title: Circulating microRNAs in patients with aneurysmal dilatation of coronary arteries

status: Public on Mar 18 2022

city: Poznań

first: Tomasz

middle: P.

last: Lehmann

address: Święcickiego 6

institute: Poznan University of Medical Sciences

summary: To understand the mechanism of coronary artery aneurysmal dilatation, we identified and compared the expression of circulating miRNAs in three groups of patients. Group 1 enrolled patients with aneurysmal dilatation of coronary arteries (n = 20), Group 2 included patients with angiographically confirmed coronary artery disease (CAD), whereas Group 3 included 20 patients with normal coronary arteries. The miRNAs were isolated from plasma and profiled using PCR arrays miRCURY LNA Serum/Plasma Focus PCR Panels. We demonstrated that the plasma miRNAs levels were significantly different in Group 1 in collation with Group 2 and Group 3 (fold change > 2 and p < 0.05). The comparison of Group 1 with Group 3 identified twenty-one significantly up-regulated and two down-regulated miRNAs in patients with aneurysmal coronary artery dilatation compared to the control groups. Moreover, we identified six up-regulated and two down-regulated miRNAs in patients with CAD compared to the controls. The third comparison revealed four up-regulated and three down-regulated miRNAs in Group 1, when compared to CAD patients. In conclusion, this study demonstrates the specific signature of plasma miRNA, namely up-regulated and down-regulated, in patients with abnormal dilatation of coronary arteries and the comparison between the groups consisting of atherosclerotic and control patients.

overall_design: qPCR of circulating miRNA expression profiling. Plasma samples have been collected and analysed for 3 groups of donors : 1 - patients with aneurysmal dilatation of coronary arteries, 2 - patients with angiographically confirmed coronary artery disease, 3 - patients with normal coronary arteries (control) as described with more detailes in the summary.

first: Sylwia

last: Iwańczyk

first: Artur

last: Cieślewicz

last: Radziemski

first: Katarzyna

last: Malesza

first: Michał

last: Wrotyński

first: Paweł

last: Jagodziński

first: Marek

last: Grygier

first: Maciej

last: Lesiak

first: Aleksander

last: Araszkiewicz


title: Esrrb Regulates Specific Feed-Forward Loops to Transit from Pluripotency into Early Stages of Differentiation

status: Public on Mar 21 2022

city: Barcelona

first: Ana

last: Sevilla

state: ESP

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

country: Spain

institute: Universidad de Barcelona

summary: Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to be crucial for embryonic stem (ES) self-renewal maintenance and cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these state transitions remain elusive. Here we describe the dynamic transcriptional regulatory circuitry of ES cells that incorporate protein-coding and miRNA genes based on microRNA array expression and quantitative sequencing of short transcripts upon the downregulation of the Estrogen Related Receptor Beta (Esrrb). The data reveals how Esrrb, a key stem cell transcription factor, regulates a specific ES cell miRNA expression program and integrates dynamic changes of feed forward loops contributing to the exit of the pluripotency state upon its downregulation. Together these findings provide new insights on the architecture of the combined transcriptional post-transcriptional regulatory network in stem cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Total of 12 murine embryonic stem cell line with controllable Esrrb expression (Esrrb_R) samples; Esrrb day0, Esrrb kd day1, Esrrb kd day3 and Esrrb kd Day5; all performed in triplicates
Please note that the common reference pool includes samples s1 to s3;
s1: Esrrb Day0 Rep1
s2: Esrrb Day0 Rep2
s3: Esrrb Day0 Rep3

first: Amin

last: Mazloom

first: Huilei

last: Xu

first: Jaume

middle: J

last: Reig

last: Vasileva

first: Avi

last: Ma’ayan

first: Ihor

middle: R

last: Lemischka


title: Genome-wide maps of chromatin state in mouse and human glioblastoma cells

status: Public on Mar 20 2022

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We had performed the ATAC-seq in mouse and human glioblastoma stem cells to understand the epigenetic regulation of glioblastoma stem cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of chromatin openess in mouse and human glioblastoma stem cells

first: Linxuan

last: Zhao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Drosophila larval Wild Type and TFAM RNAi (r4-gal4>TFAM RNAi) Fat body Transcriptomes

status: Public on Mar 19 2022

city: Calgary

first: Savraj

last: Grewal

state: Alberta

address: 3330 Hospital Drive

country: Canada

institute: University of Calgary

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this RNA-Seq is to analyze the transcriptomes from wild type and TFAM RNAi fat body samples at 96 hr AEL (after egg laying) and to identify the differentially expressed genes.
Methods: Drosophila larval fat bodies were isolated from wild type and TFAM RNAi (r4-gal4) animals at 96 hrs AEL (after egg laying) of development.  mRAN profiles were generated by Next Generation Sequencing Facilities.
Results: RNA Seq differential expression analysis identified a significant change in 1758 transcripts, with 1213 transcripts showing reduced expression levels and 545 transcripts with elevated expression levels.

overall_design: Drosophila larval fatbody mRNA profiles of wild type and TFAM RNAi

middle: S

first: Shrivani

last: Sriskanthadevan-Pirahas


title: Non-Transgenic Guinea Pig Strains Exhibit Hallmarks of Human Brain Aging and Alzheimer’s Disease

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

country: USA

institute: Colorado State University

summary: Older age is the primary risk factor for most chronic diseases, including Alzheimer’s disease (AD). Current preclinical models to study brain aging and AD are mainly transgenic and harbor mutations intended to mirror brain pathologies associated with human brain aging/AD (e.g., by increasing production of amyloid precursor protein, amyloid beta [Aβ], and/or phosphorylated tau, all of which are key pathological mediators of AD). Although these models may provide insight on pathophysiological processes in AD, none completely recapitulate the disease and its strong age-dependence, and there has been limited success in translating preclinical results and treatments to humans. Here, we describe two non-transgenic guinea pig (GP) models, a standard PigmEnTed (PET) strain and lesser-studied Dunkin-Hartley (DH) strain, that may naturally mimic key features of brain aging and AD in humans. We show that brain aging in PET GP is transcriptomically similar to human brain aging, whereas older DH brains are transcriptomically more similar to human AD. Both strains/models also exhibit increased neurofilament light chain (NFL, a marker of neuronal damage) with aging, and DH animals display greater S100 calcium-binding protein B (S100β), ionized calcium-binding adapter molecule 1 (Iba1), and Aβ and phosphorylated tau— which are all important markers of neuroinflammation-associated AD. Collectively, our results suggest that both the PET and DH GP may be useful, non-transgenic models to study brain aging and AD, respectively.

overall_design: PolyA RNA-seq on cortex isolated from Pigmented and Hartley Guinea Pigs at 5 and 15 months of age.

first: Thomas

last: LaRocca


title: Regulation of spn by Teg49 in S. aureus

city: Hanover

first: Liviu

last: Cengher

state: NH

address: 45 Dewey Field Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine

summary: We have studied the transcriptome of S. aureus SH1000 strain, isogenic Teg49 mutant strain, and isogenic plasmid complemented strain

overall_design: 1 growth point, 3 strains, RNA extraction of WT and DTeg49 and complement in SH1000 strains

first: Cengher

last: Liviu

first: Manna

last: Adhar

first: Juho

last: Cho

first: Jomkuan

last: Theprungsirikul

first: Katherine

last: Sessions

first: William

last: Rigby

first: Cheung

last: Ambrose


title: Validation of Whole Genome Methylation Profiling Classifier for Central Nervous System Tumors

city: Chicago

first: Lucas

last: Santana-Santos

state: IL

address: 710 N. Fairbanks Court, Olson 2-459

department: Pathology

institute: Northwestern University

type: Methylation profiling by genome tiling array

summary: The 2021 WHO Classification of Tumors of the Central Nervous System includes several tumor types and subtypes for which the diagnosis is at least partially reliant on utilization of whole genome methylation profiling. The current approach to array DNA methylation profiling utilizes a reference library of tumor DNA methylation data, and a machine learning-based tumor classifier. This approach was pioneered and popularized by the German Cancer Research Network (DKFZ) and University Hospital Heidelberg. This research group has kindly made their classifier for central nervous system tumors freely available as a research tool via a web-based portal. However, this classifier is not maintained in a clinical testing environment. Therefore, we validated our own DNA methylation-based classifier of central nervous system tumors. We validated our classifier using the same training and validation datasets as the DKFZ group. In addition, we performed a validation of samples tested in our own laboratory and compared the performance of both classifiers. Using the validation data set, our classifier’s performance showed high concordance (92%) and comparable accuracy (specificity 94.0% v. 84.9% for DKFZ, sensitivity 88.6% v. 94.7% for DKFZ). Receiver operator curve showed areas under the curve of 0.964 v. 0.966 for NM and DKFZ classifiers, respectively. Our classifier performed comparably well with samples tested in our own laboratory and is currently offered for clinical testing.

overall_design: 84 brain tumors used in the clinical validation of whole genome methylation profiling for central nervous system tumors profiling

first: Kwok

middle: L

last: Kam

first: David

last: Dittmann

first: Stephanie

last: De Vito

first: Matthew

last: McCord

first: Pouya

last: Jamshidi

first: Hailie

last: Fowler

first: Xinkun

last: Wang

first: Alan

middle: M

last: Aalsburgh

first: Daniel

last: Brat

first: Craig

last: Horbinski

first: Lawrence

last: Jennings


title: Oridonin delays aging through AKT signaling pathway

city: Beijing

first: yongpan

last: an

address: xueyuanlu

country: China

institute: Peking University

summary: Aging is the major risk factor for chronic diseases and disability in human. There is no effective anti-aging clinical treatment. In this study, oridonin was selected based on the drug screening strategy of Connectivity MAP (CMAP) upon transcriptomes of 102 traditional Chinese medicines (TCM) treated cell lines. Oridonin is an anti-inflammatory drug and diterpenoid isolated from Rabdosia rubescens. Oridonin exhibited a variety of pharmacological activities, including anti-tumor, antibacteria and anti-inflammation. Here, we found that oridonin inhibited cellular senescence in human diploid fibroblasts (2BS and WI-38), indicated by decreased senescence-associated β-galactosidase (SA-β-gal) staining. Compared with the elderly control group, the positive cell rate in the oridonin intervention group was 48.5%, and the cell shape was similar to young cells. Oridonin prolonged the lifespan of yeast by 14.6%~48.9%, and prolonged the average life span of naturally aged mice by 21.6%. It also increased the healthspan of aged mice. In addition, oridonin also improved doxorubicin-induced cellular senescence and mouse senescence. Compared with the model group, the percentage of SA-β-gal positive cells in the oridonin treatment group was reduced to 59.8%. It prolonged the average life span of mice by 53.8% as well as the healthspan. Mechanistically, we show that oridonin delayed aging through the AKT signaling pathways and reverses the genetic changes caused by doxorubicin-induced cell senescence. Therefore, oridonin may be an ideal candidate for the development of anti-aging drugs, and it also provides therapeutic potential in other diseases.

