title: Gene expression data from diabetic human adipose-derived stem cells (d-hASC) treated with 1uM oleacein

summary:
Gene expression profiling reveals multiple biological functions of oleacein in diabetic model.
We evaluated the effects of oleacein on diabetic human adipose-derived stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of oleacein in a diabetic adipose stem cell-based tool.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and oleacein treated hASCs samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed.ar space) were considered as differentially expressed genes (DEGs). The fold change value around top 500 genes (FC=1.18)were extracted and sorted in descending order, for clustering and more focused enrichment analysis.


title: Peripheral blood mononuclear cell hyperresponsiveness in patients with premature myocardial infarction without traditional risk factors

status: Public on Jul 19 2023

city: Nijmegen

first: Niels

middle: P

last: Riksen

state: Gelderland

address: Geert Grooteplein Zuid 10

department: Afdeling Interne Geneeskunde - Department of Internal Medicine

country: Netherlands

institute: Radboud UMC

type: Expression profiling by high throughput sequencing

summary:
An increasing number of patients develop a myocardial infarction (MI) in the absence of standard modifiable risk factors (SMuRFs). Atherosclerosis is characterized by a chronic arterial wall inflammation in which monocyte-derived macrophages play a pivotal role. Trained immunity – a long lasting hyperreactive state of innate immune cells – might contribute to the development of atherosclerosis. This study investigated whether trained immunity is observed in this specific patient group.
20 SMuRFless MI patients who suffered an atherothrombotic myocardial infarction > 1 year and < 4 years before inclusion were recruited. All patients were younger than 50 years of age during the index event. Patients were matched to 18 healthy controls without coronary atherosclerosis as determined by a coronary CT-scan. Blood samples were obtained two weeks after interrupting statins in patients and starting aspirin therapy in controls to match relevant medication use. Circulating inflammatory parameters and monocytes were analyzed, with an in-depth focus on peripheral blood mononuclear cell (PBMC) function, and monocyte phenotype, RNA expression and epigenetic histone markers.
PBMCs from SMuRFless patients showed higher cytokine production upon ex vivo stimulation. Although baseline RNA expression and monocyte activations markers were largely unchanged, enrichment of the transcriptionally permissive histone marker H3K4me3 on the promoter region of cytokine genes was observedIL-10 genes was observed. This existed without differences in systemic inflammation.
Circulating monocytes in young SMuRFless MI patients have a hyperresponsive functional and epigenetic phenotype, indicative of trained immunity. In the absence of traditional risk factors, this could be a promising target for future therapy in these patients.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for monocytes from patients with matched healthy controls without coronary atherosclerosis
----------------------
Authors state "Due to privacy concerns, it was requested that we only provide the count data and not the raw sequencing data itself."

first: Jan-Quinten

last: Mol

first: Julia

last: van Tuijl

first: Siroon

last: Bekkering

first: Charlotte

middle: C

last: van der Heijden

first: Sander

middle: J

last: Damen

first: Benjamin

last: Cossins

first: Liesbeth

last: van Emst

first: Tim

middle: M

last: Nielen

first: Laura

last: Rodwell

first: Yang

last: Li

first: Gheorghe

last: Pop

first: Mihai

middle: G

last: Netea

last: van Royen

first: Saloua

last: El Messaoudi


title: Salivary miRNA profiles in COVID-19 patients with different disease severity [Plasma]

city: Milan

first: Irma

last: Saulle

address: G.B. Grassi 74

country: Italy

institute: University of Milan

summary: The oral mucosa is the first site of SARS-CoV-2 entry and replication, and it plays a central role in the early defense against infection. Thus, SARS-CoV-2 viral load, miRNAs, cytokines, and neutralizing activity (NA) were assessed in saliva and plasma from mild (MD) and severe (SD) COVID-19 patients.  Here we show that of the 84 miRNAs analysed, 8 are differently express in plasma and saliva of SD. In particular: 1) miRNAs let-7a-5p, let-7b-5p, let-7c-5p are significantly downregulated; and 2) miR-23a and b, miR-29c, as well as three immunomodulatory miRNAs (miR-34a-5p, miR-181d-5p, miR-146) are significantly upregulated. The production of pro-inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-9 and TNFα) and chemokines (CCL2 and RANTES) increase in both saliva and plasma of SD and MD. Notably, disease severity correlates with NA and immune activation.  Monitoring these parameters could help to predict disease outcome and identify new markers of disease progression.

overall_design: This study included a total of 20 COVID-19-positive patients (as determined by SARS-CoV-2 molecular test of nasopharyngeal swabs) enrolled from a larger cohort hospitalized at the Infectious Diseases Unit, Policlinic “Riuniti” of Foggia (Italy), between March 1st and May 31st,2020. Patients were divided into Mild Patients (MD; n=10) and Severe Patients (SD; n=10) according to COVID-19 disease severity and following the National Institute of Health (NIH) guidelines for COVID-19 treatment. Age and sex matched Uninfected Subjects (HC) (n= 10) were included

first: Claudia

last: Vanetti

first: Micaela

last: Garziano


title: Down regulation of Monocyte miRNAs: Implications for Immune Dysfunction and Disease Severity in Drug-Resistant Tuberculosis

city: Chennai

first: Ramalingam

last: Bethunaickan

state: Tamil Nadu

address: No.1.  Mayor Satya murthy Road, Chetpet

department: Immunology

country: India

institute: ICMR-National Institute for Research in Tuberculosis

summary: Monocyte miRNAs govern both protective and pathological responses during tuberculosis through their differential expression and emerged as potent target for biomarker discovery and host-directed therapeutics. Thus, our profound interest is to look at the miRNA profile of sorted monocytes across TB disease spectrum (drug-resistance TB (DR-TB), drug-sensitive TB (DS-TB) and latent TB) and healthy individuals (HC) to understand the underlying pathophysiology and their regulatory mechanism.

overall_design: Blood sample from four categories; 1. Healthy controls (HC) (n=6), 2. Latent TB (LTB) (n=6), 3. Drug-sensitive pulmonary tuberculosis (DS-TB) (n=6) and 4. Drug-resistant pulmonary tuberculosis (DR-TB) (n=6) were collected. After nCounter miRNA assay, QC metrics were performed using nSolver 4.0 software as per the guidelines, before proceeding with further analysis. 2 samples each from the groups, HC and DR-TB were filtered from further analysis before proceeding with normalization owing to the poor ligation QC values below the threshold.  The final number of samples used for normalization and further analysis included 20 samples.

first: Pavithra

last: Sampath

first: Aishwarya

last: Janaki

first: Madhavan

last: Dhanapal

first: Uma

middle: D

last: Ranganathan

first: Manju

last: Moorthy

first: Athul

last: Menon

first: Lekshmi

last: Madhav

first: Gopalakrishna

last: Ramaswamy

first: Alangudi

last: Natarajan

first: Syed

last: Hissar


title: RNA-Seq of Primary and Recurrent DSRCT Tumors

city: New Orleans

first: Sean

middle: Bong

last: Lee

state: LA

address: 1700 Tulane Ave

department: Pathology

country: USA

institute: Tulane University School of Medicine

summary: Desmoplastic small round cell tumor (DSRCT) is a rare pediatric cancer caused by the EWSR1-WT1 fusion oncogene. Despite initial response to chemotherapy, DSRCT has a recurrence rate of over 80% leading to poor patient prognosis with a 5-year survival rate of only 15-25%. Owing to the rarity of DSRCT, sample scarcity is a barrier to understanding DSRCT biology and developing effective therapies. Here, we performed RNA-sequencing on a novel pair of primary and recurrent DSRCT tumors harvested from the same patient 5-years apart. To gain insights into gene expression alterations associated with recurrence, we performed pathway analysis on Gene Ontology Biological Processes and KEGG pathways. Upregulated pathways in the recurrent tumor included DNA repair and mRNA splicing related pathways, while downregulated pathways included immune system function and focal adhesion. We further examined the expression of previously identified EWSR1-WT1 regulated targets, a large number of which were enriched in the recurrent tumor. Overall, this study provides novel understanding of DSRCT biology and a new RNA-seq data set to advance future studies.

overall_design: RNA sequencing was performed on a set of primary and recurrent DSRCT samples from the same patient. Gene expression and pathway alterations were examined

middle: B

first: Justin

middle: W

last: Magrath


title: Role of ALDH1A1 in PARPi resistance in ovarian cancer

city: Columbus

first: Qi-En

last: Wang

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

summary: Poly (ADP-ribose) Polymerase (PARP) inhibitors (PARPi) are approved to treat recurrent ovarian cancer with BRCA1 or BRCA2 mutations, and as maintenance therapy for recurrent platinum sensitive ovarian cancer (BRCA wild-type or mutated) after treatment with platinum. However, the acquired resistance against PARPi remains a clinical hurdle. Our previous study has demonstrated that PARPi can enhance the Aldehyde dehydrogenase (ALDH) activity in ovarian cancer cells, mainly through inducing expression of ALDH1A1, an isoform of the ALDH family. In addition, an ALDH1A1 selective inhibitor can synergize with olaparib in killing EOC cells carrying BRCA2 mutation in both in vitro cell culture and the in vivo xenograft animal model. In order to elucidating the mechanism by which ALDH1A1 renders PARPi resistance to ovarian cancer, we performed RNA-seq analysis to identify genes whose expression can be regulated by ALDH1A1.

overall_design: PEO1 cells were transfected with ALDH1A1 siRNA and control siRNA for 48 h. RNA was isolated and subjected to mRNA sequencing.

first: Kousalya

last: Lavudi

first: Shurui

last: Cai

last: Li


title: Particulate matter 10 exposure affects intestinal functionality in both inflamed 2D intestinal epithelial cell and 3D intestinal organoid models

