title: ATF4 Protects the Heart from Failure by Antagonizing Oxidative Stress

city: Dallas

first: GUANGYU

last: ZHANG

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UTsouthwestern Medical Center

summary: Cellular redox control is maintained by generation of reactive oxygen/nitrogen species balanced by activation of antioxidative pathways. Disruption of redox balance leads to oxidative stress, a central causative event in numerous diseases including heart failure. Redox control in the heart exposed to hemodynamic stress, however, remains to be fully elucidated. Here, we show that production of cardiomyocyte NADPH (nicotinamide adenine dinucleotide phosphate), a key factor in redox regulation, is decreased in pressure overload-induced heart failure. As a consequence, the level of reduced glutathione is downregulated, a change associated with cardiac cell death, fibrosis, and cardiomyopathy. We report that the pentose phosphate pathway (PPP) and mitochondrial serine/glycine/folate metabolic signaling, two major NADPH-generating pathways in the cytosol and mitochondria, respectively, are induced in the heart by pressure overload. We identify ATF4 (activating transcriptional factor 4) as an upstream transcription factor controlling the expression of multiple enzymes in these two pathways. Consistent with this, joint pathway analysis (JPA) of transcriptomic and metabolomic data reveals that ATF4 preferably controls oxidative stress and redox-related pathways. Overexpression of ATF4 in cardiomyocytes in culture leads to a significant increase in NADPH-producing enzymes whereas silencing of ATF4 decreases their expression. Further, stable isotope tracer experiments reveal that ATF4 overexpression in vitro strongly augments metabolic flux within these two pathways. In vivo, cardiomyocyte-specific deletion of ATF4 exacerbates cardiomyopathy in the setting of pressure overload and accelerates the development of heart failure, attributable, at least in part, to an inability to increase the expression of NADPH-generating enzymes. Taken together, our findings reveal that ATF4 plays a critical role in cardiac homeostasis under conditions of hemodynamic stress by governing both cytosolic and mitochondrial production of NADPH.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: There is 18 sample in this RNA-seq data. The samples 1-6 all treat with sham surgery which can be divided into two groups: 3 samples for ctrl group and 3 samples for cKO group. The samples 7-12 all treat with TAC surgery for 3 days, which can also be divided into two groups: 3 samples for ctrl group and 3 samples for cKO group. The samples 13-18 all treat with TAC surgery for 7 days, which can also be divided into two groups: 3 samples for ctrl group and 3 samples for cKO group.

first: Xiaoding

last: Wang

first: Guangyu

last: Zhang

first: Subhajit

last: Dasgupta

first: Chao

last: Li

first: Qinfeng

first: Lin

last: Tan

first: Philip

middle: L

last: Lorenzi

first: Beverly

last: Rothermel

first: Philipp

last: Scherer

last: Hill


title: gene expression profiles in ankles from CAIA mice model

status: Public on May 16 2022

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: To identify a candidate epigenetic regulator in RA pathogenesis, gene expression microarray analysis was conducted using mRNA obtained from whole ankle tissue in collagen antibody-induced arthritis (CAIA) mice and two control mice (CtrlP and CtrlL)

overall_design: collagen antibody induced arthritis (CAIA): 5 mg of anti-collagen 2 monoclonal antibody cocktail (Chondrex, USA, Redmond) was administered on day 0, followed by 50 μg of LPS on day 3 i.p. RNA was extracted from ankle tissues of Control, LPS control and CAIA mice.

first: Katsuhide

last: Igarashi


title: Dual interactions of K27M mutant nucleosomes with PRC2 and MLL1 shape the cancer epigenetic landscape [CUT&RUN, HEK293]

status: Public on May 15 2022

city: Rehovot

first: Efrat

last: Shema

address: Herzl St 234

department: Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer associated mutations in genes encoding histones dramatically reshape chromatin patterns and support tumorigenesis, despite their low prevalence. Lysine to Methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate Polycomb activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial chromatin patterns associated with K27M expression. We find that K27M-mutant nucleosomes not only sequester PRC2, but also bind preferentially to MLL1, thus leading to genome-wide redistribution of H3K4me3. K27M-mediated deregulation of both repressive and activating chromatin marks maintains ‘bivalent’ chromatin, supporting a poorly differentiated cellular state. This study provides evidence for widespread effects of the K27M oncohistone on multiple core epigenetic pathways, and highlights the use of single-molecule tools to reveal mechanisms of chromatin deregulation in cacner.

overall_design: Cut&Run analysis of HEK293 cell line. CUT&RUN assay was done as described in Skene et al (2017) with slight modifications as follows. Cells were harvested and counted with 200000 cells per reaction. Permeabilized cells, bound to Concanavalin A-coated beads were mixed with individual primary antibody  and incubated overnight at 4°C while rotating. Secondary antibody, anti-rabbit HRP was used as a negative control.

first: Noa

last: Furth

first: Danielle

last: Algranati

first: Bareket

last: Dassa


title: Gene expression of hCG-treated rat mammosphere culture

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

country: USA

institute: Fox Chase Cancer Center

summary:
We previously showed that recombinant human chorionic gonadotropin (r-hCG) induces mammary gland differentiation and inhibits mammary tumorigenesis in rats. The present study investigates the impact of r-hCG on the stemness of mammary epithelial cells by using a rat model.
We performed microarray analysis of RNA isolated from mammospheres formed by normal mammary epithelial cells extracted from rats treated for 21 days either with r-hCG  or vehicle (control).

overall_design: Female Sprague Dawley rats at age 55 days were treated daily via intraperitoneal injection with 100 IU/day r-hCG;  or vehicle control (phosphate buffered saline) for 21 days. Rat mammary gland 4&5 from three animals from each group were resected 21 days after the last day of treatment. Mammary epithelial cell enriched single cells were plated in 6-well ultra-low attachment plate. The formation of mammosphere was checked daily. After 7 days of culture, the mammospheres were used for RNA extraction and Affymetrix microarray analysis.

first: Yanrong

last: Su

first: Michael

last: Slifker

first: Thomas

last: Pogash

first: Ricardo

last: Lopez de Cicco

first: Theresa

middle: D

last: Nguyen

first: Jose

last: Russo


title: METTL3 preferentially enhances non-m6A translation of epigenetic factors and promotes tumorigenesis (meRIP, RIP and polysome-seq)

city: Beijing

first: Yufeng

last: Gao

state: Beijing

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

type: Expression profiling by high throughput sequencing

summary: Methyltransferase-like 3 (METTL3) is the best known m6A methyltransferase of the N6-adenosine-methyltransferase complex that functions in the reversible epi-transcriptome modulation of m6A modification. Besides acting as a m6A methyltransferase, METTL3 also regulates mRNA translation as well as other biological processes either through m6A “reader”-mediated downstream effect or directly binding to m6A sites, but the underlying mechanism and biological significance of these cytoplasmic events remain undefined. Here, we demonstrated that METTL3 inhibition significantly delayed gastric tumorigenesis in patient-derived xenograft model. Intriguingly, global METTL3-binding profiling revealed METTL3 occupied numerous oncogenic mRNAs without m6A signals, indicating a novel mechanism independent of m6A machinery. Furthermore, METTL3 was observed to translocate from nucleus to cytoplasm during gastric carcinogenesis, and its cytoplasm-to-nucleus ratio was correlated with cancer progression. In addition, the nuclear retention of METTL3 nearly abolished its tumor-promoting activity. Mechanistically, METTL3 interacted with PABPC1 to promote RNA looping, thus facilitating the translation of multiple oncogenic mRNAs. Taken together, our findings indicate an unexpected role of METTL3 as an important translational regulator independent of either m6A-“writer” or -“reader” activities and suggest METTL3 as a therapeutic target in gastric cancer.

overall_design: Examination the cytoplasmic function of METTL3 in human gastric cancer

first: Xueju

last: Wei

first: Jingnan

last: Pi

first: Yue

last: Huo

first: Qinglv

first: Fang

last: Wang

first: Yu

last: Jia


title: RNA sequencing of ETV6-NCOA2 expression in CD34 positive cord blood cells

first: Gilgi

last: Friedlander

address: Hertzel st

summary: Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. Their pathogenesis is largely unknown, and their treatment is challenging. We have previously discovered the specific association between recurrent t(8;12)(q13;p13) chromosomal translocation, creating ETV6-NCOA2 fusion, with T/Myeloid leukemias. Here we report that the ETV6-NCOA2 initiates T/Myeloid leukemia in preclinical models and examine the expression profile induced by ETV6-NCOA2 in CD34+ cord blood progenitors in-vitro.

overall_design: Gene expression examination of ETV6-NCOA2 or empty vector in CD34 positive cord blood cells in-vitro. 3 replicates each (for each biological replicate, at least three different cord blood samples were mixed)

first: Shai

last: Izraeli

first: Hila

last: Fishman


title: TRAF4 promotes the malignancy of ovarian high-grade serous carcinoma by activating YAP pathway

city: Guangzhou

first: Xiaolin

last: Luo

state: Guangdong

address: 651 Dongfeng East Road

department: Gynecology Oncology

institute: Sun Yat'sen University Cancer Center

summary: Ovarian high-grade serous carcinoma (HGSC) accounts for the majority of deaths caused by epithelial ovarian cancer. The precise molecular changes attributable for the pathogenesis of HGSC are still largely unknown. TRAF4 has been identified to be up-regulated in some cancers. However, the association between TRAF4 and the malignancy of HGSC has not been elucidated before. In this study, we aim to explore the prognostic value and function of TRAF4 in HGSC. The results of immunohistochemistry in 174 cases of HGSC showed that high expression of TRAF4 was significantly associated with a shorter overall survival (p=0.005) and recurrence-free survival (p=0.003) in HGSC. Knock-down of TRAF4 inhibited the malignancy of ovarian cancer cells, and over-expression of TRAF4 increased cell malignancy both in vitro and in vivo. Moreover, mechanism studies demonstrated that TRAF4 promoted cell malignancy by activating YAP pathway in HGSC. In conclusion, TRAF4 could be a prognostic biomarker for HGSC and increase HGSC cell malignancy by activating YAP pathway, which may serve as a potential therapeutic target for HGSC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ovarian cancer cells and its knockdown derivatives (siTRAF4).