overall_design: WI-38 cells were first induced with 1μM doxorubicin for 12 hours, and then treated with oridonin or DMSO-containing medium for 48 hours.

first: Yongpan

last: An

first: Zhengwei

last: Xie

first: Baoxue

last: Yang


title: HTG mRNA expression for Progessive versus Stable disease in breast cancer RADICAL trial patients

city: London

first: Olivier

middle: Emmanuel

last: Pardo

address: Hammersmith Hospital, Du Cane Road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College

summary: Background: AZD4547 is a potent and selective inhibitor of FGFR-1, 2 and 3 receptor tyrosine kinases. Phase 1 studies both in Europe and Japan have shown that the compound is well tolerated and shows activity in patients with solid tumours. Here, we hypothesised that AZD4547 could reverse resistance to AIs such as anastrozole and letrozole.   Methods: After a safety run-in study in which 6 patients had PK and safety assessments on combined AI plus AZD4547, we recruited 52 eligible patients with metastatic breast cancer who had progressed on treatment with anastrozole or letrozole. The primary objective of the phase lla study was to assess the efficacy of AZD4547 based on the change in tumour size when used in combination with either anastrozole or letrozole in ER positive breast cancer patients who have progressed on treatment with either anastrozole or letrozole in any setting.  Results:. According to centrally reviewed RECIST criteria, five partial response (PR) and 8 stable disease (SD) patients were observed from a total of 50 assessable cases, giving a Clinical Benefit Rate (PR + SD) of 26% (95% CI: 14.6-40.3%). RNA-Seq was done on a subset of patients’ samples: 6 differentially-expressed-genes could distinguish those who benefited from the addition of AZD4547. Eleven patients had retinal pigment epithelial detachments (RPEDs) either in one or both eyes which was asymptomatic and reversible, although RPED recurred in one patient on re-treatment. Twenty six (50%) and 7(13%) patients had elevated phosphate and calcium, respectively.   Conclusions: in a group of unselected ER positive women with aromatase inhibitor-resistant metastatic breast cancer, FGFR pathway inhibition combined with letrozole or anastrozole provided clinical benefit in a significant proportion of patients with manageable toxicity.

overall_design: Relative expression of mRNA was assessed on FFPE samples using the HTG EdgeSeq Oncology Biomarker Panel.

middle: E

first: Raoul

middle: C

last: Coombes

first: Michael

last: Seckl


title: Type I Innate Lymphoid Cells Control Leukemia Stem Cell Fate and Limit Development of Acute Myeloid Leukemia

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

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

overall_design: Refer to individual Series


title: Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress

city: Dallas

first: Ganesh

middle: V.

last: Raj

state: TX

address: 5323 Harry Hines Blvd., JA5.150

department: Urology

institute: UT Southwestern Medical Center

summary: Triple-negative breast cancer (TNBC) has a poor clinical outcome, due to a lack of actionable therapeutic targets. Herein we define lysosomal acid lipase A (LIPA) as a viable molecular target in TNBC and identify a stereospecific small molecule (ERX-41) that binds LIPA. ERX-41 induces endoplasmic reticulum (ER) stress resulting in cell death, and this effect is on target as evidenced by specific LIPA mutations providing resistance. Importantly, we demonstrate that ERX-41 activity is independent of LIPA lipase function but dependent on its ER localization. Mechanistically, ERX-41 binding of LIPA decreases expression of multiple ER-resident proteins involved in protein folding. This targeted vulnerability has a large therapeutic window, with no adverse effects either on normal mammary epithelial cells or in mice. Our study implicates a targeted strategy for solid tumors, including breast, brain, pancreatic and ovarian, whereby small, orally bioavailable molecules targeting LIPA block protein folding, induce ER stress and result in tumor cell death.

overall_design:
MDA-MB-231 and BT-549 cells were cultured in RPMI1640 (Gibco) supplemented with 10% FBS, 0.2% Normocin and 1% penicillin-streptomycin. SUM-159 cells were cultured in F-12 (Gibco) supplemented with 10% FBS, 0.2% Normocin and 1% penicillin-streptomycin.
Cells were treated with DMSO or ERX-41. For mRNAseq samples, ERX-41 treated cells were treated with 1 uM of ERX-41 for 2 or 4 hours. For CRISPR screen samples, ERX-41 treated cells were treated with 0.25 uM (1st screen) or 0.5 uM (2nd screen) for 3 weeks.

first: Xihui

last: Liu

middle: V


title: mRNA expression profiling of PBMCs from Behcet’s disease

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

summary: Behçet’s disease (BD) is a chronic vasculitis characterized by systemic immune aberrations. However, a comprehensive understanding of the immune disturbances in BD and how they contribute to BD pathogenesis is lacking. Here, we performed single-cell and bulk RNA sequencing to profile peripheral blood mononuclear cells (PBMCs) and isolated monocytes from BD patients and healthy controls. This dataset is the bulk RNA sequencing part (next generation sequencing-based genome-wide transcriptional profiling), which contains the transcriptional profilings of  freshly isolated PBMCs from19 samples (10 healthy controls and 9 BD patients).

overall_design: Transcriptional profiling of peripheral blood mononuclear cells (PBMCs)  from 19 samples (10 healthy controls and 9 BD patients).

first: Xiaoman

first: Jinjing

first: Xin

last: Yu

first: Jijun

first: Xiaoya

last: Pei

first: Heping

first: Hua

last: Chen

first: Hou-Zao


title: DNA methylation profiles in pneumonia patients reflect changes in cell types and pneumonia severity

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

type: Methylation profiling by high throughput sequencing

summary:
Immune cell type composition changes with age, potentially weakening the response to infectious diseases. Profiling epigenetics marks of immune cells can help us understand the relationship with disease severity. We therefore leveraged a targeted DNA methylation method to study the differences in a cohort of pneumonia patients (both COVID-19 positive and negative) and unaffected individuals from peripheral blood.
This approach allowed us to predict the pneumonia diagnosis with high accuracy (AUC = 0.92), and the PCR positivity to the SARS-CoV-2 viral genome with moderate, albeit lower, accuracy (AUC = 0.77). We were also able to predict the severity of pneumonia (PORT score) with an R2 = 0.69. By estimating immune cellular frequency from DNA methylation data, patients under the age of 65 positive to the SARS-CoV-2 genome (as revealed by PCR) showed an increase in T cells, and specifically in CD8+ cells, compared to the negative control group. Conversely, we observed a decreased frequency of neutrophils in the positive compared to the negative group. No significant difference was found in patients over the age of 65.
The results suggest that this DNA methylation-based approach can be used as a cost-effective and clinically useful biomarker platform for predicting pneumonias and their severity.

overall_design: Targeted DNA methylation profiling in a cohort of pneumonia patients and unaffected individuals from peripheral blood. Patient age, clinical diagnosis, PCR positivity information provided.

first: Colin

last: Farrell

first: Dennis

last: Montoya

first: Tarık

last: Gören

first: Ramazan

last: Sabırlı

first: İbrahim

last: Türkçüer

first: Özgür

last: Kurt

first: Aylin

last: Köseler

first: Matteo

last: Pellegrini


title: SHP2 inhibitor augments murine liver regeneration via cytoprotective and proproliferative pathway enhancement identified by RNA sequencing

status: Public on Mar 17 2022

city: Rochester

first: Ryan

last: Watkins

state: MN

address: 200 First St SW

department: Surgery

institute: Mayo Clinic

summary: Disruption of the liver’s innate ability to regenerate represents an “undruggable” clinical challenge associated with poor patient outcomes. Yes-associated protein (YAP), a transcriptional co-activator which is repressed by the Hippo pathway, is instrumental in liver regeneration. We have previously described an alternative, Hippo-independent activation of YAP mediated by tyrosine-protein phosphatase non-receptor type 11 (SHP2) inhibition. Herein, we examined the effects of YAP activation with a selective SHP1/SHP2 inhibitor, NSC-87877, on liver regeneration in murine partial hepatectomy models. In our studies, NSC-87877 led to accelerated hepatocyte proliferation, improved liver regeneration, and decreased markers of injury following partial hepatectomy. Evaluation of these effects in mice with hepatocyte-specific Yap/Taz deletion demonstrated dependence on these molecules for the enhanced regenerative response. Furthermore, administration of NSC-87877 to murine models of non-alcoholic steatohepatitis was associated with improved survival and decreased markers of injury post-hepatectomy. Evaluation of transcriptomic changes in the context of NSC-87877 administration revealed reduction in fibrotic signaling and augmentation of cell cycle signaling. Cytoprotective changes included downregulation of Nr4a1, an apoptosis inducer. Collectively, the data suggest that SHP2 inhibition induce a YAP-dependent pro-proliferative and cytoprotective enhancement of liver regeneration.

overall_design: Murine whole liver lysates mRNA profiles at baseline, 40 hours post-hepatectomy, and 40 hours post-hepatectomy treated with NSC-87877 (15 mg/kg/day)

first: Rory

last: Smoot


title: Airway Aging and Methylation Disruptions in HIV-associated Chronic Obstructive Pulmonary Disease [methylation]

city: Vancouver

first: Janice

last: Leung

state: BC

address: Room 166, 1081 Burrard Street

institute: Centre for Heart Lung Innovation, University of British Columbia

summary:
Purpose:To identify whether accelerated aging can be observed in the airways of PLWH with COPD, manifest by a unique DNA methylation signature.
Methods: Bronchial epithelial brushings from PLWH with and without COPD and HIV-uninfected adults with and without COPD (n=76) were profiled for DNA methylation and gene expression. We evaluated global Alu and LINE-1 methylation and calculated the epigenetic age using the Horvath clock and the methylation telomere length estimator. To identify genome-wide differential DNA methylation and gene expression associated with HIV and COPD, robust linear models were used followed by an expression quantitative trait methylation (eQTM) analysis.
Results:Epigenetic age acceleration and shorter methylation estimates of telomere length were found in PLWH with COPD compared to PLWH without COPD and uninfected patients with and without COPD. We identified CpG sites, genes, and eQTM-gene pairs associated with the interaction between HIV and COPD.
Conclusions: Methylation age acceleration is observed in the airway epithelium of PLWH with COPD, a process that may be responsible for the heightened risk of COPD in this population. Their distinct methylation profile, differing from that observed in patients with COPD alone, suggests a unique pathogenesis to HIV-associated COPD that warrants investigation into the candidate genes identified.

