks in mice. Our approach provides a scalable in vitro model of the human ATOH1 lineage that yields cerebellar granule cells within 48 days as well as a strategy for identifying uniquely human cellular and molecular characteristics.

overall_design: ATOH1 TRAP-seq of hPSCs differentiated towards the cerebellar granule cell lineage (ATOH1+) at day 28 in vitro

first: Hourinaz

last: Behesti

first: Mary

middle: E

last: Hatten

first: Arif

last: Kocabas

first: Thomas


title: Expression data from human alveolar macrophages (AMs)

status: Public on Dec 08 2021

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

institute: Karolinska Institutet


title: Expression data from human alveolar macrophages (AMs) of fetal versus adult origin

summary:
The impact of cell origin on human lung macrophage identity and function remains unknown. In this study we characterized human alveolar macrophages of fetal versus adult origin.
We used microarray to define the gene signatures of human alveolar macrophages derived from CD116+CD64+ fetal monocytes, CD116+CD64- fetal precursors, and CD34+ HSPCs in MISTRG humanized mice.

overall_design: Human cells with an alveolar macrophage surface phenotype (CD45+CD11b+HLA-DR+CD206+CD169+) were purified from MISTRG mice 13 weeks after intrahepatic transplantation of newborn mice with either adult (2 x 10^5 CD34+ HSPCs) or fetal precursors (2 x 10^5 CD34-Lin-CD116+CD64- or CD34-Lin-CD116+CD64+ fetal liver cells). HSPC-engrafted MISTRG mice were injected intravenously with 2 μg of PE-conjugated anti-human CD45 antibody (HI30, BioLegend) before lung harvest to exclude IV CD45-PE+ pulmonary intravascular macrophages from the sorted CD45+CD11b+HLA-DR+CD206+CD169+ subset as described (Evren et al., 2021)

first: Elza

last: Evren


title: Expression data from different types of human alveolar macrophage (AM) precursors

summary:
Despite their importance in lung health and disease, it remains unknown how human alveolar macrophages develop early in life. In this study we identified the fetal progenitor of human alveolar macrophages.
We used microarray to define the gene signatures of human CD14+ blood monocytes (adult AM precursors), CD116+CD64+ fetal liver monocytes, and CD116+CD64- fetal AM precursors.

overall_design: Cells were purified by immunomagnetic separation followed by cell sorting. We used buffy coat from healhty donors as a source of CD14+CD16- blood monocytes and fetal liver from second trimester as a source of fetal monocytes and fetal AM precursors.


title: High-grade Ovarian Cancer Associated H/ACA snoRNAs Promote Cancer Cell Proliferation and Survival

city: Sherbrooke

first: Laurence

last: Faucher-Giguère

state: Québec

address: 3201 rue jean Mignault

department: Microbiology and Infectiology

institute: Université de Sherbrooke

summary: Small nucleolar RNAs (snoRNAs) are an omnipresent class of non-coding RNAs involved in the modification and processing of ribosomal RNA (rRNA). There are two types of snoRNAs, box C/D, which typically guide 2’-O-methylation, and box H/ACA, which guide pseudouridylation. As snoRNAs are required for ribosome production, the increase of which is a hallmark of cancer development, their expression would be expected to increase in proliferating cancer cells. However, the contributions of H/ACA box and C/D box snoRNAs to the biology of cancer cells remain unclear. To understand the contribution of snoRNAs to cancer progression and aggressiveness we examined their abundance patterns in high-grade serous ovarian carcinomas (HGSC) and serous borderline tumors (SBT), using a newly developed snoRNA sensitive sequencing technique. Surprisingly, the results indicate that while abundance of a selected group of H/ACA snoRNAs increases, most C/D snoRNAs remain stable or decrease in HGSC compared to SBT. This suggests that induction of ribosome biogenesis and translation in HGSC does not require a general increase in snoRNAs expression but depends upon the upregulation of a handful of key H/ACA snoRNAs. This subgroup accurately discriminates between SBT and HGSC underlining their potential as biomarkers of tumor aggressiveness. Remarkably, knockdown of HGSC associated H/ACA snoRNAs, but not their host genes, inhibits cell proliferation and induces apoptosis of model ovarian cancer cell lines. Together our data indicate that specific H/ACA snoRNAs promote tumor aggressiveness through the induction of cell proliferation and resistance to apoptosis.