first: Jihong

last: Liu


title: ETV6-NCOA2 expression profile in T/M mixed-phenotype acute leukemia [ETV6_NCOA2_Mouse_in_vitro]

summary: Exparession profiling of lineage negative bone marrow cells from C57B/6 mice expressing either ETV6-NCOA2, KAT6-NCOA2 or empty-vector after five days in in-vitro culture.

overall_design: Gene expression examination in murine lineage negative cells expressing either ETV6-NCOA2, KAT6-NCOA2 or empty vector after five days in in-vitro culture.


title: ETV6-NCOA2 expression profile in T/M mixed-phenotype acute leukemia [ETV6-NCOA2 human]

summary: Exparession profiling of ETV6-NCOA2 at different stages of disease dEmpty vectorelopment: CD34 cord blood cells transduced with ETV6-NCOA2-GFP or with empty vector-GFP, CD34 cord blood cells transduced with ETV6-NCOA2-NGFR or ETV6-NCOA2-NGFR + NOTCH1-L1601PdP-GFP and transplanted in NSGS mice, and ETV6-NCOA2 patient derived xenografts.

overall_design: Expression profiling of ETV6-NCOA2 in human: CD34 positive cord blood cells transduced with ETV6-NCOA2 or empty vector, cultured five days in-vitro (n=3), ETV6-NCOA2 (n=3) or ETV6-NCOA2+NOTCH1-L1601PdP (n=5) transduced in CD34 positive cord blood cells and transplanted in NSGS mice, or ETV6-NCOA2 patient-derived xenografts (n=4).


title: Dual interactions of K27M mutant nucleosomes with PRC2 and MLL1 shape the cancer epigenetic landscape (ATAC-seq)

first: Efrat

last: Shema

overall_design: ATAC-seq analysis conducted on SU-DIPG13, SU-DIPG6 and SU-DIPG48 cells

first: Noa

last: Furth

first: Danielle

last: Algranati

first: Bareket

last: Dassa


title: High-throughput sequencing and analyses of the TCR repertoire

city: Shijiazhuang

first: Lei

last: Bao

address: Zhongshan road 361

institute: Hebei Medical University

summary: We co-cultured T cells with Mo-DCs exposed to ConA for 24 h and used multiplex PCR and next-generation sequencing to detect the TCRα repertoire.The length of the amino acids of CDR3 in each group was 4–59 amino acids, and all presented a normal distribution. Moreover, the length of the amino acids of CDR3 was not different between ConA and control groups. The number of clonotypes and unique clonotypes in the ConA group was increased significantly compared with that in control groups. However, the difference of high-frequency CDR3 amino-acid clonotypes between ConA and control groups was not significant (cutoff = 0.2%). Our results for the V and J gene segments of TCR diversity showed a marked increase in the number of clonotypes in the ConA group. The Shannon–Wiener Diversity Index of ConA was lower than that in the control group, and the top-20 V and J gene segments of ConA showed a higher usage frequency than that in the control group, but the difference between ConA and the control group was not significant. Collectively, these data indicated that ConA could reduce CDR3 diversity and augment usage of high-frequency CDR3.

overall_design: 3 samples of ConA, 3 samples of Cim, 3 samples of Cy, 3 samples of DNCB,3 samples of SDS and 3 samples of Control

first: Wu

last: Yao


title: Dual interactions of K27M mutant nucleosomes with PRC2 and MLL1 shape the cancer epigenetic landscape (MARS-seq)

overall_design: Bulk MARS-seq of DIPG cell culture


title: Human coronary plaque T cells are clonally expanded and display cross-reacting viral/self-antigen specificities

city: Stanford

first: Patricia

last: Nguyen

state: California

address: 300 Pasteur Dr

department: Cardiovascular Medicine

institute: Stanford University

summary:
Background:
Coronary artery disease is an incurable, life-threatening disease that was once considered primarily a disorder of lipid deposition. Coronary artery disease is now also characterized by chronic inflammation‚ notable for the buildup of atherosclerotic plaques containing immune cells in various states of activation and differentiation. Understanding how these immune cells contribute to disease progression may lead to the development of novel therapeutic strategies.

Methods:
We used single-cell technology and in vitro assays to interrogate the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity.

Results:
In addition to macrophages, we found a high proportion of αβ T cells in the coronary plaques. Most of these T cells lack high expression of CCR7 and L-selectin, indicating that they are primarily antigen-experienced memory cells. Notably, nearly one-third of these cells express the HLA-DRA surface marker, signifying activation through their TCRs (T-cell receptors). Consistent with this, TCR repertoire analysis confirmed the presence of activated αβ T cells (CD4<CD8), exhibiting clonal expansion of specific TCRs. Interestingly, we found that these plaque T cells had TCRs specific for influenza, coronavirus, and other viral epitopes, which share sequence homologies to proteins found on smooth muscle cells and endothelial cells, suggesting potential autoimmune-mediated T-cell activation in the absence of active infection. To better understand the potential function of these activated plaque T cells, we then interrogated their transcriptome at the single-cell level. Of the 3 T-cell phenotypic clusters with the highest expression of the activation marker HLA-DRA, 2 clusters expressed a proinflammatory and cytolytic signature characteristic of CD8 cells, while the other expressed AREG (amphiregulin), which promotes smooth muscle cell proliferation and fibrosis, and, thus, contributes to plaque progression.

Conclusions:
Taken together, these findings demonstrate that plaque T cells are clonally expanded potentially by antigen engagement, are potentially reactive to self-epitopes, and may interact with smooth muscle cells and macrophages in the plaque microenvironment.

overall_design:
We performed scRNA-seq on human coronary arteries collected from 12 donors, along with paired blood samples from 3 of the donors. These data contain sequenced alpha beta T cells.
*** Raw data are not included, due to patient confidentiality. ***

first: Roshni

last: Chowdhury

first: Jessica

last: D'addabbo

first: Xianxi

last: Huang

first: Stefan

last: Veizades

first: Koki

last: Sasagawa

first: Jan

last: Sokol

first: Paul

last: Cheng

first: David

last: Louis

first: Alexandria

last: Tso

first: Annie

last: Jensen

first: Vishnu

last: Shankar

first: Ben

last: Wendel

first: Isaac

last: Bakerman

first: Grace

last: Liang

first: Tiffany

last: Koyano

first: Robyn

last: Fong

first: Allison

last: Nau

first: Herra

last: Ahmad

first: Jayakrishnan

last: Gopakumar

first: Robert

last: Wirka

first: Andrew

middle: S

last: Lee

first: Jack

last: Boyd

first: Joseph

middle: Y

last: Woo

first: Thomas

last: Quertermous

first: Gunsagar

last: Gulati

first: Siddhartha

last: Jaiswal

first: Yueh-Hsiu

last: Chien

first: Charles

middle: K

last: Chan

first: Mark

middle: M

last: Davis


title: Dual interactions of K27M mutant nucleosomes with PRC2 and MLL1 shape the cancer epigenetic landscape

first: Efrat

last: Shema

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

overall_design: Refer to individual Series


title: Dual interactions of K27M mutant nucleosomes with PRC2 and MLL1 shape the cancer epigenetic landscape (Cut&Run)

overall_design: Cut&Run analysis of patient-derived DIPG cells. Performed on SU-DIPG using primary antibodies: anti-histone H3K27M, anti-histone H3K27ac, anti-histone H3K27me3, anti-histone H3K4me3, anti-MLL1 and anti-EZH2. Secondary antibody anti-rabbit HRP was used as a negative control.

first: Noa

last: Furth

first: Danielle

last: Algranati

first: Bareket

last: Dassa


title: Transcriptome response to endoplasmic reticulum stress in rat oligodendrocyte precursor cells

city: Louisville

first: Michal

last: Hetman

state: Kentucky

address: 511 South Floyd Street, MDR609A

department: Department of Neurological Surgery

institute: University of Louisville

summary: In the US, there are approximately 12,000 new cases of traumatic spinal cord injury (SCI) each year. Currently there are no neuroprotective treatments to improve outcome of SCI. Our previous research has revealed that endoplasmic reticulum stress response (ERSR) is an important contributor to oligodendrocyte death and subsequent white matter loss and locomotor impairment after contusive spinal cord injury in mice. ERSR affects activity of multiple transcription factors regulating either pro-survival- or apoptosis-promoting genes. Therefore, we characterized transcriptomic changes in ERSR-challenged oligodendrocytes as a first step to identify new targets for therapies that may attenuate their loss after SCI.

overall_design: Total RNA for library construction was obtained from cultured rat oligodendrocyte precursor cells (OPCs) which are often used as a convenient model of oligodendrocytes. These cells were originally isolated from adult rat spinal cords by our collaborator Dr. Scott Whittemore.  Only low passage cells were used (up to passage 6). OPCs were treated with the ERSR inducer tunicamycin (0 or 5 µM) for 2- or 8h (4 samples from each experiment, 3 independent experiments were analyzed resulting in 12 samples, total). The two time points selected (both preceding cell death) were used to increase the probability of identifying important transcriptomic components of the ERSR that determine its outcome on oligodendrocyte survival.

first: Eric

middle: C

last: Rouchka

first: Benjamin

middle: J

last: Harrison


title: The MEF2C oncogene opposes Notch signalling in T versus B lineage decision and drives leukemia in the thymus context [ChIP-Seq]

status: Public on May 14 2022

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Overexpression of the oncogene MEF2C opposes NOTCH signalling in T versus B lineage decision, driving leukemia in the thymus context

overall_design: Binding of transcription factors MEF2C,  BRD4, histone modification of Loucy cell line, with overexpression of MEF2C on or of DL1 of with ICN overexpressed.