overall_design: Epigenome-wide associattion study

first: Don

middle: D

last: Sin


title: Airway Aging and Methylation Disruptions in HIV-associated Chronic Obstructive Pulmonary Disease


title: RNAseq analysis of FACS-isolated  astrocytes from the striatum of 11-14 month-old knock-in Hdh140 mice after astrocyte-targeted expression of GFAP or JAK2ca

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

summary:
We analyzed the transcriptional profile of  striatal  astrocytes from 1) Hdh140 mice infected with AAV-GFP,  2) astrocytes from Hdh140 mice infected with AAV-JAK2ca (+ AAV-GFP, at the same total virus load).
We show that JAK2ca activates the JAK2-STAT3 patwhay in striatal astrocytes, induces reactive changes and activates a proteostasis signature.

overall_design: Total RNA was extracted from GFP+ astrocytes isolated by FACS from knock-in Hdh140 mice injected with an AAV targeting astrocytes and encoding GFP alone (ASTRO-HD-GFP group, N=5) or JAK2ca and GFP (ASTRO-HD-JAK2ca group, N=6).

first: Laurene

last: Abjean

first: Miriam

last: Riquelme-Perez

first: Marie-Ange

last: Palomares

first: Jean-François

last: Deleuze

first: Solène

last: Brohard

first: Carole

last: Escartin


title: Airway Aging and Methylation Disruptions in HIV-associated Chronic Obstructive Pulmonary Disease [RNA-seq]


title: Expression data from germ cell tumor patient-derived cells

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

summary: Patient-derived cancer cells (PDCs) were established by three-dimensional (3D) spheroid culture from testicular germ cell tumor (GCT) specimens. Microarray expression analysis revealed that cancer stem-like cell-related genes were upregulated in 3D culture condition compared with two-dimensional (2D) culture condition.

overall_design: RNAs were prepared from GCT PDCs (GCT-A and -B) which were cultured in 3D or 2D culture condition, and then subjected to Affymetrix microarray analysis.

first: Takeshi

last: Namekawa

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Profiling the knee joints of mice with Type 1 diabetes mellitus

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Type 1 diabetes mellitus (T1DM) affects 9.5% of the population. T1DM is characterized by severe insulin deficiency that causes hyperglycemia and leads to several systemic effects. T1DM has been suggested as a risk factor for articular cartilage damage and loss, which could expedite the development of osteoarthritis (OA). OA represents a major public health challenge by affecting 300 million people globally, yet very little is known about the correlation between T1DM and OA. In this study we aimed to understand the role of T1DM in OA by evaluating whether pre-existing T1DM exacerbates the development of knee post traumatic osteoarthritis (PTOA).

overall_design: Right knee joints of 10-week-old C57Bl/6J (Ctrl) and STZ injected C57BL/6J (T1DM) mice were injured using a tibial compression injury model. Hindlimbs were collected from uninjured and injured mice at 7-days post-injury. Subsequently, knee joints were isolated, about ~1mm tissue was cut from the end of femur and tibia and digested to obtain single cell suspensions. After depleting CD45+ immune cells and Ter119+ erythrocytes, the remaining cells were sequenced to obtain single-cell level gene expression profiles.

first: Gabriela

last: Loots


title: Type I Innate Lymphoid Cells Control Leukemia Stem Cell Fate and Limit Development of Acute Myeloid Leukemia [1]

first: Zhenlong

last: Li

summary: Type I innate lymphoid cells (ILC1s) are critical regulators of inflammation and immunity in mammalian tissues. However, their functional roles in cancer are largely undefined. We found that a high concentration of normal murine ILC1s induced leukemia stem cell (LSC) apoptosis. At a lower concentration, ILC1s prevented LSCs from differentiating into leukemia progenitors and promoted their differentiation into non-leukemic cells, thus blocking the production of terminal myeloid blasts. All of these effects, which required ILC1s to produce interferon-γ after cell–cell contact with LSCs, converged to suppress leukemogenesis in vivo. Conversely, ILC1s’ anti-leukemia potential waned when JAK-STAT and PI3K-AKT signaling was inhibited. The relevant anti-leukemic properties of normal ILC1s were operative in humans and impaired in AML patients. Collectively, our findings reveal crucial functions of ILC1s as anti-cancer immune cells seemingly suitable for AML immunotherapy, and provide a new potential strategy to treat AML and/or prevent relapse of the disease.

overall_design: Identification of the ILC1 regulatory pathways in AML

first: Jianhua

last: Yu


title: Gene expression during conidia germination in Neurospora crassa on PDA

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Conidia germination is critical for fungi to colonize various habitats. We sampled RNA expression at four stages of conidia germination, including fresh conidia (15min), polar growth (120min), doubling of long axis (240min), and first hyphal branching (360min) in Neurospora crassa. Cultures were made onPDA, iand two biological replicates were collected for all data points. The growth was under a labratory condition of 25C and constant light.

overall_design: mRNA were sampled and compared from four time points across conida germination in Neurpsora crassa on different media

last: Lopez-Giraldez

first: Jeffrey

middle: P

last: Townsend

first: Zheng

last: Wang


title: Understanding the role of Type 1 diabetes mellitus in osteoarthritis

summary: Type 1 diabetes mellitus (T1DM) affects 9.5% of the population. T1DM is characterized by severe insulin deficiency that causes hyperglycemia and leads to several systemic effects. T1DM has been suggested as a risk factor for articular cartilage damage and loss, which could expedite the development of osteoarthritis (OA). OA represents a major public health challenge by affecting 300 million people globally, yet very little is known about the correlation between T1DM and OA. In this study we aimed to understand the role of T1DM in OA by evaluating whether pre-existing T1DM exacerbates the development of knee post traumatic osteoarthritis (PTOA). Here we describe the transcriptomic differences between the knee joints of STZ injected C57BL/6J mice (T1DM) and control mice

overall_design: Bulk RNA-seq of knee joints of STZ injected C57BL/6J mice (T1DM) and control mice

middle: G

first: Aimy

last: Sebastian


title: Multi-omics analysis of RNA binding, splicing and turnover alterations induced by mutant U2AF1 in myeloid malignancies.

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

summary:
Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA binding motifs; yet how they affect splicing and promote cancer remains unclear. The U2AF1/U2AF2 heterodimer is critical for 3’ splice site (3’SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure detecting contacts between U2AF1 and the 3’SS AG at single-nucleotide resolution (fractionated eCLIP-seq or freCLIP-seq). Our data reveal that U2AF1 S34F and Q157R mutants establish new 3’SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding (eCLIP-seq and freCLIP-seq), splicing (RNA-seq) and turnover (TimeLapse-seq or TL-seq) data, we predicted that U2AF1 mutations directly affect stress granule components. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies.
Keywords: splicing, RNA binding, U2AF1, U2AF2, S34F, Q157R, hotspot mutations, 3'SS, 3' splice site, myeloid malignancies, eCLIP, freCLIP, RNA-seq, RNA turnover, TimeLapse-seq, TL-seq, RNA granules, stress granules, stress response, biomolecular condensates, MDS, AML

overall_design: In this study, we performed high-throughput sequencing of RNA isolated by enhanced crosslinking immunoprecipitation (eCLIP-seq) to determine the function of WT U2AF1 alongside two cancer-associated U2AF1 mutants (S34F, Q157R) in the context of a human hematopoietic cell line. U2AF1 and U2AF2 eCLIP-seq were performed in 2 biological replicates, with also 1-2 technical replicates. Human erythroid leukemia (HEL) cell lines were stably transduced with either wild type U2AF1 (WT) or mutant U2AF1 (S34F, Q157R). Central to this work was the development of (fr)eCLIP-seq – for fractionated eCLIP-seq, a modification of eCLIP that enabled us to separate a light and a heavy fraction, dissecting U2AF1 from U2AF2 RNA binding signals within the 3’SS region in vivo. U2AF1 freCLIP-seq was performed in 2-4 biological replicates. RNA-seq and TimeLapse-seq (TL-seq, providing RNA turnover data) were performed in biological duplicates. Uninduced cells were used as controls in RNA-seq. Unlabeled and uninduced cell samples were used as controls in TL-seq.

first: Poorval

last: Joshi

first: Joshua

middle: T

last: Zimmer

first: Matthew

last: Simon

first: Toma

last: Tebaldi

first: Stephanie

last: Halene


title: Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin [CUT&RUN]

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: lncRNAs regulate protein functions via formation of protein-RNA complexes. Previous studies have shown that expression of viral lncRNA, polyadenylated nuclear RNA (PAN RNA) is essential for inducible viral genomic looping and distal gene activation during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation. Here we show an underlying molecular mechanism and regulation of KSHV latency by a viral lncRNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. Knock-out of the viral RNA binding protein, ORF57 protein, leads to decreased inducible and static viral genomic loops in latent chromatin and a failure to form RNA polymerase II aggregates in the nucleus during reactivation. We identified that CHD4's enzymatic activity silences viral gene expression by preventing nuclear aggregate formation. Furthermore, integrated genomic and proteomic studies together show that KSHV episomes frequently tether near the host cell centromeres and colocalize with a CHD4 protein complex, ChAHP. KSHV episomes detached from these sites when reactivation is triggered, and PAN RNA binds and inhibits CHD4 DNA binding in vitro. Our studies suggest that CHD4 exhibits strong repressor function by preventing inducible enhancer-promoter looping, and is therefore important for the ability of KSHV to establish and maintain latency in a “poised” state at specific host genomic loci.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Examination of genome-wide binding of host and viral proteins on the human and KSHV genome using CUT&RUN. Experiments were performed in KSHV naturally infected human primary effusion lymphoma (PEL) cell line BCBL-1 and wild type or ORF57-Stop recombinant KSHV infected iSLK cells.