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: A growing body of evidence suggests that particulate matter (PM10) enters the gastrointestinal (GI) tract directly, causing the GI epithelial cells to function less efficiently, leading to inflammation and an imbalance in the gut microbiome. PM10 may, however, act as an exacerbation factor in patients with inflamed intestinal epithelium, which is associated with inflammatory bowel disease. In this study, we established chronically inflamed intestinal epithelium models utilizing two-dimensional (2D) human intestinal epithelial cells (hIECs) and 3D human intestinal organoids (hIOs), which mimic in vivo cellular diversity and function, in order to examine the deleterious effects of PM10 in human intestine-like in vitro models. Inflamed 2D hIECs and 3D hIOs exhibited pathological features, such as inflammation, decreased intestinal markers, and defective epithelial barrier function. In addition, we found that PM10 exposure induced a more severe disturbance of peptide uptake in inflamed 2D hIECs and 3D hIOs than in control cells. This was due to the fact that it interferes with calcium signaling, protein digestion, and absorption pathways. The findings demonstrate that PM10-induced epithelial alterations contribute to the exacerbation of inflammatory disorders caused by the intestine. According to our findings, 2D hIEC and 3D hIO models could be powerful in vitro platforms for the evaluation of the causal relationship between PM exposure and abnormal human intestinal functions.

overall_design: Comparision of gene expression profile in control, PM10, Inflammed, Inflammed+PM10 treated intestinal epithelial cells


title: The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/drosophila/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis but was known to comprise three proteins, of which two were conserved in mammals. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian orthologs. Nonetheless, the yeast MTC is arranged differently from its mammalian counterpart. The yeast MTC features a mostly mutually stabilizing core comprising Ime4/Mum2/Vir1 and the mRNA binding component Kar4, and an auxiliary hub comprising Slz1/Dyn2. The MTC core subunits when in a complex have both m6A-dependent and m6A-independent functions in meiosis. Kar4 also has a mechanistically separate function from the MTC during mating. Our findings expand the relevance of yeast as a model for unravelling m6A-dependent and independent functions of MTCs.

overall_design:
ChIP-seq of yeast MTC components under various conditions.
Please note that the processsed data file generated from both *_1 and *_2 samples is linked to the corresponding *_1 sample records.

first: Imke

last: Ensinck

first: Harshil

last: Patel


title: Hierarchical phosphorylation of HOXB13 by mTOR dictates its activity and oncogenic function in prostate cancer [RNAseq_HOXB13]

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

summary: Dysregulation of mTOR signaling plays a critical role in promoting prostate cancer (PCa) growth. HOXB13, a homeodomain transcription factor, is known to influence the androgen response and PCa development. Recently, HOXB13 was found to complex with mTOR on chromatin. However, the functional crosstalk between HOXB13 and mTOR remains elusive. We now report that mTOR directly interacts with and hierarchically phosphorylates HOXB13 at threonine 8 and 41 then serine 31 to promote its destabilization by the E3 ligase SKP2 while enhancing its oncogenic properties. Expression of HOXB13 harboring phosphomimetic mutations at the mTOR-targeted sites stimulates PCa cellular growth both in vitro and in murine xenografts. Transcriptional profiling studies revealed a phospho-HOXB13-dependent gene signature capable of robustly discriminating between normal prostate tissues, primary and metastatic PCa samples. This work uncovers a previously unanticipated molecular cascade by which mTOR directly phosphorylates HOXB13 to dictate a specific gene program with oncogenic implications in PCa.

overall_design: Triplicate RNA-seq experiments in LNCaP cells with shRNA-mediated knockdown of HOXB13 rescued with either WT HOXB13 , HOXB13 3A phospho mutant (T8, T41 and S31 mutations to alanine) or empty vector (EV) conrol treated with 10nM R1881 or vehicle (EtOH) control for 24h.

first: Yonghong

last: Chen

first: Catherine

middle: R

last: Dufour


title: RNA-seq of cultured prefrontal cortex brain tissue from C57BL/6 mouse

city: Guangzhou

first: Zhonghui

last: Tang

state: Guangdong

address: No. 74 Zhongshan Second Road, Guangzhou

country: China

institute: Sun Yat-sen University

summary: FGF2 plays important roles in neural progentor cells prolifration and differency, however, the effects of FGF2 on neuronal cell culture are controversial and its effects on human embryonic prefrontal cortex tissues after culture have not been studied, therefore, we firstly investigated the effect of FGF2 on human embryonic cortex tissue and repeated with P0 mice embryonic prefrontal tissues after culture.

overall_design: We performed RNA-seq on P0 mouse cultured brain tissue treated with or without FGF2. Prefrontal cortex brain cells were harvested as describrd in P0 mouse cortical brain neurons in vitro culture. 1-2 million cells were used for library construction.

first: Rong

last: Liu

first: Wei

last: Dong


title: Effect of suppression of ERDMAN_2020 on whole-genome transcriptomic profiling of Mycobacterium tuberculosis Erdman by RNA Seq

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

institute: Translational Health Science and Technology Institute

summary: The main objective of this study is to analyze changes in whole-genome transcriptomic profile of ERDMAN_2020(-) strain of Mycobacterium tuberculosis Erdman after ATc-dependent conditional depletion of ERDMAN_2020 by RNA Seq. Total 798 transcripts were found differentially regulated in three biological replicates with log2 fold change ≥ 1 and p-value ≤ 0.05 from. ERDMAN_2020 belongs to MerR family of transcription regulators. Treatment of ERDMAN_2020(-) strain with 50ng/ml ATc for 4 days resulted in accumulation of 338 transcripts and suppression of 460 transcripts, compared to the empty vector control.

overall_design: mRNA profile of M. tuberculosis Erdman after conditional depletion of ERDMAN_2020 by 4 days of treatment with 50ng/ml anhydrotetracycline (ATc).

first: Pramila

last: Pal


title: Differential effects of sugar and fat on adipose tissue inflammation

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Obesity has become a worldwide pandemic. Low grade inflammation initiated from adipose tissue further promotes deterioration of the health of these individuals. However, the early events that lead to the release of inflammatory factors from adipose tissue have not been well characterized. In order to separate out the effects of glucose and lipids on adipose tissue, we used an adipose-specific knockout of txnip mouse model. In the absence of TXNIP, excess basal glucose uptake by adipocytes lead to modestly increased adiposity. We found a clear uncoupling of two events that are generally assumed to be regulated together: adipose macrophage number increase and their activation. Adipocytes exposure to excess glucose led to an increase of macrophage numbers without activation while metabolic rescuing with a ketogenic diet led to macrophage activation without an analogous increase in macrophage count. We identified multiple factors that contributed to the increase in macrophage number including elevated FFA (free fatty acids) and reduced extracellular matrix whereas decreased adiponectin production was associated with macrophage activation.

overall_design: eWAT mRNAseq of WT and TXNIP adipose specific KO animals on control and ketogenic diets, mRNAseq of CD64+ cells isolated from eWAT of WT and adipose specific KO animals on control and ketogenic diet

first: Tracey

last: Avequin

first: Kin

last: Lau

first: Althea

middle: N

last: Waldhart

first: Hannah

last: Guak

first: Holly

last: Dykstra

first: Connie

last: Krawczyk


title: Transcriptomes of pressure overloaded left ventricle in 4-week age mice

city: Shanghai

first: Bozhong

last: Shi

address: 1678, Dongfang road, Pudong district

institute: Shanghai Children's Medical Center

summary: neonatal ascending aorta constriction (nAAC) or sham surgery was performed in newborn mice within 24h (n=5 vs 5). At the 4th week, left ventricles were collected and used for RNA sequencing.

overall_design: comparative gene expression profiling analysis of RNA-seq data for the left ventricle of nAAC mice and sham mice

first: Xiaomin

last: He

first: Jinghao

last: Zheng


title: Molecular Characterisation of Adipocyte Cells from a Patient with ROHHAD Syndrome

city: Bristol

first: Claire

last: Perks

address: 5 Tyndall Avenue

department: Bristol Medical School

institute: University of Bristol

summary: To better characterise adipose cells from a child with ROHHAD syndrome, we performed next-generation sequencing (NGS) and bioinformatic analyses on these cells compared to tissue from an age- and sex-matched control. The two most up-/down-regulated genes were validated using QPCR.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of adipose cells from a child with ROHHAD compared to normal control adipose tissue from an age- and sex-matched child.

first: K

last: Biernacka

first: C

last: Hawton

first: J

last: Hamilton-Shield


title: Loss of the importin Kpna2 causes infertility in male maice by disrupting the translocation of testis-specific transcription factors

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

summary: Karyopherin proteins mediate the movement between the nucleus and cytoplasm of specific proteins that are essential for spermatogenesis. Through a loss-of-function approach, we here examine the specific role of Karyopherin Subunit Alpha 2 (Kpna2) in spermatogenesis and male fertility. The factors determined were (i) the spatial distribution of KPNA2 in the testis using immunofluorescence; (ii) the morphological and functional consequences of Kpna2 deficiency in terms of sperm production, quality, and motility, and fertility in knock-out and wild-type mice; and (iii) the transcriptomic consequences of Kpna2 deficiency in knock-out compared to wild-type mice by RNA-seq analysis. KPNA2 was found expressed in the cytoplasm of primary spermatocytes and the nucleus and cytoplasm of secondary spermatocytes and spermatid cells. Ablation of Kpna2 in male mice reduced their size, affected sperm motility, increased sperm abnormalities, and led to dysregulation of testis gene expression and ultimately to infertility. Impaired mRNA expression mainly affected clusters of genes expressed in spermatids and spermatocytes. Downregulated genes include a set of genes that participate in cell adhesion, extracellular matrix (ECM) organization, and ECM-receptor interaction. We detected the enrichment of some transcription factors that bind to regions around transcription start sites of downregulated genes. We propose an essential role of Kpna2 in spermatogenesis via the disrupted translocation of testis specific transcription factors that control the expression of genes related to ECM organization in the seminiferous tubules.

overall_design: Differential gene expression analysis in mice Kpna2 knockout testis compared to wild-type testis.

