title: Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability

city: Basel

first: Attila

last: Becskei

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: The half-life of mRNAs, as well as their translation, increases proportionally to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the coupling in yeast displays a dichotomous behavior regarding the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs even though they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality-dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell-cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.

overall_design: To investigate the translational status of transcripts, with respect to the number of ribosomes associated with them, we carried out polysome profiling of yeast BY4743 isogenic strains and carried out RNASeq of each of the fractions with them corresponding to specific number of ribosomes.

first: Sayanur

last: Rahaman

first: Simone

last: Faravelli

first: Sylvia

last: Voegeli


title: Transcriptome analysis of familial dysautonomia reveals tissue-specific gene expression disruption in the peripheral nervous system

status: Public on Sep 28 2023

city: Boston

first: Susan

last: Slaugenhaupt

state: MA

address: 185 Cambridge St

department: Center for Genomic Medicine

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: Familial Dysautonomia (FD) is a rare recessive neurodevelopmental disease caused by a splice site mutation in the Elongator acetyltransferase complex subunit 1 (ELP1) leading to tissue-specific skipping of exon 20 and reduction of the ELP1 protein, distinctly in the central nervous system (CNS) and peripheral nervous system (PNS).  Here we performed a transcriptome-wide study to dissect the molecular mechanisms underlying FD in specific neuronal tissues from the FD phenotypic mouse which expresses human ELP1, including the dorsal root ganglion (DRG), trigeminal ganglion (TG), medulla (MED), cortex, and spinal cord (SC). We focused our analyses on differentially expressed genes (DEGs) representing the most dominant transcriptomic alterations; and on genes in co-expression modules that are highly correlated with full-length ELP1 expression (ELP1 dose-responsive genes). We identified higher number of DEGs (342) in the PNS (DRG, TG) as compared to the CNS (MED, SC, Cortex) (143). ELP1 dose-responsive genes are only found in DRG, TG, and MED, not in Cortex or SC, tissues. Gene Ontology analyses of both DEGs and ELP1-dose-responsive genes highlight the regulation of neurotransmitters. The transcriptome-wide signals were highly convergent between PNS tissues (DRG and TG) but not among CNS tissues. Those convergent genes were enriched for known protein-protein interactions and cell type-specific markers defining myelinated neurons and peptidergic nociceptors. Our findings support the involvement of specific neuronal subtypes underlying the PNS phenotypes in FD. Our study comprehensively investigates transcriptome-wide alterations in FD neuronal tissues and identifies the functional dysregulations in the peripheral nervous system contributing to disease.

overall_design: 3-month old FD and Control mice were dissected for cortex, dorsal root ganglion, medulla, spinal cord and trigeminal ganglion neurons and paired-end mRNA-seq was performed.  124 Libraries were generated.

first: Ricardo

last: Harripaul

first: Elisabetta

last: Morini

first: Dadi

last: Gao

last: Slaugenahaupt


status: Public on Sep 29 2023

city: Guwahati

first: Narayana

middle: H

last: Mohan

state: Assam

address: Rani

department: ICAR-National Research Centre on Pig

country: India

institute: Indian Council of Agricultural Research

summary: We report the application of next generation sequencing for examining muscle development in two different breeds of pigs (Hampshire and Mali). Muscle samples (n=2/breed) were subjected to RNA isolation, cDNA library preparation and sequencing.The transcriptome analysis shows significant differences in the expression pattern of genes associated with muscle development in Hampshire and Mali.

overall_design: Transcriptome analysis of muscle from two pig breeds with varying muscularity was conducted to provide insights into muscle development.

first: Prajwalita

last: Pathak

first: Lipika

last: Buragohain

first: Juri

last: Deka

first: A

middle: K

last: Das

first: R

last: Thomas

last: Singh

first: Jaya

last: Bharati

first: D

last: Sarma

first: V

last: Gupta

first: B

middle: C


title: MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity

type: Methylation profiling by high throughput sequencing

summary: We report the application of methylated DNA immunopreciptation (MeDIP)-next generation sequencing for examining methylome in two different breeds of pigs. Two muscle samples from each animal/breed processed to isolated DNA. DNA was isolated from two muscle samples (one per breed) was used for methylated DNA immunoprecipitation (MeDIP). 5 methyl cytosine regions were immunoprecipitated and processed for next generation sequencing in Hiseq 2500 (Illumina). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment (BWA) (version 0.7.17). The MeDIP data generated was used for identification of differentially methylated regions (DMRs) across the chromosome between the breeds using Burrrows Eheeler Alignment (BWA version 0.7.17. Uniquely mapped reads were processed further with MEDIPS. A total of 1545 and 25 DMRs (P<0.1) were identified across the pig chromosome and mitochondrial DNA respectively.

overall_design: Methylome analysis of muscle from two pig breeds with varying muscularity was conducted to provide insights into muscle development.


title: Host transcriptional responses to SARS-CoV-2 infection in a human nose organoid model

city: Houston

first: Sarah

middle: Yvette

last: Ponce

state: TX

address: 1 Baylor Plaza

department: HGSC

institute: Baylor College of Medicine

summary: As a means to identify host transcriptional responses to SARS-CoV-2 infection, we generated RNA-seq data on the human nose organoid model HNO2043. We sampled HNO204 cells infected with SARS-CoV-2 and Mock control cells at 6hrs, 72hrs, and 6 days post-infection, and we profiled these samples for gene expression. Comparisons of the HNO204 transcriptional response to SARS-CoV-2 in relation to transcriptional responses observed in other models and patient samples would suggest the existence of distinct host responses to SARS-CoV-2 depending on cellular context.

overall_design: We determined the transcriptional response of a human nose organoid (HNO) line infected with SARS-CoV-2. **RAW DATA NOT PROVIDED DUE TO PATIENT PRIVACY CONCERNS**

first: Chad

last: Creighton

first: Yiqun

last: Zhang

first: Pedro

last: Piedra

first: Vasanthi

last: Avadhanula


title: Trib1 regulates mouse LDL metabolism through Cebpa-mediated regulation of the LDL receptor in hepatocytes.

city: philadelphia

first: Katherine

last: Quiroz-Figueroa

state: Pennsylvania

address: 11-135 Smilow Center for Translational Research, 3400 Civic Center Blvd

department: Division of Translational Medicine and Human Genetics, Department of Medicine

institute: University of Pennsylvania

summary: The Tribbles homolog 1 protein (TRIB1), encoded by the gene TRIB1, has been identified by genome-wide association studies (GWAS) as likely to be causal of a remarkable number of cardiometabolic traits, including plasma lipids, hepatic steatosis, adiponectin levels, and coronary artery disease. In its best-known function, Tribbles 1 interacts with the ubiquitin ligate COP1 protein to target the transcription factors CCAAT/enhancer-binding protein alpha and beta (CEBP a/b) for proteasomal degradation. We have previously published that specific Trib1 deletion in mice increased de novo lipogenesis, hepatic steatosis, and plasma triglycerides, attributable at least in part to increased protein levels of hepatic Cebpa. However, the mechanism by which Trib1 regulates plasma lipids and specifically LDL-C metabolism remained unknown. In this experiment our aim was to identify possible molecular interactions by which hepatic Trib1 regulates specifically LDL-C metabolism dependently of Cebpa expression.  To do this, we compared total gene expression in livers of wild type mice, Trib1, Cebpa and Trib1;Cebpa hepatic deleted mice.  Gene expression data was then used in Ingenuity Pathway analysis to identify upstream transcription factors that might be responsible for the gene expression changes observed.

overall_design: Four groups of mice were used for this experiment: wild type Trib1 Flox/Flox, Cebpa Flox/Flox and Trib1;Cebpa Flox/Flox. The mice were 20-21 weeks of age when injected with adeno associated virus (AAV) encoding Cre recombinase (AAV_Cre). The mice were injected in 2 different cohorts with a total n=6 mice per group. Mice were euthanized at 4-week post injection of AAV, and RNA collected from whole liver tissue.

first: Daniel

middle: J

last: Rader

first: Nicholas

last: Hand

first: John

middle: W

last: Tobias


title: ChIP-seq data from pika Epas1 knock in MAF and RNA-seq data from mouse, rat, rabbit and Tibetan pika fibroblasts

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National institute of biological sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MAF from pika Epas1-3FLAG knock-in mice were extracted and immortalized. After 12h DMOG treatment, cells were conducted for the ChIP-seq (Bmal1,Flag). We found that in knock-in mice fibroblasts, EPAS1-3FLAG can bind to similar E-box locus compared with BMAL1. Fibroblasts from mouse, rat, rabbit and Tibetan pika were extracted (and Tibetan pika fibroblasts were immortalized). RNA was extracted at 90% confluency. We found that Per2 mRNA level was significantly lower in Tibetan pika fibroblasts compared with other species.

sample_organism:
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus
Ochotona curzoniae

overall_design: To evaluate the binding site of Epas1 and the mRNA level of core clock genes in different species

first: Ziqing

last: Yu

first: Jiawen

last: Wang

first: Eric

middle: E


title: RGS1 Modulates Autophagic and Metabolic Programs and Is a Critical Mediator of Human Treg Function

city: Cambridge

first: Franck

last: Rapaport

address: 350 Water Street

department: PMCB

institute: Sanofi

summary: Regulatory T cells (Tregs) are critical mediators of immune tolerance and play a diametric role in cancer and autoimmunity. Tumor-infiltrating Tregs are often associated with poor prognosis in solid tumors, as their enrichment in the tumor microenvironment contributes to immunosuppression. Conversely, dysregulation in the Treg compartment can disrupt self-tolerance, leading to autoimmunity. Herein, we describe a novel regulator of Tregs, the GTPase activator, Regulator of G Protein 1 (RGS1), RGS1, demonstrating that RGS1-deficient human Tregs show downregulation of Treg-associated genes and are less immunosuppressive. These RGS1-deficient Tregs exhibit perturbations to the FOXP3-c-MYC transcriptional axis and downstream metabolic and autophagy programs by shifting their energy demands toward glycolysis and rendering them less autophagic. Taken together, RGS1 may serve as an apical node of Treg function by regulating the FOXP3-c-MYC transcriptional axis, thereby providing a therapeutic rationale for targeting RGS1 for treatment of cancer and autoimmune diseases.