first: Yoshihiro

last: Izumiya

first: Mel

last: Campell

first: Ashish

last: Kumar

first: Yuanzhi

last: Lyu

first: Yuichi

last: Yanagihashi

first: Chanikarn

last: Chantarasrivong

first: Kazushi

last: Nakano

first: Ryan

last: Davis


title: Link between GRHL2 Motifs and Intratumor Heterogeneity of Cis-Regulatory Elements Results in Poor Outcome in Luminal Breast Cancer: A Single-cell Chromatin Accessibility Analysis

status: Public on Mar 16 2022

city: Koto-ku

first: Reo

last: Maruyama

state: Tokyo

department: Cancer Institute

institute: Japanese Foundation For Cancer Research

summary: In breast cancer patients, tumor heterogeneity is associated with prognosis and therapeutic response; however, the epigenetic diversity that exists in primary tumors remains unknown. Using a single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq), we obtained the chromatin accessibility profiles of 12,452 cells from 16 breast cancer patients including 11 luminal, 1 luminal-HER2, 1 HER2+, and 3 triple-negative subtypes. Via this profiling process, tumors were classified into cancer cells and the tumor microenvironment, highlighting the heterogeneity of disease-related pathways including estrogen receptor (ER) signaling. Furthermore, the coexistence of cancer cell clusters with different ER binding motif enrichments was identified in a single ER+ tumor. In a cluster with reduced ER motif enrichment, we identified GRHL2, a transcription factor, as the most enriched motif, and it cooperated with FOXA1 to initiate endocrine resistance. Coaccessibility analysis revealed that GRHL2 binding elements potentially regulate genes associated with endocrine resistance, metastasis, and poor prognosis in patients that received hormonal therapy. Overall, our study suggests that epigenetic heterogeneity could lead to endocrine resistance and poor prognosis in breast cancer patients and it offers a large-scale resource for further cancer research.

overall_design:
Sixteen breast cancer samples collected by core needle biopsies from surgical specimens were objected to scATAC-seq analysis.
***Raw data not available due to patient privacy concerns***

first: Kohei

last: Kumegawa

first: Yoko

last: Takahashi

first: Sumito

last: Saeki


city: Saitama City

first: Katsunori

last: Yanai

address: 1-847, Amanuma-cho, Omiya-ku

institute: Jichi Medical University, Saitama Medical Center

summary:
Background: Age-dependent renal impairment contributes to renal dysfunction in both the general population and young and middle-aged patients with renal diseases. Pathological changes in age-dependent renal impairment include glomerulosclerosis and tubulointerstitial fibrosis. The molecules involved in age-dependent renal impairment are not fully elucidated. MicroRNA (miRNA) species were reported to modulate various renal diseases, but the miRNA species involved in age-dependent renal impairment are unclear. Here, we investigated miRNAs in age-dependent renal impairment, and we evaluated their potential as biomarkers and therapeutic targets.
Methods: We conducted an initial microarray profiling analysis to screen miRNAs whose expression levels changed in kidneys of senescence-accelerated resistant (SAMR1)-10-week-old (wk) mice and SAMR1-50wk mice and senescence-accelerated prone (SAMP1)-10wk mice and SAMP1-50wk mice. We then evaluated the expressions of differentially expressed miRNAs in serum from 13 older patients (>65 years old) with age-dependent renal impairment (estimated glomerular filtration ratio <60 mL/min/1.73 m2) by a quantitative real-time polymerase chain reaction (qRT-PCR) and compared the expressions with those of age-matched subjects with normal renal function. We also administered miRNA mimics or inhibitors (5 nmol) with a nonviral vector (polyethylenimine nanoparticles: PEI-NPs) to SAMP1-20wk mice to investigate the therapeutic effects.
Results: The qRT-PCR revealed a specific miRNA (miRNA-503-5p) whose level was significantly changed in SAMP1-50wk mouse kidneys in comparison to the controls. The expression level of miRNA-503-5p was upregulated in the serum of the 13 patients with age-dependent renal impairment compared to the age-matched subjects with normal renal function. The administration of a miRNA-503-5p-inhibitor with PEI-NPs decreased the miRNA-503-5p expression levels, resulting in the inhibition of renal fibrosis in mice via an inhibition of a pro-fibrotic signaling pathway and a suppression of glomerulosclerosis in mice by inhibiting intrinsic signaling pathways.
Conclusion: miRNA-503-5p may represent a biomarker for age-dependent renal impairment, and the inhibition of miRNA-503-5p had no effect on age-dependent renal impairment. However, the inhibition of miRNA-503-5p had therapeutic effects on renal fibrosis and glomerulosclerosis.

overall_design: 10-week-old SAMR1 mice (n=4), 50-week-old SAMR1 mice (n=4), 10-week-old SAMP1 mice (n=4), 50-week-old SAMP1 mice (n=4)


title: Enhanced cortical neural stem cell identity through short SMAD/WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells.

city: Berlin

first: Yechiel

last: Elkabetz

address: Ihnestraße 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Cerebral organoids exhibit broad regional heterogeneity accompanied by limited cortical cellular diversity under a variety of derivation methods, suggesting inadequate patterning of early neural stem cell (NSC) starting populations. Here we show that a short combined Dual SMAD/WNT inhibition course during early organoid establishment is sufficient for yielding robust and lasting cortical identity with efficient suppression of non-cortical fates in organoid NSCs. In contrast, other widely used methods are inconsistent in their cortical specification capacity. Furthermore, combined inhibition selectively enriches for outer radial glia (oRG) cells in organoids that demarcate well-defined outer sub-ventricular (oSVZ)-like regions. Finally, combined inhibition enables superior NSC radial organization, further facilitates the generation of molecularly distinct deep and upper cortical layer neurons, and uncovers cortex-specific microcephaly defects. Thus, combined inhibition is critical for establishing a rich cortical cell repertoire, for enabling fundamental cytoarchitectural features of cortical development, and for meaningful disease modeling.

overall_design:
Single cell RNA-sequencing of brain organoids from 4 iPSC lines across 3 derivation protocols after 50 days and 80 days in culture. Bulk RNA-Seq of H9-derived microcephaly and wild-type organoids.

Please note that raw data is not provided as it requires controlled access.

first: Daniel

last: Rosebrock

first: Sneha

last: Arora

first: Naresh

last: Mutukula

first: Rotem

last: Volkman

first: Elzbieta

last: Gralinska

first: Anastasios

last: Balaskas

first: Amèlia

last: Aragonés Hernández

first: René

last: Buschow

first: Björn

last: Brändl

first: Franz-Josef

last: Müller

first: Peter

middle: F

last: Arndt

first: Martin

last: Vingron


title: Inherited defect in ST6GalNAc1 reveals roles of sialylation in intestinal homeostasis

city: Bethesda

first: Han-Yu

last: Shih

state: MD

address: 10 Center Drive Rm 5S261

institute: National Eye Institute

summary: Chronic inflammatory bowel disease (IBD) causes disability, suffering and risk of colon cancer in over 30 million people globally. Here, we investigate 3 kindreds of IBD with mutations in the N-acetylgalactosamide alpha-2,6-sialyltransferase 1/ST6GALNAC1 (ST6) glycosyltransferase gene that is uniquely expressed in the goblet cells (GCs). These mutations cause defective sialic acid (SA) conjugation, elimination of the onco-antigen S-Tn (Sialyl-Tn), and altered glycosylation of the MUC2 protein, a key component of intestinal mucus. Decreased MUC2 sialylation increases susceptibility to bacterial proteolytic degradation and compromises the gastrointestinal (GI) mucus barrier. Mice harboring the patient ST6 mutations recapitulate human colitis and reveal that defective sialylation causes dysbiosis, butyrate overproduction, and impaired GI stem cell proliferation during injury. Thus, this new genetic disease illustrates how sialylation controls host-microbe homeostasis and reveals several new potential approaches to IBD treatment.

overall_design: Integrated analysis of RNA-seq and ATAC-seq data from Wild-type and St6galnac1 intestinal epithelial cells.

first: Yikun

last: Yao

first: Girak

last: Kim

first: Samantha

last: Shafer

first: Zuojia

last: Chen

first: Jialie

last: Luo

first: Satoshi

last: Kubo

first: Yanlong

last: Ji

first: Weiming

last: Yang

first: Sebastian

last: Perner

first: Chrysi

last: Kanellopoulou

first: Ann

last: Park

first: Ping

last: Jiang

first: Safa

last: Baris

first: Elif

middle: K

last: Aydiner

first: Deniz

last: Ertem

middle: J

last: Mulder

first: Neil

last: Warner

first: Anne

last: Griffiths

first: Chani

last: Topf-Olivestone

first: Michal

last: Kori

first: Lael

last: Werner

first: Jodie

last: Ouahed

first: Michael

last: Field

first: Chengyu

last: Liu

first: Benjamin

last: Schwarz

first: Sundar

last: Ganesan

first: Jian

last: Son

first: Henning

last: Urlaub

first: Thomas

last: Oellerich

first: Stacy

middle: A

last: Malaker

first: Lixin

last: Zheng

first: Carolyn

last: Bertozzi

first: Yu

last: Zhang

first: Helen

last: Matthews

first: Will

last: Montgomery

first: Jiansheng

first: Scott

last: Snapper

first: Aleixo

last: Muise

first: Dror

last: Shouval

first: Ahmet

last: Ozen

first: Kuan-Ting

last: Pan

first: Chuan

last: Wu


title: Autism-like behaviors and cerebellar dysfunction in the Bmal1 mutant mouse ameliorated by mTORC1 inhibition

city: Duluth

first: Ruifeng

last: Cao

address: 1035 University Dr

department: Biomedical Sciences

institute: University of Minnesota

summary: Although circadian and sleep disorders are frequently associated with autism spectrum disorders (ASD), it remains elusive whether clock gene disruption can lead to autistic-like phenotypes in animals. The essential clock gene Bmal1 has been associated with human sociability and its missense mutations are identified in ASD. Here we report that global Bmal1 deletion led to significant social impairments, excessive stereotyped and repetitive behaviors, as well as motor learning disabilities in mice, all of which resemble core behavioral deficits in ASD. Furthermore, aberrant cell density and immature morphology of dendritic spines were identified in the cerebellar Purkinje cells (PCs) of Bmal1 knockout (KO) mice. Electrophysiological recordings uncovered enhanced excitatory and inhibitory synaptic transmission and reduced firing rates in the PCs of Bmal1 KO mice. Differential expression of ASD- and ataxia-associated genes (Ntng2, Mfrp, Nr4a2, Thbs1, Atxn1, and Atxn3) and dysregulated pathways of translational control, including hyperactivated mammalian target of rapamycin complex 1 (mTORC1) signaling, were identified in the cerebellum of Bmal1 KO mice. Interestingly, the antidiabetic drug metformin reversed mTORC1 hyperactivation and alleviated major behavioral and PC deficits in Bmal1 KO mice. Importantly, conditional Bmal1 deletion only in cerebellar PCs was sufficient to recapitulate autistic-like behavioral and cellular changes akin to those identified in Bmal1 KO mice. Together, these results unveil a previously unidentified role for Bmal1 disruption in cerebellar dysfunction and autistic-like behaviors. Our findings provide experimental evidence supporting a putative role for dysregulation of circadian clock gene expression in the pathogenesis of ASD.