overall_design: Ribodepleted TGIRT-Seq librairies were generated from RNA samples originating from three serous borderline tumors and three high grade serous carcinoma tissues.

last: Faucher-Giguere

first: Audrey

last: Roy

first: Gabrielle

last: Deschamps-Francoeur

first: Sonia

last: Couture

first: Ryan

last: Nottingham

first: Alan

last: Lambowitz

first: Michelle

middle: S

last: Scott

first: Sherif

last: Elela


title: Polymorphonuclear cells show features of dysfunctional activation during fatal sepsis

city: Brno

first: Marco

last: De Zuani

address: Pekarska, 53

department: CTM

country: Czech Republic

institute: FNUSA - ICRC

summary: Sepsis and septic shock remain leading causes of morbidity and mortality for patients in Intensive care unit. In their early phase, immune cells produce various cytokines which lead to the prompt activation of the immune system. Polymorphonuclear leukocytes (PMNs) respond to different signals producing inflammatory factors and executing their antibacterial mechanisms, resulting in the engulfment and elimination of invading pathogens. However, long-term activation caused by various inflammatory signals produced during sepsis progression, can lead to the alteration of PMN signaling and subsequent defects in their functionality. Here we analyzed the PMNs samples from 34 patients in septic shock, we focused on PMNs gene expression and proteome changes caused by septic shock. We reveal that, compared to those of patients who survived, PMNs from patients who had a fulminant outcome were characterized by a dysfunctional hyper-activation, showing an altered metabolism, higher longevity and recent exit from cell cycle. We believe that this multi-omics approach, although limited, served to pinpoint the alterations in PMNs’ functionality, which may be reverted by targeted treatments.

overall_design: RNAseq of human polymorphonuclear cells isolated from the peripheral blood of patients affected by septic shock

first: Marcela

last: Hortova-Kohoutkova

first: Petra

last: Laznickova

first: Kamila

last: Bendickova

first: Ondrej

last: Mrkva

first: Ivana

last: Andrejcinova

first: Alexandra

last: Mytnikova

last: Polansky

last: Koci

first: Veronika

last: Tomaskova

first: Vladimir

last: Sramek

first: Martin

last: Helan

first: Jan

last: Fric


title: Single-cell RNA sequencing (scRNAseq) data from postnatal day (P) 5 Nes-Cfp/+ cerebella from Wild type (non-irradiated) and Irradiated (at P1) pups

city: Ann Arbor

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: We performed large-scale single cell profiling of dissociated whole postnatal day (P) 5 cerebella from 4 male NestinCFP/+ pups that were either irradiated at P1, or their control littermates in two replicate experiments.

overall_design: Using automated microwell array platforms and mRNA capture beads, we generated single-cell RNA-seq profiles of dissociated neonatal cerebellum cells from control and injured pups.

first: N

last: Bayin

first: Peter

last: Sims

last: Joyner


title: Conditional deletion of Pdcd1 identifies the cell-intrinsic action of PD-1 on functional CD8 T cell subsets for anti-tumor efficacy

city: Boston

first: Eric

last: Muise

state: MA

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

summary: PD-1 blockade has a profound effect on the ability of the immune system to eliminate tumors but many questions remain about the cell types involved and the underlying mechanisms of immune activation. To shed some light on this, the cellular and molecular events following inhibition of PD-1 signaling was investigated in the MC-38 colon carcinoma model using constitutive (PD-1 KO) and conditional (PD1cKO) PD-1 KO mice as well as in wild type mice treated with an anti-PD-1 antibody. The impact on both tumor growth and the development of tumor immunity was assessed. In the PD-1cKO mice, a complete deletion of Pdcd1 in tumor infiltrating T cells (TILs) after tamoxifen treatment led to the inhibition of tumor growth of both small and large tumors. Extensive immune phenotypic analysis of the TILs by flow and mass cytometry identified 22-different T cell subsets of which specifically 5-CD8 positive ones expanded in all three models after PD-1 blockade. All 5 subsets expressed granzyme B and secreted IFNγ. Gene expression analysis of the tumor further supported the phenotypic analysis in both PD-1cKO and PD-1 Ab treated mice and showed an upregulation of pathways related to CD4 and CD8 T cell activation and enhanced signaling through co-stimulatory molecules and IFNγ. Altogether, using PD-1 cKO we define the intrinsic nature of PD-1 suppression of CD8 T cell responses in tumor immunity.