first: Paula

last: Navarrete-López

first: María

last: Maroto

first: Raúl

last: Fernández-González

first: Eva

last: Pericuesta

first: Marta

last: Lombó

first: Priscila

last: Ramos-Ibeas


title: Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model

city: Kiryat Shmona

first: Ari

last: Meerson

address: 2 Tarshish St.

country: Israel

institute: MIGALGalilee Research Institute

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: Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo

city: ZHENG ZHOU

first: shuai

last: zhang

address: China Henan Zhengzhou Agricultural Road No. 63 (450002)

institute: Henan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Dynamic alteration of the epitranscriptome exerts regulatory effects on the lifecycle of oncogenic viruses in vitro. However, little is known about these effects in vivo because of the general lack of suitable animal infection models of these viruses. Using a model of rapid-onset Marek’s disease lymphoma in chickens, we investigated changes in viral and host mRNA N6-methyladenosine (m6A) modification during Marek’s disease virus (MDV) infection in vivo. We found that the expression of major epitranscriptomic proteins varies among viral infection phases, reprograming both the viral and the host epitranscriptomes.Specifically, the METTL3/14 complex was suppressed during the lytic and reactivation phases of the MDV lifecycle, whereas its expression was increased during the latent phase and in MDV-induced tumors. METTL3/14 overexpression inhibits, whereas METTL3/14 knockdown enhances, MDV gene expression and replication. These findings reveal the dynamic features of the mRNA m6A modification program during viral replication in vivo, especially in relation to key pathways involved in tumorigenesis.

first: Guoqing

last: Zhuang

first: Aijun

last: Sun


title: Plasma kynurenine mediated pathological communication between gut microbiota and ventricular remodeling in children with pressure overload

first: Bozhong

last: Shi

summary: Abnormally elevated plasma kynurenine (Kyn) was detected in the patient cohort and single nuclues sequecing revealed its molecular role

overall_design: Comparative gene expression profiling analysis of snRNA-seq data for the left ventricle tissue of high Kyn patients and normal Kyn patients

first: Xiaomin

last: He


title: Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model [RNA-Seq]

summary:
Obesity associates with anxiety disorders in adult humans, rodents and fish, although there is also evidence to the contrary.
Moreover, it is unknown if this association is developmentally regulated, and which genes are involved.
RNA-sequencing differences between caffeine-induced anxious zebrafish larvae, which exhibited greater thigmotaxis, erratic swimming and higher whole-body cortisol levels than matched controls,
and high fat diet-fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls, were revealed.
There were 231 genes common to both models (padj<0.05) and 75% of the transcripts upregulated (>1.5 fold) in the anxiety model were downregulated (<0.67 fold) in obese larvae.
Immune system pathways were overrepresented among these inversely regulated genes.

overall_design:
Profile analyses of RNA-seq poly(A)+ and miRNA data were carried out on two zebrafish larval models (15 days post fertilization[dpf]),
one of anxiety (induced by a half hour exposure to 100 mg/liter caffeine [CAF], compared to no treatment [NO])
and the other of obesity (induced by feeding 6 dpf larvae a high fat diet  [HFD, egg yolk-based] until 15 dpf, compared to a standard diet [SD]).
Both models were optimized and validated, the anxiety model by behavioral and cortisol level tests and the obesity model by histology-based adiposity analysis.
RNA was extracted from pools of 30 larvae per replicate (3 replicates per treatment [NO, CAF, SD, HFD]), euthanized by ice-cold water and snap-frozen in liquid nitrogen.

first: Hila

last: Yehuda

first: Hermona

last: Soreq


title: Single cell RNA sequencing reveals mechanisms underlying a senescence-like phenotype of Alveolar Macrophages during Aging

city: Rochester

first: Jie

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Alveolar Macrophages (AMs) are unique innate immune cells that reside in the alveolar space and accommodate the ever-changing needs of the lungs against internal and external challenges. During homeostasis, AMs maintain themselves through self-renewal without input from adult hematopoietic stem cells. Currently, little is known regarding the influence of aging on AM dynamics, heterogeneity and transcriptional profiles. Here, we identified CBFβ as an indispensable transcription factor that ensures AM self-renewal. Deficiency in CBFβ led to decreased proliferation and self-renewal ability of AMs. Moreover, with single cell RNA sequencing analysis of AMs from young and aged mice, we discovered that despite similarities in the transcriptome of proliferating cells, AMs from the aged mice exhibited reduced embryotic stem cell-like features. Aged AMs also showed diminished capacity for DNA repair, potentially contributing to impaired cell cycle progression and elevation of senescence markers. In accordance with the analysis, we observed reduced number of AMs in aged mice, which had defective self-renewal ability and were more sensitive to the reduction of GM-CSF. Interestingly, decreased CBFβ was observed in the cytosol of AMs from aged mice. A similar senescence-like phenotype was also found in human AMs. Taken together, we conclude that AMs in the aged host harbor a senescence-like phenotype, potentially mediated by the activity of CBFβ.

overall_design: Single cell RNA sequencing of FACS sorted Alveolar Macrophages (CD11c+ Siglec F+) from lung homogenate  of young (~2-month-old) and aged (~22-month-old) mice

first: Yue

last: Wu

first: Bibo

last: Zhu

first: Ying

last: Li


title: Single-Cell Analysis of Aging Mouse Dentate Gyrus

city: Berkeley

first: Danica

last: Chen

address: 335 Morgan Hall

institute: University of California, Berkeley

summary: The dentate gyrus of the hippocampus is a brain region involved in learning, memory formation, and spatial coding. We performed single-cell RNA-sequencing of the dentate gyrus of young and old mice to identify the age-induced changes.

overall_design: Mouse dentate gyri were microdissected and single cells were isolated via enzymatic dissociation. Viable cells were collected via fluorescence-activated cell sorting and subjected to 10x Genomics single-cell RNA-sequencing. Libraries were seqeucned with Illumina NovaSeq 6000 28x94 Flow Cell SP, paired-end.

first: Wei

last: Mu

first: Rika

last: Ohkubo

first: Chih

middle: L

last: Wang


title: Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model [miRNA-Seq]

summary:
Obesity associates with anxiety disorders in adult humans, rodents and fish, although there is also evidence to the contrary.
Moreover, it is unknown if this association is developmentally regulated, and which genes are involved.
RNA-sequencing differences between caffeine-induced anxious zebrafish larvae, which exhibited greater thigmotaxis, erratic swimming and higher whole-body cortisol levels than matched controls,
and high fat diet-fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls, were revealed.
There were 231 poly(A)+ genes common to both models (padj<0.05) and 75% of the transcripts upregulated (>1.5 fold) in the anxiety model were downregulated (<0.67 fold) in obese larvae.
Immune system pathways were overrepresented among these inversely regulated genes.

first: H

first: A


title: JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis [ChIP-Seq]

city: shanghai

first: li

last: peng

institute: PSC

summary: JASMONATE-ZIM DOMAIN (JAZ) proteins are key regulators in the JA signaling pathway and function to repress the expression of JA-responsive genes. We found that JAZ proteins directly interact with several chromatin-associated Polycomb proteins to mediate repressive chromatin modifications at part of JA-responsive genes and thus their transcriptional repression in Arabidopsis.

overall_design: Nuclei were extracted from liquid-cultured LHP1:Flag seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with anti-Flag M2 magnetic beads (Sigma). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on NovaSeq 6000 (Illumina). Three biologically independent samples treated by 5µM JA or mock (5000x diluted ethanol) have been analyzed.

first: Xiao

last: Luo

first: Li

last: Peng

first: Yuehu

last: i He


title: JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis [RNA-Seq]

overall_design: For RNA-seq analysis, total RNAs were extracted from 6 day-old seedlings treated with or without 5-µm JA for 3hr. Three samples including WT (mock), lhp1 (mock), and WT (JA) were analyzed for RNA-seq (each sample with three biological replicates).

first: Yang

last: Ou

first: Yuehui


title: Overexpression of human TLR8 alters the bone marrow erythropoietic niche and causes fatal anemia in SLE-prone mice

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary:
The goal of this study was to understand the cause of anemia in lupus prone mice expressing humn TLR8. This was found to be due to a block in erythroblast differentiation form the CFUE to proerythroblast stage, a step that occurs within erythroblastic islands.
We analyzed 19,309 bone marrow EBI cells and 4,794 spleen EBI cells that formed 22 clusters of cells.
We confirmed the block in CFUE differentiation and found a defect in central macrophages that caused failure of erythroblast adherence

overall_design: We compared sequences of single cells from isolated and dissociated bone marrow and spleen erythroblastic islands from male lupus prone mice (Sle1.Yaa) expressing a human TLR8 transgene with sequences of single cells from isolated bone marrow erythroblastic islands from Sle1.Yaa controls using 10X genomics V3.1 platform

first: Anne

last: Davidson


title: JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [9C, 9D, 9E & 9F]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (9C_190620, 9D_190326, 9D_190404, 9E_200707, 9E_200709, 9F_201001, 9F_201008).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Gene expression modification in lungs of rats exposed to TiO2 by inhalation

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

summary: In this work we study the pulmonary toxicological properties of titanium dioxide using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation.  Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 13 week old female Sprague Dawley rats were exposed by inhalation to TiO2 (1.5, 5 or 15 mg/m3). TiO2-induced gene expression profile in rat lung was performed 3, 30 and 180 days post exposure (3 time points). Each time point is composed of 6 control,  6 exposed rats. A total of 72 samples (microarrays) was used.

first: Sarah

middle: A

last: Valentino

first: Mylène

last: Lorcin

first: Sylvie

last: Sébillaud

first: Laurent

last: Gaté


title: Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes [DNA-Seq]

