title: Muscle injury causes gene expression changes that are related to long-term changes in stem cell DNA methylation [RNA-Seq]

first: Tal

last: Michaeli

summary: Injury to muscle brings about the activation of stem cells, which then generate new myocytes to replace the damaged tissue.  We now demonstrate that this activation causes a dramatic change in the stem cell methylation pattern that prepares them epigenetically for terminal myocyte differentiation.  These demethylation and de novo methylation events occur at regulatory elements associated with genes involved in myogenesis.  Local injury of one muscle brings about an almost identical epigenetic change in satellite cells from other muscles in the body, as well.  Furthermore, this same methylation state is also generated in muscle stem cells of female animals following full-term pregnancy, even in the absence of any injury.  In all of these cases, which appear to be mediated by circulating factors, the new methylation profile is then stably maintained in resident muscle stem cells and thus represents a molecular memory of previous physiological events that is probably programmed to provide a mechanism for adapting to the environment. Here we show the changes in gene expression that accompany the changes in DNA methylation.

overall_design:
Muscle injury was carried out on hind-limb muscles from 8.5-9 month old mice, virgin and pregnant, by piercing multiple times with a 23-gauge needle. Satellite cells were isolated from the injured muscles according to specific markers and subjected to expression studies using RNA-Seq. At least 3 replicates in each condition.
[Third-party reanalysis]  Mature quadriceps muscle samples were taken from the project "An RNASeq normal tissue atlas for mouse and rat", by the Boehringer Ingelheim Pharma GmbH & Co. KG Target Discovery Research center, and added as additional samples in the system. Accession numbers for those samples were SAMEA104310458, SAMEA104310459 and SAMEA104310460, of the project PRJEB22693 (ENA database, https://www.ebi.ac.uk/ena/browser/view/PRJEB22693).

middle: F

first: Ofra

last: Sabag

first: Jonathan

last: Monin

first: Yuval

last: Nevo

last: Gielchinsky

first: Benjamin

middle: P

last: Berman

first: Howard

last: Cedar

first: Yehudit

last: Bergman


title: Raw RNA-seq data of MEF cells treated with MGH-CP1

status: Public on Dec 01 2022

city: Worcester

first: Junhao

last: Mao

state: MA

address: 55 N Lake Ave

department: MCCB

country: USA

institute: UMass Medical School

type: Expression profiling by high throughput sequencing

summary: Raw RNA-seq data of MEF cells treated with control vehicles (DMSO) and MGH-CP1 (1uM in DMSO)for 2 and 4 days

overall_design: Wild type and Lats1/2 DKO MEF cells are treated with vehicles (DMSO) or MGH-CP1 (1uM in DMSO) for 2 days and 4 days

first: Lihua

last: Zhu

first: Xu

last: WU

first: Qi

last: Li

first: Rui

first: Yang

last: Sun


title: Genome-wide contacts of rDNA units detected by 4C procedure in human genome [new]

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for PCR amplification were selected upstream from EcoRI site (coordinate 30487 in the sequence with Accession number U13369.1): 5' TTCGCCTACGGATTTCTAGAAAATAA 3' and 5' AAAAGAAGCTCAAGTACATCTAATCTAA 3' (new primers).

overall_design: Analysis of rDNA genome-wide contacts in HEK 293T cells using 4C approach.

middle: A

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: Effects-based Monitoring of Contaminants of Emerging Concern in Great Lakes Tributaries: Calculating the Risk of Fish Developing Liver Toxicity and Cancer

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

summary: Today, many contaminants of emerging concern can be measured in waters across the United States, including the tributaries of the Great Lakes. However, just because the chemicals can be measured does not mean that they necessarily result in harm to fish and other aquatic species. Complicating risk assessment in these waters is the fact that aquatic species are encountering the chemicals as mixtures, which may have additive or synergistic risks that cannot be calculated using single chemical hazard and concentration-response information. We developed an in vitro effects-based screening approach to help us predict potential liver toxicity and cancer in aquatic organisms using water from specific Great Lakes tributaries: St. Louis River (MN), Bad River (WI), Fox River (WI), Manitowoc River (WI), Milwaukee River (WI), Indiana Harbor Canal (IN), St. Joseph River (MI), Grand River (MI), Clinton River (MI), River Rouge (MI), Maumee River (OH), Vermilion River (OH), Cuyahoga River (OH), Genesee River (NY), and Oswego River (NY). We exposed HepG2 cells for 48hrs to medium spiked with either field collected water (final concentration of environmental samples in the exposure medium were 75% of the field-collected water samples) or purified water. Using a deep neural network we clustered our collection sites from each tributary based on water chemistry. We also performed high throughput transcriptomics on the RNA obtained from the HepG2 cells. We used the transcriptomics data with our Bayesian Inferene for Sustance and Chemical Toxicity (BISCT) Bayesian Network for Steatosis to predict the probability of the field samples yielding a gene expression pattern consistent with predicting steatosis as an outcome. Surprisingly, we found that the probability of steatosis did not correspond to the surface water chemistry clustering. Our analysis suggests that chemical signatures are not informative in predicting biological effects. Furthermore, recent reports published after we obtained our samples, suggest that chemical levels in the sediment may be more relevant for predicting potential biological effects in the fish species developing tumors in the Great Lakes basin.

overall_design: There are 8 samples exposed to control water, and 4 samples each are exposed to surface water from each site, with the exception of MIWI where only 3 samples were exposed to surface water.

middle: D

first: Marina

last: Evich

first: John

middle: E

last: Mylroie

first: Quincy

last: Teng

first: Natalia

last: Garcia Reyero

first: Mitchell

last: Wilbanks

first: Edward

middle: J

last: Perkins


title: Coronavirus replication is controlled by both host and viral RNA m6A methylations

city: Hangzhou

first: Yaowei

last: Huang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

summary: N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role in virus life cycle. However, whether m6A methylation can modulate replication of coronaviruses, which contain the largest known RNA genomes, remains elusive. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of genome, and that PEDV infection alters the expression pattern of host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has an opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulates coronavirus replication.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: MeRIP-seq of poly(A)-RNA from Mock or PEDV-infected MARC-145 and S10-3 cells in two replicates.

first: Yangfan

last: Zhou

first: Chun-Miao

last: Ji

first: Zhike

last: Lu

first: Jianzhao

last: Liu

first: Yao-Wei


title: Krill oil protects dopaminergic neurons from age-related degeneration through temporal transcriptome rewiring and suppression of several hallmarks of aging

status: Public on Nov 30 2022

city: Lørenskog

first: Hilde

last: Loge Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

summary: There is accumulating evidence that interfering with the basic aging mechanisms can enhance healthy longevity. Many cellular processes contribute to aging and are referred to as “hallmarks of aging”; by presumption, interventional/therapeutic strategies targeting on multiple ageing hallmarks could be more effective to delay ageing than targeting on one hallmark. While the health-promoting qualities of marine oils have been extensively studied, the underlying molecular mechanisms are not fully understood. Lipid extracts from Antarctic krill are rich in long-chain omega-3 fatty acids (eicosapentaenoic acid/EPA and docosahexaenoic acid/DHA), choline, and astaxanthin. Here, we investigated whether krill oil promotes healthy aging in the small roundworm C. elegans. We show that krill oil rewires distinct gene expression programs that contribute to attenuate several aging hallmarks, including oxidative stress, proteotoxic stress, senescence, genomic instability, and mitochondrial dysfunction. In a C. elegans model of Parkinson´s disease, krill oil protects dopaminergic neurons from aging-related degeneration, decreases alpha synuclein aggregation, and improves dopamine-dependent behavior and cognition. Mechanistically, krill oil increases neuronal resilience through temporal transcriptome rewiring to promote anti-oxidative stress and inflammation via healthspan regulating transcription factors such as SNK-1. However, also krill oil promotes DA neuron survival through regulation of synaptic transmission and neuronal functions via PBO-2 and RIM-1.  Collectively, krill oil rewires global gene expression programs and promotes healthy aging via abrogating multiple ageing hallmarks, shedding light on further pre-clinical and clinical explorations.

overall_design: Age synchronized wildtype and PD animals were grown on regular medium of medium supplemented with krill oil. These animals were harvested as day 1, day 3, day 6 adults and RNA isolation was performed the same day. Briefly, the animals were washed x2 with sterilized milliQ water, and collected in 1.5ml Eppendorf. The worm pellets were dispensed in 600 µl of TRI reagent or trizol and transferred to tube with sterile beads to homogenize the animals. From here RNA isolation for tissue was followed as described in the Direct-zol RNA Miniprep Kits protocol section. The isolated RNA was dissolved in 10 µl nuclease free water and the quality was analyzed in bioanalyser.

first: Tanima

last: SenGupta

first: Yohan

last: Lefol

first: Lisa

last: Lirussi

first: Veronica

last: Suaste

first: Torben

last: Luders

first: Swapnil

last: Gupta

first: Yahyah

last: Aman

first: Kulbhushan

last: Sharma

first: Evandro

last: Fang

last: Nilsen


title: Stress induced accelerated aging in mouse eye [ChIP-seq]

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

state: California

address: 837 Health Sciences Rd, Gillespie Neuroscience Research Facility, Room#2226, Bench#8

department: Physiology & Biophysics

institute: UC Irvine

summary: Aging, a universal process that affects all cells in an organism, is a major risk factor for a group of neuropathies called glaucoma, where elevated intraocular pressure is one of the known stresses affecting the tissue. Our understanding of molecular impact of aging on response to stress in retina is very limited, therefore we developed a new mouse model to approach this question experimentally. Here we show that susceptibility to response to stress increases with age and is primed on chromatin level. We demonstrate that program activated by stress caused by ocular hypertension is similar to natural aging and involves activation of inflammation and senescence. Finally, we show that multiple instances of pressure elevation cause accelerated aging of young retina as measured on transcriptional and epigenetic level and is accompanied by changes in chromatin modifications. Our data suggests that molecular mechanism of aging is regulated at the level of epigenetic activation and repression and, therefore, might be modifiable. Lastly, this work further emphasizes the importance of early diagnosis and prevention as well as age-specific management of age-related eye-diseases, including glaucoma.

overall_design: From the RNA-Seq analysis results we observed that recurrent stress on young tissue induced changes in IOP stress response in transcription were similar to aged retina. We then hypothesized that dynamics of H3K27Ac levels in young retinas upon repetitive stress will be similar to aged retinas upon one-time stress. To test this hypothesis we performed ChIP-Seq anti-H3K27Ac antibody.

first: Qianlan

last: Xu

first: Cezary

last: Rydz


title: Hedgehog signaling is essential to maintain epithelial identity during larynx and foregut morphogenesis.