first: Jules

middle: P

last: Meijerink

first: Kirsten

last: Canté-Barrett


title: The MEF2C oncogene opposes Notch signalling in T versus B lineage decision and drives leukemia in the thymus context


title: Identification of antimalarial compounds that inhibit Apicomplexan AP2 transcription factor proteins in the human malaria parasite Plasmodium falciparum

status: Public on May 13 2022

city: STATE COLLEGE

first: Timothy

last: Russell

address: W122 Millennium Science Complex

institute: Pennsylvania State University

summary: Transcription time course of Plasmodium falciparum parasite asexual blood stage progression in the presence of antimalarial drug CID5750730 (Compound C)

overall_design: Two-condition experiment, drug treated vs. DMSO vehicle control. Time points: 7 time points per condition. Biological replicates: 1 per condition

first: Russell

last: Timothy

first: K

middle: E

last: De Silva

first: Valerie

last: Crowley

first: Kathryn

last: Shaw-Saliba

first: Namita

last: Dube

first: Gabrielle

last: Josling

first: A

last: Pasaje

first: Irene

last: Kouskoumvekaki

first: Gianni

last: Panagiotou

first: C

last: Niles

first: Marcelo

last: Jacobs-Lorena

first: Denise

last: Okafor

first: Francisco-Javier

last: Gamo

first: Manuel

last: Llinás


title: The MEF2C oncogene opposes Notch signalling in T versus B lineage decision and drives leukemia in the thymus context [array]

first: Rico

last: Hagelaar

summary: Overexpression of the oncogene MEF2C oposses NOTCH signalling in T versus B lineage decision, driving leukemia in the thymus context

overall_design: LOUCY cell lines under multiple conditions are used for RNA extraction and hybridization on Affymetrix microarrays. Overexpression of MEF2C in the presence and absence of NOTCH stimuli, provides insight in MEF2C function in opposing NOTCH signalling in T-cell differentiation. Mimicing the bi-phenotypic lymphoid tumors, resembling a human mixed phenotype acute leukemia (MPAL).

first: Jules

last: Meijerink


title: Topical, immunomodulatory epoxy-tiglianes induce biofilm disruption and healing in acute and chronic skin wounds [HDFa]

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary: The management of antibiotic-resistant, bacterial biofilm infections in chronic skin wounds is a significant clinical challenge.  Despite advances in diagnosis, many patients do not derive benefit from current anti-infective/antibiotic therapies.  Here we report a novel class of epoxy-tiglianes and demonstrate their antimicrobial activity (modifying bacterial growth and inducing biofilm disruption), with structure/activity relationships established against important human pathogens.  In vitro, the lead candidate, EBC-1013 stimulated PKC-dependent neutrophil ROS induction and NETosis, and increased expression of wound healing associated cytokines, chemokines and antimicrobial peptides in keratinocytes and fibroblasts.  In vivo, topical EBC-1013 induced rapid resolution of infection with increased matrix remodelling in acute thermal injuries.  In chronically-infected, diabetic wounds, treatment induced cytokine/chemokine production, inflammatory cell recruitment and complete healing (in 6/7 wounds) with ordered keratinocyte differentiation.  These results highlight a non-antibiotic approach involving contrasting, orthogonal mechanisms of action: targeted biofilm disruption and innate immune induction in the treatment of chronic wounds.

overall_design: Single colour, Illumina Human HT12v4 Beadarrays.

first: Lydia

last: Powell

first: Jason

last: Cullen

first: Tom

last: DeRidder

first: Pei-Yi

last: Yap

first: Wenya

last: Xue

first: Carly

last: Pierce

first: Manon

middle: F

last: Pritchard

first: Georgina

last: Menzies

first: Muthanna

last: Abdulkarim

first: Jennifer

last: Adams

first: Joana

last: Stokniene

first: Lewis

middle: W

last: Francis

first: Mark

last: Gumbleton

first: Jenny

last: Johns

first: Katja

last: Hill

first: Adam

middle: V

last: Jones

first: Peter

middle: G

last: Parsons

first: Paul

last: Reddell

first: David

last: Thomas


title: Silk scaffolding drives self-assembly of functional and mature human brain organoids

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich


title: Real-time quantitative PCR analysis of mouse liver tissue and liver cells

city: Jiangmen

first: Xiu

last: Zhou

address: Pengjiang

department: School of Biotechnology and Health Sciences

institute: Wuyi University

summary: Diets rich in fat is a major cause of common chronic liver diseases in worldwide and nutritional food has been widely used to counteract the metabolic disorders such as non-alcoholic fatty liver disease (NAFLD). The present study investigated the effects of oleuropein-enriched extract from Jasminum grandiflorum L. flowers (OLE-JGF), a medicinal plant that is also widely consumed as a beverage in China, in high fat diet (HFD) fed mice and oleic acid (OA)-treated AML-12 cells. Treatment of HFD-fed mice with 0.6% (w/w) OLE-JGF for 8 weeks significantly reduced the plasma levels of ALT, TC and LDL-C without changing the liver weight. Additionally, OLE-JGF administration significantly suppressed the mRNA expressions of the inflammatory mediators MCP-1 and CD68 in the liver of HFD-fed mice. Importantly, treatment with OLE-JGF significantly downregulated the key lipogenic enzymes (ACC and FAS) and their upstream transcription factor SREBP-1c in the liver. In the same time, mitochondrial DNA and UCP2 were upregulated along with increased expression of mitochondrial biogenic promoters including LKB1 and its downstream gene PGC-1α, Nrf2 and Tfam, but not changed AMPK in liver. In vitro, treatment of OLE for 24 h significantly increased the cell viability and decreased the TG level in OA-induced AML-12 cells. OLE significantly inhibited ACC mRNA expression and upregulated LKB1, PGC-1α and Tfam mRNA levels in OA-treated cells. In addition, OLE significantly increased the binding level of LKB1 to PGC-1α promoter in OA-induced cells. These findings indicate that OLE-JGF attenuates hepatocyte damage in HFD-fed mice and OA-induced liver cells, may be partly attributed to upregulation of LKB1-PGC-1α axis, which mediates hepatic lipogenesis and mitochondrial biogenesis. Our study provides a scientific basis for the benefits of J. grandiflorum flower as a supplement for met-abolic disease and potential use of OLE for the treatment of chronic liver diseases.

overall_design: qPCR gene expression profiling. Equal amount total RNA from each donor was pooled prior to gene expression analysis.Animal experiment Chow, HFD and HFD-JGF groups of 4-9 mice in each group were used as independent replicates.  Cell test Control, OA, OLE three groups each more than or equal to three independent repeated test

first: Xuan

last: Zhao

first: Yalin

last: Wang

first: Yapeng

last: Li

first: Yinzheng

last: Xie

first: Weiming

last: Fang

first: Yi

last: Ou

first: Ji-Ming

last: Ye

first: Dongli

first: Ri-hui

last: Wu


title: RNA-seq study on muscles of LGMD-R12 patients and controls

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Limb-girdle muscular dystrophy R12 (LGMD-R12) is caused by two recessive mutations in the anoctamin-5 gene. Our main aim was to identify genes and pathways that underlie LGMD-R12 and explain differences in the molecular predisposition and susceptibility between three different thigh muscles that are severely (semimembranosus), moderately (vastus lateralis) or mildly (rectus femoris) affected in this disease.

overall_design: We performed transcriptomics on these three differently affected muscles in 16 male LGMD-R12 patients and 15 age-matched male controls.

first: Kristl

last: Claeys

first: Christophe

last: Depuydt


title: Topical, immunomodulatory epoxy-tiglianes induce biofilm disruption and healing in acute and chronic skin wounds

first: Glen

last: Boyle


title: Inflammation modulates intercellular adhesion and mechanotransduction in human epidermis via ROCK2

city: geneva

first: Wolf

middle: Henning

last: Boehncke

address: Rue Michel servet 1

institute: Univeristy of Geneva

summary: The cytoskeletal mechanisms regulating inflammatory responses in the epidermis are not well described. Here we addressed this question by inducing a psoriatic phenotype in human keratinocytes and reconstructed human epidermis using a cytokine stimulation model.We report the results from RNA-seq  in N/TERT keratinocytes treated with M5 or both M5 and ROCK2 inhibitor KD025.

overall_design: N/TERT keratinocytes treated 24h with M5 or both M5 and ROCK2 inhibitor KD025.

first: Maria

last: Shutova

first: Julia

last: Borowczyk

first: Barbara

last: Russo

middle: H


title: Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

summary: Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms and may influence prognosis. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG).  Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations are thought to converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have non-overlapping, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional dysregulation in Idh2R172K cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of IDH1/2 and TET2 mutations, providing support for the optimization of genotype-specific therapies in myeloid neoplasms.

overall_design: Lin-cKit+Sca1+ cells from 3-4 month old +/+; Vav-Cre (control), Idh1LSL-R132H/+;Vav-Cre, Idh2LSL-R140Q/+;Vav-Cre, and Idh2LSL-R172K/+;Vav-Cre mice were analyzed. For each genotype,  4 pools of 2 mice each (each forming a biological replicate), were analyzed.

first: Jerome

last: Fortin

first: Ming-Feng

last: Chiang

first: Jonathan

last: Foox

first: Cem

last: Meydan

first: Parameswaran

last: Ramachandran

first: Ari

last: Melnick

first: Christopher

last: Mason


title: Condition-Specific Mapping of Operons (COSMO) Using Dynamic and Static Genome Data

city: Cape Town

first: Tracey

last: Calvert-Joshua

state: Western Cape

address: Robert Sobukwe Road, Bellville

department: South African National Bioinformatics Institute (SANBI)

country: South Africa

institute: University of the Western Cape

summary: An operon is a set of adjacent genes which are transcribed into a single messenger RNA. Operons allow prokaryotes to efficiently circumvent environmental stresses. It is estimated that about 60% of the Mycobacterium tuberculosis genome is arranged into operons, which makes them interesting drug targets in the face of emerging drug resistance. We therefore developed COSMO - a tool for operon prediction in M. tuberculosis using RNA-seq data. We analyzed four algorithmic parameters and benchmarked COSMO against two top performing operon predictors. COSMO outperformed both predictors in its accuracy and in its ability to distinguish operons activated under distinct conditions.

overall_design:
The RIF samples were obtained from two Mtb patients and RNA-sequenced. The lineages and drug resistance profiles were confirmed using the TBProfiler tool  (Phelan et al., 2019) in Galaxy (https://galaxy.sanbi.ac.za/) (Jalili et al., 2020). Except for the WT family, all other strains were RIF resistant. The 64 samples consisted of six biological replicates from L2 (Beijing family) and six biological replicates from L4 (Family X). For each of the aforementioned samples, half of the biological replicates were high MIC strains (150 µg/ml) and the other half, were low MIC strains (40 µg/ml). We also isolated three biological replicates of naturally produced rpOB mutants (L2) and three wildtype (WT) strains (L2).
Most biological replicates had a minimum of three technical replicates, with the exception of the WT strains. All strains were grown under RIF stress (experimental) and no RIF-stress conditions (control) – with the exceptions again of the WT strains, which were only exposed to control conditions. Under RIF-stress conditions, the low and high MIC strains were exposed to a ¼ MIC treatment.


title: Impact of circadian rhythm in obtaining reference profiles of exRNAs in healthy individuals