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Senescent cells are one source of the chronic inflammation that contributes to the diseases and debilities of aging. Whereas cellular senescence in fibroblasts is well documented, how this process is orchestrated in epithelial cells, the origin of human carcinomas, is much less understood. We used normal primary human oral keratinocytes (NOKs) to elucidate senescence programs in a prototype mucosal epithelial cell that undergoes senescence spontaneously. We employed widely-accepted assays to characterize senescence phenotypes in these cells and found that p21WAF1/CIP1 is not a reliable marker of senescence for NOKs, as it is for fibroblasts. We performed transcriptome analysis by RNA-seq and proteomic analysis of secreted proteins, both non-vesicular and those associated with extracellular vesicles (EVs). NOKs, while sharing with fibroblasts certain important aspects of inflammation, such as upregulation of the NF-κB, interferon, and p38MAPK pathways, also exhibit novel senescence associated characteristics. In two of the donors, we observed an expected repression of DNA repair genes, correlating with downregulation of E2F1 mRNA and protein, but saw a divergent result for the third donor. We were able to highlight potential senolytic targets. Our secretome analysis led us to propose additions to the senescence associated secretory phenotype, including HSP60, which we found on the surface of EVs. Moreover, EVs from senescent NOKs can create inflammation by stimulating interferon pathway signaling in THP-1 monocytes in culture. Our results highlight important senescence changes in epithelial cells in terms of how these cells contribute to chronic inflammation, aging, and age-related diseases.

overall_design: DNA-seq analysis of cellular senescence in normal human oral keratinocytes

first: Rachael

middle: E

last: Schwartz

first: Maxim

last: Shokhirev

first: Gerald

middle: S

last: Shadel


title: Gene expression modification in lungs of rats exposed to carbon nanotube by inhalation [Mitsui]

summary: In this work we study the pulmonary toxicological properties of Mitsui using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 13 week old female Sprague Dawley rats were exposed by inhalation to Mitsui (0.15 - 0.5 or 1.5 mg/m3). Mitsui-induced gene expression profile in rat lung was performed 3, 30 and 180 days post exposure (3 time points). Each time point is composed of 6 control, 6 exposed rats. A total of 72 samples (microarrays) was used.


title: Molecular correlates of vaccine-induced protection against typhoid fever

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

department: Oxford Vaccine Group, Department of Paediatrics

institute: University of Oxford

summary: Typhoid fever is caused by the Gram-negative bacterium Salmonella enterica serovar Typhi. Bulk RNA-sequencing (RNA-seq) data were generated from blood samples obtained from adult human volunteers enrolled in a vaccine trial involving two vaccines against typhoid fever, a plain polysaccharide vaccine, ViPS and a glycoconjugate vaccine, ViTCV. The participants were then challenged with S. Typhi in a controlled human infection model (CHIM).

overall_design: Whole blood RNA sequencing was performed using paired-end RNA sequencing. Blood samples were taken at several time points post-vaccination and post-challenge to monitor the changes in molecular signatures.

first: Irina

last: Chelysheva

first: Daniel

last: O'Connor


title: Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq]

status: Public on Jul 18 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. Collection of RNA-expression data from multiple PDX models was performed to generate a library of RNA-sequencing data which may be utilized to compare tumors from different subtypes or treatment groups.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ER+ and triple negative mammary tumors were grown orthopedically in mice for 8 weeks. Tumor cells from each PDX were profiled by bulk RNA-sequencing to determine differentially expressed genes and gene signatures between models with the goal of furthering the fields of oncogenesis, metastasis and drug resistance.

first: J

last: Harrell

first: Amy

last: Olex

first: Mikhail

last: Dozmorov

first: Julia

last: Altman

first: David

last: Boyd

first: Emily

last: Zboril


title: Forkhead Box F1 acts as a novel prognostic biomarker and induces caspase-dependent apoptosis in bladder cancer

first: Yining

last: Hao

state: Shanghai Municipality

address: No. 197 Ruijin Second Road, Huangpu District

institute: Shanghai Ruijin Hospital

summary: Down-regulated expression of Forkhead Box F1 (FOXF1) in malignant tumors were reported in several kinds of cancer before, but its role in bladder cancer (BC) was not clear. This study aims to demonstrate the prognostic value and of FOXF1 in BC patients. Here, a retrospectively recruited BC cohort and public datasets were utilized to identify the predictive ability of FOXF1 and its relationship between clinical information in BC patients. The expression level of FOXF1 is notably higher in BC tissues than para-cancerous mucosae. Low FOXF1 expression is correlated to unfavorable clinicopathological features and poor prognosis. Further, in bladder tumor cells, the expression levels of FOXF1 mRNA and protein were tested by quantitative real-time PCR and western blot. The viability of cells was examined by CCK-8, EdU, and clonogenic capacity assays. Cell apoptosis was detected by flow cytometry. We note that FOXF1 activating could impair cell viability and induce apoptosis in BC. Then, caspase 3 as a downstream gene of FOXF1 was spotted by RNA-Seq and PPI. The anti-tumor effect of FOXF1 were also validated in animal models. In conclusion, down-regulated FOXF1 expression is a potential independent indicator for unfavorable clinical outcomes of BC patients, FOXF1 inhibits BC cells proliferation and induces cell apoptosis via caspase signaling pathway. This study exhibits FOXF1 express pattern, demonstrates the prognostic predictive ability of FOXF1 and prove the anti-tumor mechanisms of FOXF1 in BC, it has reference value to clinical decision, activation FOXF1 expression could be used as a new strategy in tumor therapeutics.

overall_design: human bladder cancer cell line T24, FOXF1-activated and negative control, 3 replicates per group

first: Danfeng

last: Xu

first: Chenghe

last: Wang


title: Gene expression modification in lungs of rats exposed to DQ-12 by endotracheal instillation

first: Carole

last: Seidel

summary: In this work we study the pulmonary toxicological properties of cristalline silica DQ-12 using molecular toxicological approache. For this, we exposed Sprague Dawley rats by endotracheal instillation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 13 week old female Sprague Dawley rats were exposed by endotracheal instillation to DQ-12 (10 mg/rat). DQ-12-induced gene expression profile in rat lung was performed 1, 30 and 180 days post exposure (3 time points). Each time point is composed of 6 control,  6 exposed rats. A total of 36 samples (microarrays) was used.

first: Sarah

last: Valentino

first: Mylène

last: Lorcin

first: Sylvie

last: Sébillaud

first: Laurent

last: Gaté


title: Liquid Biopsy: Examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for molecular tumor markers

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

country: Germany

institute: University of Ulm

summary: The present study aims to clarify whether patients suffering from head and neck squamous cell carcinoma (HNSCC) could be recognized based on platelet mRNA sequencing (RNAseq). Sequencing analysis of RNA derived from platelets of tumor patients and healthy donors revealed significantly differentially expressed RNA encoding 618 genes. Among them, we identified RNA coding for 49 genes characteristically expressed in epithelial cells. Additionally, in tumor patient’s platelets we observed RNA coding for genes involved in tumor progression by contributing to proliferation, metastasis or angiogenesis. Furthermore, 41 non-coding RNAs involved in transcription and translation have been identified. Results were verified by quantitative RT-PCR on platelet RNA derived from a second tumor patient / healthy donor cohort. However, in order to identify a combination of a certain set of genes allowing the identification of HNSCC based on platelet RNAseq further research is necessary.

overall_design: 15 samples in total: 5 blood platelet of tumor patients, 5 blood platelet of healthy donors, 5 tumor tissue of patients

first: Lisa

middle: T

last: Huber

first: Johann

last: Kraus

first: Marco

last: Groth

first: Thomas

last: Hoffmann

first: Cornelia

last: Brunner


title: Haemophilus influenzae Outer membrane vesicles inhalation contributes to steroid-resistant asthma

city: Changchun

first: Ying

last: Zhang

state: Select...

address: 1 Xinmin Street

institute: Department of Pediatric Respiratory, The First Hospital of Jilin University

summary: Asthma is the most common chronic respiratory disease. Asthma that cannot be well controlled by steroid treatment is called steroid-resistant asthma. Steroid-resistant asthma accounts for only 5% of all asthma cases, but it accounts for 80% of asthma healthcare costs. Nontypeable Haemophilus influenzae (NTHi), as a Gram-negative bacterium, can release outer membrane vesicles (OMVs) and transfer biomolecules to host cells and the external environment by carrying lipopolysaccharides, proteins, peptidoglycans, outer membrane proteins, cell wall components, proteins, nucleic acids, ion metabolites, and signaling molecules. Thus, it plays a role in obtaining nutrition, stress, toxin delivery, adhesion, host immune surveillance evasion, and host immune response regulation. It becomes an essential way in bacterial pathogenesis. To further clarify whether NTHi OMVs could be inhaled to induce steroid-resistant asthma, we isolated and purified NTHi OMVs. In vivo experiments showed that NTHi OMVs could be inhaled and enter airway epithelial cells. Cosensitization with OVA induces steroid-resistant asthma in mice. Furthermore, through high-throughput sequencing, we found that the NTHi OMVs and OVA co-sensitized mice had significantly enriched inflammatory and immune-related signaling pathways, and the transcription and secretion of IL-1β were increased was the potential cause of SRA.

overall_design: mice were atomized with NTHi OMVs on day-10 and intraperitoneal injected with 50 μg OVA (Sigma) in 200 μL 0.9% saline on day 0. On days 12-15 of the experiment, mice in the OVA+NTHi OMVs group were given 15ml 2% OVA atomization, while mice in the Control group were given an equal amount of 0.9% saline atomization. Lung tissue was obtained for sequencing


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion (CUT&Tag)

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

summary: Persistent exposure to antigen during chronic infection or cancer renders T cells dysfunctional. The molecular mechanisms regulating this state of exhaustion are thought to be common in infection and cancer, despite obvious differences in their microenvironments. We discovered that NFAT5, an NFAT family member lacking an AP-1 docking site, is highly expressed in exhausted T cells responding to chronic infection and tumors but is a central player selectively in tumor-induced exhaustion. While NFAT5 overexpression in CD8+ T cells reduced tumor control, NFAT5 deletion improved tumor control by promoting the accumulation of tumor-specific CD8 T cells that expressed less TOX and PD-1 and produced more cytokines specifically among precursor exhausted cells. Conversely, NFAT5 did not promote T cell exhaustion during chronic infection. While NFAT5 expression was induced by TCR triggering, its transcriptional activity was specific to the tumor microenvironment and required hyperosmolarity. NFAT5 thus promotes CD8 T cell exhaustion in a tumor-selective fashion.