overall_design: total RNA-seq and footprint experiments from the cerebellar tissue of Bmal1 knockout and wildtype mice, 3 biological replicates form each condition for RNA-seq; 2 biolgical replicates from each condition for footprint experiments.

first: Christos

last: Gkogkas

first: Kun

last: Fang


title: Differential gene expression profiling of conventional (Tconv), regulatory (Treg), follicular (TFH) helper and follicular regulatory (TFR) T-cells from control vs OX40L-Jagged-1 treated NZBWF1/j mice

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

institute: UIC

overall_design:
Tconv, Treg, TFH and TFR subsets (n=3)  from control vs OX40L-JAG1 treated mice were compared for differential gene expression pattern.
23-week-old female NZBWF1/j mice were injected (i.p.) with recombinant mouse OX40L (2mg/kg body weight) and mouse JAG1 (2mg/kg body weight)  once a week for three consecutive weeks. Age and sex-matched control mice received PBS. On week 26, mice were sacrificed and Tconv (CD4+CXCR5-GITR-) cells, Tregs (CD4+CXCR5-GITR+), TFH (CD4+CXCR5+PD1Hi GITR-/low), and TFR (CD4+CXCR5+PD1Hi GITRHi) cells were sorted and subjected to RNA-seq analysis.

first: Bellur

middle: S

last: Prabhakar

first: Zarema

last: Arbieva

first: Mark

last: Maienschein-Cline

first: Feferman

last: Leonid


title: Gene expression during conidia germination in Neurospora crassa on Bird medium at 37C

first: Francesc

last: Lopez

summary: Conidia germination is critical for fungi to colonize various habitats. We sampled RNA expression at four stages of conidia germination, including fresh conidia (15min), polar growth (120min), doubling of long axis (240min), and first hyphal branching (360min) in Neurospora crassa. Cultures were made on Bird medium, and two biological replicates were collected for all data points. The growth was under a labratory condition of 375C and constant light.

last: Lopez-Giraldez

first: Jeffrey

last: Townsend

first: Zheng

last: Wang


title: A Preliminary Study of Whole Blood Transcriptome Analysis Using RNA Sequencing in Repetitive Low-Level Blast Exposure in Career Breacher

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary: Repetitive low-level blast exposure is one of the major occupational health concerns in the US mil-itary service members and law enforcement, and the underlying biological mechanisms remain controversial. Therefore, this study is to identify gene expression using RNA sequencing in the whole blood sample from experienced breachers and unexposed control. We performed experi-mental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System in whole blood samples from 15 experienced breachers and 14 age, sex, race matched unexposed control. We identified 10 significantly dysregulated genes between experienced breacher and unexposed control with FDR corrected < 0.05. One upregulated gene included LINC00996 (long intergenic non-protein coding RNA 996) and 9 downregulated genes including IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin associ-ated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobu-lin heavy variable 4-34). Dysregulated of these genes’ expression are associated with nervous system development and organismal development. The dysregulated gene expression reported in our study is functionally associated with chronic inflammation and immune response in repeti-tive low-level blast exposure, which may have a negative influence on neurological health.

overall_design: RNA-seq on blast vs. control

first: Jessica

last: Gill


title: Genome-wide maps of H3K9Ac in wild type and sinhcaf mutant zebrafish embryos

status: Public on Mar 15 2022

city: Wuhan

first: Binbin

last: Tao

address: No. 7 Donghu South Road

institute: Institute of Hydrobiology

summary: H3K9Ac ChIP-Seq was conducted to investigate whether loss of sinhcaf increases the histone acetylation in the promoter region of kinesin family genes.Increased H3K9Ac ChIP-Seq peaks upon sinhcaf loss were detected in the kif26ab promoter region.

overall_design: Examination of H3K9Ac in wild type and sinhcaf mutant zebrafish embryos by CHIP-Seq


title: Gene expression during conidia germination in Neurospora crassa

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

overall_design: Refer to individual Series


title: RNA-Seq analysis of traumatic and degenerative tears of subacromial bursal tissues of human shoulder joint

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Objective: To identify transcript level differences between traumatic and degenerative tears of subacromial bursal tissues in shoulder joint using RNA-seq. Methods: Bursal tissues were collected from female and male patients with traumatic or degenerative tears during arthroscopic surgery (N=32). Differentially expressed transcript  between traumatic and degenerative tears were detected by RNA-seq and biological processes were identified computationally. RNA-seq results were selectively validated by real-time qPCR. Results: We identified 334 protein-coding transcripts differentially expressed between traumatic and degenerative tears in females and 167 in males at a fold-change greater than |2| and a P < 0.05. In females, XIRP2, MYL1, MYBPC1, TNNT1, and LMOD2, were the highly expressed in traumatic tears and TPSD1, CDSN, RCVRN, LTBP4, and PTGS1 were prominently repressed in traumatic tears. Transcripts elevated in traumatic tears represented muscle cell differentiation and development, and muscle contraction whereas those elevated in degenerative tears represented cell activation, neutrophil granulation, immune response,  and protein transport. In males, AZGP1, CNTFR, COL9A1, ZNF98 and EREG were highly elevated in traumatic tears whereas MYL2, HOXD11, SLC6A7, CADM1, and MMP17 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented metabolic processes, catabolic processes, and transmembrane protein transport while processes related to cell cycle were mainly repressed in traumatic tears. We also identified a number of novel lncRNAs differentially expressed between traumatic and degenerative tears in both females and males. Conclusions: This study increases our molecular understanding of bursal tissues in patients with rotator cuff tendinopathy based on the nature of disease that is trauma or degeneration. These finding also provide new insights into sex-based transcript differences that could inform clinical decision making in treating patients with traumatic and degenerative shoulder injuries.

first: Muhammad

first: Lei

last: Cai

first: Eric

last: Tycksen

first: Aaron

last: Chamberlain

first: Jay

last: Keener


title: The PAF1 complex promotes 3‘ processing of pervasive transcripts [3'-seq]

city: Beijing

first: wei

middle: zi

last: guo

state: Beijing

address: ZhongGuanCun

institute: tsinghua university

summary: The PAF1 complex (PAF1C) functions in multiple transcriptional and co-transcriptional processes. Although many aspects of the requirement for PAF1 in coding gene transcription have been heavily studied, the function of PAF1C at sites of non-coding transcription is poorly understood.  eRNAs and PROMPTs are pervasive transcripts transcribed by RNA Polymerase II and rapidly degraded after 3’ endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C depletion results in near universal 3’ end processing defects in pervasive transcripts, leading to transcription termination dysregulation. Mechanistically, PAF1C recruits Integrator to chromatin through direct interactions promoting timely cleavage and transcription termination of pervasive transcripts. We also show that PAF1C recruits Integrator to the promoters of coding genes, where PAF1C then dissociates from the Integrator complex upon entry into processive elongation. Our results demonstrate an unexpected function for PAF1C in limiting the length and accumulation of pervasive transcripts, while highlighting a general requirement for PAF1C in Integrator recruitment.

overall_design: Examination of transcription termination defects upon PAF1 depletion

first: Xinhong

last: Liu

first: Ziwei

last: Guo

first: Han

last: Jing

first: Bo

last: Peng

first: Bin

last: Zhang

first: Xiaoyu

last: Hu

first: Haitao

last: Li

first: Charles

last: David

first: Mo

last: Chen


title: Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single cell transcriptomics

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: An increasing number of studies suggests that embryonic development is a highly plastic process and that lineage specification can proceed via alternative routes not encompassed in canonically defined germ layers. Despite these recent revisions to fate maps, the differentiation of pluripotent stem cells (PSCs) to specific lineages tends to continue to focus on defined germ layer differentiation. Thus although recent studies suggest that the visceral organs originate from both embryonic and extra-embryonic lineages, PSC differentiation has focused on generating definitive and gut endoderm solely via an embryonic trajectory. To better resolve the lineage trajectories during development and during corresponding in vitro differentiation, we used MARS-seq to generate a single-cell RNA-seq datasets from mouse embryos expressing a Foxa2Venus reporter and in vitro embryonic stem cell (ESC) differentiation towards definitive endoderm. We coupled this data to a new simplified computational approach to compare cell types, both within our own transcriptomes and across different datasets. Based on this analysis, we captured the central intermediate in the transition between extra-embryonic and embryonic endoderm. When we assessed in vitro ESC differentiation in a number of different endoderm protocols, we found no evidence for this transient intermediate population during differentiation, only traditional embryo-like populations. We then directly tested the capacity of extra-embryonic endoderm to generate organ specific cell types, exploiting our previously defined cell culture system for naïve extra-embryonic endoderm (nEnd). We found that nEnd exhibited gene expression states that reflects early extra-embryonic identity and could be further differentiated to embryonic gut organoids. Taken together, this suggests self-renewing extra-embryonic nEnd represents a source of definitive organ cell types and suggests that in vitro differentiation should take full advantage of the recent observations about developmental plasticity.

overall_design: The in Vivo study contains 41 samples from 4 developmental stages of Foxa2-Venus mouse embryos. There are 12 samples of E6.5, 8 samples of E7.5, 17 samples of E8.5, 4 samples of E9.5. The single cells were specifically sorted for Foxa2-Venus protein. The in Vitro study contains 34 samples from 10 experimental stages. The single cells were sorted for Gsc-GFP and Hhex-RedStar or E-cad and Cxcr4.