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The effect of increasing concentrations of haemoglobin in the starting material on the results of RNA seq using plasma isolated from healthy donors.

overall_design: 18 samples from 6 subjects, 3 time points (8:30am, 2:30pm, 6:30pm) from each subject.


title: Tabula Sapiens

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary: Tabula Sapiens is a single cell transcriptomic atlas of 24 human tissues and organs.

overall_design:
Various tissues. The raw data is accessible from a public AWS bucket (s3://czb-tabula-sapiens/).
contributor: The Tabula Sapiens Consortium


title: Effect of Celastrol on LncRNAs and mRNAs Profiles of Cerebral Ischemia-Reperfusion Injury in Transient Middle Cerebral Artery Occlusion Mice Model

first: Xiangna

last: Guo

address: South Shatai Road, Baiyun District

institute: Southern Medical University

summary: Celastrol plays a significant role in cerebral ischemia-reperfusion injury. Although previous studies have confirmed that celastrol post-treatment has a protective effect on ischemic stroke, the therapeutic effect of celastrol on ischemic stroke and the underlying molecular mechanism remain unclear. In the present study, focal transient cerebral ischemia was induced by transient middle cerebral artery occlusion (tMCAO) in mice and celastrol was administered immediately after reperfusion. We performed lncRNA and mRNA analysis in the ischemic hemisphere of adult mice with celastrol post-treatment through RNA-Sequencing (RNA-Seq). A total of 50 differentially expressed lncRNAs (DE lncRNAs) and 696 differentially expressed mRNAs (DE mRNAs) were identified between the sham and tMCAO group, and a total of 544 DE lncRNAs and 324 DE mRNAs were identified between the tMCAO and tMCAO+celastrol group. Bioinformatic analysis was done on the identified deregulated genes through gene ontology (GO) analysis, KEGG pathway analysis and network analysis. Pathway analysis indicated that inflammation-related signaling pathways played vital roles in the treatment of ischemic stroke by celastrol. Our study suggests celastrol treatment can effectively reduce cerebral ischemia-reperfusion injury. The bioinformatics analysis of lnRNAs and mRNAs profiles in the ischemic hemisphere of adult mice provides a new perspective in the neuroprotective effects of celastrol, particularly with regards to ischemic stroke.

overall_design: LncRNAs and mRNAs Profiles in three groups of mice, including sham group, tMCAO group and cela group.

first: Jiandong

last: Liu

first: Chunshui

last: Lin

first: Zaisheng

last: Qin


title: Bulk Sequencing of CD45- cells from HD and SSc patients

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

summary: Skin cells were depleted from CD45+ and dead cells using microBeads, purity 95%. CD45- cells were RNA sequenced (bulk) to find differentially regulated genes between healthy donors and scleroderma patients (SSc)

overall_design: CD45- cells were isolated from 3 punch biopsies (4mm) od 3 patients or healthy donors. Samples were group-pooled to compensate for HLA-DR differences.

first: Verena

last: Raker

first: Kerstin

last: Steinbrink

first: Sabrina

last: Muecklich

first: Jessica

last: Haub


title: Breast Cancer Chemotherapy Induces Vascular Dysfunction and Hypertension

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

summary:
Cardiovascular disease is the major cause of mortality in breast cancer survivors. Chemotherapy contributes to this risk. Accordingly, we aimed to define the mechanisms of long-term vascular dysfunction caused by neoadjuvant chemotherapy (NACT) and identify novel targets for pharmacological intervention.
We studied human mammary arteries from women who had undergone NACT for breast cancer using docetaxel, doxorubicin and cyclophosphamide  and women with no history of such treatment matched for key clinical parameters. Mechanisms were further explored in wild-type and Nox4-/- mice and human microvascular endothelial cells.
Endothelium-dependent relaxation was severely impaired in patients after NACT, while endothelium-independent responses remain normal. This was mimicked by 24-hour exposure of arteries to NACT agents ex vivo. When applied individually, only docetaxel significantly impaired endothelial function in human vessels.

overall_design: Vascular rings (mammary artery) from 6 female patients, with no history of NACT, were incubated with 100 nM docetaxel (Cayman Chemicals) and vehicle (solvent) as a control (paired design). The vessels were incubated in a buffer containing: Hank's Balanced Salt Solution (HBSS; Gibco), 20 mM Hepes (Gibco) and gentamicin with glutamine in an incubator at 37°C in a humidified atmosphere for 24 hours. After incubation, vascular function was measured or rings were placed in RNAlater (Ambion) for gene expression and RNAseq studies. RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research) and treated with DNase I. RNAseq profiling was performed by Genewiz (United Kingdom).

first: Piotr

last: Szczepaniak

last: Siedlinski

first: Tomasz

last: Guzik


title: Targeting gamma-glutamyltransferase 1 on myeloid-derived suppressor cells prevents tumor progression caused by G-CSF in neutropenic mouse model

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Myeloid-derived suppressor cells (MDSCs) are one of the major immunosuppressive cells that accumulate in tumor-bearing hosts. Since MDSCs suppress anti-tumor immunity and promote tumor progression, they are promising targets for cancer immunotherapy. Granulocyte colony-stimulating factor (G-CSF) is an agent for the treatment of chemotherapy-induced febrile neutropenia in patients with cancer. However, several reports reveal that G-CSF would play crucial immune-related adverse roles in tumor progression through MDSCs. In this study, we showed that MDSCs differentiated in the presence of G-CSF in vitro exhibited the enhanced proliferation and immunosuppressive activity compared with those differentiated without G-CSF. RNA-seq analysis demonstrated that G-CSF enhanced the immunosuppressive function of MDSCs through the upregulation of gamma-glutamyltransferase (GGT) 1. Moreover, in the EL4 lymphoma-bearing neutropenic mouse model, the administration of recombinant G-CSF increased MDSCs and attenuated anti-cancer effect of chemotherapy. We showed that the combination of GGsTop, a GGT inhibitor, with G-CSF could prevent tumor growth caused by G-CSF, without affecting the promoting myelopoiesis by G-CSF. These results suggest that targeting GGT1 on MDSCs can eliminate the effect of G-CSF in promoting tumor growth. GGsTop could be an attractive combination agent when receiving G-CSF treatment for febrile neutropenia in patients with cancer.

overall_design: We performed an RNA-seq analysis, comparing gene expression profile of in vitro MDSCs differentiated with or without G-CSF.

first: Masashi

last: Tachibana


title: Single-cell RNA sequencing of right atrial blood mononuclear cells offers a novel approach to studying nasopharyngeal carcinoma.

city: Foshan

first: Guoyi

last: Zhang

address: Tumor Center, First People's  Hospital of Foshan, Foshan, Guangdong

institute: Tumor Center, Foshan First People's Hospital

summary: We collected blood samples from the right atrium of newly diagnosed patients with nasopharyngeal carcinoma (NPC) for the first time, and performed single-cell RNA sequencing of mononuclear cells. We then compared the profiles of cells from atrial blood with those of peripheral venous blood and found that a great difference in the gene expression profiles of T cells and B cells. We speculate that this difference is due to the pulmonary circulation and peripheral capillaries. We also analyzed the data of patients with EBV to provide data for the study of the relationship between EBV and NPC. This study also provides a unique single-cell sequencing dataset that will be a valuable resource in further elucidating the roles of mononuclear cells in NPC pathogenesis.

overall_design:
In this study, to explore the characteristic changes in RABMCs in NPC patients at the single-cell level, we performed scRNA-seq on MCs (mononuclear cells) isolated from RAB (right atrial blood) and PVB (cubital vein blood) samples collected from ten patients with newly diagnosed (untreated) nonmetastatic NPC.
***Please note that 8 sample records represents 8 raw data files obtained from 10 patients, and that the 'readme.txt' describes which raw data each processed data file was generated***

first: GUOYI

last: ZHANG

first: BAOGUO

last: XIE

first: GANG

last: DU


title: A genetics screen uncovers the role of RNA-binding protein RBP45D in flowering time under heat and DCL3-independent RNA-directed DNA methylation

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: In the canonical RdDM, small interfering RNAs (siRNAs) are produced through the slicer activity of DICER-LIKE 3 (DCL3). Here, we describe the Arabidopsis thaliana prors1 (LUC) transgenic system in which transcriptional gene silencing (TGS) through RdDM is independent of DLC3. To identify players in the DCL3-independent pathway, a forward genetics screen was performed with the prors1 (LUC) system to identify suppressor mutants in which TGS is released. Among already known components of RdDM, we identified RNA-binding protein RBP45D. RBP45D promotes DNA methylation changes, and a lack of RBP45D results in a late flowering phenotype especially under heat, presumably mediated by elevated FLC levels. A lack of RBP45D did not influence the pre-mRNA splicing of known RdDM genes, suggesting that RBP45D involvement in the RdDM might be direct. RBP45D is localized to the nucleus where it is associated with snRNAs and snoRNAs. RBP45D promotes siRNA production originating from the transgene and we hypothesize that this function is direct and not indirect.

overall_design: Examination of differential gene expression in the Arabidopsis rbp-kd1 and -kd2 mutants in comparison to Col-0


title: Single-cell transcriptomic and epigenetic analyses in the embryonic mouse cerebellum

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: In this study we performed single-cell RNA sequencing and single-nuclei ATAC-seq of E12.5- E14.5 mouse cerebella to reveal molecular and epigenetic features of various cerebellar cell types or cell states.

overall_design: Single-cell or single-nuclei suspensions of embryonic mouse cerebellum were prepared following the protocols recommended by 10x Genomics. Subsequently, samples were processed with the 10X Genomics Chromium Kits.

first: James

last: Li


title: Expression profiling of 1-day old C. elegans adult crh-1(syb385) versus wild-type

city: Reno

first: Pedro

last: Miura

state: Nevada

address: 1664 N VIRGINIA ST MS 0314

department: Biology

institute: University of Nevada, Reno

summary: Stranded, ribo-depleted RNA-Seq of circ-crh1 mutant versus wild-type

overall_design: Total-RNA profiles of three independent replicates of wild type and circ-crh-1 knockout [crh-1(syb385)] 1-day adult worms.