overall_design: Total RNA from tumors from either  wild-type MC38 mice  treated with anti-PD1 antibody muDX400, or conditional Pdcd1 (PD1) KO mice, was sequenced.

first: Sukanya

last: Raghavan

first: Manjiri

last: Sathe

first: Wendy

last: Blumenschein

first: Elaine

last: Pinheiro

first: Rene

last: de Waal Malefyt


title: Thyroid Hormone effects on hiPSC-derived cardiomyocytes (hiPSC-CM). Identification of target genes and pathways by RNA-Seq analysis

city: Rome

first: Alessandra

last: Ulivieri

address: Via Don Carlo Gnocchi 3

department: Laboratory of Biomedical Research

institute: Niccolò Cusano University Foundation

summary: QT prolongation represents a dangerous and potentially life-threatening electrical event affecting the heart. Thyroid hormones (THs) are critical for cardiac development and heart function. However, little is known about THs influence on ventricular repolarization and controversial effects on QT prolongation are reported. Aim of this study was to characterize the direct effects of THs on the cardiac repolarization of human Induced Pluripotent Stem Cell derived cardiomyocytes (hiPSC-CM). RNA Seq analysis of hiPSC-CM treated with Thyroid Hormone T3 indicates significant deregulation in genes involved in cardiac pathways, in particular in ion homeostasis.

overall_design: Gene expression profile of control (EtOH) and T3 treated commercial hiPSC-CM

first: Luca

last: Lavra

first: Fiorenza

last: Magi

last: Morgante

first: Leila

middle: B

last: Salehi

first: Salvatore

last: Sciacchitano


title: Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

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

sample_organism:
Drosophila melanogaster
unidentified plasmid

overall_design: Refer to individual Series


title: Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue [plasmid]

summary: Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

overall_design: We generated a population of Drosophila embryos in each of which reporter gene expression is driven by one genomically integrated reporter element from a pool of wild type enhancers or enhancers in which all binding sites for one or more selected TFs have been mutated. Each tested enhancer was tagged with several distinct 20-base degenerate sequence tags in the 3' UTR of the reporter gene. We dissociated embryonic cells and FACS-sorted informative populations, and reporter gene molecules were counted by a Unique Molecular Identifier (UMI) amplification strategy. We detected RNA and DNA levels by high-throughput sequencing of tagged reporter gene amplicons and normalized gene expression (RNA UMI counts) by dividing by DNA UMI counts to generate a measure of enhancer activity.

first: Colin

last: Waters

first: Yuliya

last: Sytnikova

first: Tiziana

middle: M

last: Cafarelli

first: David

last: Hill

first: Martha

last: Bulyk


title: Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue [Drosophila melanogaster]


title: Neonatal and Adult Human Intervertebral Disc scRNA-seq

status: Public on Dec 07 2021

city: Los Angeles

first: Wensen

last: Jiang

state: CA

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: We report the single-cell RNA-seq (scRNA-seq) data for human neonatal and adult human intervertebral disc (IVD) scRNA-seq. We sequenced cells harvested from three IVDs of a neonatal baby and one IVD from an adult cadaver.

overall_design: Examining cell atlases and transcriptomes of neonatal human IVD and adult human IVD, and make comparison between them.