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

summary:
Purpose: This study seeks to determine the role of Hedgehog signaling in larynx development.
Methods: To determine how Hedgehog signaling directs larynx epithelial morphogenesis we used genomic approaches to identify a novel set of Hedgehog target genes within the early larynx. To this end, we performed bulk RNA-seq on 3-pooled E10.5 (32-35S) larynx tissues from wild-type (2 replicates) and Shh-/- (2 replicates) embryos. From this experiment we identified 1873 differentially expressed genes (p-value <0.05).
Results: Hedgehog is essential for maintaining the identity of foregut-derived epithelial cells within the larynx vocal folds. In the absence of HH signaling these epithelial cells undergo specific transcriptional changes to initiate a partial epithelial-to-mesenchymal transition, migrate out of the epithelial layer and under go cell death. The layer is then replaced by a different population of cells.

overall_design: Bulk RNA-seq on 3-pooled E10.5 larynx tissues in wild-type and Shh-/- embryos (32-35S).

first: Janani

last: Ramachandran

first: Weiqiang

last: Zhou

first: Anna

last: Bardenhagen

first: Hongkai

last: Ji


title: Muscle injury causes long-term changes in stem cell DNA methylation [RRBS]

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

type: Methylation profiling by high throughput sequencing

summary: Injury to muscle brings about the activation of stem cells, which then generate new myocytes to replace the damaged tissue. We now demonstrate that this activation causes a dramatic change in the stem cell methylation pattern that prepares them epigenetically for terminal myocyte differentiation. These demethylation and de novo methylation events occur at regulatory elements associated with genes involved in myogenesis. Local injury of one muscle brings about an almost identical epigenetic change in satellite cells from other muscles in the body, as well. Furthermore, this same methylation state is also generated in muscle stem cells of female animals following full-term pregnancy, even in the absence of any injury. In all of these cases, which appear to be mediated by circulating factors, the new methylation profile is then stably maintained in resident muscle stem cells and thus represents a molecular memory of previous physiological events that is probably programmed to provide a mechanism for adapting to the environment.

overall_design: Muscle injury was carried out on hind-limb muscles from 8.5-9 month old mice, virgin and pregnant, by piercing multiple times with a 23-gauge needle. Satellite cells were isolated from the injured or contralateral muscles according to specific markers and subjected to methylation studies using the RRBS protocol. At least 4 mice in each group.

first: Ofra

last: Sabag

first: Jonathan

last: Monin

first: Yuval

last: Nevo

last: Gielchinsky

first: Benjamin

last: Berman

first: Howard

last: Cedar

first: Yehudit

last: Bergman


title: Stress induced accelerated aging in mouse eye [ATAC-seq]

overall_design: To understand the chromatin remodeling events that occur after IOP elevation in young and aged retinas, we performed ATAC-seq on retinas isolated two days after the 30 mmHg IOP treatment.  3-month-old bulk retinas (N=6) was set as control group to 18-month-old bulk retinas (N=6) in the natural aging related differential analysis of genome-wide chromatin accessibility in wildtype mouse.  For mice at each age (3 month or 18 month), unilateral untreated retinas (N=3) were set as control group to unilateral IOP (constant 30mmHg IOP for 1 hour) treated retina (N=3) in the intraocular pressure elevation related differential analysis of genome-wide chromatin accessibility in wildtype mouse.


title: SCOPE-seq Analysis of Intra-operative Labeling Specificity of 5-ALA for Glioblastoma

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway

institute: Columbia University

summary: Glioblastoma (GBM) is the most common and aggressive malignant primary brain tumor, and surgical resection is a key part of the standard-of-care. In fluorescence-guided surgery (FGS), fluorophores are used to differentiate tumor tissue from surrounding normal brain. The heme synthesis pathway converts 5-aminolevulinic acid (5-ALA), a fluorogenic substrate, to the fluorophore protoporphyrin IX (PpIX). The resulting fluorescence is thought to be specific to transformed glioma cells, but this specificity has not been examined at single cell level. Here, we performed paired single cell imaging and RNA sequencing of individual cells (SCOPE-seq2) on human GBM surgical specimens with visible PpIX fluorescence from patients who received 5-ALA prior to surgery. SCOPE-seq2 allows us to simultaneously measure PpIX fluorescence by imaging and unambiguously identify transformed glioma cells from single-cell RNA-seq (scRNA-seq). We observed that 5-ALA treatment results in labeling that is not specific to transformed tumor cells. In cell culture experiments, we further demonstrated untransformed cells can be labeled by 5-ALA directly or by PpIX secreted from surrounding transformed cells. In acute slice cultures from mouse glioma models, we showed that 5-ALA preferably labels GBM tumor tissue over non-neoplastic brain tissue at bulk level, and that this contrast is not due to blood-brain-barrier disruption. Taken together, our findings support the use of 5-ALA as an indicator of GBM tissue, but not as a specific marker of transformed glioma cells.

overall_design: Performed SCOPE-seq2 on single cells dissociated from human GBM surgical specimens with visible intra-operative 5-ALA fluorescence.

first: Zhouzerui

last: Liu


title: 786-0 renal cell carcinoma cell line Everolimus treatment

city: Chapel Hill

first: Bhavani

last: Krishnan

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

summary: We present transcriptome profiling of 786-0 renal cell carcinoma cell lines both with and without Everolimus, an mTOR inhibitorhbn

overall_design: 786-0 cells were treated with either a control DMSO vehicle or 10um Everolimus, an mTOR inhibitor, for 4 hours

first: William

middle: Y

last: Kim


title: DNA methylome and transcriptome sequencing to define pathways involved in the activation of microglia

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Microglia cells are macrophages which reside in the brain, and become activated during the inflammatory processes involved in neurodegenerative and autoimmune disorders. An understanding of the molecular processes involved in this activation process could lead to the development of new neuroprotective therapies. To reveal molecular mechanisms involved in microglia activation, we performed RNA-seq and MBD-isolated genome sequencing (MiGS or MBD-seq) on both naïve and peak microglia derived from the mouse experimental autoimmune encephalomyelitis (EAE) model. The EAE model reflects some of the histological and immunological features of multiple sclerosis (MS) in humans. Mice genetically engineered to label Ccr2 with red fluorescent protein (rfp) and Cx3cr1 with green fluorescent protein (gfp) (“red-green mice” as described in Saederup et al., 2010 and Mizutani et al., 2012) were employed and microglia (positive for gfp) were separated from infiltrating monocytes using flow cytometry.

overall_design: Microglia cells were purified and pooled from the brains of 30 mice per condition for both the naïve (before EAE induction) and peak (peak of EAE induction) timepoints of the EAE mouse model. DNA and RNA were extracted, and RNA-seq and MiGS were performed for each timepoint. MiGS was performed for two biological replicates. Due to the difficulty of obtaining the materials, the RNA-seq was not replicated.

first: Jeffrey

middle: M

last: Bhasin

first: Haiyan

first: Nagarajavel

last: Vivekananthan

first: Richard

last: Ransohoff


title: Expression profile of Ewing sarcoma

status: Public on Nov 29 2022

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

country: Germany

institute: Technical University of Munich, TUM University Hospital

summary: The expression profile in Ewing tumors was analyzed and correlated with glucose uptake (SUVmax) measured in 18F-FDG-PET imaging

overall_design: 19 samples (sample_XX) from 17 patients (patient_XX) with Ewing sarcoma were analyzed

first: Oxana

last: Schmidt

first: Stefan

last: Burdach


title: Next Generation Sequencing Quantitative Analysis of Wild Type and RALY knock-down HCT 116 cells Transcriptomes

city: Gwang-ju

first: Kim

last: Donggun

address: 123 cheomdangawgi-ro, buk-gu

department: Life science

country: South Korea

institute: Gwangju Institute of Science and Technology

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression and alternative RNA splicing. The goals of this study are to compare alternative splicing in RALY knock-down cells to identify the function of RALY in alternative splicing transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods:  mRNA profiles of RALY knock-dowed HCT 116 cells and non-silencing shRNA treated HCT 116 cells generated by deep sequencing, in duplicate, using Illumina Hiseq 2500.
Results: Using an we mapped about more than 60 million reads per sample to the human genome (GRCh38)  and identified 58,884 transcripts in WT and RALY knock-downed HCT 116 cells with Hisat2. rMATS analysis of RNA-seq data demonstrate  significant effects of RALY on 4,046 skipped exon splicing and other alternative splicing events.
Conclusions: Our study represents the first detailed analysis of transcriptomes in RALY KD cells, with biologic duplicates, generated by RNA-seq technology. The splicing analysis workflows reported here should provide a framework for the RALY function in the splicing.

overall_design: RALY knockdown

first: Haihong

last: Shen

first: Donggun


title: Ssc-miR-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene

city: Guiyang

first: wei

last: yuan

state: Guizhou Province

address: Huaxi District

department: College of Animal Science

institute: Guizhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: The TYRP1 gene can affect melanogenesis in melanocytes of the Xiang pigs, and ssc-miR-221-3p targets the TYRP1 gene to affect melanogenesis in melanocytes of the Xiang pigs.