first: David

last: Knupp

first: Alexander

last: van der Linden


title: A genetics screen uncovers the role of RNA-binding protein RBP45D in flowering time under heat and DCL3-independent RNA-directed DNA methylation (WGBS)

type: Methylation profiling by high throughput sequencing

summary: RNA-directed DNA methylation (RdDM) is a prominent pathway in plants to defend against invasive nucleic acids. In the canonical RdDM, 24-nt small interfering RNAs (siRNAs) are produced through DICER-LIKE 3 (DCL3). Here, we describe the Arabidopsis thaliana prors1 (LUC) transgenic system in which transcriptional gene silencing (TGS) is independent of DLC3. In a forward genetics screen performed with this system, already known components of RdDM and RNA-binding protein RBP45D were identified. RBP45D promotes DNA methylation, and a lack of RBP45D causes late flowering especially under heat, presumably mediated by elevated FLC levels. RBP45D is localized to the nucleus where it is associated with snRNAs and snoRNAs. RBP45D maintains siRNA production originating from the transgene, but does not promote mRNA levels or influence pre-mRNA splicing of known RdDM genes. We hypothesize that RBPD45 facilitates DCL3-independent siRNA production through stabilisation of either the precursor RNA or the – not yet identified – slicer protein.

overall_design: Examination of differential methalytion in the Arabidopsis thaliana rbp-ko-1 (KO27) mutant in comparison to Col-0


title: Genome-wide DNA accessibility maps after Sirt6 inactivation in muscle stem cells [ATAC-seq]

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Sirt6, the NAD+-dependent deacetylase, has been described to deacetylate H3K9, H3K18, and H3K56. However, analysis of the acetylation status revealed that loss of Sirt6 caused a massive increase of histone H3K56ac levels but no detectable change of histone H3K9ac and H3K18ac, indicating that SIRT6 is the dominant deacetylase for H3K56ac in muscle stem cells (MuSCs). Further, we investigate genome transposase-accessible chromatin in the absence of Sirt6 in MuSCs using high throughput sequencing (ATAC-seq).

overall_design: ATAC-seq experiment to determine genome-wide open chromatin in control (wild type) and Sirt6 knockout primary muscle stem cells.

first: Angelina

last: Georgieva

first: Stefan

last: Günther


title: RNA-sequencing of wild-type versus SETD2-null 786-O and HKC cells.

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

summary: RNA-seq analysis was performed from wild-type and SETD2-null cells in order to gauge changes in gene expression following loss of SETD2 methylation activity. We identified 4 genes that were commonly upregulated and 11 that were commonly downregulated.

first: C


title: Genome-wide H3K56ac profiling after Sirt6 knockdown in mESCs [ChIP-seq]

summary: Sirt6, the NAD+-dependent deacetylase, has been described to deacetylate H3K9, H3K18, and H3K56. However, analysis of the acetylation status revealed that loss of Sirt6 caused a massive increase of histone H3K56ac levels but no detectable change of histone H3K9ac and H3K18ac, indicating that SIRT6 is the dominant deacetylase for H3K56ac in muscle stem cells (MuSCs). Further, we investigate genome-wide H3K56ac profiling in the absence of Sirt6 in MuSCs and mouse embryonic stem cells (mESCs) using high throughput sequencing (ChIP-seq).

overall_design: ChIP-seq experiment to determine genome-wide H3K56ac distribution in scrabled control and Sirt6 knockdown mouse embryonic stem cells


title: Reprogramming of three-dimensional chromatin architecture   drives human dilated cardiomyopathy

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

summary: Here we generated the first reference 3D chromatin contact maps from 101 biobanked human heart tissue samples through HiChIP (H3K27ac), in situ Hi-C, ChIP-seq, ATAC-seq and RNA-seq profiling. We discovered that the active regulatory elements and their connectome were extensively reprogrammed in DCM and contributed to transcription dysregulation implicated for DCM development. Higher-order chromatin structures indicated that the overall genome architecture was largely invariant in DCM and chromatin accessibility did not alter DCM-specific H3K27ac loops. This provided insight to the mechanistic hierarchies between higher-order chromatin structures, cis-regulatory elements and differential chromatin accessibilities in DCM, suggesting the importance of sequence-specific transcription factors. Intriguingly, we uncovered that the DCM-specific H3K27ac loops anchors exhibited a strong enrichment for Heart And Neural Crest Derivatives Expressed 1 (HAND1), a key transcription factor involved in early cardiogenesis. In line with this, its protein expression was upregulated in human DCM hearts and mouse failing hearts. Functional analyses by ectopic overexpression of HAND1 in human iPSC-derived cardiomyocytes induced cell hypertrophy and abnormal electrophysiology. Moreover, cardiomyocyte-specific overexpression of HAND1 in the mouse heart resulted in cardiomyocyte enlargement, increased heart weight/body weight ratio and dilated left ventricle. Echocardiography showed that cardiomyocyte-specific Hand1 overexpression in the mouse heart led to cardiac dysfunction and remodeling. Thus, aberrant activation of HAND1 in adult cardiomyocytes recapitulated the phenotypes observed in human DCM and indicated the involvement of a partial reactivation of a developmentally earlier cell identity program in the disease.

overall_design: H3K27ac HiChIP, In-situ Hi-C, H3K27ac ChIP-seq, HAND1 ChIP-seq, ATAC-seq, RNA-seq for human non-failing and failing (DCM) heart tissues. H3K27ac HiChIP, H3K27ac ChIP-seq, HAND1 ChIP-seq, RNA-seq for human iPSC-derived cardiomyocytes.

first: Yuliang

last: Feng

first: Wei

last: Hunag

first: Liuyang

last: Cai


title: Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Non-silencing Control and EP300 Knockdown Transcriptomes

city: Worcester

first: Magnolia

last: Pak

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Purpose: The goal of this study is to identify p300-regulated genes.

overall_design: Method: Expression profiles of MCF10AT cells expressing two independent EP300 shRNAs and the cooresponding non-silencing controls were generated by RNA-Seq, in triplicates, using Illumina.

first: Michael

middle: R

last: Green


title: Topical, immunomodulatory epoxy-tiglianes induce biofilm disruption and healing in acute and chronic skin wounds [HEKa]

status: Public on May 12 2022

city: Brisbane

first: Glen

last: Boyle

address: 300 Herston Road Herston

institute: QIMR Berghofer Medical Research Insitute

summary: The management of antibiotic-resistant, bacterial biofilm infections in chronic skin wounds is a significant clinical challenge.  Despite advances in diagnosis, many patients do not derive benefit from current anti-infective/antibiotic therapies.  Here we report a novel class of epoxy-tiglianes and demonstrate their antimicrobial activity (modifying bacterial growth and inducing biofilm disruption), with structure/activity relationships established against important human pathogens.  In vitro, the lead candidate, EBC-1013 stimulated PKC-dependent neutrophil ROS induction and NETosis, and increased expression of wound healing associated cytokines, chemokines and antimicrobial peptides in keratinocytes and fibroblasts.  In vivo, topical EBC-1013 induced rapid resolution of infection with increased matrix remodelling in acute thermal injuries.  In chronically-infected, diabetic wounds, treatment induced cytokine/chemokine production, inflammatory cell recruitment and complete healing (in 6/7 wounds) with ordered keratinocyte differentiation.  These results highlight a non-antibiotic approach involving contrasting, orthogonal mechanisms of action: targeted biofilm disruption and innate immune induction in the treatment of chronic wounds.

overall_design: Single colour, Illumina Human HT12v4 Beadarrays.

first: Lydia

last: Powell

first: Jason

last: Cullen

first: Tom

last: DeRidder

first: Pei-Yi

last: Yap

first: Wenya

last: Xue

first: Carly

last: Pierce

first: Manon

last: Pritchard

first: Georgina

last: Menzies

first: Muthanna

last: Abdulkarim

first: Jennifer

last: Adams

first: Joana

last: Stokniene

first: Lewis

last: Francis

first: Mark

last: Gumbleton

first: Jenny

last: Johns

first: Katja

last: Hill

first: Adam

last: Jones

first: Peter

last: Parsons

first: Paul

last: Reddell

last: Thomas


title: RNA seq of naïve CD8+ T cells expanded in different cytokines (along with our re-engineered cytokine) to find differences in t cell function, marturation and metabolic reprogramming.

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Cytokine therapy is limited by undesirable off-target side effects as well as terminal differentiation and exhaustion of chronically stimulated T cells. Here, we describe the signaling properties of a potentially unique cytokine by design, where T cell surface binding and signaling are separated between 2 different families of receptors. This fusion protein cytokine, called OMCPmutIL-2, bound with high affinity to the cytotoxic lymphocyte-defining immunoreceptor NKG2D but signaled through the common γ chain cytokine receptor. In addition to precise activation of cytotoxic T cells due to redirected binding, OMCPmutIL-2 resulted in superior activation of both human and murine CD8+ T cells by improving their survival and memory cell generation and decreasing exhaustion. This functional improvement was the direct result of altered signal transduction based on the reorganization of surface membrane lipid rafts that led to Janus kinase-3–mediated phosphorylation of the T cell receptor rather than STAT/AKT signaling intermediates. This potentially novel signaling pathway increased CD8+ T cell response to low affinity antigens, activated nuclear factor of activated T cells transcription factors, and promoted mitochondrial biogenesis. OMCPmutIL-2 thus outperformed other common γ chain cytokines as a catalyst for in vitro CD8+ T cell expansion and in vivo CD8+ T cell–based immunotherapy.

overall_design: RNA-seq

first: Alexander

middle: S

last: Krupnick

first: Anirban

last: Banerjee


title: Genome-wide H3K56ac profiling after Sirt6 inactivation in MuSCs [ChIP-seq]

first: Marek

last: Bartkuhn

overall_design: ChIP-seq experiment to determine genome-wide H3K56ac distribution in control (wild type) and Sirt6 knockout MuSCs

first: Angelina

last: Georgieva

first: Stefan

last: Günther


title: Thymic involution caused by repeated cocaine administration includes apoptotic cell loss followed by ectopic adipogenesis

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima

department: Forensic medicine

institute: Tokyo Medical and Dental University

summary:
To obtain insight into the  changes in thymus caused by repeated cocaine administration, we performed transcriptome analysis.
Total RNAs from the control and cocaine groups (day 7) were subjected to DNA microarray analysis.

overall_design: We analyzed thymus from 1 control rat and 1 cocaine-administered (20mg/kg, daily for 7days) rat using the ClariomS platform.