first: Dmitriy

last: Sheyn


title: Open chromatin analysis of CD4+ Tcells from maternal immune activation (MIA) exposed offspring

first: Eunha

last: Kim

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: We report differentially regulated chromatin accessibility of CD4+ T cells in MIA offspring

overall_design: For ATAC-seq, chromatin accessibility was compared between MIA naïve CD4+ T cells with those of PBS offspring

first: Jun

last: Huh


title: Maternal inflammation promotes autoimmune susceptibility in offspring


title: Modelling SARS-CoV-2 Infection in Mice Using Lentiviral hACE2 Vectors Suggests Two Modes of Immune Responses to SARS-CoV-2 Infection

city: Jerusalem

first: Lior

last: Nissim

address: Hadassah Medical School, Hadassah Ein-Kerem

department: Biochemistry and Molecular Biology

country: Israel

institute: The Hebrew University of Jerusalem

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of individuals worldwide, causing a severe global pandemic. Mice models are wildly used to investigate viral infection pathology, antiviral drugs, and vaccine development. However, since wild-type mice do not express human angiotensin-converting enzyme 2 (hACE2), which mediates SARS-CoV-2 entry into human cells, they are not susceptible to infection with SARS-CoV-2 and are not suitable to simulate symptomatic COVID-19 disease. HACE2 transgenic mice could provide an efficient model, but they are expensive, not always readily available and practically restricted to specific strain(s). Since additional models are needed to study the disease at varying genetic and immune backgrounds, there is a dearth of mouse models for SARS-CoV-2 infection. Here we report the application of lentiviral vectors to generate hACE2 expression in mouse lung epithelial cells (LET1) as well as in interferon receptor knock-out (IFNAR1-/-) mice.  Lenti-hACE2 transduction supported SARS-CoV-2 replication both in vitro and in vivo, simulating mild acute lung disease1. Gene expression analysis revealed two modes of immune responses to SARS-CoV-2 infection: one in response to the exposure of mouse lungs to SARS-CoV-2 particles in the absence of productive viral replication, and the second in response to a productive infection.  This approach expands our knowledge on the role of type-1 interferon signaling in COVID-19 disease, and can be further implemented for a range of COVID-19 studies and drug development.

overall_design: 8 samples of mouse lung:  Lenti-control_1*  Lenti-control 2 *  Lenti-hACE2_1*  Lenti-hACE2_2*  Lenti-control+SARS-CoV-2(dpi 2)*  Lenti-control+SARS-CoV-2(dpi 4)*  Lenti-hACE2+SARS-CoV-2(dpi 2)**  Lenti- hACE2+SARS-CoV-2(dpi 4)**

first: Chaja

last: Katzman

first: Inbal

last: Gazy

first: Tomer

last: Israely

first: Sharon

last: Melamed

first: Boaz

last: Politi

first: Assa

last: Sittner

first: Yifat

last: Yahalom-Ronen

first: Shay

last: Weiss

first: Reem

last: Rass

first: Rachel

last: Zamostiano

first: Eran

last: Bacharach

first: Marcelo

last: Ehrlich

first: Nir

last: Paran


title: Rutaecarpine inhibits glioblastoma migration by activating the aryl hydrocarbon receptor (AhR) signaling pathway

city: Beijing

first: Yiyun

last: Liu

address: 18 Shuangqing Road, Haidian District, Beijing

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

summary: Glioblastoma is the most frequent and aggressive primary astrocytoma in adults. The high migration ability of the tumor cells is an important reason for the high recurrence rate and poor prognosis of glioblastoma. Recently, emerging evidence has shown that the migration ability of glioblastoma cell was inhibited upon the activation of aryl hydrocarbon receptor (AhR), suggesting potential anti-tumor effects of AhR agonists. Rutaecarpine is a natural compound with potential tumor therapeutic effects which can possibly bind to AhR. However, its effect on the migration of glioblastoma is unclear. Therefore, we aim to explore the effects of rutaecarpine on the migration of human glioblastoma cells U87 and the involvements of the AhR signaling pathway. The results showed that: (i) compared with other structural related alkaloids, like evodiamine and dehydroevodiamine, rutaecarpine was a more potent AhR activator, and has stronger inhibitory effect on the glioblastoma cell migration; (ii) rutaecarpine decreased the migration ability of U87 cells in an AhR-dependent manner; (iii) AhR mediated the expression of a tumor suppressor interleukin 24 (IL24) induced by rutaecarpine, and AhR-IL24 axis was involved in the anti-migratoryeffects of rutaecarpine on the glioblastoma. Besides IL24, other motility related genes were proposed to participate in the migration regulation process of rutaecarpine by RNA-Seq analysis. These data suggest that rutaecarpine is a natural AhR agonist that could inhibit the migration of glioblastomaandbe a potential candidate for developing therapeutic drug against glioblatoma.