overall_design:
To investigate the mRNAs and miRNAs affecting melanogenesis in melanocytes in Xiang pigs.
We screened genes and miRNAs affecting melanin in Xiang pigs by transcriptome sequencing, and experimentally verified whether there is a directional regulatory relationship between the screened genes and miRNAs and whether they can jointly affect melanogenesis in Xiang pigs.

first: Wei

last: Yuan

first: Hai

last: Qin

first: Huan

last: Bi

first: Depeng

last: Zhao

first: Yiyu

last: Zhang

last: Chen


title: Tagmentation (CUT&Tag) assay for ATF4 in HCT116 (Human colorectal cancer) cells

city: Beijing

first: Zhimin

last: Jiang

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

summary: To determine the biological function of ATF4 in the modulation of downstream target genes, we performed Tagmentation (CUT&Tag) assay in HCT 116 (Human colorectal cancer) cells

overall_design: Then  CUT&Tag assay analysis were performed and the modulation of downstream target genes were identified.

first: Hui

last: Guo

first: Zusen

last: Fan


title: Single-cell RNA-sequencing of virus-specific GP33+CD8+ T cells from day 33 post-LCMV Cl13 infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. However, when CD4+ T cell help is present, a heterogenous population of virus-specific CD8+ T cells are present. Here, we applied scRNA-seq to distinguish CD8+ T cell heterogeneity during LCMV Clone 13 infection.

overall_design: GP33+ CD8+ T cells were FACS-sorted from LCMV Cl13-infected mice on day 33 post- infection (2 mice) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol

first: Moujtaba

last: Kasmani

first: Paytsar

last: Topchyan


title: Differential expression of microRNAs in adipose tissue with aging and caloric restriction

city: Alcorcon

first: Gema

last: Medina-Gomez

state: Madrid

address: Avda de Atena s/n

department: Ciencias Básicas de la Salud

country: Spain

institute: Universidad Rey Juan Carlos

summary: To further analyze the effect of aging and caloric restriction in the microRNA expression, we have employed microarray expression profiling as a discovery platform to identify differentially expressed microRNAs in middle-aged animals and the impact of caloric restriction in the microRNA expression profile. Subcutaneous and visceral adipose tissue were extracted from 3 groups of mice: 3 month-old, 12 month-old fed ad libitum and 12 month-old fed with a caloric restricted diet. Comparisons between young and middle-aged animals in subcutaneous and visceral adipose tissue, and between the 12 month old ad libitum and 12 month old caloric restricted diet in both adipose depots were made.

overall_design: microRNA expression was analyzed in 2 different adipose tissue depots: subcutaneous (scWAT) and epidydimal (eWAT) adipose tissue. For the scWAT, 5 samples from 3 month-old animals, 4 samples from 12 month old ad libitum animals and 3 samples from 12 month old caloric restriction were studied. For the eWAT, 5 samples from 3 month-old animals, 4 samples from 12 month old ad libitum animals and 4 samples from 12 month old caloric restriction were studied.

last: Medina Gomez

first: Patricia

last: Corrales


title: Identification of heterogeneous networks and plasma-monocytes crosstalks in multiple myeloma stratified by R-ISS system through single-cell sequencing

city: Chengdu

first: gong

last: bo

address: 四川省成都市青羊区一环路西二段32号

institute: Sichuan Provincial People’s Hospital

summary:
Purpose: to identify new potential pathways and therapeutic targets to kill plasma cells and affect their microenvironment in stage R-ISS III MM patients.
Methods: We performed single-cell RNA sequencing of bone marrow samples obtained from nine MM patients and from two normal controls including pseudotime analysis, SCENIC analysis,cell–cell communication networks,large-scale chromosomal CNV analysis.The new markers that we reported originally were verified by qPCR, flow cytometry and immunofluorescence staining.
Results: We identified two R-ISS-related modules, namely, “protein metabolism” (module 2) and “cell proliferation” (module 1). The gene expression pattern in pseudotime suggested that the gene activation in module 2 provides a substantial basis for the malignant proliferation of plasma cells during MM progression. We found that STAT1 may activate LETM1 to promote MM progression via the C-type lectin receptor signaling pathway. And PDIA6 was putatively activated by the UQCRB regulon to participate in oxidative phosphorylation. Moreover, a subcluster of monocytes exclusively found in stage III and specifically expressed CCL3L1, CCL3, and CXCL2 was modulated by ATF3. CCL3/CCL5/CCL3L1–CCR1, CCL4–SLC7A1, CD47–SIPRA, SEMA4A–PLXND1, and LILRB4–LAIR1 were identified as the active ligand–receptor pairs in plasma–monocyte communications in stage III.
Conclusions: we systematically analyzed the molecular events and the regulated networks in the progression of the R-ISS stages, and the results suggested a promising landscape for the treatment of MM.

overall_design: We performed single-cell RNA sequencing of bone marrow samples obtained from nine MM patients and from two normal controls to investigate the heterogeneity among the stages stratified by R-ISS (Revised International Staging System)

first: Ling

last: Zhong

first: Bo

last: Gong


title: Single-cell RNA-sequencing of CD44+ CD4+ T cells from day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (scRNA-Seq)

summary: CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, following transient CD4+ T cell depletion, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. Here, we applied scRNA-seq to determine the CD4+ T cell subsets that repopulate following transient CD4+ T cell depletion, during LCMV Clone 13 infection.

overall_design: CD44+ CD4+ T cells were FACS-sorted from control or CD4+ T cell-depleted mice on day 21 post-LCMV Cl13 infection (2 mice per condition) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) according to manufacturer’s protocol.


title: RNA-sequencing of primary and secondary bacterial pneumonia

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

institute: University of Colorado Denver, Anschutz

summary: Influenza infection is substantially worsened by the onset of secondary pneumonia caused by bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). The bidirectional interaction between the influenza-injured lung microenvironment and MRSA is poorly understood. By conditioning MRSA ex vivo in bronchoalveolar lavage fluid collected from mice at various timepoints of influenza infection, we found that the influenza-injured lung microenvironment dynamically induces MRSA to increase cytotoxin expression while decreasing metabolic pathways. LukAB, a SaeRS two-component system dependent cytotoxin, is particularly important to the severity of post-influenza MRSA pneumonia. LukAB’s activity is likely shaped by the post-influenza lung microenvironment, as LukAB binds to (and is activated by) heparan sulfate (HS) oligosaccharide sequences shed from the epithelial glycocalyx after influenza. Our findings indicate that post-influenza MRSA pneumonia is shaped by bidirectional host-pathogen interactions: host injury triggers changes in bacterial expression of toxins, the activity of which may be shaped by host-derived HS fragments.

overall_design: We analyzed whole lung RNA-sequencing analysis on control mice (IN Saline D0 + IT Saline D10), influenza A/PR/8/34 infection alone (IN PR8 D0 + IT Saline D10), USA300 MRSA primary pneumonia (IN Saline D0 + IT MRSA D10), and PR8 with MRSA secondary pneumonia (IN PR8 D0 + IT MRSA D10).

first: Kaori

last: Oshima

first: Eric

last: Schmidt


title: MRSA temporal adaptation to the healthy and influenza injured lung microenvironment

summary: Influenza-induced respiratory failure is substantially worsened by secondary bacterial infections such as methicillin-resistant Staphylococcus aureus (MRSA). The bidirectional interaction between the influenza-injured lung microenvironment and MRSA is poorly understood. By conditioning MRSA ex vivo in bronchoalveolar lavage (BAL) fluid collected from mice at various timepoints of influenza infection, we found that influenza-injured lung microenvironment induces MRSA to increase cytotoxin expression while decreasing metabolic pathways.  This overall increase in MRSA virulence was dependent upon SaeRS, a bacterial two-component system. Once expressed by MRSA, these influenza-induced toxins (such as Hla and LukAB) interact with host heparan sulfate (HS) fragments shed into the airspace. Highly-sulfated HS fragments augmented Hla- and LukAB-toxicity in vitro and in vivo. Our findings indicate that post-influenza MRSA pneumonia is shaped by bidirectional host-pathogen interactions: host injury triggers changes in bacterial expression of toxins, the activity of which are then shaped by host-derived HS fragments.

overall_design: We analyzed Staphycoccus aureus, WT and SaePQRS mutant strains, RNA cultured in cell-free bronchoalveolar lavage (BAL) fluid for 12 hours collected from mice given intranasally (IN) saline and influenza (PR8, 30k FFU), recovered for 3, 7, 10, 21 days.

first: Alex

last: Horswill


title: Stress induced accelerated aging in mouse eye

first: Dorota

last: Skowronska-Krawczyk

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

overall_design: Refer to individual Series


title: Mechano-regulated RNA binding protein hnRNPC contributes to RNA homeostasis in heart failure

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

summary: Cardiac pathologies are characterized by intense remodeling of the extracellular matrix (ECM) that eventually leads to heart failure. Cardiomyocytes respond to the ensuing biomechanical stress by re-expressing fetal contractile proteins via transcriptional and post-transcriptional processes, like alternative splicing (AS). Here, we demonstrate that the heterogeneous nuclear ribonucleoprotein C (hnRNPC) is upregulated and relocates to the sarcomeric Z-disk upon ECM pathological remodeling. At this site, the protein participates to the localized translation of mRNAs encoding sarcomeric proteins. Alterations in hnRNPC expression and localization can be mechanically determined and affect the AS of numerous mRNAs involved in mechanotransduction and cardiovascular diseases. We thus propose that cardiac ECM remodeling serves as a switch in RNA metabolism by directly impacting an associated regulatory protein of the spliceosome apparatus. These findings offer new insights on the mechanism of mRNAs homeostasis mechanoregulation in disease conditions.