overall_design:
To investigate the function of RGS1 in human Tregs, we knocked down RGS1 via siRNA (siRGS1) and used a non-targeting scrambled control siRNA (siNT) for comparison
We then performed RNAseq on ex vivo expanded Tregs with siRGS1 and siNT knockdowns on 5 human Treg donors
Comparative gene expression profiling analysis of RNAseq data from siRGS1 and siNT human Tregs

first: Alyssa

middle: L

last: Flynn

first: Joseph

last: Gans

first: Javier

last: Escobedo

first: Cheng

last: Zhu

first: Ana-Maria

last: Florescu

first: Srinivas

last: Shankara

first: Stephen

last: Madden

first: Peter

middle: S

last: Kim

first: Lily

middle: I

last: Pao


title: Sex-specific role for SLIT1 in regulating stress susceptibility

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Major depressive disorder (MDD) is a pervasive and debilitating syndrome characterized by mood disturbances, anhedonia, and alterations in cognition. While the prevalence of MDD is twice as high for women compared to men, little is known about the molecular mechanisms that drive sex differences in depression susceptibility. We discovered that Slit Guidance Ligand 1 (SLIT1), a secreted protein essential for axonal navigation and molecular guidance in cellular migration, is downregulated in the ventromedial prefrontal cortex (vmPFC) of depressed women compared to healthy controls, but not depressed men. This sex-specific downregulation of Slit1 was also observed in the vmPFC of mice exposed to chronic variable stress. To identify a causal, sex-specific role for SLIT1 in depression-related behavioral abnormalities, we performed knockdown (KD) of Slit1 expression in the vmPFC of male and female mice. When combined with stress exposure, vmPFC Slit1 KD reflected the human condition by inducing a sex-specific increase in anxiety- and depression-like behavioral abnormalities in female mice with no effect seen in male mice. Further, we found that vmPFC Slit1 KD caused a pronounced reduction in dendritic arborization and concomitant alterations to electrophysiological properties of vmPFC pyramidal neurons in females. Additionally, RNA-sequencing analysis of the vmPFC following Slit1 KD in female mice revealed an augmented transcriptional stress signature. Together, our findings establish a crucial role for SLIT1 in regulating neurophysiological and transcriptional responses to stress within the vmPFC, and provide mechanistic insight into novel signaling pathways and molecular factors influencing sex differences in depression susceptibility.

overall_design: RNA-sequencing analysis of the vmPFC following Slit1 KD in female mice.

first: Yentl

middle: Y

last: van der Zee

first: Casey

last: Lardner

first: Philipp

last: Mews

last: Nestler

first: Orna

last: Issler


title: Cytosolic DNA accumulation promotes breast cancer immunogenicity via a STING-independent pathway

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Immune checkpoint blockade (ICB) has revolutionized cancer treatment. However, ICB alone has demonstrated only benefit in a small subset of patients with breast cancer. We here reported that the tumoral cytosolic ssDNA is associated with tumor-infiltrating lymphocyte in patients with triple negative breast cancer. TREX1 deficiency triggered a STING-independent innate immune response via DDX3X. Cytosolic ssDNA accumulation in tumors due to TREX1 deletion is sufficient to drastically improve the efficacy of ICB.

overall_design: RNA from control and TREX1-depleted tumors (via CRISPR-Cas9) treated with or without ICB were analyzed for global gene expression levels


title: Suture-anchored cutaneous tension induces persistent hypertrophic scarring in a novel murine model [RNA-Seq]

city: Shanghai

first: Yashu

last: Li

address: No,1665, Kongjiang Road, Yangpu District

department: Department of Plastic Surgery

institute: Xinhua hospital, Shanghai Jiaotong University

summary: Hypertrophic scars arise from dysregulated wound healing under prolonged mechanical tension, causing disfiguring fibrosis. However, limited preclinical models replicate key features of human tension-induced scarring. We developed an innovative murine model utilizing suture anchoring to impose persistent transverse-axial stretch across healing incisions, mimicking excessive wound tension that leads to hypertrophy clinically. Dorsal paired incisions were generated in mice, with wound edges on the upper back sutured to the rib cage while leaving wound edges on the lower back relaxed. This localized anchoring restrained wound contraction, maintaining high tension throughout remodeling analogous to scars widening under stress. Stretched upper wounds developed profound fibrotic changes compared to relaxed controls. Scars induced by suture-anchored tension displayed macroscopic hypertrophy, hardness, erythema, and pruritis up to 3 months. Histologically, scars induced by suture-anchored tension were hypercellular, hypervascular, hyperproliferative with disorganized extracellular matrix deposition, and displayed molecular hallmarks of hypertrophic fibrosis. MRNA sequencing revealed the fibrogenic signature in suture-anchored tension induced hypertrophic scars, which exhibited transcriptional overlap with mechanically-stretched scars, human hypertrophic and keloid scars.

overall_design: To identify the global transcriptome of hypertrophic scars generated in stretched group (HS) and normal scars formed in control group (NS), mRNA sequencing was conducted upon scar samples 2 weeks post excision. Comparative gene expression profiling analysis of mRNA-seq data for HS and NS.

first: Dale

last: Xu

first: Weifeng

last: He

first: Kaiyang

last: Lv


title: Suture-anchored cutaneous tension induces persistent hypertrophic scarring in a novel murine model

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of alloantigen-specific TEa CD4+ T cells after heart transplantation

first: Dawei

last: Zou

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

summary: Alloreactive CD4+ T cells play a central role in allograft rejection, We used single cell RNA sequencing (scRNA-seq) to analyze the cell states of alloreactive CD4+ T cells in periphery and allografts to better understand how alloreactive CD4+ T cells drive allograft rejection.

overall_design: C57BL/6 (B6) mice received adoptive transfer of congenically marked naïve WT or Ldha-/- TEa (TCR transgenic) CD4+ T cells, specifically recognizing the BALB/c I-EÎ± major alloantigen. Subsequently, these mice underwent transplantation of BALB/c hearts. After 7 days post-transplantation, we isolated WT TEa cells from both spleens and heart allografts, along with Ldha-/- TEa cells from the spleens, for single-cell RNA sequencing (scRNA-seq) analysis.

first: Guohua

last: Wang

first: Yin

last: Zheng

first: Wenhao

last: Chen


title: Single cell RNA-seq of brain cells from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice

city: Uppsala

first: L.

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: In this single cell RNAseq analysis, we analyzed brain cells from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice

overall_design: Brain single cells from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice were sorted into 384-well-plates and RNA-sequenced using the SmartSeq2 method

first: Johanna

last: Andrea

first: Christer

last: Betsholtz


title: Genomic annotation of a non-coding region deleted on 4q25 [ATAC-seq]

city: nantes

first: Julien

last: Barc

address: 8 quai moncousu

country: France

institute: INSERM

summary: we identified 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2).

overall_design: ATAC-seq has been performed to identify the accessible chromatin regions and annotate the 4q25 region

first: Manon

last: Baudic

first: Estelle

last: Baron

first: Enora

last: Fremy

first: Adrien

last: Foucal

first: Jean-Jacques

last: Schott


title: Impact of ZAP-70 kinase inhibitors on  gene expression in murine xenograft models of malignant T-cell lymphoma

city: Barcelona

first: Cristina

last: Hernandez

address: Calle Natzaret 115-117

country: Spain

institute: Vall D'Hebron Institute of Oncology

summary: T-cell lymphoma (TCL) is a group of lymphomas derived from mature T and NK cells, often characterized by an aggressive clinical course with limited effective treatments available. Emerging evidence underscores the pivotal role of T cell receptor signaling (TCR) in the pathobiology of T cell lymphomas. ZAP-70, a protein tyrosine kinase belonging to the Syk / ZAP-70 family, is expressed in T lymphocytes and in NK cells and is an essential kinase in the proximal signaling of the TCR. The main objective of this project is to study the therapeutic potential of blocking TCR signaling by specific inhibition of the ZAP-70 protein. For this, we have developed two ZAP-70 kinase inhibitory molecules and have analyzed their antitumor efficacy in T-cell lymphoma xenografts. All this would emulate what has been observed in B-cell lymphomas, where signaling through the B-cell receptor is crucial for the survival and growth of tumor cells and blocking this pathway is of enormous therapeutic efficacy. Based on the results of the research proposed here, we will be able to establish the basis for further early phase clinical trials.

overall_design: We conducted RNA sequencing analysis on subcutaneous T-cell lymphoma tumors derived from T-cell lymphoma xenografts that had undergone 1 week treatment with either a ZAP-70 inhibitor candidate (2 candidates tested), as well as the vehicle group receiving the vehicle treatment(n=6/group).

first: Pau

last: Abrisqueta

first: Marta

last: Crespo

first: Laura

last: Palomo


title: The Impact of RNA Extraction Method on Ribosomal-depleted RNA Sequencing (RNA-Seq) Experiments in a Translational Setting

city: Ann Arbor

first: Logan

middle: Alexander

last: Walker

state: MI

address: 109 Zina Pitcher Pl, Lab 3838 (loganaw)

department: Biophysics

institute: University of Michigan, Ann Arbor

summary:
Background
Ribosome depleted RNA-seq is well suited for understanding coding- and noncoding transcript expression in clinical samples with diverse input RNA quality and mass. Current choices for RNA extraction include phase-separation (e.g., ThermoFisher TRIzol) approaches to column-based (e.g., Norgen Spin Columns) approaches. Each method, however, has been noted to have differing effects on the properties of the extracted nucleic acids, precluding the straightforward bioinformatic comparison of data generated by the two methods.
Methods
In this study, we present differences in data differing only in total RNA extraction approaches (phase separation vs. column) from clinical samples processed by the same tissue bank and sequencing facility personnel. We use data from seven samples with libraries generated from RNA extracted with both extraction methods to characterize the effect of ‘differentially extracted’ genes (DExGs) on transcriptomic profiles. We then use another set of 148 samples extracted with one or the other method to confirm the differences observed in the 7-sample dataset.
Results
The large number of samples employed in this study allows us to find significant differences in important quality control parameters as well as many DExGs between the two methods. We identify several biophysical properties which are potential drivers of these differences.
Conclusions
We show that partial correction of extraction method mediated differences can be achieved but full correction is not possible. These results lay the foundation for principled decision making of RNA extraction methods for use in clinical samples in a translational environment, particularly in light of recent reagent shortages during the COVID-19 pandemic.