overall_design: NFAT5 KO cells were obtained from LN and spleen of CD4-Cre+/- NFAT5flox/flox mice. CD8 T cells were enriched by negative selection following the manufacturer’s protocol (Stemcell) and plated at 0.4 106 cells /24-well with anti-CD3/28 antibodies and 20U/mL IL-2 24h pre-transduction. Viral supernatants were supplemented with 20U/mL IL-2, Polybrene at 8ug/mL, and 0.5mL were added to the CD8 T cells. Cells were spun for 60min at 1800RPM at 32°C and incubated for 24h followed by a resting period of 24h were cells when taken off stimulation. To induce exhausted cells were passed on a new anti-CD3 coated plate every 2 days. After a total of three rounds of stimulation, CD8 T cells were sorted and processed for CUT&RUNseq

first: Daniela

last: Cropp

first: Joao

last: Lourenco


title: Synaptosome RNA and bulk RNA sequencing of Alzheimer's disease and control mouse frontal cortex tissue

city: Seattle

first: Paul

middle: Nils

last: Valdmanis

state: WA

address: 1705 NE PACIFIC ST.

department: Department of Medicine: Division of Medical Genetics

institute: University of Washington

summary: We measured RNA synaptic localization differences in human AD patient samples. We performed RNA sequencing to identify mislocalized coding and non-coding RNAs and contrasted findings with global expression differences in human frontal and temporal lobe tissue as well as an APP/PSEN1 AD mouse model. We discovered significant mRNA localization differences in AD tissue including upregulation of genes related to cell differentiation and adhesion, and downregulation of genes related to cellular component organization ion transport. In addition, we identified major differences among circular RNAs (circRNAs) localized to synapses. Among our data, we discovered two unique isoforms of circGSK3β that are differentially expressed in AD. Furthermore, we found that expression of these distinct isoforms affects tau phosphorylation in neural cell culture. These discoveries substantiate the importance of circRNAs in the brain and in neurodegenerative disease. Identifying differences in synaptic-localized mRNAs and circRNAs opens new avenues to understanding AD synaptic pathology and identifying potential therapeutic targets.

overall_design: Synaptosomes were prepared from mouse frontal cortex tissue homogenate including wild-type and the APP/PSEN1 transgenic Alzheimer's disease mouse model. Both isolated synaptosomes and bulk homogenate were RNA-sequenced.

first: Samuel

last: Smukowski

first: Eli

last: Kaufman


title: Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [ChIP-seq]

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

summary: We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique).Histone modifications analysis suggested there was histone modifications reprogramming in the B. napus hybrids compeared with parents.

overall_design: Comparative histone modifications (H3K4me3 and H3K27me3) analysis for HZ62 (seedling, flower bud and silique) and its parents.

first: Meng

last: Ma

first: Qing

first: Jinxiong

last: Shen


title: Cathepsin V is correlated with the prognosis and tumor microenvironment in liver cancer

first: wen

last: zhang

address: xiangyin road

institute: naval medical university

summary: Recent studies have shown that high cell cycle activity negatively correlates with antitumor immunity in certain cancer types. However, a similar correlation has not been proven in liver cancer.We downloaded transcriptomic profiles of TCGA-LIHC (the cancer genome atlas-liver hepatocellular carcinoma) and assessed the cell cycle distribution of samples using single sample gene set enrichment analysis (ssGSEA), termed the cell cycle score (CCS). We obtained cell cycle-related differentially expressed prognostic genes and identified CENPA, CDC20 and CTSV using LASSO regression. We studied the effect of CTSV on clinical features and immune alterations in liver cancer based on TCGA-LIHC data. In vitro and in vivo experiments were performed to validate the role of CTSV in liver cancer using liver cancer cell lines and tissues.We found that the CCS closely correlated with the clinical features and prognosis of patients in TCGA-LIHC. Analysis of differentially expressed genes (DEGs), univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression identified cathepsin V (CTSV) with prognostic significance in LIHC. Importantly, single-gene survival analysis of CTSV using microarray and sequencing data indicated that high levels of CTSV expression correlated with an unfavorable prognosis in various cancers. Gene set enrichment analysis (GSEA) revealed that high CTSV expression closely correlated with decreased expression of metabolic genes and increased expression of cell cycle genes. Furthermore, difference and correlation analyses of the relationship between CTSV expression and immune infiltrates, determined using CIBERSORT and TIMER algorithms, revealed that CTSV expression correlated with macrophages and CD4+ T cells. In vitro and in vivo experiments revealed that knockdown of CTSV inhibited liver cancer cells proliferation. Immunohistochemical staining showed that high CTSV expression correlated with macrophage infiltration in liver cancer tissues, predicted a poor prognosis, and may serve as a biomarker for HCC therapy.In conclusion, CTSV is a novel cell cycle prognostic gene that can affect HCC cells proliferation, and a potential biomarker for HCC therapy.

overall_design: To further validate our conclusion about  functions of  gene CTSV in liver cancer, we established Huh7 cell lines in which the target gene CTSV has been knocked down by shRNA and control cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at the same time points.Comparative gene expression profiling analysis of RNA-seq data for Huh7 cells(Con) and its KD derivatives (ShCTSV).

first: Junyu

last: Liu

first: Jin

last: Ding

first: Beifang

last: Ning


title: Gene expression modification in lungs of rats exposed to carbon black by inhalation

first: Carole

last: Seidel

summary: In this work we study the pulmonary toxicological properties of Printex using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.

overall_design: 13 week old female Sprague Dawley rats were exposed by inhalation to Printex (5, 15 or 50 mg/m3). Printex-induced gene expression profile in rat lung was performed 3, 30 and 180 days post exposure (3 time points). Each time point is composed of 6 control, 6 exposed rats. A total of 72 samples (microarrays) was used.

first: Sarah

last: Valentino

first: Mylène

last: Lorcin

first: Sylvie

last: Sébillaud

first: Laurent

last: Gaté


title: Extracellular matrix stiffness regulates microvascular stability by controlling endothelial paracrine signaling to determine pericyte fate

city: Qingdao

first: Dong

last: Wang

email: dongwang@qdu.edu.cn, dwang2100@163.com

address: 38 Dengzhou Road

institute: Qingdao University

summary: Background:  The differentiation of pericytes into myofibroblasts causes microvascular degeneration, extracellular matrix (ECM) accumulation, and tissue stiffening, characteristics of fibrotic diseases. It is unclear how pericyte-myofibroblast differentiation is regulated in the microvascular environment. Our previous study established a novel two-dimensional platform for coculturing microvascular endothelial cells (ECs) and pericytes derived from the same tissue. This study investigated how ECM stiffness regulated microvascular ECs, pericytes, and their interactions.  Methods: Primary microvessels were cultured in the TGM2D medium. Stiff ECM was prepared by incubating ECM solution in regular culture dishes for one hour followed by PBS wash. Soft ECM with Young’s modulus of approximately 6 kPa was used unless otherwise noted. Bone grafts were prepared from the rat skull. Immunostaining, RNA sequencing, qRT-PCR, western blotting, and knockdown experiments were performed on the cells. Results:  Primary microvascular pericytes differentiated into myofibroblasts (NG2+αSMA+) on stiff ECM, even with the TGFβ signaling inhibitor A83-01. Soft ECM and A83-01 cooperatively maintained microvascular stability while inhibiting pericyte-myofibroblast differentiation (NG2+αSMA-/low). We thus defined two pericyte subpopulations: primary (NG2+αSMA-/low) and activated (NG2+αSMA+) pericytes. Soft ECM promoted microvascular regeneration and inhibited fibrosis in bone graft transplantation in vivo. As Integrins are the major mechanosensor, we performed qRT-PCR screening of Integrin family members selected from RNA sequencing data. We found that Integrin β1 (Itgb1) was the major subunit downregulated by soft ECM and A83-01 treatment. Knocking down Itgb1 suppressed myofibroblast differentiation on stiff ECM. Interestingly, ITGB1 phosphorylation (Y783) was mainly located on microvascular ECs on stiff ECM, which promoted EC secretion of paracrine factors, including CTGF, to induce pericyte-myofibroblast differentiation. CTGF knockdown or monoclonal antibody treatment partially reduced myofibroblast differentiation, implying the participation of multiple pathways in fibrosis formation.  Conclusions: Microvascular ECs mediate ECM stiffness-induced pericyte-myofibroblast differentiation through paracrine signaling.

overall_design: to investigate the effect of stiffness and TGFβinhibitor A83-01 on microvessels and pericyte-myofibroblast differentiation


title: Global transcriptional response to electron acceptors AKB and pyruvate in K562 cells

city: Haining

first: Mikael

last: Bjorklund

state: Zhejiang

address: 718, Haizhoudong Road, Xiashi Street

institute: Zhejiang University-University of Edinburgh Institute

summary: We report the effects of two metabolites alpha-ketobutyrate and pyruvate on transcription of K562 cells. Increased cell size associates with electron acceptor limitation. Using four replicates per condition, we find that electron acceptors alleviate endoplasmic reticulum stress response in these cells as evidenced by reduction of amino acid transporter as well as ATF4 and CHOP expression.