first: Kana

last: Unuma

first: Homare

last: Kaga

first: Takeshi

last: Funakoshi

first: Koichi

last: Uemura


title: ATAC-seq and ChIP-seq studies after Sirt6 inactivation in MuSCs/mESCs

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

overall_design: Refer to individual Series


title: Transcriptome-wide impact of season and progesterone in the medio-basal hypothalamus of the goat

city: Nouzilly

first: Hugues

last: Dardente

address: INRA

department: INRAE - Centre Val de Loire

institute: INRAE

summary: Here we used RNAseq to compare the transcriptomes of the medio-basal hypothalamus of goats killed at two different times of the year (end of January and mid-May) and under different hormonal conditions (follicular and luteal phase, in January only). The current experiment was designed to identify the impact of photoperiod upon the transcriptome and to compare it with that of the ewe. The current design also tested the potential impact of progesterone (P4) upon this transcriptome; ewes were treated with a vaginal fluogestone acetate sponge during the breeding season (January) and killed either 2 days (follicular phase) or 8 days (luteal phase) after estrumate treatment and sponge removal.

overall_design: The study was performed in adult Alpine goats. The experiment included 18 goats: 5 for January/Follicular phase; 5 for January/Luteal phase and 8 for mid-May/Anestrus. RNA was extracted from each goat MBH. Then, for each condition two random equimolar mixes of mRNA were used for RNAseq --> 2 biological replicates.


title: Transcriptome-wide impact of progesterone in the medio-basal hypothalamus of the ewe

summary: Here we used RNAseq to assess the impact of progesterone (P4) on the transcriptome of the medio-basal hypothalamus of ewes. Ewes were treated with a vaginal fluogestone acetate sponge in mid-February. The sponge was removed in early March and ewes received a PMSG injection. Animals were then killed either 2 days (follicular phase) or 12 days (luteal phase) later.

overall_design: The study was performed in adult ewes of the Ile-de-France breed (hereafter IF). The experiment included 20 ewes : 10 in Follicular phase and 10 in Luteal phase. RNA was extracted from each ewe MBH. Then, for each condition 5 random equimolar mixes of mRNA (n=2 per mix) were used for RNAseq --> 5 biological replicates.


title: Transcriptomic analyses of NF1-mutant melanoma

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

summary: RNA analysis of 770 genes (Pan Cancer IO 360) related to the tumor microenvironment on NF1-MUT and matched NF1-WT samples for reference.

overall_design: Multiplex gene expression analysis covers 770 genes from 24 different immune cell types and 48 gene-derived signatures measuring biological variables crucial to the tumor-immune interaction including cell proliferation, angiogenesis and immune inhibitory mechanisms, among others.

first: George

last: Jour


title: Effect on gene expresssion in HeLa cells treated for 8 hours and 24 hours with 1 micromolar CTT25136

city: Heidelberg

last: Reid

address: Waldhofer Strasse

institute: WMT AG

summary:
To investigate the effect the small molecule CTT251236 has on gene expression in HeLa cells following 8 hours and 24 hours of treatment
We performed gene expression profiling analysis using data obtained from RNA-seq of solvent treated cells (control) and cells treated for 8 hours and for 24 hours. Each condition was performed in triplicate.

overall_design: Comparative gene expression profiling analysis of HeLa cells treated with CTT251236

first: Reid

last: George


title: Gene expression profile at single cell level of cerebrospinal fluid cells derived from one breast cancer leptomeningeal metastases patient

city: Shanghai

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

summary: Cerebrospinal fluid cells derived from one breast cancer leptomeningeal metastases patient

overall_design: Cerebrospinal fluid cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of mCherry signal and analyzed using scRNAseq.

first: Haoyu

last: Ruan


title: Various forms of calorie restriction, but not a nonrestricted low-fat diet, reverse obesity-associated tumor growth and lung metastasis in a mouse model of triple-negative breast cancer-RRBS

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

summary: lean control, obese, and formerly obese C57BL6N mice which underwent weight loss via low-fat diet or various forms of calory restriction were injected with E0771 cells and tumor growth was monitored

overall_design: DNA was extracted from contralateral normal mammary tissue and subject to RRBS

first: Michael

last: Coleman

first: Laura

last: Bowers

first: Stephen

middle: D

last: Hursting


title: Various forms of calorie restriction, but not a nonrestricted low-fat diet, reverse obesity-associated tumor growth and lung metastasis in a mouse model of triple-negative breast cancer


title: Transcriptome-wide impact of food-restriction on the medio-basal hypothalamus of the ewe.

summary: Here we used RNAseq to compare the transcriptomes of ewes fed ad libitum VS food-restricted ewes (hereafter AL and RES, respectively). Body Condition Score was used as an index to validate the impact of food restriction.

overall_design: The study was performed in adult ewes of the Ile-de-France breed. The experiment included 30 ewes in each group (ad lib and food-restricted) and was repeated the following year giving a grand total of 60 ewes fed ad lib and 60 food-restricted ewes. RNA was extracted from each ewe. Then, for each condition four random equimolar mixes of mRNA from 15 ewes were used for RNAseq --> 4 biological replicates.


title: Gene expression profiling of HUVECs with different HtrA2/Omi

city: Chengdu

first: Haoran

last: Tai

state: Sichuan

address: #783 Xindu Avenue

department: Department of Histology and Embryology

institute: Chengdu Medical College

summary: Our previous experiments suggested that HtrA2/Omi could regulate the transcription of certain genes through its PDZ domain. Here, we used an inducible Tet-On system to mimic stress-induced HtrA2/Omi upregulation and RNA sequencing to study its influence.

overall_design: Lentivirus transduced HUVECs with an inducible Tet-On  expression system were used for RNA sequencing. There were 4 groups and each group contains 3 independent replicates.


title: Various forms of calorie restriction, but not a nonrestricted low-fat diet, reverse obesity-associated tumor growth and lung metastasis in a mouse model of triple-negative breast cancer-RNAseq

overall_design: RNA was extracted from contralateral normal mammary tissue and subject to RNAseq


title: ATAC-seq in precursor and differentiated ER-Hoxb8 cells

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

institute: University of Münster

overall_design: Precursor and day 3 differentiated WT and C/EBPδ KO ER-Hoxb8 cells were harvested, washed and cryopreserved in 50% FBS/ 40% growth media/ 10% DMSO using a freezing container at -80 °C overnight. Sequence analysis was performed by mapping the paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) to the genome using the BWA algorithm with default settings (“bwa mem”). Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed. BAM files were used to perform peak calling with MACS2, using paired-end mode with a bandwidth of 200 and q-value cutoff of 0.01. BedGraph files were converted to BigWig format for visualization with the Integrative Genomics Viewer (IGV) using bedGraphToBigWig. Differential accessibility analyses for all possible comparisons between WT and/or C/EBPδ KO in day 0 and day 3 groups were carried out with GUAVA v1. Differential peaks were defined as those merged intervals within a window of 5000 bp upstream and 3000 bp downstream of the transcription start site (TSS) showing an adjusted p-value < 0.05 and log2 fold change ≥ ±1.5.

first: Saskia-Larissa

last: Jauch-Speer

first: Nadine

last: Ludwig

first: Bruna

last: Véras De Carvalho

first: Leonie

last: Martens

first: Jonas

last: Wolf

first: Achmet

middle: I

last: Chasan

first: Anika

last: Witten

first: Birgit

last: Markus

first: Bernhard

last: Schieffer

first: Thomas

last: Vogl

first: Jan

last: Rossaint

first: Monika

last: Stoll

first: Johannes

last: Roth

first: Olesja

last: Fehler


title: Transcriptional signature of CD4hiCD38hi T cells from patients with Plasmodium falciparum or Plasmodium knowlesi malaria

city: Chermside

first: Simon

last: Apte

state: QLD

address: Rode Rd

department: The Prince Charles Hospital

institute: Queensland Department of Health

summary: We observed by flow cytometry a population of CD4 T cells expressing very high levels of the coreceptor CD4 and the ectoenzyme CD38 (termed CD4hiCD38hi) in the peripheral blood of patients from Sabah and Papua with Plasmodium falciparum or Plasmodium knowlesi malaria. CD4hiCD38 T cells express genes associated with type 1 regulatory T cells.

overall_design: PBMCs isolated from adult patients with P. falciparum or P. knowlesi malaria in Papua or Sabah were sorted by flow cytometry into populations of CD4hiCD38hi T cells or CD4norm T cell populations. Immediately following the sort, the cells were stimulated with PMA and Ionomycin for 3 hours and then lysed and gene expression was analysed using the nCounter Custom Codeset Watkins_1_c3950. CD4hiCD38hi T cells and CD4norm T cells were sorted from 6 patients with P. falciparum from Sabah and 6 from Papua, and also from 6 patients with P. knowlesi from Sabah.

first: Denise

last: Doolan


title: Histone deacetylase 3 facilitates TNF α -mediated NF-κB activation through suppressing CTSB induced RIP1 degradation and is required for host defense against bacterial infection [ChIP-seq]

city: Hang Zhou

first: Liping

last: Yang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: Histone deacetylases (HDACs), as important enzymes regulating acetylation, participate in a series of cell physiological process. Here we reported that HDAC3-deficient macrophages had elevated expression of multiple cathepsins and over-expressed cathepsins such as cathepsin B (CTSB) caused remarkable degradation of receptor (TNFRSF)-interacting serine-threonine kinase 1 (RIP1), which resulted in reduced TNFα mediated NF-κB activation and inflammatory response. Consistent with these findings, mice with macrophage specific knockout of HDAC3 were impaired in inflammatory response and susceptible to pseudomonas aeruginosa infection. Thus, our studies uncovered important roles of HDAC3 in the regulation of cathepsin-mediated lysosomal degradation and RIP1-mediated inflammatory response in macrophages as well as in host defense against bacterial infection.

overall_design: Examination the level of histone acetylation on Vector and HDAC3 knockout RAW264.7

first: Genhong

last: Cheng

first: Heng

first: Feng

last: Xu


title: Role of Amh and Activin B in testis development

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS


title: Histone deacetylase 3 contributes to the anti-viral innate immunity of macrophages through interacting with FOXK1 to regulate STAT1 and STAT2


title: Histone deacetylase 3 contributes to the anti-viral innate immunity of macrophages through interacting with FOXK1 to regulate STAT1/2 transcription [RNA-seq]

summary: It is well known that IFNα/β activates the JAK/STAT signaling pathway and suppresses viral replication through induction of interferon stimulated genes (ISGs). Here we reported that knockout of HDAC3 from macrophages resulted in decreased expression of STAT1 and STAT2, leading to a defective anti-viral immunity in cells and mice. Further studies showed that HDAC3 interacted with a conserved transcription factor Forkhead Box K1 (FOXK1), co-localized with FOXK1 at the promoter of STAT1 and STAT2, and was required for protecting FOXK1 from lysosomal system mediated degradation. Constantly, FOXK1 deficient macrophages also showed low STAT1 and STAT2 expression with defective response to virus. Thus, our studies uncovered the biological importance of HDAC3 on regulating antiviral immunity of macrophages through interaction with FOXK1 to regulate the expression of STAT1 and STAT2.