first: Michaela

last: Rothova

first: Alexander

last: Nielsen

first: Martin

last: Proks

first: Yan

last: Wong

first: Alba

middle: R

last: Riveiro

first: Madeleine

last: Linneberg-Agerholm

first: Eyal

first: Ido

last: Amit

first: Ala

last: Trusina

first: Joshua


title: Genome-wide ERa DNA-binding in MCF7 cells revealed by ChIP-seq

city: Cambridge

first: Zhaojie

state: MA

address: 300 Tech Sq

institute: H3 Biomedicine

summary: In the cellular setting, both H3B-6545 and H3B-9709 were confirmed to be non-degraders and had similar global DNA-binding patterns.

overall_design: ERalpha CHIPSEQ in MCF7 cells treated with H3B-6545, H3B-9709, Fulvestrant, Tamoxifen and E2

first: Zhenhua

last: Wu

first: Craig

last: Furman

first: Xiaoling

last: Puyang

first: Manav

last: Korpal


title: Mammary Gland microRNA profiling in female mice receiving flaxseed or its oil and secoisolariciresinol diglucoside components

city: Toronto

first: Elena

last: Comelli

state: Ontario

address: 1 king's college circle, MSB5354

department: Nutritional Sciences

institute: University of Toronto

summary: Breast cancer is one of the most leading causes of cancer mortality in the world. A growing body of evidence demonstrates the association between flaxseed (FS) consumption and the reduction of breast cancer risk. Flaxseed (FS) is an oilseed rich in n-3 polyunsaturated fatty acids (PUFA), α-linolenic acid (ALA), in dietary phytoestrogen lignan, secoisolariciresinol diglucoside (SDG), and in fiber. Early-life exposure to FS or to its isolated components was associated with the improvement of the mammary gland (MG) morphogenesis and differentiation, and prevention of the MG carcinogenesis. Here, we investigated the effect of FS as a whole food and its isolated oil (FSO) and lignan (SDG) on the MG microRNA (miRNA) signature, in female mice at a late stage of development. We identified a diet-specific MG miRNA signature. Significantly deregulated miRNAs in response to the 3-weeks intervention were associated with breast cancer. Identified miRNAs targeted genes enriched in MG growth and development and in cancer. These miRNAs could be used as potential biomarkers for breast cancer.

overall_design:
4-5 weeks of age female C57BL/6 mice, were randomized into 4 groups (n=6/group) to receive: i) Basal AIN-93G, ii) 10% FS, iii) 3.67% FSO or iv) 0.15% SDG for 3 weeks. After the intervention, the mice were sacrificed and the mammary gland (4th left) was collected for total RNA extraction and miRNA profiling using Nanostring technologies.
Please note that two samples ('Mammary Gland- Basel Diet-female05' and 'Mammary Gland- 3.67% Flaxseed Oil-female05') were excluded from the final analysis because less than 75% of miRNA probes had values above the background (the samples were quality-filtered).
Please note that both txt files and the RCC files contain raw miRNAs data (there is no difference between them) and were included to facilitate their download/use by the scientific community.

first: Amel

last: Taibi

first: Diana

first: Zhen

last: Lin

first: Lilian

last: Thompson


title: Genome-wide Screening in the Haploid System Reveals Slc25a43 as a Target Gene of Oxidative Toxicity

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

summary: Reactive oxygen species (ROS) are extensively assessed in physiological and pathological studies; however, the genes and mechanisms involved in antioxidant reactions are elusive. To address this knowledge gap, we used a forward genetic approach with mouse haploid embryonic stem cells (haESCs) to generate high-throughput mutant libraries, from which numerous oxidative stress-targeting genes were screened out. We performed proof-of-concept experiments to validate the potential inserted genes. Slc25a43 (one of the candidates) knockout (KO) ESCs presented reduced damage caused by ROS and higher cell viability when exposed to H2O2. Subsequently, ROS production and mitochondrial function analysis also confirmed that Slc25a43 was a main target gene of oxidative toxicity. In addition, we identified that KO of Slc25a43 activated mitochondria-related genes including Nlrx1 to protect ESCs from oxidative damage. Overall, our findings facilitated revealing target genes of oxidative stress and shed lights on the mechanism underlying oxidative death.

overall_design: Comparison of the transcriptomes between WT-ESCs, Slc25a43-KO ESCs, and Nlrx1-OE ESCs by RNA-seq analysis.

first: Wenhao

last: Zhang

first: Jinxin

first: Yiding

last: Zhao


title: Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin [Capture Hi-C]

first: Clifford

last: Tepper

overall_design: The overall goal of these studies was to define the long-range chromatin interactions occurring within the KSHV genome as well as between the KSHV and human host cell genomes both during latency and viral reactivation. These were defined in an unbiased manner using Hi-C analysis, which is chromosome conformation capture (3C) combined with next-generation sequencing (NGS). A modified protocol, referred to as Capture Hi-C, was utilized to selectively enrich interactions involving KSHV by performing target enrichment with a custom-designed KSHV genomic capture probe library. Experiments were performed in three different KSHV naturally infected human primary effusion lymphoma (PEL) cell lines (TREx-F3H3-K-Rta BCBL-1, BC1 and BC3) and wild type or ORF57-Stop recombinant KSHV infected iSLK cells.

first: Yoshihiro

last: Izumiya

first: Mel

last: Campell

first: Ashish

last: Kumar

first: Yuanzhi

last: Lyu

first: Yuichi

last: Yanagihashi

first: Chanikarn

last: Chantarasrivong

first: Kazushi

last: Nakano

first: Ryan

last: Davis


title: Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin


title: The mitochondrial metabolic enzyme Hexokinase 2 regulates stem cell function and differentiation by increasing chromatin openness and the accessibility of stem cell genes [RNA-Seq]

first: Aaron

last: Schimmer

state: CA-ON

address: 101 College St

institute: Princess Margaret Cancer Centre

summary: Mitochondrial metabolites regulate the function and differentiation of leukemic and normal stem cells by affecting epigenetic marks.  However, it is less understood how mitochondrial enzymes localize to the nucleus to control stem cell function. We discovered that the mitochondrial metabolic enzyme Hexokinase 2 (HK2) localizes to the nucleus in leukemic and normal hematopoietic stem cells. Overexpression of nuclear HK2 increased leukemic stem cell (LSC) properties and decreased differentiation while selective knockdown of nuclear HK2 promoted differentiation and decreased stem cell function. The nuclear localization of HK2 was phosphorylation dependent and required active import and export. Nuclear HK2 regulated LSC and differentiation independent of its enzymatic and metabolic activity. HK2 interacted with nuclear proteins that regulate chromatin openness and increased chromatin accessibilities at sites associated with the LSC+ signature and DNA damage repair. Consistent with these effects, nuclear HK2 increased repair of DNA damage and contributed to the mechanism by which LSCs resist DNA damaging agents. Thus, we describe a non-canonical mechanism by which mitochondrial enzymes regulate gene expression and stem cell function independent of their metabolic function.

overall_design: Gene expression analysis upon knock-down of Nuclear HK2.

first: Geethu

middle: E

last: Thomas


title: The mitochondrial metabolic enzyme Hexokinase 2 regulates stem cell function and differentiation by increasing chromatin openness and the accessibility of stem cell genes [ChIP-Seq]

overall_design: Examination of nuclear HK2 interaction with DNA or DNA bound proteins


title: The PAF1 complex promotes 3‘ processing of pervasive transcripts [PRO-Seq]

first: wei

last: guo

overall_design: Examination of transcription level upon PAF1 and INTS11 depletion

first: Xinhong

last: Liu

first: Ziwei

last: Guo

first: Han

last: Jing

first: Bin

first: Xiaoyu

last: Hu

first: Charles

last: David

first: Mo

last: Chen


title: Gene expression regulation in MCF7 cells by H3B-6545, H3B-9709, Fulvestrant and Tamoxifen

first: Zhaojie

last: Zhang

summary: In the cellular setting, both H3B-6545 and H3B-9709 were confirmed to be non-degraders and had nearly identical impact on global gene expression changes

overall_design: RNASEQ in MCF7 cells treated with H3B-6545, H3B-9709, Fulvestrant and Tamoxifen

first: Zhenhua

last: Wu

first: Craig

last: Furman

first: Xiaoling

last: Puyang

first: Manav

last: Korpal


title: A low sugar diet enhances Drosophila body size in males and females via sex-specific mechanisms

status: Public on Mar 14 2022

city: Vancouver

first: Elizabeth

last: Rideout

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: The University of British Columbia

summary: We report sex differences in mRNA levels between male and female Drosophila larvae reared on a diet containing sugar (1S) vs a -low-sugar diet (0S)

overall_design: mRNA profiles of third instar larvae reared on a 1S or 0S diet

first: Jason

middle: W

last: Millington


title: RNA-Seq analysis of traumatic and degenerative tears of tendon tissues of human shoulder joint

first: Muhammad Farooq

last: Rai

summary: Objective  To identify transcript level differences between traumatic and degenerative tears of tendon tissues in shoulder joint using RNA-seq.  Methods  Tendon tissues were isolated from female and male patients with traumatic or degenerative tears during arthroscopic surgery (N = 31). Differentially expressed transcript were identified and biological processes enriched in traumatic and degenerative tears were probed computationally. Expression pattern of selected transcripts was validated by real-time qPCR.  Results  We identified 339 and 336 transcripts differentially expressed between traumatic and degenerative tears in females and males respectively at a fold-change greater than |2| and a p-value  0.05. In females, GSTM1, MT1G, S1008A, ACSM3, DSC, FAM110C and VNN2 were the most prominent transcripts elevated in traumatic tears and CHAD, CLEC3A, IBSP, TNMD, APLNR, and CPA3 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented catabolic processes, immune response, and metabolic processes while those repressed in traumatic tears represented tissue morphogenesis and developmental processes, angiogenesis, and extracellular matrix organization. In males, ELOA3B, CXCL8, ADM, TNS4 and SPOCK1 were the most prominent transcripts elevated in traumatic tears and MYL2, TNNC1, MB, CPA3, APLNR, and CA3 were most highly repressed in traumatic tears. Transcripts elevated in traumatic tears represented localization of endoplasmic reticulum, chromosome organization, leukocyte/neutrophil degranulation, and protein transport whereas those repressed in traumatic tears represented muscle development, blood circulation (angiogenesis), and muscle cell differentiation. Numerous novel lncRNAs were also identified to be differentially expressed between traumatic and degenerative tears in both sexes.  Conclusions and Clinical Relevance  This study improves our molecular understanding of tendon tissues in patients with rotator cuff tendinopathy based on underlying etiology (trauma and degeneration). It also provides new insights into sex-based transcript differences that may help drive clinical decision making in female and male patients with traumatic and degenerative shoulder injuries.