overall_design: mRNA proflies of K562 cells treated with alpha-ketobutyrate, pyruvate compared to untreated control cells

first: Yuchen

last: Cheng


title: Single cell RNAseq of murine gliomas induced by PDGFB overexpression

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

summary: Glioblastoma progression remains elusive, especially in its first stages. Here, by simultaneous transfer of PDGFB and genetic barcode in mouse brain, we triggered gliomagenesis in univocally labelled cells in vivo, hence enabling direct tracing of glioblastoma evolution from the earliest possible stage. We observed an unexpectedly high incidence of clonal extinction events and progressive clonal size divergence, even after the acquisition of a malignant phenotype. Computational modelling suggests these dynamics as the consequence of a clonal-based cell-cell competition. Bulk and single-cell transcriptome analyses, coupled to lineage tracing, revealed that the strongest correlation with clonal size unbalancing is shown by Myc transcriptional targets. Additionally, higher levels of Myc signalling discriminate "winner" from "loser" clones in early gliomagenesis. These results agree with recent understanding of the Myc-mediated induction of supercompetitive phenotype in mammalian embryo. Our findings shed light on aspects of glioblastoma evolution inaccessible by conventional retrospective approaches and highlight the potential of the combined use of clonal tracing and transcriptomic analyses in this field.

overall_design:
Gliomas induced by in-utero somatic gene transfer of PDGFB in embryonic telencephalic ventricles were collected at about 40 days from the birth. Tumor masses were dissociated, tumor cells were enriched by FACSorting exploiting the GFP expression.
The resulting samples were pooled two by two prior to 10X partitioning.

first: Davide

last: Ceresa

first: Irene

last: Appolloni


title: Effect of Cell-Adhesive Nanofibril on 3D spheroid hepatic differentiation-related gene expression

status: Public on Jul 17 2023

city: Chuncheon-si

first: Kim

last: Wijin

address: Kangwondaehak-gil

institute: kangwon national university

summary: To investigate the effect of Cell-Adhesive Nanofibril on the hepatic differentiation process of 3D iPSC spheroids, we established hepatic organoids that underwent a stepwise hepatic differentiation process with or without Cell-Adhesive Nanofibril.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of hepatic organoids subjected to stepwise hepatic differentiation with and without Cell-Adhesive Nanofibril.

first: Jinhee

last: Park

first: Ju-Hyun


title: Bulk RNAseq of murine gliomas driven by overexpression of PDGFB

overall_design:
Gliomas obtained by in-utero somatic gene transfer of PDGFB in embryonic telencephalic ventricles.
Bulk mRNAseq of 12 PDGFB-driven mouse gliomas, at different times after PDGFB transduction. Cells were obtained ex-vivo after brain dissociation and FACS-sorting. Both glioma (marked by expression of fluorescent proteins) and glioma-surrounding (negative for endogenous fluorescence) cells were collected by FACSorting.


title: IL-12 Virotherapy Induces Immune Equilibrium in Melanoma That is Overcome by Blockade of Innate Inflammatory Cytokine

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: Viral vectors deliver therapeutic cargo with the natural adjuvant effect of a pathogen. We engineered a non-replicating herpes simplex virus 1, d106S-IL12, to deliver IL-12 to the tumor microenvironment, resulting in a type I interferon response, rapid production of T cell recruiting chemokines, and accumulation of melanoma-specific CD8 T cells. We immunologically defined a long-term, stable immune equilibrium, whereby mice neither succumbed nor fully cleared their tumors. We profiled the immune equilibrium induced by d106S-IL12, identifying blockade of innate inflammatory cytokines, TNFα, IL-1β, or IL-6 as possible synergistic interventions. Single-cell RNA-sequencing demonstrated that d106S-IL12 induced a loss of Tregs and a shift towards Th1 responses, while blockade of inflammatory cytokines repolarized macrophages towards a less suppressive phenotype. Blockade of each cytokine resulted in downregulation of overlapping inflammatory pathways, shifting immune equilibrium towards tumor clearance. These results suggest targeting innate inflammatory cytokines could enhance immunotherapy efficacy while potentially mitigating toxicity.

overall_design: CD45+ cells were sorted by FACS from B16-Nectin1 melanoma tumors inoculated into C57BL/6 mice that had received one of the following intratumoral treatments: PBS, TNF⍺ blockade, IL6R blockade, IL1β blockade, d106S virus, d106S-IL12 virus, or d106S-Il12 virus in combination with blockade of TNF⍺, IL6R, or IL1β.

first: Michael

middle: J

last: Walsh

first: Lestat

last: Ali

first: Patrick

last: Lenehan

first: David

last: Knipe


title: Conserved transcriptomic signatures and protein markers in cellular senescence models

city: Zografou

first: Dionysia

last: Skea

address: Zografou Campus, 9, Iroon Polytechniou str

country: Greece

institute: NTUA

summary: Cellular senescence is described as an irreversible cell cycle arrest induced in response to various stresses. Senescent cells are characterised by heterogeneous signalling alterations, complex secretory phenotype, known as senescence-associated secretory phenotype (SASP), and diverse transcriptomic profile. With the aim to investigate senescence heterogeneity and identify conserved transctiptomic alterations and universal senescence markers, we performed RNA-seq and multiplex proteomic analysis in proteasome inhibition-induced and stress-induced premature senescence models of HFL1 and BJ human fibroblasts. Our data revealed diverse transcriptomic signatures, but also, 231 common differentially expressed genes related to cell division and ECM remodelling, and enriched pathways that remained conserved among the different models with senescence onset. Moreover, we identified a subset of proteins and validated them in replicative senescent models. These proteins are involved in cell cycle arrest and promote a pro-inflammatory environment in premature and replicative senescence models. We suggest that the simultaneous analysis of p21, p-c-JUN, BCL-xL and survivin in cellular lysates, and IL-8, GM-CSF, GDF-15 and GROa in culture supernatants can provide a powerful tool for the identification and monitoring of senescent cells and can support the assessment of the efficacy of potential senotherapeutic approaches.

overall_design: Comparative gene expression profiling analysis of proteasome-inhibition-induced and stress-induced premature senescent HFL1 and BJ cells versus their respective untreated proliferating control cells.

first: Christos

last: Fotis

first: Nikos

last: Tsolakos

first: Vicky

last: Pliaka

first: Kleio-Maria

last: Verrou

first: Leonidas

last: Alexopoulos


title: Transgenic pig over-expressing leptin as a model for female infertility

city: Jinan

first: Rusong

last: Zhao

state: Shandong

address: 44 Wenhua xi Road

department: Center for Reproductive Medicine

institute: Shandong University

summary: Infertility is a growing global health concern affecting millions of couples worldwide. Both overweight and underweight individuals face reproductive issues, resulting in infertility. Due to small size and short life, mice are not necessarily suitable animal models for human infertility. While, pigs having large size, anatomical and physiological similarities with human are considered as more ideal animal model of human disease. Leptin is a well-known adipokine that serves as an endocrine signal between adiposity and fertility. However, the exact mechanisms underlying leptin's effects on reproductive function remain unclear. To shed light on this, our study focused on pigs genetically engineered to overexpress leptin. These leptin-overexpressing pigs exhibited several reproductive abnormalities, including reduced body weight and size, decreased back fat thickness, and displayed late onset of puberty, and irregular estrous behavior characterized by increased inter-estrous interval and more breeding attempts until pregnancy. This reproductive impairment in leptin pigs was followed by hormonal imbalances and altered steroidogenesis. Bulk RNA sequencing of the ovaries revealed neutrophilic infiltration followed by upregulation of inflammation related genes. To gain a deeper understanding of the cellular levels, we employed single-nucleus RNA sequencing (snRNA-seq), and found that leptin overexpression triggered immune response, suppressed follicle development and luteinization, imposing metabolism dysfunction and hormone imbalance in ovary. Further, trends of phenotypical infertility symptoms and endocrine changes in underweight female patients mirrored the alterations observed in our leptin pigs. These findings suggest that leptin-overexpressing pigs could serve as a valuable animal model for studying infertility and investigating potential therapeutic interventions.

overall_design: Leptin overexpressed pig (C013) was re-cloned and the cloned offspring (♂) were mated with the Duroc/Landrace/Yorkshire sow (DLY, ♀) to obtain the F1 generation, and then the F1 generation was further crossed to obtain the F2 generation. The offspring (F2-generation) with leptin overexpression were then screened out by PCR, qPCR, and immunoblotting, etc. The body weight, body size and estrus of leptin overexpressed sows and control group were monitored. The changes in body weight and body size were plotted, and the pubertal onset and inter-estrous interval were calculated. The breeding efficiency of leptin overexpressed sows was explored by mating with fertile male and pregnancy was monitored. The serum profile of reproductive hormones was evaluated using radio immune assay (RIA) and enzyme linked immunosorbent assay (ELISA). Next, the ovaries of leptin and control sows were collected and protein abundance and mRNA expression of steroidogenic enzymes and apoptotic markers were evaluated at tissue and cell levels. Meanwhile, the back fat thickness of leptin overexpressed sows was measured by ultrasonography and serum levels of circulating fatty acids were measured by gas chromatography. Finally, the ovarian samples were sent for the transcriptomic profiling.

first: Yixiao

last: Chen

first: Hongjiang

last: Wei

first: Hongye


title: EZH2 mutants in isogenic cell lines

city: Columbus

first: Julian

last: Aldana

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

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

overall_design: Refer to individual Series


title: RNA-Seq analysis of EZH2 mutants in isogenic cell lines

summary: The Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2) is an essential epigenetic modifier able to methylate lysine 27 on histone H3 (H3K27) to induce chromatin compaction, protein complex recruitment and ultimately transcriptional repression. Hematologic malignancies, including Diffuse Large B cell lymphoma (DLBCL) and Acute myeloid leukemia (AML) have shown a high EZH2-mutation frequency (>20%) associated with poor clinical outcomes. Particularly, two distinct oncogenic mutations, so-called gain-of-function (Y641F and A677G) and loss-of-function (H689A and F667I) are found in the catalytic domain of EZH2. In this study, a comprehensive multi-omics approach was employed to characterize downstream effects of H3K27me3 deposition driven by EZH2 mutations. Human embryonic kidney cells (HEK293T) were transfected to generate three stable EZH2 mutants: EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I), which were validated via immunoblotting and DIA-MS-based histone profiling assay. Subsequently, constructs were analyzed under a comprehensive multi-omics approach including: 1) Cleavage Under Targets and Tagmentation (CUT&Tag); 2) chromatin accessibility characterization using the assay for transposase-accessible chromatin with sequencing (ATAC-Seq); 3) transcriptomics (RNA-Seq); 4) label-free whole-cell proteomics, acquired with a Bruker timsTOF Pro HPLC-MS/MS with Ion Mobility, and 5) MS-based untargeted metabolomics, in positive and negative ionization MS/MS mode, acquired with an Agilent 6545 QTOF with a 1290 UHPLC system and HILIC column. Total coverage comprised over 21,000 chromatin regions, 18,000 transcripts, 6,000 proteins and 400 metabolic features. Pair-wise comparison using univariate and supervised multivariate statistical methods revealed significant differences between constructs in each omic level. Furthermore, effector pathway analysis combining omics data revealed distinctive reprogramming effects for each EZH2 mutant.