overall_design: iCLIP-seq : Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) of hnRNPC1/C2 in normal human dermal fibroblasts (NHDFs)

first: Fabiana

last: Martino

first: Ana

last: Rubina Perestrelo

first: Nandan

last: Mysore Varadarajan

first: Helena

last: Durikova

first: Vladimir

last: Horvath

first: Francesca

last: Cavalieri

first: Frank

last: Caruso

first: Waleed

middle: S

last: Albihlal

first: André

last: Gerber

first: Mary

last: O’Connell

first: Stepanka

last: Vanacova

first: Stefania

last: Pagliari

first: Giancarlo

last: Forte


title: Fetal and maternal liver expression post gestational exposure to perfluorooctanoic acid (PFOA) or hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) in CD-1 mice

city: Research Triangle Park

first: Suzanne

last: Fenton

state: North Carolina

address: 111 TW ALEXANDER DR

department: Mechanistic Toxicology Branch

institute: Division of the National Toxicology Program, National Institute of Environmental Health Sciences

summary: Multiple per- and polyfluoroalkyl substances (PFAS) have been associated with adverse liver outcomes in adult humans and toxicological models, but effects on the developing liver or biologic pathways involved are not known. We performed whole-transcriptome gene expression analysis to investigate the molecular mechanisms of liver toxicity in the dam and female fetuses after exposure to two different PFAS, perfluorooctanoic acid (PFOA) and its replacement, hexafluoropropylene oxide-dimer acid (HFPO-DA, commonly referred to as GenX).

overall_design: Pregnant CD-1 mice were exposed via daily oral gavage from embryonic day (E) 1.5-17.5 to PFOA (0, 1, or 5 mg/kg) or GenX (0, 2, or 10 mg/kg). Maternal and fetal livers were collected, RNA was isolated (N=5 per dose/group), and transcriptome-wide gene expression was quantified.

first: Bevin

last: Blake

first: Trina

last: Phan

first: Helen

last: Nguyen

first: Colette

middle: N

last: Miller

first: Deepak

last: Mav

first: Ruchir

middle: R

last: Shah

first: Michele

last: Balik-Meisner

first: Dhiral

last: Phadke


title: Human CMV-specific vs IAV-specific CD8 TCM cells

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

summary: We compared CD8 TCM cells specific for a CMV epitope (pp65495-503) and an influenza A virus (IAV) epitope (M158-66) of the same healthy adults and identified genes whose expression are altered in CMV-specific compared to IAV-specific TCM cells.

overall_design:
Transcriptional profiling of CMV-specific vs IAV-specific CD8 TCM cells from healthy human. Goal was to determine the differentially expressed genes between these two antigen-specific CD8 TCM cells.
CMV-specific vs IAV-specific CD8 TCM cells. Biological replicates: 2 CMV-specific replicates, 2 IAV-specific  replicates.

first: Guobing

last: Chen

first: Nan-ping


title: lncRNA H19/Let7b/EZH2 axis regulates somatic cell senescence

city: Philadelphia

first: Christian

last: Sell

state: Pennsylvania

address: 245 N 15th St, Room

department: Biochemistry

institute: Drexel University

summary: Long non-coding RNAs (lncRNAs) regulate diverse cellular processes and are associated with many age-associated diseases. However, the function of lncRNAs in cellular senescence remains largely unknown. Here we characterize the role of lncRNA H19 in senescence. We show that H19 levels decline as cells undergo senescence, and depletion of H19 results in premature senescence. We find that repression of H19 is triggered by the loss of CTCF and prolonged activation of p53 as part of the senescence pathway. Mechanistically, the loss of H19 drives senescence via increased let7b mediated targeting of EZH2. We further demonstrate that  H19 is required for senescence inhibition by the mTOR inhibitor rapamycin, where it maintains lncRNA H19 levels throughout the cellular lifespan and thus prevents the reduction of EZH2 that would otherwise lead to cellular senescence. Therefore, lncRNA H19 is crucial in maintaining the balance between sustained cell growth and the onset of senescence.

overall_design: CUT&TAG

first: Manali

last: Potnis


title: Transcriptome analysis of transgenic Kimchi cabbage with Arabidopsis thaliana Phytochrome B.

status: Public on Nov 28 2022

city: Gwangju,Korea

first: Jeong-Il

last: Kim

address: Chonnam National University, Gwangju 61186, Korea

department: Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University

institute: Chonnam national university

summary: We report here NGS RNA-seqencing datasets with wild-type (Chiifu) and kimchi cabbage with Arabidopsis thaliana Phytochrome B (named AtPHYB) grown under optimal temperature (22℃) condition.

overall_design: B. rapa whole plant: 22; 2weeks old (non-heat treated), NT; Non-transgenic Kimchi cabbage, AtPHYB; Kimchi cabbage with Arabidosis thaliana Phytochrome B, G564E; Kimchi cabbage with AtPHYB mutant which 564 amino acid G to E.


title: Effect of Combination Therapy with Anti-PD-1 Antibody and dasatinib on Liver Metastases in an Experimental Mouse Model

city: Hiroshima

first: RYO

last: YUGE

state: Hiroshima

address: 1-2-3, Kasumi Minamiku

country: Japan

institute: Hiroshima University Hospital

summary:
In order to investigate whether dasatinib, a stromal inhibitor, could increase the sensitivity to immunotherapy for metastatic colorectal cancer, we generated a mouse model of liver metastasis.
We performed a comprehensive gene expression profiling analysis by extracting toral RNA from liver metastases of mice treated with immunotherapy alone or with immunotherapy and dasatinib.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver metastases of mice that received only immunotherapy with anti-PD-1 antibody and those that received immunotherapy and dasatinib

first: Ryo

last: Yuge

first: Hiroki

last: Kadota


title: Chromatin occupancy and chromatin status of K562 cells with a mutation causing exclusive expression of N-terminally truncated GATA1 (GATA1s).

city: Hirosaki

first: Rika

last: Kanezaki

address: 5 Zaifucho

institute: Hirosaki University Graduate School of Medicine

summary: Children with Down syndrome (DS) are at high risk of transient abnormal myelopoiesis (TAM) and acute megakaryoblastic leukemia (DS-AMKL). GATA1 gene mutations are detected in almost all TAM and DS-AMKL samples, leading to exclusive expression of short GATA1 protein (GATA1s) lacking of N-terminal domain (NTD). However, it remains to be clarified how GATA1s is involved with both disorders. To investigate how the loss of GATA1 NTD is involved in the molecular mechanisms of leukemogenesis in DS, we established the K562 GATA1s (K562-G1s) clones expressing only GATA1s by CRISPR/Cas9 genome editing. The K562-G1s clones expressed KIT at higher levels compared to the wild type K562 (K562-WT). With Chromatin-Immunoprecipitation (ChIP) studies, we found that both GATA1 and GATA1s were bound upstream of the KIT gene. To understand the status of the KIT gene in K562-WT and one of K562-G1 subclone, C1 #26, we also performed ChIP-seq of histone modifications. Although the ChIP-seq signals of C1 #26 tended to be slightly lower than those of K562-WT, the activation status of the KIT gene demonstrated by the histone modifications was not significantly different between K562-WT and C1#26. Chromosome conformation capture (3C)-modified proximity assays revealed the difference in the conformation of the KIT gene between the K562-WT and C1 #26. We found that the lack of the NTD of GATA1 altered the genomic structure of the KIT gene, resulting in dysregulation of KIT expression. These results suggest that the NTD of GATA1 is essential for proper genomic conformation and gene expression regulation of the KIT gene and that perturbation of this mechanism might be involved in the pathogenesis of TAM and DS-AMKL.

overall_design: Chromatin and  RNA samples from K562-WT and K562-G1 subclones were analyzed.

first: Tsutomu

last: Toki

first: Etsuro

last: Ito


title: Transcriptomics‐based analysis of the causes of “sugar receding” in ‘Feizixiao’ litchi (Litchi chinensis Sonn.) pulp

city: Haikou

first: Junjie

last: Peng

address: renmmin 58 street

institute: Hainan university

summary: Transcriptome sequencing of ‘Feizixiao' litchi pulp at 35, 63 and 69 days after anthesis

first: Jingjia

last: Du

first: Wuqiang

last: Ma

first: Xian

last: Shui


title: Adaptations in nucleus accumbens neuron subtypes mediate negative affective behaviors in fentanyl abstinence II

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

summary: We used RNAseq to evaluate baseline expression of NPAS+ VP translatomes in comparison to bulk VP translatomes.

overall_design: We performed gene expression profiling in ribosome-associated mRNA from two different mouse genotypes (NPAS-Cre x Rpl22-HA or Rpl22-HA with Cre AAV in the VP) at baseline

first: Gessynger

last: Morais-Silva

first: Rianne

last: Campbell

first: Hyungwoo

last: Nam

first: Mary

middle: K

last: Lobo

first: Seth

last: Ament


title: Dysregulated H19/Igf2 expression disrupts cardiac-placental axis during development of Silver Russell Syndrome-like mouse models

status: Public on Nov 25 2022

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
Abstract: Dysregulation of the imprinted H19/IGF2 locus can lead to Silver-Russell Syndrome (SRS) in humans. However, the mechanism of how abnormal H19/IGF2 expression contributes to various SRS phenotypes remains unclear, largely due to incomplete understanding of the developmental functions of these two genes. We previously generated a mouse model with humanized H19/IGF2 ICR (hIC1) on the paternal allele that exhibited H19/Igf2 dysregulation together with SRS-like growth restriction and perinatal lethality. Here we dissect the role of H19 and Igf2 in cardiac and placental development utilizing multiple mouse models with varying levels of H19 and Igf2. We report severe cardiac defects such as ventricular septal defects (VSDs) and thinned myocardium, placental anomalies including thrombosis and vascular malformations, together with growth restriction in mouse embryos that correlated with the extent of H19/Igf2 dysregulation. Transcriptomic analysis using cardiac endothelial cells of these mouse models shows that H19/Igf2 dysregulation disrupts pathways related to extracellular matrix (ECM) and proliferation of endothelial cells. Our work links the heart and placenta through regulation by H19 and Igf2, demonstrating that accurate dosage of both H19 and Igf2 is critical for normal embryonic development, especially related to the cardiac-placental axis.
Methods: E12.5 hearts were lysed with Collagenase, Dispase II, and DNase I. Cardiac endothelial cells were collected using MACS CD31 microbeads and RNA was isolated using RNeasy Micro kit. After confirming RNA integrity using Bioanalyzer, mRNA library was generated from 25ng RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II RNA Library Prep Kit. Library quality was assessed by Bioanalyzer and TapeStation. Sequencing was performed on NovaSeq 6000. Quality of raw fastq reads was assessed using FastQC version 0.11.5. Reads were aligned to the GRCm38/mm10 reference using STAR version 2.4.0i with default parameters and maximum fragment size of 2000 bp. Properly paired primary alignments were retained for downstream analysis using Samtools version 1.9. Count matrices were generated using FeatureCounts version 1.6.2 against RefSeq gene annotation and read into DESeq2 to perform normalization and statistical analysis.