middle: A

first: Pearlly

last: Yan

first: Ralf

last: Bundschuh


title: Cadmium-induced oxidative stress, histopathology, and transcriptomic changes in the hepatopancreas of Fenneropenaeus merguiensis

status: Public on Sep 27 2023

city: Zhanjiang City

first: Ju

last: Zhimin

address: 1 Haida Road, Mazhang District

institute: Guangdong Ocean University

summary: This paper aimed to elucidate the potential mechanisms of cadmium's impact on the hepatopancreas of F. merguiensis through physiological, histological, and transcriptomic analyses. Transcriptomic analysis also indicated that cadmium exposure induced the expression of genes related to detoxification and apoptosis, such as heat shock proteins, metallothionein, and Caspase-3, suggesting it has adverse effects on the normal physiological functions of F. merguiensis.

overall_design: Healthy Fenneropenaeus merguiensis were reared at Guangdong Ocean University's Donghai Island Base. They were acclimated for a week in holding tanks with specific water conditions and fed three times daily with a special feed. Water was refreshed daily. The study had two parts: a preliminary trial to find the effect of cadmium chloride at 72-hour LC50 and the main trial. Shrimps were placed in tanks and exposed to varying concentrations of cadmium chloride, 30 shrimps per tank, three tanks for each concentration, totaling 540 shrimps, water and conditions were kept stable, mortality was monitored every 2 hours, and survival rates were noted at 24, 48, and 72 hours. Based on the preliminary results, the main experiment was conducted, shrimps were divided into two groups (30 each, three replicates per concentration, totaling 180 shrimps), and two cadmium concentrations were used: 0.0 mg/L (control) and 0.5 mg/L (72 h-LC50). Experimental conditions remained the same as in the preliminary trial.

first: Zhimin

last: Ju

first: Yiguo

last: Lei

first: Charles

middle: B

last: Ndandala

first: Panmei

last: Wang

first: Junliang

last: Luo

first: Huafang

last: Liang


title: SARS-CoV-2 infection

first: Sarah

last: Ponce


title: LncRNA of human Fibroblast-like synoviocytes of rheumatoid arthritis and osteoarthritis

city: Guangzhou

first: Shibai

last: Xiao

address: guangzhou avenue, NO.1023

institute: Nanfang Hospital, Southern Medical University

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

summary: To further development of  lncRNA expression differences, we have employed whole lncRNA microarray expression profiling as a discovery platform to identify lncRNA with the potential to distinguish

overall_design: total RNA of Fibroblast-like synoviocytes in vitro obtained from three patients with RA and OA was extracted by TRIzol® reagent

first: Min

last: Yang


title: Divergent roles for STAT4 in shaping effector differentiation of ILC1 and NK cells during gut inflammation I

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

summary: Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1) require the transcription factor STAT4 to elicit rapid effector responses and protect against pathogens. Herein, by combining genetic and transcriptomic approaches, we revealed that STAT4 played an unexpected divergent role in regulating effector differentiation of murine ILC1 and NK cells, during intestinal inflammation. Stat4 deletion in Ncr1-expressing cells led to an increased generation of cytotoxic ILC1 in the inflamed large intestine. By contrast, Stat4-deficient NK cells showed impaired terminal differentiation, characterized by lower levels of IRF-8 and KLRG1. STAT4 expression in NCR+ innate lymphocytes restrained gut inflammation and controlled both systemic  IFN-g levels and the number of type 2 adaptive T cells in the large intestine. Collectively our data shed light on shared and distinctive mechanisms of transcriptional regulation driven by STAT4 in NK cells and ILC1 required for protection during intestinal inflammation.

overall_design: Mice were administered with DSS for 7 days. NK cells were isolated from the lamina propria of the large intestine. NK cells from the spleen of untreated mice were used as control.

first: Stephen

middle: R

last: Brooks

first: Gianluca

last: Scarno

first: Giuseppe

last: Sciumè


title: The single cell transcriptomic profiling in iPSC derived Midbrain Organoid of POLG Disease

city: Bergen

first: Kristina Xiao

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: To investigate the transcriptomic profile and molecular mechanisms using single cell RNA sequecning (scRNA-seq) analysis for the iPSC derived midbrain organoids from the patient of POLG Disease

overall_design:
Examination of single cell transcriptomic profile in iPSC-derived midbrain organoids from: Control samples, Patient sample, Patient sample treated with nicotinamide riboside (NR) at a concentration of 1mM and the midbrain organoids were exposed to NR over 2 months.
*** Submitter declares that raw data cannot be deposited due to the sensitive nature of the data. ***

first: Kristina

middle: X

first: Anbin

last: Chen

first: Tsering

last: Yangzom


title: Postnatal Subventricular Zone Injury Predicts Motor Impairment in Preterm Infants Following Intestinal Disease

city: Durham

first: Adrian

middle: Aryeh

last: Epstein

state: NC

address: 300 N Duke St

department: Pediatrics

institute: Duke Univeristy School of Medicine

summary: Following intestinal perforation in neonatal mice there is an injury to the subventrcular zone stem cell niche. These files are the raw data from mouse SVZ in controls and mice with modeled instestinal perforation.

overall_design: On postnatal day 5, mice were divided into controls and modeled intestinal perforation. After 48 hours, the SVZ was dissected for single nuclear RNAseq.

first: Eric

last: Benner

first: Vaibhav

last: Jain

first: Simon

middle: G

last: Gregory


title: Divergent roles for STAT4 in shaping effector differentiation of ILC1 and NK cells during gut inflammation


title: Complementary HLH Susceptibility Factors Converge on CD8 T-cell Hyperactivation

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis


title: Gene expression profile (RNAseq) in atrophic gastrocnemius muscle of wild type, ZEB1 and ZEB2 knock out mice

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

institute: IDIBAPS/ICREA

summary:
Purpose: Characterize the gene expression profile of gastrocnemius muscle in wild type, ZEB1 and ZEB2 knock out mice subjected to 36 hours of fasting
Methods: RNA sequencing of RNA from total gastrocnemius muscle after 36h of fasting from the three genotypes used in this study: ZEB1-control, ZEB1-KO, ZEB2-control, ZEB2-KO. Males and females were used from the four genotype (ZEB1flx/flx, ZEB1flx/flx;HSACre, ZEB2flx/flx, ZEB2flx/flx;HSACre).
Results: Knockout of ZEB1 or ZEB2 results in differential gene expression in atrophic gastrocnemius muscle
Conclusions: Comparison of wild type, ZEB1 and ZEB2 KO muscles displayed differential gene expression profiles after fasting

overall_design: RNA sequencing of total RNA from ZEB1 and ZEB2 HSA-Cre knocked-down muscles and their respective controls. Two mice of each genotype was used per sample. At least two sample per genotype were used for RNA sequencing.

first: Chiara

last: Ninfali

first: Anna

last: Esteve-Codina


title: Circular RNA sequencing of chondrocytes treated with or without cholesterol

city: Hangzhou

first: Fengchao

last: Zhao

address: No.79 Qingchun Road

institute: he First Affiliated Hospital, Zhejiang University School of Medicine

summary: Purpose: Circular RNA sequencing was used to find out differentially expressed CircRNAs between chodrocytes treated with or without cholesterol.Methods:chondrocyte CircRNAs profiles of cholesterol (10ug/ml) treated samples.

overall_design: We treated chondrocytes cell line C28/I2 cells with cholesterol for 48 hours. All last, the negative control (ctrl) samples and cholesterol treated Ch) samples were collected.

first: Jiarui

last: Li


title: CRISPR/Cas9-mediated activation of NR5A1 steers female human embryonic stem cell-derived bipotential gonadal-like cells towards a steroidogenic cell fate.

city: Helsinki

first: Juha

middle: Samuli

last: Tapanainen

state: Uusimaa

address: Haartmaninkatu 8

department: Obstetrics and Gynaecology

country: Finland

institute: University of Helsinki

summary: The nuclear receptor subfamily 5 group A member 1 (NR5A1), encoding steroidogenic factor 1 (SF-1), has been identified as a critical factor in gonadal development in animal studies. A previous study of ours suggested that upregulation of NR5A1 during early gonadal differentiation in male (46,XY) human pluripotent stem cells steers the cells into a more mature gonadal cell type. However, the detailed role of NR5A1 in female gonadal differentiation has yet to be determined. In this study, by combining the processes of gonadal differentiation and conditional gene activation, we show that NR5A1 induction predominantly upregulates the female gonadal marker inhibin subunit α (INHA) and steroidogenic markers steroidogenic acute regulatory protein (STAR), cytochrome P450 family 11 subfamily A member 1 (CYP11A1), cytochrome P450 family 17 subfamily A member 1 (CYP17A1), hydroxy-delta-5-steroid dehydrogenase (HSD3B2) and hydroxysteroid 17-beta dehydrogenase 1 (HSD17B1). In contrast, NR5A1 induction did not seem to affect the bipotential gonadal markers gata binding protein 4 (GATA4) and Wilms tumour suppressor 1 (WT1) nor the female gonadal markers r-spondin 1 (RSPO1) and wnt family member 4 (WNT4). Differentially expressed genes were highly associated with adrenal and ovarian steroidogenesis pathways. Moreover, time-series analysis revealed different dynamic changes between male and female -induced samples, where continuously upregulated genes in female gonadal differentiation were mostly associated with adrenal steroidogenesis. Thus, in contrast to male gonadal differentiation, NR5A1 is necessary but not sufficient to steer human embryonic stem cell (hESC)-derived bipotential gonadal-like cells towards a more mature somatic, female cell fate. Instead, it seems to direct bipotential gonadal-like cells more towards a steroidogenic-like cell population. The information obtained in this study helps in elucidating the role of NR5A1 in gonadal differentiation of a female stem cell line.

overall_design: Total of 7 samples with 3 technical replicates each, collected at days 4, 6, 8, and 10 of differentiation of human embryonic stem cells (H9-DDdCas9VP192-NR5A1 clone 10)  into gonadal-like cells. At days 6, 8, and 10, samples were collected separately from both NR5A11 induced (IND) and non-induced (CTRL) treatment conditions.

first: Laura

last: Danti

first: Karolina

last: Lundin

first: Kirsi

last: Sepponen

first: Dawit

last: Yohannes

last: Kere

first: Timo

last: Tuuri


title: Divergent roles for STAT4 in shaping effector differentiation of ILC1 and NK cells during gut inflammation II

first: Mattia

last: Laffranchi

overall_design: Stat4fl/fl and Ncr1DStat4 mice were administered with DSS for 7 days. NK cells were isolated from the lamina propria of the large intestine by FACS sorting.

first: Giuseppe

last: Sciumè

first: Gianluca

last: Scarno

first: Julija

last: Mazej


title: Transcriptomic analysis of periapical tissue biopies to understand dental pain.