overall_design: Gene expression profiling analysis was performed via RNA-Seq in a set of stable transfected HEK293T cell lines with EZH2 mutants, including EZH2(WT), EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I) to investigate the effects of common single point mutations in the active site of EZH2.


title: Heterogenity of memory CD4 T cells

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

summary: Analysis of single cell gene transcription by mouse influenza virus specific CD4 T cells examined 40 days after infection.

overall_design: 4 TRACE reporter mice, that enable identification of memory T cells by EYFP expression, were infected with influenza A virus (WSN) intranasally. After 40 days, the mice were injected with fluorescently labelled anti-CD45-PE to enable exclusion of memory CD4 T cells within the blood. Lung and spleen CD4 cells were isolated using magnetic beads and then co-cultured with bone marrow dendritic cells presenting influenza virus antigens. After 4 hours, the cells were stained with surface antibodies and AbSeq tagged anti-ICOS and anti-PD1 antibodies. EYFP+ memory CD4 T cells from the spleen and lung and naive (EYDP negative CD44low) CD4 from the spleen were FACS sorted and analysed by BD Rhapsody scRNAseq for gene expression (targeted) and CDR3 sequence of T cell receptors.

first: MacLeod

last: Megan

first: Noonan

last: Jonathan


title: Side-population trophoblasts from first and third trimester pregnancies

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

type:
Expression profiling by array
Third-party reanalysis

summary: Gene expression microarrays investigating the transcriptome of matched populations of human side-population trophoblasts and cytotrophoblasts isolated from first and third trimester placentae

overall_design: Publically available .cel files of matched first trimester side-population trophoblasts and cytotrophoblasts were downloaded from NCBI GEO (GSE57834). The first trimester data was compared to healthy third trimester control samples (GSE123551).

last: Fan

first: Jasper

last: Perry

first: Lawrence

last: Chamley

first: Joanna

last: James


title: Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [RNA-seq]

first: Wenying

last: Zhong

summary: We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique). Transcriptome analysis suggested that gene expression level altered in hybrids compared with parents.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HZ62 (seedling, flower bud and silique) and its parents.

first: Meng

last: Ma

first: Qing

last: Zhang

first: Jinxiong

last: Shen


title: H3K27me3 CUT&Tag analysis of EZH2 mutants in isogenic cell lines

overall_design: Genome-wide analysis of H3K27me3 via Cleavage Under Targets and Tagmentation (CUT&Tag) in a set of stable transfected HEK293T cell lines with EZH2 mutants, including EZH2(WT), EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I) to investigate the effects of common single point mutations in the active site of EZH2.


title: Early rotarod training aggravates injury and impairs functional recovery after spinal cord injury

city: Beijing

first: Junhao

last: Deng

state: Beijing

address: Fuxing Road,  Beijing, 100853, People’s Republic of China.

institute: Chinese PLA General Hospital

summary: Mice with rotarod training showed significant differences in the expression of trophic factors and cytokines, histological repair, and functional recovery when compared with the mice without training. To exlore the potential mechanism, we applied the next-generation sequence to compare the transcriptome profile between two groups. We found that there were 1299 DEGs between two groups with 586 upregulated genes and 713 downregulated genes. GO enrichment analysis revealed that DEGs, especially the downregulated genes, were primarily associated with revascularization biological process like angiogenesis, regulation of vasculature development, regulation of angiogenesis, and cellular component including postsynapse, neuron to neuron synapse, etc. On the other hand, KEGG pathway analysis showed that those significantly altered genes, also downregulated DEGs in particular, were mainly enriched in the PI3K-Akt signaling pathway.

overall_design: Explore the gene expression profile between mice with or without rotarod training after SCI. Mice were randomly assigned to two groups: SCIT (mice with rotarod training) and SCI (mice without rotarod training).

first: Deng

last: Junhao

last: Fanqi

first: Zhang

last: Licheng

first: Tang

last: Peifu


title: ATAC-Seq analysis of EZH2 mutants in isogenic cell lines

last: Aldana

overall_design: Genome-wide analysis of chromatin accesibility was performed via via Assay for Transposase-Accessible Chromatin with sequencing (ATAC-Seq) in a set of stable transfected HEK293T cell lines with EZH2 mutants, including EZH2(WT), EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I) to investigate the effects of common single point mutations in the active site of EZH2.


title: A Population of Tumor-Infiltrating CD4+ T-cells Co-expressing CD38 and CD39  is Associated with Checkpoint Inhibitor Resistance

city: Aurora

first: Ann

last: Strange

state: CO

address: 12801 E. 17th Ave, 8th floor

department: Division of Medical Oncology

institute: CU Anschutz

summary: We previously showed that elevated peripheral blood frequencies of a population of T-cells defined by the marker set CD3+CD4+CD127-GARP-CD38+CD39+ were associated with checkpoint immunotherapy resistance in metastatic melanoma patients. In this study we sought to further understand the role(s) of this population of ectoenzyme expressing T-cells (Teee). Using RNA-sequencing and flow cytometry to evaluate Teee from the peripheral blood of metastatic melanoma patients, we found that Teee were proliferative, apoptotic, had exhaustion associated phenotypes, and had high expression of inhibitory molecules. Co-culture of patient Teee with autologous T-cells in vitro resulted in suppression of proliferation of the target T-cells. Using single-cell RNA-sequencing datasets, we identified distinct clusters of cells with a Teee gene signature present in melanoma, non-small cell lung cancer and bladder cancer patients’ tumors. Teee were not present in healthy bladder tissue. Using multispectral immunofluorescence of melanoma patient FFPE tumor samples, we were able to identify CD4+ T-cells co-expressing CD38 and CD39 in the tumor microenvironment, which preferentially associated with Ki67- CD8+ T-cells. Finally, we found that high baseline intra-tumor frequencies of cells with a Teee gene signature were associated with checkpoint immunotherapy resistance and poor overall survival in metastatic melanoma patients. These results build upon our previous findings, demonstrating that a novel population of CD4+ T-cells co-expressing CD38 and CD39 are found in the periphery and tumor of patients and are associated with checkpoint immunotherapy resistance.

overall_design: In this study we sought to address the roles of Teee in immunotherapy resistance by investigating their phenotype contrasted against CD38/CD39 single positive populations, determining their presence in the microenvironment of various solid tumors, and evaluating the relationship of intra-tumor Teee to immunotherapy resistance.   Cryopreserved peripheral blood mononuclear cells (PBMCs) were obtained from previously collected baseline samples (i.e. prior to start of therapy) as part of the clinical studies S15-00906 (NCTS15-00906), MCC15400 (NCT0117646122), CA209-064 (NCT0178393823) and MCC15651/ (NCT011764745).  RNAseq analysis was performed.

first: Ankita

last: Mitra

first: Brian

last: Thompson

first: Carol

middle: M

last: Amato

first: Igor

last: Dolgalev

first: Jonathan

last: Hester-McCullough

first: Amrutesh

last: Puranik

first: Tomoaki

last: Muramatsu

first: Diana

last: Kimono

first: Melinda

last: Vassallo

first: Jeffrey

last: Weber

first: David

last: Woods


title: CD4 Polarized T cells Reduce the Expansion of Tumor Infiltrating Lymphocytes in Melanoma Patients Treated with Adoptive Cell Therapy [RNA-seq]


summary:
Background: Adoptive cell therapy (ACT) with tumor infiltrating lymphocytes (TIL) is effective in treating PD-1 refractory melanoma, but requires adequate ex vivo expansion of TIL.
Methods: CD4+ and CD8+ TIL from metastatic melanoma patients treated with TIL ACT were analyzed by RNA-seq (n=12) and ChIP-seq of acetylated histone 3 (n=19). Patients were grouped into “TIL high” and “TIL low” based on division at the median number of TIL infused. The number of TIL infused and CD4+ TIL frequency were correlated with overall survival (OS).
Results: The number of TIL infused correlated with longer OS (R2=0.57, p=0.00076), and the percent of CD4+ infused was negatively correlated with the total number of TIL infused (R2=0.64, p=0.00047). RNA-seq analysis of CD4+ TIL showed increases in Th2/Th17/Treg transcripts and pathways in the TIL low group. ChIP-seq analysis of CD8+ TIL showed decreased acetylation in the TIL low group in genes upregulated during CD8+ activation.
Conclusion: The numbers of TIL infused were associated with increased overall survival, while RNA-seq suggested that polarized CD4+ cells in the transferred TIL were associated with decreased overall expansion. These data suggest that improper CD4+ TIL polarization may reduce expansion and treatment efficacy.

overall_design: Multi-omic analysis of tumor infiltrating lymphocytes expanded from melanoma patients enrolled in clinical trials NCT01005745, NCT01659151 and NCT01701674 for the treatment of melanoma. Anlyses include RNA-seq, panH3ac ChIP-seq and DNA methylation microarray. No healthy controls are included in the study design. Experimental design involved comparison of patients with high TIL expansion vs those with low TIL expansion.

first: Amod

last: Sarnaik


title: CD4 Polarized T cells Reduce the Expansion of Tumor Infiltrating Lymphocytes in Melanoma Patients Treated with Adoptive Cell Therapy [ChIP-seq]

first: Caro


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [8K and 8L]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (8K_200319, 8L_201001, 8L_201008).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [9A, 9B, 9C]