overall_design: Human glioblastoma cell line U87 mRNA profiles exposed to 10^-4 M rutaecarpin for 48 hours

first: Yangsheng

last: Chen

first: Ruihong

last: Zhu

first: Li

last: Xu

first: Heidi

middle: Q

last: Xie

first: Bin

last: Zhao


title: RNA silencing by CRISPR in plants does not require Cas13

city: Manhattan

first: David

last: Cook

state: KS

address: 1712 Claflin Road, 4024 Throckmorton Plant Sciences Center

department: Plant Pathology

institute: Kansas State University

type: Non-coding RNA profiling by high throughput sequencing

summary: The associated experiments document the production of small RNA (sRNA) during the expression of Cas13 and crRNA, crRNA alone, or controls from agrobacterium spot infiltration in Nicotiana benthamiana. We document the specific production of sRNA corresponding to the guide sequence of the targeted mRNA. In cases where a multi-guide crRNA or a hairpin were expressed, abundent sRNA are produced correspinding to the target mRNA, but outside of the corresponding guide sequence site.

overall_design: small RNA sequencing from N. benthamiana leaves. Two experimental designs were used. One, termed spot, collected leaf tissue at 5 days post agrobacterium-mediated expression of constructs. The other, termed TRV, collected upper, non-infiltrated leaf, following systemic movement of TRV expression cassette.

first: Veerendra

middle: K

last: Sharma


title: Transcriptomics analysis of SUMO1 and SUMO2 U2OS knockout (KO) cell lines

city: Baltimore

first: Michael

middle: J

last: Matunis

address: 615 N. Wolfe Street

institute: Johns Hopkins University

summary: CRISPR-Cas9 was used to individually knock out SUMO1 and SUMO2 expression in U2OS cells. The transcriptomes of SUMO1 and SUMO2 knockout (KO) cell lines were analyzed using RNA-sequencing.

overall_design: Examination of the effects of loss of SUMO1 and SUMO2 on the global transcriptome of U2OS cells.

first: Danielle

last: Bouchard


title: GM-CSF Production by Non-Classical Monocytes Controls Antagonistic LPS-driven Functions In Allergic Inflammation

status: Public on Dec 06 2021

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

summary: Lipopolysaccharide (LPS) can either promote or prevent T helper-2 (Th2) cell-allergic responses. However, the underlying mechanism remains unknown. We show here that LPS activity switches from pro-pathogenic to protective depending on the production of GM-CSF by non-classical monocytes. In the absence of GM-CSF, LPS can favor pathogenic Th2 cell responses by supporting the trafficking of lung migratory dendritic cells (mDC2s) into the lung-draining lymph node. However, when non-classical monocytes produce GM-CSF, LPS and GM-CSF synergize to differentiate monocyte-derived DCs (moDCs) that instruct mDC2s for Th2 cell suppression. Importantly, only allergens with cysteine protease activity trigger GM-CSF production by non-classical monocytes. Hence, the therapeutic effect of LPS is restricted to allergens with this enzymatic activity. Treatment with GM-CSF, however, restores the protective effects of LPS. Thus, GM-CSF produced by non-classical monocytes acts as a rheostat that fine-tunes the pathogenic and therapeutic functions of LPS.

overall_design: Monocytes were sorted from bone marrow of B6 mice, stimulated with media +/- 5ng GM-CSF for 3 hours, and RNA-seq was performed.