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Dental pain from apical periodontitis is an infection induced-orofacial pain condition that presents with diversity in pain phenotypes among patients. While 60% of patients with a full-blown disease present with the hallmark symptom of mechanical allodynia, nearly 40% of patients experience no pain. Furthermore, a sexual dichotomy exists, with females exhibiting lower mechanical thresholds under basal and diseased states.  We conducted a transcriptomic assessment of periapical biopsies (peripheral diseased tissue) from patients with persistent apical periodontitis. our study found several unique differentially expressed genes (DEGs) between symptomatic and asymptomatic patients, as well as novel candidate genes between sexes within the same pain group.

overall_design: Surgical biopsies from symptomatic male (SM), asymptomatic male (AM), symptomatic female (SF), and asymptomatic female (AF) patients were collected and processed for bulk RNA sequencing. Three samples per symptom condition were profiled using an Illumina HiSeq 3000 system.

first: Nikita

last: Ruparel

first: Armen

last: Akopian

first: Biraj

last: Patel

first: Zhao

last: Lai


title: Effect of depletion of conrtol, Rasa1 KO, Nf2 KO, Rasa1 KO, and Rasa1/Nf2 KO in S1 tumorspheres

city: ChunCheon-si

first: Jun Won

last: Park

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

summary:
To transcriptomic differences among control, Nf2 KO, Rasa1 KO, and double KO S1 tumorspheres
We then performed gene expression profiling analysis using data obtained from RNA-seq of control, Nf2 KO, Rasa1 KO, and double KO S1 tumorspheres.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for conrtol, Rasa1 KO, Nf2 KO, Rasa1 KO, and Rasa1/Nf2 KO S1 tumorspheres.

first: Jun

first: Jong

last: Kwon

first: Jeong-Seop

last: Oh


title: Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele: a single tertiary center experience

city: Fuzhou

first: Yanting

last: Que

address: No. 88, Jiaotong Road, Taijiang District, Fuzhou City, Fujian Province

institute: Fujian Medical University

summary:
Routine karyotyping combined with CMA testing should be provided for fetuses with omphalocele. WES is an option if karyotype and CMA tests are normal. In addition, if conventional karyotype, CMA detection and WES detection are normal, then further molecular biology methods can be used to rule out disease phenotypes like BWS syndrome.
We analyzed the ultrasonographic features, genetic characteristics, and maternal and fetal outcomes of fetuses with omphalocele and provide a reference for perinatal management of such cases.

overall_design: Chromosomal analysis and chromosomal microarray analysis (CMA) were performed

last: Lin


title: BRAFV600E expression in intestinal tissue promotes a cholesterol metabolic gene signature that sustains hyperplasia and characterizes serrated colorectal neoplasia (RNA-Seq)

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

summary: BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis are poorly characterized. We investigated the impact of short-term (3 days) and long-term (6 months) expression of BrafV600E in the intestinal tissue of an inducible mouse model. We show that BrafV600E perturbs the homeostasis of intestinal epithelial cells, with impaired differentiation of enterocytes emerging after prolonged expression of the oncogene. Moreover, BrafV600E leads to a persistent transcriptional reprogramming with enrichment of numerous gene signatures indicative of proliferation and tumorigenesis, and signatures suggestive of metabolic rewiring. We focused on the top-ranking cholesterol biosynthesis signature and confirmed its increased expression in human serrated lesions. Functionally, the cholesterol lowering drug atorvastatin prevents the establishment of intestinal crypt hyperplasia in BrafV600E-mutant mice. Overall, our work unveils the long-term impact of BrafV600E expression in intestinal tissue and suggests that colorectal cancers with mutations in BRAF might be prevented by statins.

overall_design: 9 samples

first: Alessandro

last: Rufini

first: Catrin

last: Pritchard

first: Pooyeh

last: Farahmand

first: Hong

last: Cai

first: Paulina

last: Rzasa


title: An mRNA-based universal vaccine candidate confers improved cross-protection against heterosubtypic influenza viruses in mice

city: Shanghai

first: Feifei

last: Xiong

address: 350 Anshun Rd，Shanghai

institute: Shanghai Institute of Biological Products

summary: The single-cell transcriptional profiling of T cells in the spleens of vaccinated mice revealed that the mRNA-based vaccine significantly promoted CD8+ T cells and memory T cells by prime-boost immunization.

overall_design: The single-cell transcriptional profiling of cells in spleens 7 days post-prime and boost immunization was performed to gain further insights into the cellular and molecular mechanisms involved in the mRNA-based universal vaccine.

first: Chi

last: Zhang

first: Baoyuan

last: Shang

first: Mei

last: Zheng

first: Qi

last: Wang

first: Yahong

last: Ding

first: Jian

last: Luo

first: Xiuling

last: Li


title: High throughput sequencing in ARID1A knockout MDA-MB-231 cells [H3K4me1 histone modification ChIP-seq]

first: Zhonghua

last: Tao

address: No. 270, Dong’an Road

institute: Fudan University Shanghai Cancer Center

summary: ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high throughput sequencing (ChIP–seq) to investigate H3K4me1 histone modification of ARID1A knockout and control MDA-MB-231 cells.

overall_design: We performed H3K4me1 ChIP-seq in ARID1A knockout and control MDA-MB-231 cells.

first: Xinyu

last: Chen

first: Yu

last: Yang

first: Leihuan

last: Huang

first: Ting

last: Ni

first: Xichun

last: Hu


title: Single-cell RNA sequencing of kidney from idiopathic membranous nephropathy patients

city: Kunshan

first: Manman

last: Shi

address: South Zuchongzhi Road

institute: Traditional Chinese Medicine Hospital of Kunshan

summary: We characterized the renal parenchymal cell and immune cell profiles of IMN renal tissues and discovered the distinct expression signatures of myeloid cell, T cell and B cell subsets.

overall_design: In order to explore the molecular mechanism of IMN, we collected renal tissue samples from 3 IMN patients and 1 healthy controls and performed analysis by single-cell RNA sequencing.

first: Yuxin

first: Huan

first: Zicheng

last: Ling

first: Xue

first: Chaojun

last: Liu

first: Yuhua

last: Ma


title: High throughput sequencing in ARID1A knockout MDA-MB-231 cells [H3K27ac histone modification ChIP-seq]

summary: ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high throughput sequencing (ChIP–seq) to investigate H3K27ac histone modification of ARID1A knockout and control MDA-MB-231 cells.

overall_design: We performed H3K27ac ChIP-seq in ARID1A knockout and control MDA-MB-231 cells.


title: High-throughput sequencing in ARID1A knockout MDA-MB-231 cells [ATAC-seq]

summary: ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To investigate global chromatin remodeling, we performed ATAC–seq in ARID1A knockout and control MDA-MB-231 cells.

overall_design: We performed ATAC-seq in ARID1A knockout and control MDA-MB-231 cells.

first: Bin


title: High-throughput sequencing in ARID1A knockout MDA-MB-231 cells [RNA-seq]

summary: ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. Next-generation sequencing analysis was performed in control and ARID1A knockout MDA-MB-231 cells to investigate global gene expression changes.

overall_design: We performed RNA-seq in ARID1A knockout and control MDA-MB-231 cells.


title: High-throughput sequencing in ARID1A knockout MDA-MB-231 cells

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

overall_design: Refer to individual Series


title: High-throughput sequencing in ARID1A knockout MDA-MB-231 cells [H3K4me3 histone modification ChIP-seq]

summary: ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) to investigate H3K4me3 histone modification of ARID1A knockout and control MDA-MB-231 cells.

overall_design: We performed H3K4me3 ChIP-seq in ARID1A knockout and control MDA-MB-231 cells.


title: Gene expression profile, population of macrophages and lymphocytes of the spleen in conditions of liver regeneration after 70% resection in mice

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

summary:
The aim of our work was to study the expression profile of spleen genes during liver regeneration, to identify possible biologically active substances that affect reparative processes and inflammation in other organs, as well as the state of the monocytic-macrophage and lymphocytic population of the spleen after liver resection.
We used microarrays for comparison of spleen gene expression on different time periods after 70% liver resection

overall_design: 4 groups were studied: the control group - intact spleen, spleen in a 1 day, 3 days and 7 days after liver resection. Each group included 3-6 samples.

first: Maria

last: Kuznetsova


title: circRNAs expression in the plasma of DM patients, DKD patients and healthy controls

city: Chongqing

first: Ziyue

last: Lin

state: Chongqing

address: Medical College Road

institute: Chongqing Medical University

summary: In order to explore the role of circRNA in diabetic kidney disease (DKD), we employed circRNAs microarray expression profile in the plasma of daibetes patients (n=6), diabetic kidney disease patients (n=6) and healthy controls (n=6). According to the microarray data, we found 2079 differentially expressed circRNA in the plasma of DKD patients compared to the healthy people, including 1182 up-regulated and 897 down-regulated.Among the differentially expressed circRNA, nine DKD-related circRNAs were chosen and further validated by qRT-PCR.The results revealed that circUBXN7 was significantly elevated in the plasma of DKD patients, and might be a diagnostic plasma marker for DKD.

overall_design: Detection of circRNAs expression in plasma of diabetic kidney disease patients, diabetes patients and healthy people. Six independent experiments were performed in each group using different donors for each experiment.


title: Light cues induce transcriptional reprogramming and protective anticipation of environmental water loss in Pseudomonas syringae

city: Ames

first: Gwyn

last: Beattie

state: IOWA

address: 2213 Pammel Dr

department: Plant Pathology, Entomology, & Microbiology

institute: Iowa State University

summary: The ecological significance of light perception in non-phototrophic bacteria remains largely elusive. In terrestrial environments, diurnal oscillations in light are often temporally coupled to other environmental changes, including increased temperature and evaporation. Here we report that light functions as an anticipatory cue that triggers protective adaptations to tolerate a future rapid loss of environmental water in leaf-associated Pseudomonas syringae pv. syringae (Pss) and other terrestrial pseudomonads. Global transcriptome analyses in Pss showed that light control occurs almost entirely through a bacteriophytochrome photoreceptor that senses red, far-red and blue wavelengths and influences 30% of the Pss genome. Bacteriophytochrome-mediated light control disproportionally upregulates water-stress adaptation functions and confers enhanced fitness when cells encounter light prior to water limitation. These data demonstrate that non-phototrophic bacteria can use light as a cue to mount an adaptive anticipatory response against a physiologically unrelated but ecologically coupled stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas syringae pv. syringae strain B278a and isogenic mutants following brief exposure to different light wavelengths

first: Bridget

middle: M

last: Hatfield

first: Breah

last: LaSarre

first: Meiling

first: Haili

last: Dong

first: Dan

last: Nettleton


title: Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’ [ChIP-seq]

city: Utrecht

first: Ronald

middle: W.