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (9A_190702, 9A_190709, 9B_190326, 9B_190404, 9C_190530).


title: Cathepsin W restrains peripheral regulatory T cells for mucosal immune quiescence

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

summary: To investigate the molecular mechanisms of how CTSW regulates pTreg cells generation and function, we performed mRNA sequencing and found a set of genes regulated by Foxp3 was differentially expressed in CTSW-deficient compared to control pTreg cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pTreg cells from WT and CTSW KO mice


title: Modulation of Amhr2 in mouse and human mesothelial cells

status: Public on Jul 16 2023

city: Bosotn

first: Maeva

middle: Yvette

last: Chauvin

address: 55 fruit st

institute: Massachusetts General Hospital

summary: Amhr2 is as a specific biomarker for mesothelial cells. In this study, we investigated the impact of Amhr2 modulation on gene expression by overexpressing it in Met5a cells, a human mesothelial cell line. Additionally, we assessed the transcriptomic profile of tumor growth in Amhr2 knock-out mice. These experiments shed light on the role of Amhr2 in mesothelial cell function and its potential implications in tumor development

overall_design: Bulk RNA sequencing of Met5a cells, overexpressing two variants of the Amhr2 receptor: Amhr2-V3(V3), which is an inactive receptor, and Amhr2-V1(V1), which is an active receptor. Bulk RNA sequencing of mouse KPCA tumors derived from wild-type mice (CON) (C57BL6J), Amhr2 heterozygous (Het) and Amhr2 knock-out mice (KO). This dataset compare the genes expression profiles between these two groups.

first: David

last: Pépin


title: The role of IL-6 and IL-27 signalling on virus specific CD4 T cell responses during LCMV Cl13 infection

status: Public on Jul 15 2023

city: London

first: James

last: Harker

address: SAF Building, South Kensington

department: NHLI

institute: Imperial College London

summary:
LCMV Clone 13 is an arenavirus that results in a persistent viral infection in mice when delivered intravenously. It has been widely used to explore the impact of chronic viral infection on CD4 T cell responses and dissect mechanisms that regulate this.
In this study we used mixed bone marrow chimeras from wildtype and cytokine reeptor deficient (gp130 or IL-6/IL-27R) mice to determine the role these cytokines on splenic CD4 T cell responses 30 days post infection

overall_design: Mixed bone marrow chimeras of CD45.1+ wildtype and CD45.2+ receptor deficient (either gp130 or IL-6/IL-27R deficient) cells were intravenously administed to irradiated WT mice. 8 weeks later mice were infected with LCMV Clone 13 intravenously. 30 days post infection the spleen was isolated and CD45.1+ and CD45.2+ PD1+CD4+ T cells (for gp130 study) or CD45.1+ and CD45.2+ TFH (for IL-6R/IL-27R study) were FACS isolated. RNA was extracted and transcriptomics performed.

first: Elina

middle: I

last: Zuniga


title: Gene analysis in pTreg cell generation

summary: To identify the potential regulators which are critical for pTreg cell generation, we differentiated naïve CD4+ T cells with or without TGF-b stimulation for 72 h and subjected them to mRNA sequence.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pTreg cell differentiation with or without TGF-b


title: Next-Generation Sequencing of Usp7 Overexpression and Knockdown Female Germline Stem Cells (FGSCs) Transcriptomes

city: Shanghai

first: Ji

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Next-generation sequencing (NGS) was performed to analyze the usp7 effects on FGSCs.

overall_design: mRNA profiles of usp7 overexpression FGSCs, usp7 overexpression FGSCs control, usp7 knockdown FGSCs and usp7 knockdown FGSCs control.

first: Yongqiang

last: Zhao


title: Integrated lncRNAs and mRNAs sequencing reveals lncRNAs regulatory network associated with lung injury in LPS-induced septic shock rats

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: Sepsis is associated with increased morbidity and mortality. Long non-coding RNAs (lncRNAs) have been associated with human diseases. Here, we used a microarray to analyze lncRNAs and mRNAs expression and functional network of lung injury in lipopolysaccharide (LPS)-induced septic shock rats.

overall_design: We established an LPS-induced septic shock model in rats. High-throughput sequencing was performed on the lung tissue to identify differentially expressed (DE) lncRNAs and mRNAs. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis was used to verify the microarray data. Gene Ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to investigate the biological functions. Establishment of coding and non-coding co-expression (CNC) and competing endogenous RNA (ceRNA) were performed to study the molecular interactions of these molecules.

first: Yanli

first: Ruo-Lan

last: Xiang

first: Xinlun

last: Tian

first: Kai-Feng

last: Xu


title: Relapsed atypical teratoid/rhabdoid tumors (AT/RT) reveal distinct features of progression on histology, epigenetics, copy number profiling, and transcriptomics

city: Hamburg

first: Lea

last: Altendorf

address: Martinistraße 52

institute: Universitätsklinikum Hamburg-Eppendorf

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Refer to individual Series


title: Relapsed atypical teratoid/rhabdoid tumors (AT/RT) reveal distinct features of progression on histology, epigenetics, copy number profiling, and transcriptomics [DNA methylation]

type: Methylation profiling by genome tiling array

summary: Here, we investigated tumor tissue from 26 patients affected by AT/RT to identify signatures of recurrences in comparison to matched primary tumor samples.

overall_design: Bisulphite converted DNA from the 56 samples were hybridised to the Illumina Infinium HumanMethylation450 or MethylationEPIC Beadchip

first: Pascal

middle: D

last: Johann

first: Emma

last: Efremova

first: Till

last: Holsten

first: Mona

last: Steinbügl

first: Karolina

last: Nemes

first: Alicia

last: Eckhardt

last: Bockmayr

first: Arend

last: Koch

first: Christine

last: Haberler

first: Manila

last: Antonelli

first: John

last: DeSisto

first: Martin

middle: U

last: Schuhmann

first: Peter

last: Hauser

first: Reiner

last: Siebert

first: Marcel

last: Kool

first: Adam

last: Green

last: Hasselblatt

middle: C

last: Frühwald

first: Ulrich

last: Schüller


title: Relapsed atypical teratoid/rhabdoid tumors (AT/RT) reveal distinct features of progression on histology, epigenetics, copy number profiling, and transcriptomics [RNA-seq]

first: Lea

last: Altendorf

summary:
Here, we investigated tumor tissue from 26 patients affected by AT/RT to identify signatures of recurrences in comparison to matched primary tumor samples.
Therefore, we performed histological analysis and DNA methylation and gene expression profiling.

overall_design: Bulk RNA sequencing data from the 26 samples were generated using Agilent technologies.

last: Johann

last: Efremova

last: Holsten

first: Michael

middle: L


title: H3K27Ac modification and gene expression in psoriasis

city: Ramat Gan

first: Dror

last: Avni

address: Derech Shiba, 2

department: Department of Medicine C

institute: Weizmann InstituteSheba Medical Center -Tel Hashomer

summary: Applying ChIP-seq with anti-acetylation of lysine 27 on Histone 3 (H3K27Ac), we report high-throughput profiling of H3K27Ac in human skin biopsies taken from psoriasis patients, both from the lesion and from adjacent non-lesion skin, and from skin biopsies from healthy match volunteers, in term of age, gender, and the biopsies place in the body. From each group we had 4 samples.   There is a clearly different H3K27 acetylation patterns in psoriatic skin compared to uninvolved or healthy volunteer skin. in many of the most over express genes in psoriasis lesion, there is enrichment of H3K27Ac. However, loss of acetylation on H3K27 is not part of the biochemical mechanism by which gene expression is decreased in psoriatic skin.  Finally, we show Many of the over express genes in psoriasis lesion, that also were enriched with H3K27Ac harbor a putative GRHL transcription factor binding site.

overall_design: ChIP-seq with anti H3K27Ac and mRNA array was applied on skin biopsies from psoriasis patients, both from the lesion and from adjacent non-lesion skin. in parallel to skin biopsies from healthy match volunteers.

first: Moamen

last: Masalha


title: Single-cell RNA-seq analysis of IDH-wildtype glioblastoma in radiation time course

city: Cleveland

first: Jeongwu

last: Lee

state: OH

address: 9500 Euclid Ave

department: Cancer Biology

institute: Lerner Research Institute, Cleveland Clinic

summary: To understand the diversity of expression states in irradiated GBM cells, we profiled about 150,000 single cells from 3 patient-derived GBM cells by single-cell RNA sequencing (by 10X Genomics).

overall_design: Patient-derived GBM cells treated with 10 Gy in vitro irradiation were sorted into single cells, and profiled by 10X.

first: Hyemin

last: Jeon


title: Fabry nephropathy transcriptome

city: Bergen

first: Oystein

last: Eikrem

address: Haukelandsveien 22

department: Department of Mecine

country: Norway

institute: Haukeland University Hospital

summary: Fabry nephropathy (FN) is a rare disorder caused by mutations in the alpha-galactosidase A gene. In this study we aim at providing a framework allowing selection of biomarkers and drug-targets. Two independent Fabry Nephropathy cohorts (FA.NO and CH.RO) were subjected to RNAseq from archival kidney biopsies taken prior and up to 10 years of Enzyme Replacement Therapy. Four compartments were laser capture microdissected (glomeruli, proximal tubuli, distal tubuli and arteries). We found several pathways that were consistently altered and that these kidney compartments’ transcriptional landscapes can be leveraged in the search for drug-targets and biomarkers.

overall_design:
RNAseq of lasermicrodissected (LCM) baseline and follow-up kidney biopsy compartments in Fabry Disease
*** Submitter declares that, based on Norwegian legislation, submission of the raw-data files is not allowed. These can be made available upon request after individual ethics appliaction to the local IRB and after approval of the Data protection officer. ***

first: Nicolas

last: Delaleu

first: Hans-Peter

last: Marti