overall_design: mRNA profiles of CD31+ cardiac endothelial cells from E12.5 wild-type, +/hIC1, △H19/+, △H19/hIC1, △3.8/+, and △3.8/hIC1 mouse embryos. 3-5 pups for each genotype in both male and female were collected.

first: Suhee

last: Chang

first: Diana

last: Fulmer

first: Stella

last: Hur

first: Joanne

middle: L

last: Thorvaldsen

first: Li

last: Li

first: Eric

last: Rhon-Calderon

first: Xiaowen

last: Chen

first: Jonathan

last: Epstein

first: Marisa

last: Bartolomei


title: Transcriptome analysis of umbilical cord blood CD34+ cells of neonates delivered from SARS-CoV-2 infected and/or vaccinated mothers

status: Public on Nov 23 2022

city: BIRMINGHAM

first: Masakazu

last: Kamata

state: AL

address: 845 19TH ST S, BBRB 842, BBRB 842

institute: University of Alabama at Birmingham

summary: We report comparative transcriptome data of CD34+ cells derived from umbilical cord blood of neonates delivered from SARS-CoV-2 infected and/or vaccinated mothers or uninfected/non-vaccinated mothers.

overall_design: Examine transcriptomics derived from CD34+ cells in the umbilical cord blood (UCB). As a donor for the UCB, we picked two groups, 1) non-vaccinated for SARS-CoV-2 vaccine and no detectable anti-SARS-CoV-2IgG in the UCB plasma and 2) 1) non-vaccinated for SARS-CoV-2 vaccine but detectable for anti-SARS-CoV-2 spike and nucleocapside IgGs in the UCB plasma

first: Kamata

last: Masakazu


title: Transcriptional analysis of hepatoxicity induced by hexafluoropropylene oxide trimer acid (HFPO-TA)

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

summary: Transcriptome sequencing identified a set of hepatic relative biological processes that responding to HFPO-TA exposure, PPAR was the most significantly enriched pathway in KEGG analysis, and genes including ALB, FABP1, CXCL12, AHSG, FGA, FGB, etc. with high degrees in PPI network, were characterized as hub genes.

overall_design: Total RNA was isolated from the induced hepatocytes exposed HFPO-TA or 0.1% DMSO, each containing 3 replicates.

first: Liang

last: Shengxian


title: Single-cell RNA sequencing on the testis from the rete testis-specific Sox17 conditioinal knockout (cKO) mice and the controls at P14.

status: Public on Nov 27 2022

city: Yayoi, Bunkyo-ku

first: Yoshiakira

last: Kanai

state: Tokyo

institute: The University of Tokyo

summary: In mammalian testes, a valve-like structure called Sertoli valve is located at the border region of the seminiferous tubule and the rete testis. Having identified Sox17 in the rete testis as a positive regulator of the valve formation, this study aim to elucidate the mechanism of Sox17-expressing rete testis to modulate the testicular homeostasis. Our scRNA-seq data demonstrate the altered gene expression levels of several growth factors in Sox17-depleted rate testis epithelia, and highlighted the altered proportion of Sertoli cells located around the proximal part of the testis. This study provides a comprehensive profile of the proximal part of the testis including the rete testis and Sertoli valve for the first time, and further illustrate the functional role of the Sox17+ rete tesits to orchestrate the testicular homeostasis.

overall_design: Comparison of mRNA profiles of the cell located at the proximal part of the testis collected from the rete testis-specific Sox17 conditioinal knockout (cKO) mice and the controls.

first: Aya

last: Uchida


title: Whole Genome Bisulfite Sequencing Facilitates Quantitative Analysis of DNA Methylation status in sperm from 2 month old and 18 month old mice

city: Shanghai

first: Wen-Long

last: Zhao

address: Guangyuan road 145#

institute: The International Peace Maternity and Child Health Hospital

summary: We report the application of whole genome bisulfite sequencing technology for high-throughput profiling of DNA methylation in mice sperm at young and aging stages. By obtaining over 500 billion bases of sequence from genomic DNA, we generated genome-wide methylation-state maps of sperm from young and aging stages. We find that 2984 differetial methylation regions(DMR) in whole genome, including 916 DMR in promoter regions betweenin sperm from young and aging stages. 591 of DMR in promoter regions were significantly hypomethylated (~59.82%) and 397 significantly hypermethylated (~40.18%) in sperm of old males.

overall_design: Examination of  different methylation regions in young and old mice sperm

first: Fei

last: Sun


title: Proteogenomic Landscape and Clinical Characterization of GH-producing pituitary adenomas/ somatotroph pituitary neuroendocrine tumors

city: Chiba

first: Hidekazu

last: Nagano

state: Chiba

address: 1-8-1 Inohana

institute: Chiba University

summary: The clinical characteristics of growth hormone (GH)-producing pituitary adenomas vary across patients. In this study, we aimed to integrate the genetic alterations, protein expression profiles, transcriptomes, and clinical characteristics of GH-producing pituitary adenomas to detect molecules associated with acromegaly characteristics. Targeted capture sequencing and copy number analysis of 36 genes and non-targeted proteomics analysis were performed on fresh-frozen samples from 121 sporadic GH-producing pituitary adenomas. Targeted capture sequencing revealed GNAS as the only driver gene, as previously reported. Classification by consensus clustering using both RNA sequencing and proteomics revealed many similarities between the proteome and the transcriptome. Gene ontology analysis was performed for differentially expressed proteins between wild-type and mutant GNAS samples identified by non-targeted proteomics analysis and involved in G protein–coupled receptor (GPCR) pathways. The results suggested that GNAS mutations impact endocrinological features in acromegaly through GPCR pathway induction. ATP2A2 and ARID5B correlated with the GH change rate in the octreotide loading test, and WWC3, SERINC1, and ZFAND3 correlated with the tumor volume change rate after somatostatin analog treatment. These results identified a biological connection between GNAS mutations and the clinical and biochemical characteristics of acromegaly, revealing novel molecules associated with acromegaly that may affect medical treatment efficacy.

overall_design: We performed RNA sequencing analyses in 45 nonfunctioning pitutairy adenoma for comparison and 60 GH-producing pituitary adenomas

first: Azusa

last: Yamato

first: Tomoaki

last: Tanaka


title: Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)

city: Chicago

first: Weiguo

last: Cui

institute: Northwestern University

summary: CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. Here, we applied spatial transcriptomics to explore cellular localization and potential interaction between key immune cell subsets during chronic LCMV Clone 13 infection.

overall_design: Spleens from Control or CD4+ T cell-depleted mice on Day 7 and Day 21 post-LCMV Cl13 infection (2 mice per condition total, conducted in two separate rounds of experiments) and were frozen fresh, stored, and processed as instructed by the Visium kit (10x Genomics). 10 μm sections were generated from frozen spleens and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Spleen tissue on Visium slides was permeabilized for 18 minutes to extract mRNA and downstream library preparation and sequencing were conducted according to manufacturer’s protocol.

first: Paytsar

last: Topchyan


title: Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [ATAC-Seq]

status: Public on Nov 22 2022

city: Stanford

first: Justyna

last: Janas

state: CA

address: 265 Campus Drive

institute: Stanford University

summary: Examination of the effects of Tip60/Kat5 depletion on chromatin accessibility dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

overall_design: Genome-wide chromatin accessibility (ATAC-seq) determined for rtTA control or Ascl1-transduced MEFs co-expressing shRNA targeting Tip60 (shTip60), shRNA targeting H2A.Z (shH2AZ), or non-targetng control shRNA (shNTC) at day2 and/or day5 of iN cell reprogramming.


title: Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.