last: Stam

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

summary: KMT2A-rearranged acute lymphoblastic leukemia (ALL) is an aggressive type of leukemia which represents the most common form diagnosed in infancy. Oncogenic KMT2A-fusion proteins recruit histone methyltransferase DOT1L which leads to misplaced H3K79 methylation inducing an abnormal transcriptomic landscape that favors leukemia development. Hence, inhibition of DOT1L represents an attractive therapeutic strategy. Unfortunately, the first-in-class DOT1L inhibitor pinometostat resulted in the development of resistance. To understand this resistance we established acquired resistance to DOT1L inhibition in a pediatric KMT2A::AFF1+ B-ALL cell line model that stably became ~35-fold more resistant to pinometostat. Interestingly, while becoming almost completely independent of DOT1L-mediated H3K79 methylation, these cells remained fully dependent on the physical presence of DOT1L, HOXA9, as well as the KMT2A::AFF1 fusion protein. Further characterization of these cells using RNA-, ChIP-, and ATAC-sequencing analyses revealed that acquired resistance to DOT1L inhibition leads to a selective loss of KMT2A-fusion driven epigenetic regulation and expression of genes such as PROM1 (encoding the hematopoietic/leukemia stem cell marker CD133) and its enhancer TAPT1, as well as other putative KMT2A::AFF1 target genes such as RUNX2, PRSS12, ZC3H12, and GNAQ. In contrast, the levels of H3K79me2 and expression of other KMT2A::AFF1 target genes, including HOXA9, MEIS1, and CDK6 remained unaffected. Concomitantly, pinometostat-resistant KMT2A::AFF1+ B-ALL cells showed upregulation of genes associated with a myeloid immunophenotype, including CD33, LILRB4/CD85k, MPEG1, CCL5, and LIMK1.  Taken together, we here present a valuable model to study the adaptive potential of KMT2A-rearranged ALL upon losing dependency on one of its main oncogenic properties.

overall_design: Acquired resistance to DOT1L inhibitor pinometostat was induced in the KMT2A::AFF1+ ALL cell line SEM, resulting in the pinometostat-resistant daughter line SEMPINO_RES. To characterize our SEMPINO_RES cells and gain insights into the underlying mechanisms of acquired resistance to DOT1L inhibition, we performed RNA-sequencing (RNA-seq), ChIP-sequencing for KMT2A, AFF1, H3K4me3, H3K79me2, and H3K27ac, as well as ATAC-sequencing on SEM and SEMPINO_RES cells cultured in both the absence and presence of 50 µM pinometostat for 7 days.

first: P

last: Schneider

first: R

first: Nicholas

middle: T

last: Crump

first: Thomas

last: Milne


title: Antigen-presenting aged neutrophils induce CD4+ T cells to exacerbate inflammation in sepsis

city: Manhasset

first: Max

last: Brenner

state: NY

address: 350 Community Dr

institute: Feinstein Institutes for Medical Research

summary: Extracellular cold-inducible RNA-binding protein (eCIRP) is a key mediator of severity and mortality in sepsis. We found that stimulation of mouse bone marrow–derived neutrophils (BMDNs) with eCIRP generated a distinct neutrophil subpopulation, characterized by cell surface markers of both antigen-presenting cells and aged neutrophils as well as expression of IL-12, which we named antigen-presenting aged neutrophils (APANs). The frequency of APANs was significantly increased in the blood, spleen, and lungs of WT mice subjected to cecal ligation and puncture–induced sepsis but not in CIRP–/– mice. Patients with sepsis had a significant increase in circulating APAN counts compared with healthy individuals. Compared with non–APAN-transferred mice, APAN-transferred septic mice had increased serum levels of injury and inflammatory markers, exacerbated acute lung injury (ALI), and worsened survival. APANs and CD4+ T cells colocalized in the spleen, suggesting an immune interaction between these cells. APANs cocultured with CD4+ T cells significantly induced the release of IFN-γ via IL-12. BMDNs stimulated with eCIRP and IFN-γ underwent hyper-NETosis. Stimulating human peripheral blood neutrophils with eCIRP also induced APANs, and stimulating human neutrophils with eCIRP and IFN-γ caused hyper-NETosis. Thus, eCIRP released during sepsis induced APANs to aggravate ALI and worsen the survival of septic animals via CD4+ T cell activation, Th1 polarization, and IFN-γ–mediated hyper-NETosis.

overall_design: After magnetic cell sorting purification, BMDN (1×10^6) were treated with eCIRP (1 µg/mL) for 2 h and the cells were then processed through the 10× Genomics single-cell RNA sequencing pipeline (i.e., barcoding and cDNA library preparation) for sequencing

first: Hui

last: Jin

first: Monowar

last: Aziz

first: Atsushi

last: Murao

first: Molly

last: Kobritz

first: Andrew

middle: J

last: Shih

first: Robert

middle: P

last: Adelson

first: Ping

last: Wang


title: Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’ [RNA-seq]

first: RW


title: The prognostic value of whole-genome DNA methylation in response to Leflunomide in Patients with Rheumatoid Arthritis

city: Shenyang

first: Chen

middle: yu

last: lan

address: Nan Jing Bei Street

institute: Department of Clinical Epidemiology and Evidence-based Medicine, the First Affiliated Hospital, China Medical University

summary: Although Leflunomide (LEF) is effective in treating rheumatoid arthritis (RA), there are still a considerable number of patients who respond poorly to LEF treatment. Till date, few LEF efficacy-predicting biomarkers have been identified. Herein, we explored and developed a DNA methylation-based predictive model for LEF-treated RA patient prognosis.

overall_design: Two hundred forty-five RA patients were prospectively enrolled from four participating study centers. A whole-genome DNA methylation profiling was conducted to identify LEF-related response signatures via comparison of 40 samples using Illumina 850k methylation arrays. Furthermore, differentially methylated positions (DMPs) were validated in the 245 RA patients using a targeted bisulfite sequencing assay. Lastly, prognostic models were developed, which included clinical chacteristics and DMPs signatures, for the preduction of LEF treatment response using machine learning algorithms.

first: Yulan

last: Chen

first: Lingyu

last: Fu


title: DNA methylome profiling of blood to identify individuals in a pair of monozygotic twins

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

institute: Korea Research Institute of Bioscience and Biotechnology

type: Methylation profiling by genome tiling array

summary: Short tandem repeat (STR) markers cannot be used to distinguish between genetically identical monozygotic (MZ) twins, causing problems in a case with an MZ twin as a suspect. Many studies have shown that in older MZ twins, there are significant differences in overall content and genomic distribution of methylation

overall_design: Bisulphite converted DNA from the 94 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip

first: Hwan-Young

last: Lee

first: Jae-Yoon

last: Kim

first: So-Yeon

first: Seon-Young

first: Jong-Lyul

first: Soong-Deok


title: Profiling the Full-Length Transcriptome of Extracellular Vesicles With Oxford Nanopore Sequencing

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

country: Canada

institute: Montreal Clinical Research Institute

summary: While numerous studies have described the transcriptomes of EVs in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-encapsulated RNA populations. Furthermore, it has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and little is known about the extent to which full-length mRNAs are present within EVs. Using Oxford nanopore long-read RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 441 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 12.72% of all reads present in EVs corresponded to known full-length transcripts, 65.34% of which were mRNAs. We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. Here we report a full-length transcriptome from human EVs, as determined by long-read nanopore sequencing.

overall_design: Total RNA from K-562 cells and EVs  was isolated and the sequencing libraries were prepared using Nanopore PCR-cDNA Barcoding Kit.

first: Juan-Carlos

last: Padilla

first: Seda

last: Barutcu

first: Ludovic

last: Malet

first: Gabrielle

last: Deschamps-Francoeur

first: Virginie

last: Calderon

first: Eunjeong

last: Kwon

last: Lécuyer


title: The phage-encoded protein PIT2 impacts bacterial quorum sensing in Pseudomonas aeruginosa by direct interaction with LasR

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

summary: Quorum sensing (QS) is the cell density-dependent virulence factor regulator in Pseudomonas aeruginosa. Here, we elucidate PIT2, a phage-encoded inhibitor of the QS regulator LasR, derived from the lytic Pseudomonas phage LMA2. PIT2 inhibits the effectors PrpL and LasA of the type 2 secretion system of P. aeruginosa and attenuates bacterial virulence towards HeLa cells and in Galleria mellonella. Using RNAseq-based differential gene expression analysis, the effect of PIT2 on the LasR regulatory network was revealed. Moreover, the specific interaction between LasR and PIT2 was determined. These data expand our knowledge on phage-encoded modulators of the bacterial metabolism, as this examples an anti-virulence protein derived from a lytic phage. From an applied perspective, this phage protein reveals and exploits an interesting anti-virulence target in P. aeruginosa. As such, it lays the foundation for a new phage-inspired anti-virulence strategy to combat multidrug resistant pathogens and opens the door for SynBio applications.

overall_design: The transcriptional landscape of cells expressing pit2 was compared to a control, a PAO1 strain harboring an empty construct.

first: Kaat

last: Schroven

first: Leena

last: Putzeys

first: Anne-laure

last: Swinnen

first: Hanne

last: Hendrix

first: Jan

last: Paeshuyse


city: University Park

first: McCauley

middle: O'Brien

last: Meyer

email: mcobmeyer35@gmail.com, mxm1357@psu.edu

state: PA

address: 241 Chemistry Building

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology, and has been proposed as a prebiotically-plausible way to accumulate RNA. Compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Transfer RNAs are essential for protein synthesis and predate the last universal common ancestor (LUCA) of all organisms, making them relevant to both extant and ancient biology. Since tRNAs are the most heavily modified RNAs known, with modifications crucial to RNA structure, function, and gene regulation, we also compared unmodified and naturally-modified tRNAs. We elucidate the effects of Mg2+ concentration, polyion charge ratio, and polyion length on tRNA structures. The approach herein, which can be applied to study other RNAs in diverse condensates, reveals that RNA can achieve native tertiary structure in a robust fashion in membraneless compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that modifications could have played a critical role in metabolic processes at the origin of life.