first: Kamaljeet

last: Kaur

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Amber

last: Papillion

first: André

last: Ballesteros-Tato

first: Beatriz

last: León


title: Comparison of organoids from Menstrual Fluid and Hormone-treated Endometrium: Novel tools for Gynaecological Research

city: Melbourne

first: Caitlin

last: Filby

state: Victoria

address: TRF L5, 27-31 Wright Street Clayton VIC 3168, Australia

department: The Ritchie Centre

country: Australia

institute: Hudson Institute of Medical Research

summary:
Background: Endometrial organoids are useful tools for studying endometrial biology but are derived from endoemtrial tissue obtained invasively from biopsies and mostly from women not taking hormonal medication. To increase the proportion of women from which endometrial organoids can be obtained, we sought to compare endometrial organoids derived from menstrual fluid and hormone-treated endometrium with standard endometrial organoids.
Purpose: To determine if organoids derived from menstrual fluid and hormone-treated endometrium share features with standard endometrial organoids.
Methods: RNA sequencing was performed on passage 3 day 7 menstrual fluid organoids (MFO), endometrial organoids from women taking hormonal medication (EMO-H) and standard endometrial organoids (EMO)
Results: to determine if organoids derived from menstrual fluid and hormone-treated endometrium share features with staandard endometrial organoids.
Conclusions: MFO and EMO-H did not cluster distinctly to EMO, indicating that they share features with EMO and may enable population-wide disease modelling. This is the first publicly available data set demonstrating the transcriptome of EMO-H.

overall_design: mRNA profiles of human mesntrual fluid organoids, endometrial organoids from women taking hormonal medication and standard endometrial organoids

first: S

last: Mortlock


title: Epigenetic landscape of murine testicular histone variants TH2A and TH2B in sperm

city: Mumbai

first: Priyanka

last: Parte

state: Maharashtra

address: J.M.Street, Parel

department: Gamete Immunobiology

country: India

institute: ICMR-National Institute for Research in Reproductive and Child Health

summary: In this study,  chromatin immunoprecipitated sequencing was done for testis specific histone variants of H2B and H2A, TH2B and TH2A to understand the epigenomics of these retained histones, using murine caudal sperm.Our in silico analysis has attributed a myriad of novel functions to sperm retained TH2B with respect to embryo development and spermatogenesis.Also, based on genomic regions, TH2B was observed to be associated with spindle assembly and various meiosis-specific genes, which is an important finding as TH2A/TH2B DKO mice have been reported to have defective cohesin release.We also observed a degree of evolutionary conservation between the TH2B-DNA linkage across human and mouse.This overlap included genes important for embryogenesis. Most importantly, heterogeneity in the epigenetic landscape of TH2A and TH2B was seen which is intriguing as TH2B and TH2A are well reported to be present in the same nucleosomes to promote open chromatin. Additionally, unlike TH2B, TH2A was enriched on the mitochondrial chromosome. We presume that TH2A is associated with mitochondrial DNA inserted in the nuclear DNA and this observation needs further validation.. A comprehensive analysis of these observations indicates novel functions for the sperm retained TH2B and TH2A.

overall_design: Native-ChIP of sperm histones TH2A and TH2B in murine caudal sperm using 8-12 weeks old BALB/c-129-E mice

first: Isha

last: Singh


title: Bulk RNAseq of OT-1 T cells in OVA-pregnant and OVA-grafted mice

first: Paige

last: Porrett

address: 701 19th Street South, Lyons Harrison Research Building Rm 728

department: Surgery

country: USA

summary:
Purpose: The molecular circuits which govern CD8 T cell fate after alloimmunization by transplantation or pregnancy are unknown. The goals of this study are to perform whole transcriptome profiling (RNA-seq) of antigen-experienced CD8 T cells in parous and grafted mice to determine whether these cells become memory or exhausted T cells.
Methods: mRNA profiles of OT-1 T cells recovered fom naive,OVA-skin grafted and OVA-parous mice were generated by bulk RNA-sequencing. OT-1 cells were FACS sorted from 10 individual mice per each of the three groups and then pooled together into three replicate samples per group. The sequence reads that passed quality filters were analyzed after aligning (STAR) with EdgeR.
Results: Comparison of OT-1 T cells from OVA-grafted and OVA-parous mice revealed 400 differentially expressed genes.
Conclusions: Skin grafting promotes the differentiation of canonical memory CD8 T cells whereas pregnancy promotes the differentiation of exhausted CD8 T cells with diminished recall capacity.