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

overall_design: Refer to individual Series


title: Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [RNA-Seq]

summary: Examination of the effects of Tip60/Kat5 depletion on gene expression dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

overall_design: Gene expression (RNAseq) of (i) MEFs transduced with shRNA targeting Tip60 (shTip60) or non-targeting control shRNA (shNTC) at days 4 and 7 post-infection, and (ii) rtTA control or Ascl1-transduced MEFs co-expressing shTip60 or shNTC at days 2 and 5 of iN cell reprogramming (corresponding to days 4 and 7 post-infection, respectively).


title: Analyses of AR stimulated by  0.1 nM DHT in LNCaP stable cell line overexpressing AR

status: Public on Nov 21 2022

city: Boston

first: Maryam

last: Labaf

state: MA

address: 100 William T Morrissey Blvd

department: Biology

institute: University of Massachusetts Boston


title: Cistrome analyses of AR stimulated by  0.1 nM DHT in LNCaP stable cell line overexpressing AR [ChIP-Seq]

summary: The molecular drivers for the AR signaling reprogramming in castration-resistant prostate cancer remain to be determined. In this study, we hypothesize that increased AR expression in conjunction with lower-level androgens, which is a typical condition in prostate cancer cells receiving androgen deprivation therapy, is a major driving force of the reprogramming. To test this, we used LNCaP model with inducible overexpression of AR to examine the acute effects of AR overexpression stimulated by low-dose DHT (0.1nM) on AR cistrome.

overall_design: A ChIP-seq analysis of AR was performed to examine AR binding stimulated by 0.1 nM DHT with overexpression of AR in LNCaP stable cell line. The stable cells were generated by stably infecting LNCaP cells with tetracycline inducible overexpression of wild-type full length AR virus. These stable cells were grown in the medium containing 10% tetracycline-free FBS.

first: Kourosh

last: Zarringhalam

first: Dong

last: Han

first: Changmeng

last: Cai


title: Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [Cut & Tag]

summary: Tip60-dependnet histone modification/occupancy dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

overall_design: Chromatin occupancy dynamics of H2A.Z, H2A.Zac and Tip60 was determined using Cut&Tag (Kaya-Okur et al., 2019) at different times of MEF-iN cell reprogramming. The impact of Tip60 depletion was assessed in rtTA control or Ascl1-transduced (i) MEFs co-expressing shTip60 or shNTC (for H2A.Z and H2A.Zac), and (ii) Tip60 conditional knockout (cKO) MEFs expressing Cre or DCre control (for H3K4me3).


title: Transcriptome analyses of AR stimulated by  0.1 nM or 10 nM DHT in LNCaP stable cell line overexpressing AR [RNA-Seq]

summary: The molecular drivers for the AR signaling reprogramming in castration-resistant prostate cancer remain to be determined. In this study, we hypothesize that increased AR expression in conjunction with lower-level androgens, which is a typical condition in prostate cancer cells receiving androgen deprivation therapy, is a major driving force of the reprogramming. To test this, we used LNCaP model with inducible overexpression of AR to examine the acute effects of AR overexpression stimulated by DHT on AR transcriptome.

overall_design: RNA-seq analyses were performed to examine gene expressions stimulated by 0.1 nM or 10 nM DHT with or without overexpression of AR in LNCaP stable cell line. The stable cells were generated by stably infecting LNCaP cells with tetracycline inducible overexpression of wild-type full length AR virus. These stable cells were grown in the medium containing 10% tetracycline-free FBS. The experiments were done in biological triplicates.


title: RNA-seq of METTL4-mediated Nuclear N6-Deoxyadenosine Methylation Promotes Metastasis through Activating Multiple Metastasis-inducing targets

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

summary: Understanding the gene profiling in METTL4/6mA/RP11-390F4.3 axis.

overall_design: Most of sample are replicates. For CRISPR-cont, METTL4-DPPW mutant clone1 and clone2 only once.

first: Kai-Wen

last: Hsu

first: Joseph

middle: C

last: Lai

first: Chuan

last: He


title: Hepatic DKK1 driven steatosis is CD36-dependent

status: Public on Nov 19 2022

city: Guangzhou

first: Yang

last: Zhen

state: China/Guangdong

address: 190 Kaiyuan Avenue, Science Park,

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: With the improvement of people's living standards and lifestyle changes, nonalcoholic fatty liver disease (NAFLD) has become one of the most common chronic liver diseases worldwide. However, few drugs are available for NAFLD, partly due to an incomplete understanding of its pathogenic mechanisms. Here, using in vivo and in vitro gain- and loss-of function approaches, we identified DKK1 as a pivotal mediator of the progression of NAFLD and its accompanying metabolic disorders in dietary obese mice. Mechanistic study reveals that DKK1 enhances the capacity of hepatocytes to uptake fatty acids through ERK-PPARγ-CD36 pathway. Moreover, DKK1 increased insulin resistance by activating the JNK signaling pathway, which in turn exacerbates disorders of hepatic lipid metabolism. These results suggest that DKK1 is a regulator of fatty acid uptake in lipid metabolism and insulin signaling, and may be a potential therapeutic candidate for NAFLD

overall_design: hepatocyte mRNA profiles of overexpression DKK1 (OE-DKK1) and green fluorescent protein negative control (GFP-NC) AML12 cells treated with 0.5mM free fatty acid (FFA ) for 24 hours.

first: Zhen

last: Yang

first: Yin-xiong

last: Li


title: Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci

city: Wuhan

first: Junpeng

last: Zhan

state: Hubei

address: 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University


title: Global hypo-methylation in a subgroup of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape

status: Public on Nov 16 2022

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

summary: We describe a new molecular subgroup of glioblastoma, the most prevalent malignant adult brain tumour, harbouring a bias towards hypomethylation at defined differentially methylated regions.

overall_design: Transcriptomic and DNA methylation analysis of patient matched iAPCs, iOPCs, iNSCs and GICs.

first: James

last: Boot

first: Gabriel

last: Rosser

first: Daliya

last: Kancheva

first: Claire

last: Vinel

first: Yau

last: Lim

first: Nicola

last: Pomella

first: Xinyu

last: Zhang

first: Loredana

last: Guglielmi

first: Denise

last: Sheer

first: Michael

last: Barnes

first: Sebastian

last: Brandner

first: Sven

last: Nelander

first: Kiavash

last: Movahedi


title: Differentially expressed tRNA-derived fragments in bovine fetuses with assisted reproduction induced congenital overgrowth syndrome

status: Public on Nov 15 2022

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

summary: Background: As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. Our recent study identified variations in tRNA expression in LOS individuals, leading us to hypothesize that variations in tRNA expression can influence the availability of their processed regulatory products, tRNA-derived fragments (tRFs). Due to their resemblance in size to microRNAs, studies suggest that tRFs target mRNA transcripts and regulate gene expression. Thus, we have sequenced small RNA isolated from skeletal muscle and liver of day 105 bovine fetuses to elucidate the mechanisms contributing to LOS. Moreover, we have utilized our previously generated tRNA sequencing data to analyze the contribution of tRNA availability to tRF abundance. Results: 22,289 and 7,737 unique tRFs were predicted in the liver and muscle tissue respectively. The greatest number of reads originated from 5′ tRFs in muscle and 5′ halves in liver. In addition, mitochondrial (MT) and nuclear derived tRF expression was tissue-specific with most MT-tRFs and nuclear tRFs derived from LysUUU and iMetCAU in muscle, and AsnGUU and GlyGCC in liver. Despite variation in tRF abundance within treatment groups, we identified differentially expressed (DE) tRFs across Control-AI, ART-Normal, and ART-LOS groups with the most DE tRFs between ART-Normal and ART-LOS groups. Many DE tRFs target transcripts enriched in pathways related to growth and development in the muscle and tumor development in the liver. Finally, we found positive correlation coefficients between tRNA availability and tRF expression in muscle (R = 0.47) and liver (0.6). Conclusion: Our results highlight the dysregulation of tRF expression and its regulatory roles in LOS. These tRFs were found to target both imprinted and non-imprinted genes in muscle as well as genes linked to tumor development in the liver. Furthermore, we found that tRNA transcription is a highly modulated event that plays a part in the biogenesis of tRFs. This study is the first to investigate the relationship between tRNA and tRF expression in combination with ART-induced LOS.

overall_design: RNA sequencing for kidney, liver, and skeletal muscle of bovine ~day 105 fetuses conceived by AI and ART.

first: Anna

last: Goldkamp

first: Yahan

first: Darren

last: Hagen


title: Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation domains in mammalian cells

status: Public on Nov 17 2022

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

summary: In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle- dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised and it undergoes degradation via ubiquitylation pathway. Knockdown of PARP1 shifted the relative dynamic equilibrium of H4K20me2 to H4K20me3 in cells. Overexpression or knockdown of PARP1 led to aberrant H4K20me1 domains genome-wide, impacting Wnt signaling pathways genes and transcription factor binding site enrichment. Therefore, SET8 mediated chromatin remodeling in mammalian cells are influenced by poly ADP-ribosylation by PARP1.

overall_design: HeLa cells were grown according to ATCC's recommendations. PARP1 knockdown were performed in HeLa cells using esiRNA for 48hrs, esiRNA against GFP was used as control. PARP1 overexpression were performed using FLAG-PARP1 plasmid transfection in HeLa cells. ChIP seq libraries were made according to New England Biolabs's recommendations. Accessible chromatin labeling was done based on UniNicE-seq protocol and library for sequencing was generated based on One-pot Universal NicE-seq protocol.

first: Pierre-Olivier

last: Estève

first: Vishnu

middle: U

last: Kumary


title: Global hypo-methylation in a subgroup of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape.

first: Silvia

last: Marino

type: Methylation profiling by genome tiling array

first: James

last: Boot

first: Gabriel

last: Rosser

first: Daliya

last: Kancheva

first: Claire


title: DNA replication initiation shapes the mutational landscape and expression of the human genome (INDUCE-Seq)

city: Cambridge

first: Julian

last: Sale

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: The interplay between active biological processes and DNA repair is central to mutagenesis. We found that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with the formation of DNA breaks at the centre of the origins and local error-prone DNA synthesis in their immediate vicinity. To support our mutational signature analysis, we performed DSBs mapping (INDUCE-seq) in parallel with RNA-seq, ATAC-seq and TOP2A/B CUT&RUN assays and show that origin activation leads to the TOP2A/B-dependent accumulation of DSBs at origins found at TSS and splice sites of both expressed and non-expressed genes in human H9 embryonic stem cells.

overall_design: INDUCE-seq analysis of H9 cells.

first: Murat

last: Pierre

first: Perez

last: Consuelo

first: Crisp

last: Alastair

first: Dobbs

last: Felix

first: Reed

last: Simon

first: Guilbaud

last: Guillaume

first: Sale

last: Julian


title: A genome-wide cell-free DNA methylation analysis identifies an episignature associated with metastatic luminal B breast cancer.