sample_organism:
Escherichia coli
synthetic construct

platform_organism:
Escherichia coli
synthetic construct

overall_design: We performed tRNA structure-seq (a type of dimethyl sulfate chemical probing followed by mutational profiling DMS-MaP-Seq) inside of peptide-rich droplets to study a T7 transcript of a single tRNA from S. cerevisiae to validate the the technique. Then, we purified natively modified tRNAs from E. coli and generated T7 transcripts of those same tRNAs and again performed tRNA structure-seq in peptide-rich droplets. For each type of RNA in each droplet condition, there were 3 independent control experiments and 3 independent DMS treatments performed.

middle: O

first: Ryota

last: Yamagami

first: Saehyun

last: Choi

first: Christine

middle: D

last: Keating

first: Philip

middle: C

last: Bevilacqua


title: Enhancing Autophagy in CD11c+ Antigen Presenting Cells as a Therapeutic Strategy for Acute Respiratory Distress Syndrome and Lung Inflammation

city: Los Angeles

last: Quach

state: CA

address: 1450 Biggy St NRT 5509

institute: University of Southern California

summary: To investigate the role of autophagy in CD11c+ APCs in a mouse model of Poly(I:C)-induced ALI/ARDS

overall_design: We generated two animal models; mice with a deletion of autophagy-related gene 5 (Atg5) specifically in CD11c+ APCs to impair autophagy and mice with overexpression of transcription factor EB (Tfeb), a regulator of autophagy, in CD11c+ APCs to constitutively induce autophagy.

first: Doumet

last: Helou

first: Meng

last: Li

first: Benjamin

last: Hurrell

first: Emiy

last: Howard

first: Pedram

last: Shafiei-Jahani

first: Pejman

last: Soroosh

first: Jing-hsiung

last: Ou

first: Babak

last: Razani

first: Virender

last: Rehan

first: Omid

last: Akbari


title: FGF21 treatment and iPSC-derived neurons

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: FGF21 analogs tested in clinical trials in metabolic diseases i.e. type 2 diabetes mellitus and non-alcoholic fatty liver disease are generally well-tolerated. FGF21 is a peptide hormone that is primarily secreted  by the liver, but it also crosses the blood-brain barrier. The bulk of literature on this subject has raised the possibility that FGF21 administration could affect alcohol use and reward behaviors. Our recent study showed that FGF21 levels were associated with recent alcohol consumption. Furthermore, our data also suggest that the effects of FGF21 in the induced pluripotent stem cell (iPSC)-derived 3D-brain organoids are associated, at least in part, with the regulation of catecholamines, neurotransmitters that play a crucial role in reward pathways. These observations potentially open the way to pharmacologic manipulation of FGF21, which in turn could have significant implications for catecholamines, and alcohol use. Current in vitro models designed to study drug action in the human brain are limited. Therefore, we used iPSC-derived neurons as a novel "cell-line based" approach to advance our understanding of drug action in the brain. Since the half-life of the naïve form of FGF21 is about 0.5-2 hours, it is not suitable for clinical use due to poor pharmacokinetic and biophysical properties . As a result, the present study was designed to identify molecular mechanisms for both the naïve form of FGF21 and a long-acting FGF21 molecule (PF-05231023) which was developed by conjugating two molecules of modified FGF21 (dHis/Ala129Cys) to an antibody scaffold.

overall_design: This study was designed to identify molecular mechanisms for the naïve form of FGF21 and a long-acting FGF21 molecule (PF-05231023) in iPSC-derived neurons.

first: Ming-Fen

last: Ho

first: Hu

first: Richard

last: Weinshilboum


title: Effect of peroxisomal proteotoxic stress on gene expression in mammalian cells

first: Akihiro

last: Yamashita

address: 3801 University Ave

institute: McGill University

summary: To establish the overall cell responses to peroxisomal proteotoxic stress, we analysed transcriptomes of NT- and LONP2-silenced cells using RNA sequencing in COS-7 and U2OS cells.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NT- or LONP2-silenced COS-7 cells and U2OS cells

first: Heidi

last: McBride

first: Olesia

last: Ignatenko

first: Kathleen

last: Watt


title: ClpP/ClpX deficiency impairs mitochondrial functions and mTORC1 signaling during spermatogenesis and meiosis

city: Shenzhen

first: Chenxi

last: Guo

address: 1 Haiyuan 1st Rd

institute: The University of Hong Kong-Shenzhen Hospital

summary:
To investigate whether ClpP/ClpX is required for maintaining mitochondrial functions in spermatocytes during meiosis and spermatogenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different spermatocytes from control, ClpP CKO, ClpX CKO groups (3 repeats for each)

overall_design: We knockedout ClpP or ClpX specifically in male mice germ cells via Stra8-Cre mice, evaluated the functions of mitochondria in control and ClpO/ClpX cKO spermatocytes.

first: Tianren

last: Wang


title: PRMT5 inhibition in MCL

city: Columbus

first: Shelby

last: Sloan

state: OHIO

address: 410 W 12th Ave

institute: Ohio State University

summary: To identify the mechanistic underpinning of the anti-tumor activity of PRMT5 inhibition in MCL, we explored transcriptomic profiles of PDX-AA cells treated in vivo for 2 weeks with PRT-382, ibrutinib, or vehicle control (n=3/group).

overall_design:
RNA-sequencing of human-CD19+ cells isolated from the spleen of PDX engrafted with human MCL and treated with vehicle control (n=3), ibrutinib (n=3), or PRT-382 (n=3).
NOTE FROM SUBMITTER: The raw data will not be uploaded due to patient privacy concerns.

first: Sloan

last: Shelby

first: Baiocchi

last: Robert

first: Alinari

last: Lapo


title: Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome.

city: Corvallis

first: Adrian

middle: F

last: Gombart

state: OR

address: 307 Linus Pauling Science Center

department: Biochemistry & Biophysics

institute: Oregon State University

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

overall_design: Refer to individual Series


title: Calcium channel β3 subunit regulates ATP-dependent migration of dendritic cells

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

country: Germany

institute: UKE

summary: To find Cacnb3-dependent transcriptomic changes after eATP stimulation, we performed RNA-sequening of WT and Cacnb3-KO BMCs in steady-state and after eATP stimulation.

overall_design: WT and Cacnb3-KO BMDCs were stimulated with 500 µM eATP for 30 minutes and 24 hours and were harvested for RNA sequencing.

middle: S

first: Friederike

last: Ufer

first: Manuel

middle: A

last: Friese


title: Cooperative regulation of coupled oncoprotein synthesis and stability in triple-negative breast cancer by EGFR and CDK12/13

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: Evidence has long suggested that epidermal growth factor receptor (EGFR) may play a prominent role in triple-negative breast cancer (TNBC) pathogenesis, but clinical trials of EGFR inhibitors have yielded disappointing results. Using a candidate drug screen, we discovered that inhibition of cyclin-dependent kinases 12 and 13 (CDK12/13) dramatically sensitizes diverse models of TNBC to EGFR blockade. This combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and translation-linked turnover of driver oncoproteins, including MYC. A genome-wide CRISPR/Cas9 screen identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, thereby rescuing MYC translational suppression and promoting MYC stability. The central roles of CCR4-NOT and 4E-BP1 in response to the combination therapy were further underscored by the observation of CNOT1 loss and rescue of 4E-BP1 phosphorylation in TNBC cells that naturally evolved therapy resistance. Thus, pharmacological inhibition of CDK12/13 reveals a long proposed EGFR dependence in TNBC that functions through the cooperative regulation of translation-coupled oncoprotein stability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for breast carcinoma cells (CAL51 and MDA-MB-231) treated with DMSO, Gefitinib, THZ531 and Gefitinib+THZ531

first: Hazel

middle: X

last: Ang

first: Kris

last: Wood

first: Luke

last: Bartelt

first: Alejandro

last: Barrera

first: Ian

last: McDowell

first: Timothy

last: Reddy


title: mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Yeast mRNA decapping-activators Pat1 and Dhh1 have been implicated in repressing translation and mRNA degardation in glucose-deprived cells, but the specific mRNAs targeted by each factor and their functions in nutrient replete cells are poorly understood. To test this, we performed ribosome profiling and RNA-Seq in WT, pat1D and pat1Ddhh1D. Further, CAGE-Seq and Rpb1-ChIP Seq were employed to determine their role in decapping mediated degradation of mRNAs

overall_design: This study includes total 26 samples, 9 for ribosome profiling from triplicates of WT, pat1D and pat1Ddhh1D; 3 from  triplicates of WT. Separately, the same total RNA dhh1D, and pat1D in duplicates,  were subjected to CAGE-Seq (4 samples) and total RNA-Seq (4 samples). pat1D and dhh1D in triplicates were subjected to Rpb1-ChIP seq (6 samples).  All strains were grown in YPD at 30ºC till the OD600 ~0.6

first: Anil

last: Kumar Vijjamarri

first: Neha

last: Gupta

first: Chisom

last: Onu

first: Xiao

last: Niu

first: Fan

last: Zhang

first: Rakesh

last: Kumar

first: Zhenguo

last: Lin

first: Miriam

middle: L

last: Greenberg


title: A PPARγ-lncRNA axis modulates thermoneutral remodeling of white adipose tissue

first: Zhengyi

address: Westwood

institute: UCLA

summary: Interplay between parenchymal energy-storing white adipose cells and thermogenic beige adipocytes contributes to obesity and insulin resistance. Irrespective of cellular origin or specialized niche, adipocytes require the activity of the nuclear receptor peroxisome proliferator activated receptor gamma (PPARγ) for proper function. Exposure to cold or adrenergic signaling enriches thermogenic cells though multiple pathways that act synergistically with PPARγ, however, the molecular mechanisms by which PPARγ licenses white adipose tissue (WAT) to preferentially adopt a thermogenic or white adipose fate in response to dietary cues or thermoneutral conditions are not fully elucidated. Here, we show that a PPARγ-long noncoding RNA (lncRNA) axis integrates canonical and noncanonical thermogenesis to restrain white adipose tissue heat dissipation during thermoneutrality and diet-induced obesity (DIO). Pharmacologic inhibition or genetic deletion of the lncRNA Lexis, enhances UCP-1 dependent and independent thermogenesis. Adipose tissue specific deletion of Lexis counteracted diet-induced obesity, improved insulin sensitivity, and enhanced energy expenditure. Single-nuclei transcriptomics revealed that Lexis regulates a distinct population of thermogenic adipocytes. We systematically map Lexis motif preferences and show that it regulates the thermogenic program through the activity of the metabolic GWAS gene and WNT modulator TCF7L2. Collectively, our studies uncover a new mode of crosstalk between PPARγ and WNT signaling that preserves white adipose tissue plasticity.