first: Muhammad

first: Lei

last: Cai

first: Eric

last: Tycksen

first: Jay

last: Keener

first: Aaron

last: Chamberlain


title: RNA-seq and ChIP-seq in MCF7 cells treated with H3B-6545, H3B-9709, Fulvestrant and Tamoxifen


title: A molecular complex of Cav1.2/CaMKK2/CaMK1a in caveolae is responsible for vascular remodeling through excitation-transcription coupling in vascular smooth muscle.

city: Nagoya

first: Yoshiaki

last: Suzuki

address: 3-1 Tanabedori, Mizuhoku

department: Molecular and Cellular Pharmacology, Graduate School of Pharmaceutical Sciences

institute: Nagoya City University

summary: Elevation of intracellular Ca2+ ([Ca2+]i) activates Ca2+/calmodulin-dependent kinases (CaMK) and promotes gene transcription. This essential signaling pathway is referred to as excitation-transcription (E-T) coupling. Although vascular myocytes can exhibit E-T coupling, the molecular mechanisms and physiological/pathological roles are unknown. Multiscale analysis spanning from single molecules to whole organisms has revealed essential steps in mouse vascular smooth muscle E-T coupling: (1) Upon depolarizing stimulus Ca2+ influx through voltage-dependent Ca2+ channel Cav1.2 activates CaMKK2, which results in phosphorylation of CaMK1a and CREB in the nucleus. (2) Within caveolae the formation of molecular complex of Cav1.2/CaMKK2/CaMK1a is promoted in the vascular myocytes. (3) Ca2+ influx through Cav1.2 localized to caveolae  directly activates CaMKK2. (4) CaMK1a is phosphorylated by CaMKK2 at caveolae and translocated to the nucleus upon membrane depolarization. In addition, RNAseq analysis revealed that sustained depolarization of mesenteric artery preparation selectively induced genes related to chemotaxis, leukocyte adhesion and inflammation, and these changes were reversed by inhibitors of Cav1.2, CaMKK2 and CaMK or disruption of caveolae. In the context of pathophysiology, when mesenteric artery was loaded by high pressure in vivo, we noted CREB phosphorylation in myocytes, macrophage accumulation at adventitia, and increased thickness and cross-sectional area of tunica media. These changes were reduced in caveolin1-KO mice or in mice treated with a CaMKK2 inhibitor STO609. In summary, E-T coupling depend on Cav1.2/CaMKK2/CaMK1a localized to caveolae, and this molecular complex converts [Ca2+]i changes to gene transcription, leading to macrophage accumulation and media remodeling for adaptation to increased circumferential stretch.

overall_design: Mesenteric artery mRNA profiles of 10 weeks old wild type (WT) mice

first: Wayne

last: Giles

first: Gerald

last: Zamponi

first: Yuji

last: Imaizumi

first: Hisao

last: Yamamura


title: Colorectal Cancer Concurrent Gene Signature Based on Coherent Patterns between Genomic and Transcriptional Alterations

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

summary: The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature.

overall_design: The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n=345).

first: Ming-Hung

last: Shen

first: Chi-Jung

last: Huang

first: Thien-Fiew

last: Ho

first: Chih-Yi

last: Hsu

first: Ying-Yih

last: Shih

first: Ching-Shui

first: Chi-Cheng


title: Elevated numbers of infiltrating eosinophils accelerate the progression of Duchenne Muscular Dystrophy pathology in mdx mice.

first: Fabio

last: Rossi

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

summary: Eosinophils are implicated in the development of many chronic diseases. However, their function in muscular dystrophy is understudied. Here we demonstrate that muscle hyper-eosinophilia could be a marker of poor outcomes in Duchenne Muscular Dystrophy.

overall_design: To assess the effect of hyper-eosinophlia on muscle homeostasis, regeneration, and repair, SiglecF+ cells from WT and IL-5Tg mice were sorted from damaged muscles and subjected to RNAseq

first: Marine

last: Theret

first: Lin

last: Tung

first: Tara

last: Stach


title: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism (synthetic viability screen)

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids from S-phase until mitosis. The acetylation of cohesin’s SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the 3D genome. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 rather promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. Using a genome-wide haploid genetic screen we reveal that acetylation rather controls cohesin’s interaction with PDS5A to restrict chromatin loop length. Our data supports a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding.

overall_design:
Genes required for viability in ∆HDAC8 cells were profiled as previously described in detail (Blomen et al., 2015). ∆HDAC8 HAP1 cells were mutagenized using a gene-trap retrovirus which was produced in HEK293T cells and concentrated either by ultracentrifugation as described previously (Blomen et al., 2015),  or employing centrifugal ultrafiltration devices. Here, retrovirus-containing medium was harvested on two consecutive days, filtered (0.45 um) and concentrated using Amicon Ultra-15 Centrifugal Filter Units with 100K MWCO (Merck-Millipore). The virus concentrates from both harvests were combined, supplemented with 8 ug/mL protamine sulfate (Sigma) and used to infect ~40 million HAP1 cells.
4 control datasets have been previously published (Blomen et al., 2015; NCBI SRA accession no. SRP058962)

first: Marjon

last: van Ruiten

first: Astrid

last: Fauster

first: Thijn

last: Brummelkamp

first: Benjamin

last: Rowland


title: The mitochondrial metabolic enzyme Hexokinase 2 regulates stem cell function and differentiation by increasing chromatin openness and the accessibility of stem cell genes [ATAC-Seq]

first: Aaron

last: Schimmer

overall_design: Investigate the role of Chromatin openess by nuclear HK2 by comparitive analysis of nuclear HK2 overexpression and Nuclear HK2 knockdown cells

first: Geethu

last: Thomas


title: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism

overall_design: Refer to individual Series


title: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism (Hi-C)

summary: Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids from S-phase until mitosis. The acetylation of cohesin’s SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the 3D genome. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 rather promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. We reveal that acetylation rather controls cohesin’s interaction with PDS5A to restrict chromatin loop length. Our data supports a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding.

overall_design: Hi-C was performed in G1 isolated cells from the following genotypes: Wild Type, ∆ESCO1, ∆HDAC8, ∆ESCO1/∆HDAC8, ∆WAPL, ∆WAPL/∆ESCO1, ∆PDS5A, ∆PDS5B and ∆PDS5A/∆HDAC8 cells. Hi-C replicate experiments were performed in all genotypes. Asynchronous Hi-C analysis was performed in Wild Type cells and ∆HDAC8 cells.

first: Ángela

last: Cacciatore

first: Démi

last: van Gent

first: Laureen

last: Willems

first: Judith

middle: H

last: Haarhuis

first: Elzo

last: de Wit


title: Single-cell transcriptomics  highlights the proinflammatory contribution of C1q-high monocytes to Behçet’s disease

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

summary: Behçet’s disease (BD) is a chronic vasculitis characterized by systemic immune aberrations. Here, we performed single-cell sequencing to profile peripheral blood mononuclear cells (PBMCs) and isolated monocytes from BD patients and healthy donors. We observed prominent expansion and transcriptional changes in monocytes in PBMCs from BD patients. Deciphering the monocyte heterogeneity revealed the accumulation of C1q-high (C1qhi) monocytes in BD. Pseudotime inference indicated that BD monocytes markedly shifted their differentiation toward inflammation-accompanied and C1qhi monocyte-ended trajectory. Further experiments showed that C1qhi monocytes enhanced phagocytosis and proinflammatory cytokine secretion, and multi-platform analyses revealed the significant clinical relevance of this subtype. Mechanistically, C1qhi monocytes were induced by activated IFN-γ signaling in BD patients, and were decreased by tofacitinib treatment. Our study illustrates BD immune landscape and the unrecognized contribution of C1qhi monocytes to BD hyperinflammation, showing their potential as therapeutic targets and clinical assessment indexes.

overall_design:
This dataset contains single-cell sequencing results of PBMCs (BD: n=4, HC: n=4) and isolated CD14+monocytes (BD: n=4, HC: n=4) . Please note that raw data are not provided as they are derived from human subjects.
***Raw data not available due to patient privacy concerns***

first: Xiaoman

last: Wang

first: Jinjing

last: Liu

first: Xin

last: Yu

first: Jijun

first: Xiaoya

last: Pei

first: Heping

first: Hua

last: Chen

first: Hou-Zao


title: Persister state-directed transitioning and vulnerability in melanoma

city: Essen

first: Alexander

last: Roesch

address: Hufelandstrasse 55

department: Department of Dermatology

institute: University hospital Essen

summary: Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. For example, melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhigh cells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhigh persister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a new dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor growth and plasticity and primes melanoma cells towards lineage-specific elimination.

overall_design: RNAseq of melanoma cells with KDM5B knockdown (WM3734Tet3G-shJARID1B or as control  WM3734Tet3G-scramble, described in Shannan et al., European journal of cancer 2019) were induced with 500 ng/ml doxycycline for 72 h and analysed in triplicate using Illumina sequencer NextSeq 500.

first: H

last: Chauvistré

first: S

last: Lueong

first: J

last: Forster

first: A


title: Three-dimensional geome study of procine livers during development and metabolic adaptation

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Liver development and metabolic adaptation are well-orchestrated by a series of signaling pathways and genes. Chromatin architecture is known to influence gene expression, yet its role in controlling liver development and metabolism remains unclear. We performed high-throughput chromatin conformation capture sequencing (HiC-seq) and integrated RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) on liver tissue that were collected from six key developmental stages (embryonic day 38 [E38] – 2 years [2y]) and a high fat diet (HFD) feeding group. Our data revealed global three-dimensional (3D) reorganization during liver development from the scales of compartment, topologically associated domain (TAD) and promoter-enhancer interaction (PEI), which consistently affects the expression level of genes known to be important for liver development and function. Comparison of 3D genome and gene expression profiles between pig liver development and human hepatocellular carcinoma (HCC) revealed similarities between fatal liver and HCC and provided potential explanation for the aberrant expression in HCC from the perspective of chromatin architecture. Moreover, the similar genome architecture and expression of genes related to lipid metabolism between nomally and HFD feeding pigs, along with the thicker back fat in HFD feeding pigs compared to normally feeding pigs, supported that pigs are resistant to nonalcoholic fatty liver disease (NAFLD). Together, our results provide a global view of dynamic chromatin interactions during liver development and metabolic adaptation induced by HFD feeding, which may open new avenues for liver research and HCC therapeutic interventions.