overall_design: Total RNA profiling of gene expression upon knock-out of Hdac3 or Foxk1 in RAW264.7 cells after stimulated with vesicular stomatitis virus for 8h


title: Transcriptomic analysis of APS organoids with and without EGF

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

summary: EGF is the main mitogen promoting the growth of Kras WT colon cancer organoids. Here we aim to elucidate changes in expression profile of organoids in a suboptimal niche, mimicking the slow proliferation conditions that a tumor senses in vivo

overall_design:
APS (APC KO, p53 KO, Smad4 KO) organoids after 7 days of growing in media in absence of EGF. Two different organoids were used, with 2 replicates per organoid.
APSMC706 and CTO19 represent two biological replicates of Apc KO p53 KO and Smad4 KO colon cancer organoids. Both of them are derived from C57BL/6 mice, and their mutations were introduced by Crispr.

first: Adrian

last: Alvarez-Varela

first: Eduard

last: Batlle


title: Arabidopsis thaliana transcriptome

city: Lausanne

first: Emanuel

last: Schmid-Siegert

address: UNIL Sorge

institute: UNIL

summary: This study aims to identify genes which help to understand similar underlying mechanism in the response to shade and wounding in Arabidopsis thaliana plants.

overall_design: 18d old petioles from wild-type or allene oxide synthase (aos) mutant plants, mock or wounded and exposed to either low or high R/FR ratios at different timepoints.

first: Anne

last: Fiorucci

first: Christian

last: Fankhauser


title: RNA sequencing of triple mutant MTOs in suboptimal growth conditions

summary: We profiled mouse tumor organoids (MTOs) in complete stem cell media and in medium without EGF or in the presence of TGFb

overall_design: Comparison of 2 different MTOs per each genotype (2x AKP + 2x APT). AKP MTOs (54 and 220) were cultured in full stem cells medium (+6) or without LY/+TGFb. APT MTOs (100 and 101) were cultured in +6 and without EGF.

first: Cañellas

last: Adrià

first: Batlle

last: Eduard


title: Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (CaptureC)

status: Public on May 23 2022

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Precise control of gene expression is essential for normal development. This is thought to rely on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs) the CDK-Mediator (CDK-MED) complex has been reported to topologically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to overall genome organisation in ESCs, but interestingly has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by the Polycomb repressive complexes (PRCs). These interactions are facilitated by CDK-MED but rely on canonical PRC1. However, through separation of function experiments, we reveal that the collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on a topology-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to support gene activation.

overall_design: Interacions were profiled by CaptureC in mouse embryonic stem cells with various genetic backgrounds before and after treatment with OHT (Med13fl/fl;Med13Lfl/fl and Pcgf4-/-;Pcgf2fl/fl) or without treatment (TetR-GFP, TetR-CDK8 and TetR-PCGF2).

first: Angelika

last: Feldmann

first: Robert

last: Klose


title: Differential gene expression in murine olfactory epithelium: effect of loss of ACE2

status: Public on May 11 2022

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

institute: Nicolaus Copernicus University

summary: RNAseq differential gene expression profiling of olfactory mucosa in young wild type,  ACE2 deficient mice. Purpose: Next-generation gene expression profiling has revolutionized analysis of molecular pathways. The goals of this study were to compare NGS-derived olfactory mucosa transcriptome profiles (RNAseq) of  wild-type mice (control) and  ACE2 knockout mice. Selected genes and pathways will be analyze further by low-throughput techniques such as real-time RT-PCR. Methods: Olfactory mucosa mRNA profiles of 2 months old wild-type (WT) and  ACE2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 S4 PE150 XP. For inspecting the quality of RNA-Seq data, the 100 most abundant genes are taken from all the samples and heatmaps were generated to observe the relation between samples/conditions. Results: Using our data analysis workflow, we mapped at least 47 million sequence reads per sample to the mouse genome (build mm10). Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa.  It is also the first study examining effects of gene knockout for ACE2 on gene expression profile in murine olfactory mucosa. We conclude that these data would help future studies in olfactory mucosa cells aimed to reveal molecular mechanisms associated with aging and biological function of ACE2 genes. RNAseq differential gene expression profiling of olfactory mucosa in wild type and ACE2 deficient mice.

overall_design: In this study 6 samples were analyzed. Analysis of 3 biological replicates for each experimental condition was performed. All mice used had C57BL/6J genetic background and were females.

first: Rafał

last: Butowt

first: Christhoper

last: von Bartheld


title: Comparison of synthetic TLR4 adjuvants PHAD and E6020 in mouse peritoneal macrophages

city: Baltimore

first: Katharina

last: Richard

state: MD

address: 685 W. Baltimore St. HSFI-380

department: Microbiology and Immunology

institute: University of Maryland School of Medicine

summary:
Toll-like receptors (TLRs), a family of pattern recognition receptors, bind microbial and host-derived molecules, leading to intracellular signaling and activation of host innate immune responses. TLR4 is unique in that ligand-mediated activation initiates two signaling cascades: the MyD88-dependent pathway, localized to the cell membrane, elicits rapid MAP kinase and NF-κB activation, and the TRIF-dependent pathway, localized to TLR4-containing endosomes, results in IRF-3 activation. Previous studies have associated adjuvanticity with the TRIF pathway. Gram-negative LPS is a potent TLR4 agonist, and structurally related molecules also signal through TLR4 to different extents. Herein, we compared two synthetic, non-toxic lipid A analogs used previously as vaccine adjuvants, monophosphoryl lipid A (PHAD®, sMPL) and E6020, for their capacity to activate TLR4-mediated innate immune responses. In primary mouse macrophages, high dose sMPL activates the MyD88-dependent signaling equivalently to E6020. In contrast to sMPL, E6020 exhibits robust activation of the TRIF pathway, including TLR4 internalization and IRF-3-dependent transcription, at all doses examined. Eritoran, a TLR4/MD2 antagonist, competitively inhibited sMPL more strongly than E6020. Despite these differences, sMPL and E6020 adjuvants induced antibody responses to a similar level and with balanced Ig isotypes, in two separate mouse immunization models. However, E6020 induced superior non-specific protection in a model of Streptococcus pneumoniae infection, compared to sMPL, which correlates with the activation of reactive nitrogen and oxygen species. These data provide evidence that a TRIF bias is not necessarily predictive of superior adjuvanticity, but may activate stronger innate defenses from infection.
TLR4 is unique among TLRs that it stimulates both the MyD88- and TRIF-dependent pathways (reviewed in Takeda K and Akira S, 2004, Semin Immunol). To compare the relative stimulatory capacities of two synthetic TLR4 agonist adjuvants, PHAD® (sMPL; Avanti Polar Lipids LLC) and E6020 (Eisai, Inc), we performed microarray analysis  of primary thioglycollate-elicited mouse peritoneal macrophages that were either cultured in media alone (control) or stimulated with 100 ng/mL (57.3 uM sMPL, 61.6 uM E6020) of the TLR4 agonists for two hours. Total RNA was extracted from three biological repicates (numbered 1-3) per treatment, and the transcriptomes analyzed individually by whole transcriptome microarray (Affymetrix Clariom D). Of the differentially expressed genes (DE genes; average of three replicates greater or equal to 2-fold difference in any comparison of treatments and false discovery rate below 0.05) almost 94% were protein-coding genes (includes those listed as either protein-coding or complex in the database), on which we focused for further analysis. sMPL induced expression of 155 protein-coding genes, including those that encode IL-1beta, TNF-alpha, Cxcl1 and Cxcl2--proteins that are associated with classic macrophage activation and are essential for inducing fever and attracting neutrophils. sMPL suppressed 15 protein-coding genes. In contrast, E6020 induced expression of 413 protein-coding genes and suppressed 88 protein-coding genes, which included all but one of the sMPL-regulated protein-coding genes. The majority of the genes induced by E6020, but not sMPL, are associated with Type I IFN expression (reference: Interferome.org database). This interferon signature points to stronger activation of the TRIF/IRF3 pathway in E6020-treated macrophages and includes genes that are secondarily induced by Type I IFNs. Similar expression of MyD88 dependent genes Il1b, Il10, and Tnf, and differential expression of TRIF-dependent genes Ifnb1, Cxcl10, and Ccl5 between the two synthetic agonists was confirmed by qRT-PCR.

overall_design: Three separate pools of thiglycollate-elicited peritoneal macrophages from 6-8 week old female C57BL/6J mice were cultured at 37 deg C, 5% CO2 under the following three conditions: media alone (control) or stimulated with 100 ng/mL (57.3 uM) sMPL, or 100 ng/mL (61.6 uM) E6020. After two hours, the RNA was harvested using Roche High Pure RNA isolation kits. RIN values ranged from 8.4 to 10.0 in the nine samples.

first: Stefanie

middle: N

last: Vogel

first: Darren

last: Perkins

first: Anup

last: Mahurkar

first: Yang

last: Song

first: Jing

last: Yin


title: Deciphering risperidone-induced lipogenesis by network pharmacology and molecular validation

city: tianjin

first: Fu

last: yun

address: 22 Qixiangtai Road, Heping District

institute: tianjin medical university

summary: Risperidone is an atypical antipsychotic that can cause substantial weight gain. The pharmacological targets and molecular mechanisms related to risperidone-induced lipogenesis (RIL) remain to be elucidated. Therefore, network pharmacology and further experimental validation were undertaken to explore the action mechanisms of RIL. In this study, RIL was systematically analyzed using integrating multiple databases through integrated network pharmacology, transcriptomics, molecular docking, and molecular experiment analysis. The potential signaling pathways for RIL were identified and experimentally validated using Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Our experimental data showed that Risperidone promotes adipocyte differentiate and lipid accumulation. And network pharmacology and GO analyses showed that risperidone induced adipocyte metabolism, differentiation, and lipid accumulation related functions. Intersecting analysis, molecular docking, and pathway validation analysis indicated that risperidone activated adipocytokine signaling pathway related genes by targeting MAPK14 (Mitogen-activated protein kinase 14), MAPK8 (Mitogen-activated protein kinase 8), and RXRA (Retinoic acid receptor RXR-alpha), thereby inhibiting long-chain fatty acid beta-oxidation by suppressing STAT3 (Signal transducer and activator of transcription 3) expression and phosphorylation. This study suggested that Risperidone increases adipocyte lipid accumulation by plausible inhibiting long-chain fatty acid beta-oxidation through targeting MAPK14, MAPK8, and RXRA.