overall_design:
Unbiased chromatin-affinity assay was applied for interactome and motif analysis.
A total of 100 million preadipocytes (pre-treated with GW1929 for 24 hours) were used for each replicate and 2 replicates were performed for each group. For negative control, RNase A and RNase H were added as the amount of 2 μg per million cells.

first: Ya

last: Cui

first: Vivien

last: Su

first: Marc

last: Tol

first: Lijing

last: Cheng

first: Xiaohui

last: Wu

first: Jason

last: Kim

first: Prashant

last: Rhajbhandari

first: Wei

last: Li

first: Peter

last: Tontonoz

first: Claudio

last: Villanueva

first: Tamer

last: Sallam

first: Dan

last: Wang


title: A PPARγ-lncRNA axis modulates thermoneutral remodeling of white adipose tissue [snRNA-seq]

overall_design: 10x Genomics single-nucleus RNA sequencing was used to compare the iWAT Lexis KO and Lexis KO at single nucleus resolution.


title: Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome [RNA-seq: eWAT]

first: Adrian

last: Gombart

summary: We performed unbiased transcriptional profiling of white adipose tissue (eWAT, epididymal white adipose tissue) from mice to determine mechanisms by which xanthohumol and tetrahydroxanthohumol supplementation could ameliorate hepatosteatosis induced by a HFD at the transcriptional level. We conducted RNA-seq analysis of total RNA of ewat obtained from mice after 16 weeks on the diet.

overall_design: eWAT RNA-seq profiling of white adipose tissue from 26 week old wild type C57BL/6J male mice fed one of four diets for 16 weeks (from age 10 weeks to 26 weeks old): LFD (low fat diet, n = 10), HFD (high fat diet, n = 10), HFD+HXN (xanthohumol 60 mg/kg body weight, n = 10), HFD+TXN (tetrahydroxanthohumol 30 mg/kg body weight, n = 9).    HFD group is used as the control/reference group for all analyses.

first: Yang


title: A PPARγ-lncRNA axis modulatesthermoneutral remodeling of white adipose tissue

last: Zhang

overall_design: Bulk RNAseq was used for gene expression from Lexis WT or KO mice iWAT


title: ClpP/ClpX deficiency impairs mitochondrial functions and mTORC1 signaling during spermatogenesis and meiosis [RNA IP m6A-seq]

first: Chenxi

last: Guo

first: Tianren


title: Opiate responses are controlled by interactions of Oprm1 and Fgf12 loci in the murine BXD family: Correspondence to human GWAS findings

city: La Jolla

first: Francesca

last: Telese

address: 9500 Gilman Drive

department: Psychiatry

institute: UCSD

summary: We analyzed time-dependent behavioral responses to morphine and naloxone obtained from a large family of young adult BXD mice (n = 63–64 strains, including C57BL/6J and DBA/2J parents, n = 4–9/strain) using new whole genome sequencing (WGS)-based genetic markers. Opiate behavioral data include locomotor and behavior responses measured over a four hour period in 15 min bins after an acute morphine injection (50 mg/kg i.p.), followed by naloxone-induced withdrawal (see Philip et al. (2010). Sexes were mapped jointly and independently for males and females using 20,000 markers and linear mixed models that account for kinship structure. We confirmed a highly significant association between locomotor response and a genomic region that overlaps Oprm1 on Chr 10 at 6.8 Mb (LOD of 11.4) 15 to 105 min after injection, with a peak at 75 min. Effects were only weakly dependent of sex. Strains that inherited B haplotypes ran 76 meters farther than those that inherited D haplotypes. We discovered a novel association between a locus on Chr 16 and a late-phase locomotor response 150 min after morphine in both sexes. This locus had a significant but transient epistatic interaction with Oprm1 at 45–90 min—well before its main additive effect was detectable. The Chr 16 locus includes one compelling candidate—fibroblast growth factor 12 (Fgf12). Null mutation of Fgf12 has been shown to cause locomotor deficits (e.g., ataxia). Single nuclei transcriptomic analysis further validated a functional epistatic relationship between Oprm1 and Fgf12, showing that their expression is correlated in a specific subtype of Drd1-expressing medium spiny neurons.

overall_design: Nucleus accumens core tissue punches from two female heterogenous stock rats were obtained from a tissue repository (Carrette et. al, 2021).

first: Yanning

last: Zuo

first: Hao

last: Chen


title: Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome [RNA-seq: ileum]

summary: We performed unbiased transcriptional profiling of ileum from mice to determine mechanisms by which xanthohumol and tetrahydroxanthohumol supplementation could ameliorate hepatosteatosis induced by a HFD at the transcriptional level. We conducted RNA-seq analysis of total RNA of ileum obtained from mice after 16 weeks on the diet.

overall_design: Ileum RNA-seq profiling of livers from 26 week old wild type C57BL/6J male mice fed one of four diets for 16 weeks (from age 10 weeks to 26 weeks old): LFD (low fat diet, n = 10), HFD (high fat diet, n = 10), HFD+HXN (xanthohumol 60 mg/kg body weight, n = 10), HFD+TXN (tetrahydroxanthohumol 30 mg/kg body weight, n = 9).    HFD group is used as the control/reference group for all analyses.


title: The miR-17~92 family miRNAs regulate non-canonical NFκB pathway by targeting Socs3 to control plasma cell differentiation

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: Germinal center (GC) reaction in the lymphoid organs is a pivotal process for humoral immune response. The miR-17~92 family miRNAs have been demonstrated that regulate TFH cell differentiation, GC reaction and antibody response. However, whether they may also have functions in B cell activation and differentiation in GC reaction remain largely unknown. Here we show that mice with deletion of miR-17~92 in B cells exhibited reduced GC B cell formation and profound impaired plasma cell (PC) differentiation as well as decreased antibody response upon protein antigen immunization or chronic LMCV infection. In an in vitro plasma cell differentiation (iGCB) system, we found that miR-17~92 deficiency results in markedly decreased in vitro plasma cell (iPC) differentiation and defective NFB activation. Moreover, we developed and performed a screen by CRISPR/small guide (sg) RNA-mediated gene editing among the target genes of miR-17~92 in iGCB culture system. Intriguingly, Socs3 deletion substantially restored iPC differentiation and NFB activation in miR-17~92 deficient B cells, suggesting that Socs3 acts as a negative regulator of NFκB pathway involved in the regulation of iPC differentiation by miR-17~92. However, IL-21-induced STAT3 activation was not affected by miR-17~92 deficiency during iPC differentiation. Mechanistically, Socs3 interacts with MAP3K14 (NIK) and that promotes the ubiquitination of NIK and subsequent proteasome-mediated degradation of NIK, thereby leading to inhibition of the processing of p100 in non-canonical NFκB pathway and PC differentiation.

overall_design: WT and TKO iGCB cells (namely, iPC 0h) or iGCB cells cultured with 40LB cells plus IL-21 for 24 hrs (iPC 24h), 48 hrs (iPC 48h) were collected after sorting. Total RNA from iPC 0 h, 24 h, 48h samples were isolated for deep sequecing in triplicate.

first: Jun

last: Xie

first: Changchun

last: Xiao

first: Padmaja


title: scENCORE: leveraging single-cell epigenetic data to predict genome conformation using graph embedding

city: New Haven

first: Matthew

last: Girgenti

address: 34 Park St

institute: Yale School of Medicine

summary: Recent advances in chromatin architecture profiling technologies, such as single-cell Hi-C (scHi-C), allow us to dissect the heterogeneity of chromosome higher-order structures across diverse cell states and different individuals. However, scHi-C experiments are still expensive and not immediately available for population-scale profiling. Here, we present scENCORE, a computational method, to reconstruct personalized and cell-type-specific higher-order chromatin structures, such as A/B compartments, directly from more cost-effective and widely available single-cell epigenetic data (e.g., scATAC-seq). We apply scENCORE on scATAC-seq data from post-mortem prefrontal cortex brains and demonstrate its utility to 1) project Mega-base scale chromatin regions into lower dimensional space by leveraging graph embedding technologies based on cell-type-specific co-variability patterns, 2) define A/B compartments via unsupervised clustering, 3) perform an alignment algorithm for multi-graph embedding to derive comparable chromatin representations and highlight dynamic chromatin compartments across cell states and individuals. Validated by Hi-C experiments using FACS-sorted cells, scENCORE can faithfully reconstruct cell-type-specific chromatin compartments. Furthermore, scENCORE uniformly constructs chromosome conformation across population-scale scATAC-seq data and discovers key 3D structural switching events associated with psychiatric disorders. In summary, scENCORE allows cost-effective cell-type-specific and personalized reconstruction that delineate higher-order chromatin structures.

overall_design: Single nuclei were isolated from human postmortem dlPFC from normal controls and two psychiatric diagnostic groups, PTSD and MDD.

first: Ziheng

last: Duan

first: Shushrruth

last: Sai

first: Ahyeon

last: Hwang

first: Che

middle: Y

last: Lee

first: Jing


title: Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation

city: Taipei

first: Pao-Yang

address: 128 Section 2, Academia Road, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: During transformation, tissue culture often carries epigenetic and genetic changes underlying somaclonal variations, leading to unpredictable phenotypes. Transformation treatments may individually and jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes have never been examined. Here, we examined the changes in methylomes and transcriptomes associated with each of the components with different combinations of treatments. We found that individual transformation components targeted specific gene sets. When T-DNA was integrated, the pathway of secondary metabolism was activated, whereas primary metabolism was repressed. The transformation treatments resulted in global hypomethylation at CHH sites enriched at promoters highly associated with downregulation. The promoters that colocalized with miniature inverted-repeat TEs (MITEs) were found to be associated with epigenetic responses to stress, and this was not observed at sites without MITEs. Our results demonstrated component-specific epigenetic regulation related to adaptation to the stress response during rice transformation.