overall_design: OVA-specific OT-1 T cells were adoptively transferred into congenic naïve mice. Mice received either no OVA exposure (Naïve), a skin graft  from an Act-mOVA mouse (gOVA), or were mated with an Act-mOVA male (pOVA). Thirty days after antigen exposure, OT-1 T cells were sorted from the spleen, pooled, and bulk RNA-sequencing was performed.


title: Late eating decreases energy expenditure, increases hunger and appetite, and modifies metabolic pathways in adipose tissue [RNA-Seq]

city: Chicago

first: Matthew

last: Piron

state: IL

address: 900 E 57th St. KCBD 8230A

institute: University of Chicago

summary: Late eating has been linked to obesity risk. It is not clear whether this is caused by changes in hunger and appetite, energy expenditure or both, nor what molecular pathways in adipose tissues are involved. We conducted a randomized crossover trial to determine the effects of late vs. early meal schedule  on the above measures while rigorously controlling for nutrient intake, fasting duration, light exposure, physical activity and sleep opportunity. Late mealtimes doubled the odds of participants reporting hunger (p<0.0001), increased 24-h ghrelin:leptin ratio (p<0.0001) and decreased waketime energy expenditure (p=0.002). Adipose biopsy directional gene expression analyses showed alterations of several pathways attributed to late mealtimes: TGF-β signaling, lipid metabolism, p38 MAPK signaling, modulation of receptor tyrosine kinases, and autophagy, indicating decreased lipolysis/increased lipid synthesis, particularly for phospholipids and membrane-bound lipids. These findings may help develop evidence-based approaches for using appropriate meal timing to prevent and/or treat obesity.

overall_design: Total RNA obtained from SubQ adipose biopsy under early or late eating protocols.

first: Nina

last: Vujović


title: Late eating decreases energy expenditure, increases hunger and appetite, and modifies metabolic pathways in adipose tissue


title: Late eating decreases energy expenditure, increases hunger and appetite, and modifies metabolic pathways in adipose tissue [array]


title: Primary neonatal mouse cardiomyocytes: empty adenovirus infection vs. Mettl14-overexpression adenovirus infection

status: Public on Dec 05 2021

city: Harbin

first: weijie

last: du

state: Heilongjiang

address: 157 Baojian Road

institute: Harbin Medical University

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

summary: The adenovirus carrying Mettl14 gene infects primary neonatal mouse cardiomyocytes, which is in contrast with the primary neonatal mouse cardiomyocytes infected with empty virus. The purpose is to explore the effect of Mettl14 on the global mRNA m6A modification level in primary neonatal rat cardiomyocytes.

overall_design: One-condition experiment, primary neonatal mouse cardiomyocytes. Biological replicates: 1 empty infection replicate, 1 overexpression infection replicate.

first: Weijie

last: Du

first: Ping

last: Pang


title: Toxocara canis- and Toxocara cati-induced neurotoxocarosis is associated with comprehensive brain transcriptomic alterations

city: Hannover

first: Christina

last: Strube

address: Bünteweg 17

department: Institute for Parasitology

institute: University of Veterinary Medicine Hannover

summary: Migration and persistence of Toxocara canis and T. cati larvae in brains of paratenic hosts, including humans, may induce the disease neurotoxocarosis (NT). Along with various clinical symptoms, neurodegenerative and neuropsychiatric disorders have been described as a consequence of the disease. As most knowledge on NT is derived from only a few published clinical cases, information regarding underlying pathomechanisms and host’s response to Toxocara remain scarce. Therefore, it was aimed to characterize the general pathogenesis as well as the respective host's reaction on the transcriptional level in brains of T. canis- and T. cati C57BL/6J mice as a model for paratenic hosts.

overall_design: Transcriptional changes in cerebra as well as cerebella of T. canis- and T. cati-infected C57Bl/6J mice compared to the uninfected control mice were analysed at days 7, 14, 28, 70, 98 and 120 post infection. In each infection group, 3 animals were included for the evaluation.

first: Patrick

last: Waindok

first: Dimitri

middle: L

last: Lindenwald

first: Elisabeth

last: Janecek-Erfurth

first: Esther

last: Wilk

first: Klaus

last: Schughart

first: Robert

last: Geffers