overall_design: The whole-genome transcriptome of the promote-lipogenesis effects of risperidone in 3T3-L1

first: WeiDong

last: Li

first: Shen

first: Yun

last: Fu

first: Ke

last: Yang


title: Evaluation of the inflammatory and osteogenic response induced by metal particles released during implantoplasty of dental implants

city: L'Hospitalet de Llobregat (Barcelona)

first: Jorge

last: Toledano

address: C/Feixa llarga s/n

institute: University of Barcelona

summary:
During implantoplasty there is a large release of metal particles that might induce a pro-inflammatory response and reduce the viability of osteogenic cells, which may compromise the results of dental implants
The analysis of the inflammatory response in macrophage cell culture (THP-1) was carried out by RT-qPCR. CCR7, TNF-α and IL-1β genes were analyzed as proinflammatory markers, while CD206, TGF-β and IL-10 were analyzed as antiinflammatory markers.  The osteogenic response was studied with human bone marrow mesenchymal stem cells (BM-MSCs). We analyzed Runx2, alkaline phosphatase (ALP) and osteocalcin (OC) genes.

overall_design: In vitro cell based assay study. The expression of genes was analysed by means of RT-qPCR. We used THP-1 and BM-MSCs cells to study the inflammatory and osteogenic response, respectively.

first: Toledano

last: Jorge

first: Bosch

last: Begoña

first: Díez-Tercero

last: Leire


title: Time-dependent transcriptomic changes in HNSCC cell lines after irradiation with photons or Carbon ions

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: We aim to identify irradiation-induced transciptional changes in HPV-positive and HPV-negative HNSCC cell lines in vitro.
Methods: Cells were seeded to tissue culture flasks and irradiated after adherence, with 0 Gy or 4 Gy carbon ions or 4 Gy photons or 8 Gy photons. Analysis was performed 4h and  48h and 72h after irradiation
Results: Analysis of the data reveals a clear difference between irradiated and unirradiated samples, as well as between HPV-positive and HPV-negative HNSCC cells
Conclusion: Transcriptomic changes are dependent on HPV Status and irradiation, but independent from the type of irradiation.

overall_design: RNAseq analysis of human HNSCC cell lines

first: Dinesh

last: Tiwari

first: Ricarda

last: Hannen

first: Ulrike

last: Schötz


title: Long non-coding RNA ELDR promotes cell cycle progression in normal oral keratinocytes through induction of a CTCF-FOXM1-AURKA signaling axis

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: Long non-coding RNAs (lncRNAs) have gained widespread attention as a potential new layer of regulation in biological processes during development and disease. The lncRNA ELDR (EGFR long non‐coding downstream RNA) was recently shown to be highly expressed in oral cancers as compared to adjacent non-tumor tissue, and we previously reported that ELDR may be an oncogene as inhibition of ELDR reduces tumor growth in oral cancer models. Furthermore, overexpression of ELDR induces proliferation and colony formation in normal oral keratinocytes (NOKs). In this study, we examined in further detail how ELDR drives the neoplastic transformation of normal keratinocytes. We performed RNA-seq analysis on NOKs stably expressing ELDR (NOK-ELDR), which revealed that ELDR enhances the expression of cell cycle-related genes. Increased expression of Aurora kinase A (AURKA) and its downstream gene targets Polo-Like Kinase 1 (PLK1), Cell Division Cycle 25C (CDC25C), Cyclin-Dependent Kinase 1 (CDK1), and Cyclin B1 (CCNB1) are significantly increased in NOK-ELDR cells, suggesting induction of G2/M progression. We further identified CCCTC-Binding Factor (CTCF) as a binding partner of ELDR in NOK-ELDR cells. We showed that ELDR stabilizes CTCF and increases its expression. Finally, we demonstrate the ELDR-CTCF axis upregulates transcription factor Forkhead Box M1 (FOXM1), which induces AURKA expression and downstream G2/M transition. These findings provide mechanistic insights into the role of the lncRNA ELDR as a potential driver of oral cancer during neoplastic transformation of normal keratinocytes.

overall_design: RNA seq analysis in ELDR over expressed normal oral keratinocytes

first: Subhayan

last: Sur

first: Robert

last: Steele

first: Ben

middle: C

last: Ko

first: Ratna

middle: B

last: Ray


title: Expression data from epethilial tom+ cells in Adenomas originated in Mex3a WT and KO animals

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary:
Mex3a labells a subpopulation of Cancer Stem cells defined by their slow proliferative behaviour. Nevertheless, the precise function of MEX3A is unknown, although it plays a role in chemoresistance. The Mex3a KO adenomas are less chemoresistant compared to their WT controls.
We used microarrays to elucidate changes in gene expression in cells with the Mex3a promoter active (tomato expressing cells)

overall_design: Mex3a tom/flox or Tom/+ / Villin CreERT2 / APC fl/+ animals were induced with 4 consecutive shots of Tamoxifen to ensure recombination of both Mex3a and APC allele,followed by treatment with 2% DSS in drinking water for five consecutive days to enhance the number of colonic adenomas. Adenomas were collected after 2 months of the retival of DSS. Tomato positive cells (readout of Mex3a promoter activation) were purified by FACs.

first: Adrián

last: Alvarez

first: Eduard

last: Batlle


title: Analyses of immune infiltrate in DIPG murine models after treatment with new oncolytic virus Delta-24-ACT

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

institute: University Hospital of Navarra

summary: To better understand the mechanism underlying the therapeutic effect of Delta-24-ACT, we evaluated the triggered immune response. Thus, we intratumorally injected Delta-24-ACT, Delta-24-RGD or PBS (mock group) 3 days after NP53 cell implantation (0D). Then, tumor immune infiltrate was analyzed by NanoString (15 days)

overall_design: Comparison between Delta-24-ACT (ACT) and Delta-24-RGD (RGD) experimental groups with mock group (PBS)

middle: M

last: Alonso


title: Histone deacetylase 3 facilitates TNF α -mediated NF-κB activation through  suppressing CTSB induced RIP1 degradation and is required for host defense against  bacterial infection

first: Liping

last: Yang

overall_design: Total RNA profiling of gene expression upon knock-out of Hdac3 in RAW264.7 cells

first: Genhong

last: Cheng

first: Heng

first: Feng

last: Xu


title: Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

summary: Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.

overall_design:
This study contains the following five indepdent experimental setups, also denoted as experimental batches:
1. RNAseq of whole hippocampal lysate of aged mice continuously infused for 6 days with young mouse CSF or artificial CSF as control (aCSF n=8, YM-CSF n=7).
2. To gain a deeper mechanistic understanding of the cellular processes induced by young CSF in OPCs we metabolically labeled nascent mRNA with 4-thiouridine (s4U) using thiol(SH)-linked alkylation and sequenced RNA (SLAMseq) from cultured OPCs 1- or 6 hr after exposure to YH-CSF (a total of 4 groups; 1hr aCSF n=4, rest n=5).
3. Sorted OPC (olig2_high) and OL (olig2_low) nuclei from 4 young and 4 aged  hippocampi (aged OL n=3, rest n=4).
4. Sorted OPC (olig2_high) nuclei from hippocampi of aged mice 1hr or 6hr following acute interacerebroventricular injection of aCSF or young mouse CSF (total of 4 groups, n=4 each).
5. Sorted OPC (olig2_high) nuclei from hippocampi of aged mice 16hr following acute interacerebroventricular injection of aCSF, young mouse CSF or aged mouse CSF (total of 3 groups, aCSF n=3, rest n=4 mice each).

first: Tal

last: Iram

first: Achint

last: Kaur

first: Saket

last: Myneni

first: Allison

last: Morningsta

first: Heather

last: Shin

first: Miguel

middle: A

last: Garcia

first: Lakshmi

last: Yerra

last: Palovics

first: Andrew

first: Oliver

last: Hahn

first: Nannan

last: Lu

first: Steven

last: Shuken

first: Michael

last: Haney

first: Benoit

last: Lehallier

first: Manasi

last: Iyer

first: Jian

last: Luo

first: Henrik

last: Zetterberg

first: Andreas

last: Keller

first: Bradley

last: Zuchero

first: Tony

last: Wyss-Coray


title: Histone deacetylase 3 and FOXK1 formed a transcriptional complex involved in regulating the expression of STAT1 and STAT2 [ChIP-seq]

first: Liping

last: Yang

overall_design: Examination the binding of HDAC3 and FOXK1 on the promoter of STAT1 and STAT2.

first: Heng

first: Feng

last: Xu

first: Genhong

last: Cheng


title: Cnot8 Eliminates Naïve Regulation Networks and Is Essential for Naïve-to-Formative Pluripotency Transition [scRNA-Seq]

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: The transition of mammalian early epiblast at different phases is characterized by the differences of pluripotent states and developmental potential, involving extensive transcriptome changes. However, the role of post-transcriptional RNA degradation modulation in cell fate transition remains largely unexplored. Here, we report that deadenylase Cnot8 of Ccr4-Not complex specifically plays a role in naïve-to-formative transition of pluripotent stem cells (PSCs). Disruption of Cnot8 results in early embryonic lethality, accompanying with the increased expression levels of naïve transcription factors in mouse epiblasts. Cnot8 depletion leads to accumulated expression abundances and increased poly(A) tail lengths of massive transcripts including mRNAs of naïve regulation networks, impairing the naïve-to-formative pluripotency conversion. Mechanistically, Cnot8 interacts with Tob1 and Pabpc1 to guarantee the prompt mRNA deadenylation and degradation of naïve regulation networks at specific time. Together, these findings delineate the mechanism underlying PSC fate transition through global degradation of mRNAs for naïve regulation networks by Cnot8.

overall_design: Total 2 scRNA-seq libraries with  wild type and Cnot8 KO ESCs (S/LIF) and 48h-EpiLCs

first: Falong