overall_design: We performed whole-genome bisulfite sequencing (WGBS) and RNA-seq to examine DNA methylation and expression in a total of nine transformation components in TNG67 with two biological replicates of leave samples

first: Jo-Wei

last: Hsieh

first: Pearl

last: Chang

first: Lin-Yun

last: Kuang

first: Yue-Ie

last: Hsing


title: Gene expression signatures of JBV cells treated with miR-145

city: Gifu

first: Kazuki

last: Heishima

address: Yanagido 1-1

country: Japan

institute: Gifu University

summary: To examine the difference of gene expression profiles between malignant melanoma cells treated with neopetasin (NP), metformin (Met), and phenformin (Phen), we have employed microarray expression profiling as a discovery platform. A2058 (human malignant melanoma) cells were treated for 8 hours with NP (3 µM), Met (5,00 µM), and Phen (50 µM).

overall_design: JBV cells treated with miR-145


title: Expression profiling of Mycobacterium smegmatis in M63 medium and M63 medium supplemented with NH4Cl for wild-type, eccCa1, eccD, esxB

city: San Francisco

first: Nadia

last: Herrera

address: 600 16th Street, GH S416 BOX 2240

department: Medicine

country: USA

institute: University of California San Francisco

summary: Mycobacterium smegmatis respond to various environmental stimuli via ESX systems. We probed the transcriptional response to nitrogen addition to the medium using a series of ESX-1 knockout mutants.

overall_design:
Expression profiling of Mycobacterium smegmatis in M63 medium and M63 medium supplemented with NH4Cl for wild-type  and eccCa1, eccD, esxB mutants
RNA was extracted from cultures grown to OD600 nm ~ 0.7-0.8. Three biological replicates (single colonies) were prepared for every strain assayed. The NEB RNA extraction kit was used as directed except for the lysis step, which was completed by bead beating the cells with 0.1 mm zirconia beads. To deplete rRNA, we used the NEB rRNA kit as directed. Samples were prepared using the NEBNext Ultra RNA library prep kit for Illumina, and barcoding oligos were used to pool the libraries. Two technical replicates were prepared for analysis. The resulting pools were sequenced with the Illumina NovaSeq in 75 nt single end reads, resulting in 15M reads per sample.

first: Herrera

last: Nadia

first: Mark

last: Voorhies

first: Anita

last: Sil

first: Rosenberg

last: Oren


title: Single-Cell Multiomics Reveals Distinct Cell States at the Top of the Human Hematopoietic Hierarchy [scATAC-seq]

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

institute: Lund University

summary: The advent of single cell (Sc) genomics has challenged the dogma of haematopoiesis as a tree-like structure of stepwise lineage commitment through distinct and increasingly restricted progenitor populations. Instead, analysis of ScRNA-seq has proposed that the earliest events in human hematopoietic stem cell (HSC) differentiation are characterized by only subtle molecular changes, with hematopoietic stem and progenitor cells (HSPCs) existing as a continuum of low-primed cell-states that gradually transition into a specific lineage (CLOUD-HSPCs). Here, we combine ScRNA-seq, ScATAC-seq and cell surface proteomics to dissect the heterogeneity of CLOUD-HSPCs at different stages of human life. Within CLOUD-HSPCs, pseudotime ordering of both mRNA and chromatin data revealed a bifurcation of megakaryocyte/erythroid and lympho/myeloid trajectories immediately downstream a subpopulation with an HSC-specific enhancer signature. Importantly, both HSCs and lineage-restricted progenitor populations could be prospectively isolated based on correlation of their molecular signatures with CD35 and CD11A expression, respectively. Moreover, we describe the changes that occur in this heterogeneity as hematopoiesis develops from neonatal to aged bone marrow, including an increase of HSCs and depletion of lympho-myeloid biased MPPs. Thus, this study dissects the heterogeneity of human CLOUD-HSPCs revealing distinct HSPC-states of relevance in homeostatic settings such as ageing.

overall_design:
Singel-Cell ATAC sequencing of hematopoietic stem and progenitors of young bone marrow.
*** The raw data cannot be shared due to EU law (derived from EU patients that are protected by GDPR) ***

first: Mikael

middle: N

last: Sommarin

first: Parashar

last: Dhapola


title: Single-Cell Multiomics Reveals Distinct Cell States at the Top of the Human Hematopoietic Hierarchy [CITE-seq]

overall_design:
Singel-Cell RNA sequencing of hematopoietic stem and progenitors across different ages.
*** The raw data cannot be shared due to EU law (derived from EU patients that are protected by GDPR) ***


title: Glial progenitor heterogeneity, key regulators and cell signaling revealed by single-cell RNA-sequencing provide insights to regeneration in spinal cord injury

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: Recent studies in brain and spinal cord have revealed the heterogenous nature of astrocytes; however, how diverse constituents of astrocyte lineage cells are regulated in adult spinal cord after injury and contribute to regeneration remains elusive.  We performed single-cell RNA-sequencing (scRNA-seq) of astrocyte lineage cells from sub-chronic spinal cord injury (SCI) models, identified and compared with the subpopulations in the acute stage data. We found the subpopulations  with distinct functional enrichment and their identities defined by subpopulation-specific transcription factors and regulons. Our analyses revealed the molecular signature, location and morphologies of potential residential neural progenitors or neural stem cells in the adult spinal cord before and after injury, and the intermediate cells enriched in neuronal markers  that could potentially transition into other subpopulations. The investigation of stage-specific cell-cell communications among astrocyte lineage cells and with other cell types in the tissue generated valuable insight into signaling pathway networks in SCI. This study has significantly expanded the knowledge of the heterogeneity and cell state transition of glial progenitors in adult spinal cord before and after injury.

first: Xizi

last: Wu

first: Raquel

last: Duran

first: Lesley

last: Chaboub

first: Andrew

last: Rolfe

first: Philip

last: Horner

first: Jiaqian


title: RNAseq of mouse RAW264.7 macrophages with CRISPR deletion of SGK1, SGK3, or SGK1/3 or treated with SGKi Sanofi-14h with or without DMXAA stimulation.

status: Public on Sep 26 2023

city: Chapel Hill

first: Johnny

middle: Victor

last: Castillo Cabrera

state: NC

address: 450 West Drive

institute: University of North Carolina

summary: The STING signaling pathway is essential for the innate immune response to DNA viruses and bacteria and is important in tumor immunity. STING binding to cGAMP or to synthetic agonists leads to the activation of the kinase TBK1 which phosphorylates the transcription factor IRF3 which promotes expression of type 1 interferons such as IFNb to block viral activity. Aberrant type 1 IFN expression is associated with human diseases including autoimmunity, HIV, and cancer. Here we identify N-[4-(1H-pyrazolo[3,4-b] pyrazin-6-yl)-phenyl]-sulfonamide (Sanofi-14h), a compound with preference for inhibition of the AGC family kinase SGK3, as an inhibitor of IFNb gene expression in response to STING stimulation of macrophages. Sanofi-14h abrogated SGK activity and also impaired activation of the critical TBK1/IRF3 pathway downstream of STING activation, notably blocking the ligand-induced interaction of STING with TBK1. Deletion of SGK1 and SGK3 in macrophages suppressed activation of IFNb transcription but did not block TBK1/IRF3 activation downstream of STING. Gene and protein expression analysis revealed that deletion of SGK1/3 in a macrophage cell line decreases basal expression of critical transcription factors required for the innate immune response, such as IRF7 and STAT1.  Additional studies reveal that other AGC kinase inhibitors block TBK1 and IRF3 activation suggesting common action on a critical regulatory node in the STING pathway. Thus, studies with Sanofi-14h have revealed both SGK-dependent and SGK-independent effects in the STING pathway and suggest a mechanism to alter type 1 IFN transcription through small molecule therapy

overall_design: Murine RAW264.7 macrophages were CRISPR edited with sgRNAs against SGK1 or SGK3 or control sgRNA. Dual SGK1/3 KO cells were also constructed. RNA was collected from cells under resting (unstimulated) conditions or after 2 hours of stimulation with the murine STING agonist DMXAA (10μg/mL). In addition, a set of WT cells were pretreated with the SGK inhibitor Sanofi-14h (500nM) or vehicle (DMSO) for 2 hours prior to stimulation.

last: Cabrera

first: Hong

last: Dang

first: Adam

last: Graves

first: Zhigang

last: Wang

first: Jose

last: Torres-Castillo

first: Kelin

last: Li

first: Zayna

last: King

first: Pengda

last: Liu

first: Jeffrey

last: Aube

first: James

last: Bear

first: Blossom

last: Damania

first: Robert

last: Hagan

first: Albert

last: Baldwin


title: CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses (ChIP-seq)

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

institute: University of Helsinki

summary: Myocardin-related transcription factors (MRTFs) are coactivators of serum response factor (SRF), and thereby regulate cytoskeletal gene expression in response to actin dynamics. MRTFs have also been implicated in heat shock protein (hsp) transcription in fly ovaries, but the mechanisms remain unclear. Here we demonstrate that in mammalian cells, MRTFs are dispensable for hsp gene induction. However, the widely used small molecule inhibitors of MRTF/SRF transcription pathway, derived from CCG-1423, efficiently inhibit hsp gene transcription in both fly and mammalian cells also in absence of MRTFs.  Quantifying RNA synthesis and RNA polymerase distribution demonstrates that CCG-1423-derived compounds have a genome-wide effect on transcription. Indeed, tracking nascent transcription at nucleotide resolution reveals that CCG-1423-derived compounds reduce RNA polymerase II elongation, and severely dampen the transcriptional response to heat shock. The effects of CCG-1423-derived compounds therefore extend beyond the MRTF/SRF pathway into nascent transcription, opening novel opportunities for their use in transcription research.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Chromatin immunoprecipitationfollowed by deep sequencing (ChIP-seq) in NIH3T3 cells of Pol II phosphorylated at serine 5 (Pol II S5P) and MAL (AC-74), and Pol II phosphorylated at serine 5 (Pol II S5P)  in S2R+  cells culture. Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins either in 37°C waterbath (S2R+ cells) or 42°C waterbath (NIH 3T3 cells). Normal mouse IgG was used as negative control.

first: Bina

last: Prajapati