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

institute: Health Research Institute of Santiago (IDIS)

summary: Breast cancers of the luminal B subtype are frequent tumors with high proliferation and poor prognosis. Epigenetic alterations have been found in breast tumors and in biological fluids. We aimed to profile the cell-free DNA (cfDNA) methylome of metastatic luminal B breast cancer (LBBC) patients using an epigenomic approach to discover potential noninvasive biomarkers. Plasma cfDNA was analyzed using the Infinium MethylationEpic array (EPIC array) in a cohort of 14 women, including metastatic LBBC patients and healthy controls.

overall_design: Fifteen nanograms of each individual sample of plasma cfDNA was bisulfite-converted using the EZ DNA Methylation Lightning Kit (Zymo Research). Subsequently, the bisulfite-modified cfDNA was then subjected to whole genome amplification (WGA) using the EpiTect Whole Bisulfitome Kit (Qiagen). After the WGA of cfDNA, the Illumina Infinium HD methylation protocol was followed using MethylationEPIC BeadChips that were analyzed in a HiScan (Illumina).


title: DNA replication initiation shapes the mutational landscape and expression of the human genome (CUT&RUN)

overall_design: TOP2A/B CUT&RUN analysis of H9 cells.


title: Genome wide mapping of binding sites of ZBTB18 and CTBP2 in glioblastoma cancer cells

status: Public on Nov 14 2022

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: CTBP2 is a transcriptional co-repressor/co-activator palying a role in EMT. We have identified CTBP2 as a protein interacting with ZBTB18, a transcriptional repressor and tumor suppressor in GBM. Here, we have performed genome wide mapping of CTBP2 and ZBTB18 binding sites in GBM to characterized their gene regulation mechanism.

overall_design: CTBP2 and ZBTB18 DNA binding profiles were obtained by chromatin immunoprecipitation followed by next generation sequencing from SNB19 glioblastoma cells. At least two biological replicates of each condition were analyzed. DNA isolated from chromatin not subjected to immunoprecipitation (Input) was sequenced as reference material.

first: Maria

last: Carro

first: Melanie

last: Boerries


title: Gene epression profile of s-spheroids and t-spheroids differentiated from iPS cells

city: Tokyo

first: Tomohiro

last: Mizutani

address: 1-5-45 Yushima, Bunkyo-ku,

department: Department of Gastroenterology and Hepatology

institute: Institute of Science Tokyo

summary: For definitive endoderm differentiation, iPS cells (day0) were treated with 100 ng ml-1 activin A and 3μM CHIR99021 for 1 day and 100 ng ml-1 activin A for the following two days. Definitive endoderm was subsequently treated with 3uM CHIR99021 and 500ng ml-1 FGF4 for mid/hindgut differentiation. Mid/hindgut floating spheroids (fl; t-Spheroids) were collected from culture medium from day6 to day 8. On day6, mid/hindgut cells were dissociated into single cells and seeded onto EZSPHERE plate to generate suspension spheroids(EZ; s-Spheroids). RNA of fl spheroids and EZ spheroids were extracted using QIAGEN RNeasy kit.

overall_design: Hindgut spheroids were induced by two different conditions (fl and EZ). Three independent culture experiments were performed in triplicate. All the data was obtained from independent two iPS lines (2F and PB001).

first: Junichi

last: Takahashi

first: Ryuichi

last: Okamoto


title: SphK-produced S1P in somatic cells is indispensable for LH-EGFR signaling-induced mouse oocyte maturation

city: New York city

first: Feifei

last: Yuan

state: NY

institute: Columbia University

summary:
To further investigate the mechanism of SphK1/2 on oocyte maturation, we established Sphk1/2gc -/- and WT mice.
We then performed transcriptomic analysis on the MGCs and cumulus cells of Sphk1/2gc-/- and WT mice at 2 h post-hCG.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the MGCs and cumulus cells of Sphk1/2gc-/- and WT mice at 2 h post-hCG.

first: Xiaoqiong

last: Hao

first: Yanying

last: Cui

first: FuXin

last: Huang

first: Xiaodan

last: Zhang

first: Yanli

last: Sun

first: Tiantian

first: Zhijuan

last: Wang

first: Wei

last: Xia

first: Youqiang

last: Su

first: Meijia


title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancer patients underlies transcriptional diversity and metastatic potential

status: Public on Nov 12 2022

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

summary: Androgen receptor (AR) drives prostate cancer (PCa) development and progression. AR chromatin binding profiles are highly plastic and form recurrent programmatic changes that differentiate disease stages, subtypes and patient outcomes. While prior studies focused on concordance between patient subgroups, inter-tumor heterogeneity of AR enhancer selectivity remains unexplored. Here we report high levels of AR chromatin binding heterogeneity in human primary prostate tumors, that unexpectedly strongly overlap with heterogeneity observed in healthy prostate epithelium. Such heterogeneity has functional consequences, as somatic mutations converge on commonly-shared AR sites in primary over metastatic tissues. In contrast, less-frequently shared AR sites associate strongly with AR-driven gene expression, while such heterogeneous AR enhancer usage also distinguishes patients’ outcome. These findings indicate that epigenetic heterogeneity in primary disease is directly informative for risk of biochemical relapse. Cumulatively, our results illustrate an extraordinary level of AR enhancer heterogeneity in primary PCa driving differential expression and clinical impact.

overall_design: Capture based STARRseq experiment on LNCaP Cell Line.

middle: A

first: Wilbert

last: Zwart


title: DNA replication initiation shapes the mutational landscape and expression of the human genome (RNA-Seq)

first: Julian

last: Sale

overall_design: Gene expression profiling analysis of RNA-seq data for H9 cells.

first: Murat

last: Pierre

first: Perez

last: Consuelo

first: Crisp

last: Alastair

first: Dobbs

last: Felix

first: Reed

last: Simon

first: Guilbaud

last: Guillaume

first: Sale

last: Julian


title: Transcriptomic profiling of peripheral immune cells reveals distinct innate immune signatures associated with disease severity in COVID-19 viremia patients

status: Public on Nov 11 2022

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: SARS-CoV-2 is an emerging mosquito-borne pathogen with increasing public health significance. To characterize interconnected immune responses to SARS-CoV-2, we here examined transcriptional signatures of CD4 and CD8 T cells, B cells, NK cells, monocytes, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs) from three individuals with naturally-acquired SARS-CoV-2 infection. Whole transcriptome analysis demonstrated that all seven immune cells among PBMCs were clustered together with disease severity regardless of cell types. mDCs and pDCs gene signatures distinct disease severity. A distinct phenotype was observed in severe patients with or without plasma viremia, demonstrating a highly impaired induction of Interferon stimulated genes (ISGs) accompanied by imbalanced type I interferon sensing and an excessive inflammatory response. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in seven major immune cells in blood from different disease severe COVID-19 patients.

overall_design: The current study comprehensively examined 7 immune cell types including CD8 T cells, CD4 T cells, B cells, and NK cells, monocytes, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs) from three different groups, including moderate patients without detectable plasma viral load (nM=5), severe patients without detectable plasma viral load (nS=5), severe patients with detectable plasma viral load (vS=5), and healthy control (HD=5, 2 are included in this dataset, another 3 were previously submitted to GEO dataset GSE132228)

first: Xiaoming

first: Ke

last: Zhao

first: Yanhui

last: Yang

first: Yelizaveta

last: Rassadkina

first: Jesse

last: Fajnzylber

first: James

last: Regan

first: Jonathan

middle: Z

last: Li

first: Mathias

last: Lichterfeld

first: Xu

middle: G

last: Yu


title: Scattered tubular epithelial cell characterization

status: Public on Nov 10 2022

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

summary: We performed bulk RNA sequencing to characterize proximal tubular epithelial cells (PTECs) and PTECs that are positive for CD24 and CD133 (presumed to be scattered tubular cells (STCs)). We found an upregulation of many STC markers in our bulk RNA sequencing data and identified a pro-inflammatory and pro-fibrotic phenotype for STCs compared to PTECs. Many forms of metabolism were downregulated in the STCs compared to PTECs.

overall_design:
We performed bulk RNA sequencing on FACS sorted cells from a human kidney single cell suspension. 7 Different human kidney samples were used to obtain 7 samples of CD13-positive cells (PTECs) and 7 samples of CD13/CD24 and CD13/CD133-positive cells (STC). The 2 cell types were compared to each other with 7 replicates per cell type. After initial analysis, we excluded sample number 6 and 7 from analysis since these samples showed high discrepancy with the other samples on a PCA plot.
**RAW DATA not provided due to patient privacy concerns**

first: Jenny

last: Eymael

last: van den Broek

first: Jitske

last: Jansen

first: Bart

last: Smeets


title: Nuclear pCHK1 as a potential biomarker of increased sensitivity to ATR inhibition

status: Public on Nov 09 2022

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Excessive genomic instability coupled with abnormalities in DNA repair pathways induce high levels of “replication stress” when cancer cells propagate. Rather than hampering cancer cell proliferation, novel treatment strategies are turning their attention toward targeting cell cycle checkpoint kinases (such as ATR, CHK1, WEE1 and others) along the DNA damage response and replicative stress response pathways, thereby allowing unrepaired DNA damage to be carried forward towards mitotic catastrophe and apoptosis. The selective inhibitor of ATR kinase elimusertib (BAY 1895344), has demonstrated preclinical and clinical monotherapy activity; however, reliable predictive biomarkers of treatment benefit are still lacking. In this study, using gene expression profiling of 24 cell lines from different cancer types and in a panel of ovarian cancer cell lines, we found that nuclear-specific enrichment of checkpoint kinase 1 (CHK1) correlated with increased sensitivity to elimusertib. Using an advanced multispectral imaging system in subsequent cell line-derived xenograft specimens, we showed a trend between nuclear phosphorylated-CHK1 (pCHK1) staining and increased sensitivity to the ATR inhibitor elimusertib, indicating the potential value of pCHK1 expression as a predictive biomarker of ATR inhibitor sensitivity.