overall_design: We generated high-throughput chromatin conformation capture (Hi-C) sequencing data, integrated RNA sequencing data and chromatin immunoprecipitation (ChIP) sequencing data of pig liver tissues at embryonic day 38 (E38), embryonic day 80 (E80),  birth day (0d), postnatal day 28 (28d), postnatal day 110 (110d) and 2 years (2y) as well as high fat diet (HFD) treatment with 1-6 replicates.

first: Luxi

first: Mingzhou


summary: Phenotypic heterogeneity and plasticity represent major drivers of tumor relapse in melanoma. Expression of the H3K4 demethylase and pRB-binding protein JARID1B/KDM5B follows a dynamic continuum across melanoma cells. Highly JARID1B-expressing cells are enriched after short-term drug treatment. However, under persistent drug-exposure, JARID1B heterogeneity is reconstituted. Using a doxycycline-titratable system and a novel chemical enhancer of JARID1B-expression, we found that JARID1Bhigh cells are transiently 'pseudo-differentiated'. Melanoma cells use this JARID1Bhigh growth-arrested state to survive drugs, but must decrease JARID1B expression again to re-enter cell cycling for long-term tumor repopulation. Overcoming the reversion to phenotypic heterogeneity by exogenous homogenization of the JARID1Bhigh phenotype causes tumor growth arrest, also in MAPKi-resistant melanoma. Mechanistically, JARID1B represents an integral checkpoint for coordinating cell differentiation via transcriptional control, stabilization of hypophosphorylated pRB, and attenuation of cytokinetic abscission. Thus, the plasticity among tumor differentiation states per se represents a novel therapeutic target, which can be chemically overcome.

overall_design: RNAseq of melanoma cells (WM3734 and CSM152 treated with Cpd1 or control for 72h and WM3734Tet3G-KMD5B cells Doxycycline-induced for 24h, 48h or 72h) were analysed in triplicate using Illumina sequencer NextSeq 500.

first: D

last: Picard

first: M

last: Remke


title: The mitochondrial metabolic enzyme Hexokinase 2 regulates stem cell function and differentiation by increasing chromatin openness and the accessibility of stem cell genes

first: Aaron

middle: D

last: Schimmer

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


title: Genome-wide analysis of gene expression after knockdown of KDM5B in melanoma cells.

summary: Analysis of the effects of KDM5B in melanoma cells at gene expression level. Knockdown of KDM5B provides important information about potential target genes of KDM5B.

overall_design: Melanoma cells (WM3734 infected with shKDM5B (62) or as control scramble (SCR)) were analysed using Illumina HumanWG-6 v3.0 expression beadchip.

first: Meenhard

last: Herlyn

first: Andrew

last: Kossenkov

first: Patricia

last: Brafford


title: The PAF1 complex promotes 3‘ processing of pervasive transcripts [ChIP-seq]

first: wei

last: guo

summary: The PAF1 complex (PAF1C) functions in multiple transcriptional and co-transcriptional processes. Although many aspects of the requirement for PAF1 in coding gene transcription have been heavily studied, the function of PAF1C at sites of non-coding transcription is poorly understood.  eRNAs and PROMPTs are pervasive transcripts transcribed by RNA Polymerase II and rapidly degraded after 3’ endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C depletion results in near universal 3’ end processing defects in pervasive transcripts, leading to transcription termination dysregulation. Mechanistically, PAF1C recruits Integrator to chromatin through direct interactions promoting timely cleavage and transcription termination of pervasive transcripts. We also show that PAF1C recruits Integrator to the promoters of coding genes, where PAF1C then dissociates from the Integrator complex upon entry into processive elongation. Our results demonstrate an unexpected function for PAF1C in limiting the length and accumulation of pervasive transcripts, while highlighting a general requirement for PAF1C in Integrator recruitment.

overall_design: Examination of H3K27ac, PAF1 and INTS11 distribution

first: Xinhong

first: Ziwei

last: Guo

first: Han

last: Jing

first: Bin

last: Zhang

first: Xiaoyu

last: Hu

first: Charles

last: David

first: Mo


title: MethylC-Seq: Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

country: Australia

institute: Monash University

summary: The impact of aging on intestinal stem cells (ISCs) has not been fully elucidated. In this study, we identified widespread epigenetic and transcriptional alterations in old ISCs. Using a reprogramming algorithm, we identified a set of key transcription factors (Egr1, Irf1, FosB) that drives molecular and functional differences between old and young states. Overall, by dissecting the molecular signature of aged ISCs, our study identified transcription factors that enhance the regenerative capacity of ISCs.

overall_design: Methylome profiles of intestinal stem cells of young (2 month) and old (22 month) mice.

first: Jose

last: Polo

first: Christian

last: Nefzger

first: Helen

last: Abud

first: Thierry

last: Jarde


title: SF3B1 homeostasis is critical for survival and therapeutic response in T cell leukemia

status: Public on Mar 13 2022

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: The production of noncanonical mRNA transcripts is associated with cell transformation. Driven by our previous findings on the sensitivity of T cell acute lymphoblastic leukemia (T-ALL) cells to SF3B1 inhibitors, we identified that SF3B1 inhibition blocks T-ALL growth in vivo with no notable associated toxicity. We also revealed protein stabilization of the U2 complex component SF3B1 via deubiquitination. Our studies showed that SF3B1 inhibition perturbs exon skipping, leading to nonsense-mediated decay and diminished levels of DNA damage response–related transcripts, such as the serine/threonine kinase CHEK2, and impaired DNA damage response. We also identified that SF3B1 inhibition leads to a general decrease in R-loop formation. We further demonstrate that clinically used SF3B1 inhibitors synergize with CHEK2 inhibitors and chemotherapeutic drugs to block leukemia growth. Our study provides the proof of principle for posttranslational regulation of splicing components and associated roles and therapeutic implications for the U2 complex in T cell leukemia.

overall_design: Examination of the role of SF3B1 in T cell leukemia.

first: Cuijuan

last: Han

first: Yalu

last: Zhou

first: Panagiotis

last: Ntziachristos


title: Unstranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

status: Public on Mar 12 2022

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Taf8 was deleted in the mouse central nervous system using our Taf8 conditional allele. To determine transcriptional changes due to Ta8 deletion in the developing CNS, unstranded RNA sequencing was performed on cortices from Taf8 deleted embryos (E14.5 Taf8lox/–NesCreT/+p53–/–)  and control embryos (E14.5 Taf8+/+NesCreT/+p53–/–).

overall_design: Four Taf8-deleted and four control samples were prepared, each from a separate mouse embryo. Unstranded RNA sequencing was undertaken on an Illumina HiSeq 2000 to produce 100bp paired-end reads.

first: Yunshun

last: Chen

first: Farrah

last: El-Saafin

first: Tim

last: Thomas

first: Anne

last: Voss


title: Genomewide expression profiling from peripheral blood of multibacillary leprosy and Erythema Nodosum Leprosum (ENL) before and after thalidomide treatment.

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

summary: Acute inflammatory episodes are common in leprosy and complicate the course of the disease. Among these episodes, Erythema Nodosum Leprosum (ENL) is more common in multibacillary patients and can cause more systemic symptoms like fever, myalgia, edema, and pain. Today, ENL is managed with thalidomide and corticosteroids, yet the exact mechanisms behind ENL remain elusive and with few pharmacological options available. In this experiment, RNA was sequenced and gene expression was measured from the blood of multibacillary patients with and without ENL in a mixed design, comparing ENL to MB and ENL before and after thalidomide treatment for 7 days.

overall_design: 37 human blood samples (statistical unit) were included. The sample size for each group are: 9 MB, 15 ENL, and 13 Thalidomide, including both sexes and with age ranging from 17 to 78 years (mean age in years = 42).

first: Thabatta

middle: L

last: Rosa

last: Leal-Calvo

first: Verônica

last: Schmitz

first: Milton

middle: O

last: Moraes

first: Maria

middle: C

last: Pessolani


title: FOXO3 expression in macrophages is lowered by high fat diet and  regulates colonic inflammation and tumorigenesis

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1324 Tulane Ave

department: Pathology

institute: Tulane Univeristy

summary: Obesity, characterized by augmented inflammation and tumorigenesis, is linked to genetic predispositions, such as FOXO3 polymorphisms. As obesity is associated with aberrant macrophages infiltrating different tissue including the colon, we aimed to identify FOXO3-dependent transcriptomic changes in macrophages that drive obesity-mediated colonic inflammation and tumorigenesis. We found that in mouse colons, high-fat-diet-(HFD)-obesity led to diminished FOXO3 levels and increased macrophages. Transcriptomic analysis of mouse peritoneal FOXO3-deficient macrophages showed significant differentially expressed genes (DEGs; FDR<0.05) similar to HFD-obese colon. These DEGs related pathways, linked to mouse colonic inflammation and tumorigenesis, were similar to those in inflammatory bowel disease (IBD) and human colon cancer. Additionally, we identified a specific transcriptional signature for the macrophage-FOXO3 axis (MAC-FOXO382), which separated the transcriptome of affected tissue from control in both IBD (p=5.2E-08) and colon cancer (p=1.9E-11), revealing its significance in human colonic pathobiologies. Further, we identified (heatmap) and validated (qPCR) DEGs specific to FOXO3-deficient macrophages with established roles both in IBD and colon cancer (IL-1B, CXCR2, S100A8, S100A9, and TREM1) and those with unexamined roles in these colonic pathobiologies (STRA6, SERPINH1, LAMB1, NFE2L3, OLR1, DNAJC28 and VSIG10). These findings establish an important understanding of how HFD-obesity and related metabolites promote colonic pathobiologies.

overall_design: RNAseq analysis of macrophages, wild type vs FOXO3 KO mice

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