overall_design: 24 cell lines of different diseases were profiled.

first: Vignesh

last: Sundararajan

first: Antje

last: Wengner

first: David


title: Expression data from male and female mice fed with two type of high fat diet (45% - 45HFD and 60%-60HFD) and matched controls fed with standard diet (STD)

city: Monza

first: Valentina

last: Murtaj

state: MI

address: Via Cadore 48

department: School of Medicine and Surgery

country: Italy

institute: University of Milano-Bicocca

summary:
High caloric regimen affects brain functions leading to metabolic dysfunction and obesity and represents a risk factor for mental illness and dementia. To better understand the mechanisms underlying this process, we evaluated the effects of a prolonged exposure to high fat diet on cerebral glucose metabolism, inflammation, neuronal plasticity and transcriptome changes.
We used Clariom S microarrays on GeneChip® Scanner 3000 7G to detect gene expression changes during high fat diet regimen inducing metabolic syndrome in young/adult male and female wt mice in anterior cortex and cerebellar region

overall_design: WT C57Bl/6J mouse strain was selected as prone to obesity during adult life. Both male and female mice were subjected to prolonged high fat diet regimen starting from 4/5 weeks old and sacrificed after 33 weeks of diet for RNA extraction and gene expression analysis. Sex-difference and gene expression changes among two high fat diet vs controls were evaluated in anterior cortex and cerebellar region

first: Silvia

last: Penati

first: Sara

last: Belloli

first: Maria

last: Foti

first: Angela

last: Coliva

last: Papagna

first: Cecilia

last: Gotti

first: Elisa

last: Toninelli

first: Remy

last: Chiaffarelli

first: Stefano

last: Mantero

first: Susanna

last: Pucci

first: Michela

last: Matteoli

last: Malosio

first: Rosa

last: Moresco


title: Synergistic activation of RARb and RARg-driven programs restores cell-types specialization during stem cell differentiation

city: Evry

first: Marco Antonio

last: Mendoza Parra

address: 2 Gaston Crémieux

country: France

institute: Genoscope

summary:
How cells respond to different external cues to develop along defined cell lineages composing complex tissues is a major question in systems biology. In this study, we studied the role of synthetic agonists targeting specific Retinoic acid receptors (RARs) on activating major gene regulatory wires driving cell specialization during nervous tissue formation issued from P19 stem cells. Specifically, we have revealed that the synergistic activation of the RAR and RAR nuclear receptors by their cognate ligands (BMS641 or BMS961) induce neuronal maturation, inlcuding specialized neuronal subtypes as well as to astrocytes and oligodendrocyte precursors.
With the help of Rar-null mutant lines, combined with the use of RAR-specific agonists, global transcriptome mapping and an in-silico modeling of transcription regulatory signalling propagation, we have highlighted major gene programs essential for optimal neuronal cell specialization. Overall, this study provides a systems biology view of the gene programs behind the previously observed redundancy between RAR receptors, paving the way for their potential use for directing cell specialization during nervous tissue formation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT P19 or rar-null mutant EC cells treated with ATRA, BMS753, BMS641, BMS961 or a combination of BMS641 & BMS961 .

first: Aysis

last: Koshy

first: Elodie

last: Mathieux

first: François

last: Stüder

first: Aude

last: Bramoulle

first: Michele

last: Lieb

first: Bruno

last: Colombo

first: Hinrich

last: Gronemeyer

first: Marco

last: Mendoza-Parra


title: TERRA regulates DNA G-quadruplex formation and ATRX loading on chromatin

city: Taipei

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

department: Molecular and Cellular Biology

institute: National Taiwan University

summary: The genome consists of non-B-DNA structures such as G-quadruplexes (G4) that are involved in the regulation of genome stability and transcription. Telomeric-repeat containing RNA (TERRA) is capable of folding into G-quadruplex and interacting with chromatin remodeler ATRX. Here we show that TERRA modulates ATRX occupancy on repetitive sequences and over genes, and maintains DNA G-quadruplex structures at TERRA target and non-target sites in mouse embryonic stem cells. TERRA prevents ATRX from binding to subtelomeric regions and represses H3K9me3 formation. G4 ChIP-seq reveals that G4 abundance decreases at accessible chromatin regions, particularly at transcription start sites (TSS) after TERRA depletion; such G4 reduction at TSS is associated with elevated ATRX occupancy and differentially expressed genes. Loss of ATRX alleviates the effect of gene repression caused by TERRA depletion. Immunostaining analyses demonstrate that knockdown of TERRA diminishes DNA G4 signals, whereas silencing ATRX elevates G4 formation. Our results uncover an epigenetic regulation by TERRA that sequesters ATRX and preserves DNA G4 structures.

overall_design: To investigate the epigenetic regulation by TERRA RNA, ATRX, H3K9me3, G4 ChIP-seq and ATAC-seq were conducted after TERRA knockdown. TERRA RNA was depleted using antisense LNA oligos for 12 hours in mouse embryonic stem cells. Scramble LNA oligos transfection serves as a control.

first: Ru-Xuan

last: Tsai

first: Kuo-Chen

last: Fang

first: Po-Cheng

last: Yang

first: I-Tian

last: Chiang

first: Yunfei

last: Chen

first: Yu-Hung

last: Hsueh

first: Hungoo

last: Lee


title: DNA replication initiation shapes the mutational landscape and expression of the human genome

first: Julian

middle: E

last: Sale

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

overall_design: Refer to individual Series


title: DNA replication initiation shapes the mutational landscape and expression of the human genome (ATAC-Seq)

overall_design: ATAC-seq analysis of H9 cells.

first: Pierre

last: Murat

first: Consuelo

last: Perez

first: Alastair

last: Crisp

first: Felix

last: Dobbs

first: Simon

last: Reed

first: Guillaume

last: Guilbaud


title: EZH2-H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis

city: Lucknow

first: Dipak

last: Datta

address: B.S. 10/1, Sector-10, Jankipuram Extension Sitapur Road

department: Cancer Biology

country: India

institute: CSIR- CDRI

summary: Triple-Negative Breast Cancer (TNBC) has a poor prognosis and adverse clinical outcomes among all breast cancer subtypes as there is no available targeted therapy. Overexpression of Enhancer of zeste homolog 2 (EZH2) has been shown to correlate with TNBC's poor prognosis, but the contribution of EZH2 catalytic (H3K27me3) versus non-catalytic EZH2 (NC-EZH2) function in TNBC progression remains elusive. We reveal that selective hyper-activation of functional EZH2 (H3K27me3) over NC-EZH2 alters TNBC metastatic landscape and fosters its peritoneal metastasis, particularly splenic. Instead of H3K27me3-mediated repression of gene expression; here, it promotes KRT14 transcription by attenuating binding of repressor Sp1 to its promoter. Further, KRT14 loss significantly reduces TNBC migration, invasion, and peritoneal metastasis. Consistently, human TNBC metastasis displays positive correlation between H3K27me3 and KRT14 levels. Finally, EZH2 knockdown or H3K27me3 inhibition by EPZ6438 reduces TNBC peritoneal metastasis. Altogether, our preclinical findings suggest a rationale for targeting TNBC with EZH2 inhibitors.

overall_design: 4T1 (Murine Breast Cancer Cell) were made stable by transducing Control (MSCV) and EZH2-Y641-F plasmids. Three different batches of validated stable cells from each group were subjected RNA seq analysis-Gene expression profiling by high throughput sequencing.

first: Ayushi

last: Verma

first: Manish

middle: P

last: Singh


title: scRNA-seq and bulk RNA-seq analysis of normoxic and hyperoxic lung in  mice

status: Public on Nov 08 2022

city: ChengDu

first: Yanrong

last: Long

address: No. 17, Section 3, Renmin South Road, Wuhou District

department: State Key Laboratory of Biotherapy

institute: Sichuan University


title: Gut microbial DNA and immune checkpoint gene Vsig4/CRIg are key antagonistic players in healthy aging and age-associated development of hypertension and diabetes

city: La Jolla

first: Shandy

last: Shahabi

address: 9500 Gilman Dr

department: Chemistry

country: USA

institute: UCSD

summary: Aging is associated with the development of insulin resistance and hypertension. Aim of this study was to identify factors regulating these processes. We studied mice with complete knockout (KO) of the neuroendocrine prohormone Chromogranin A (CgA) as a model for healthy aging. These mice display two opposite aging phenotypes: hypertension but heightened insulin sensitivity at young age, whereas the blood pressure normalizes at older age and insulin sensitivity further improves. In comparison, aging WT mice gradually lost glucose tolerance and insulin sensitivity and developed hypertension. Quantitative RT-PCR revealed increased (~35-fold) accumulation of bacterial DNA in the heart of 2-yr-old WT mice compared to only ~2-fold increase in age-matched CgA-KO mice. Similarly, RNA sequencing showed increased expression of the Vsig4 gene (which removes bacterial DNA) in the liver of 2-yr-old CgA-KO mice, which possibly accounts for the very low accumulation of microbial DNA in the heart. The reversal of hypertension in aging CgA-KO mice is possibly due to (i) low accumulation of microbial DNA (i.e., reduced inflammation), and (ii) decreased spillover of norepinephrine (measured by ultra-pressure liquid chromatography) in the heart and kidneys. The reverse is true for aging WT mice. Moreover, while aging WT mice had increased inflammation with higher plasma TNF-⍺, IFN-ɣ, CCL2 and increased mitochondrial fission, these phenotypes were the opposite in aging CgA-KO mice. We conclude that Vsig4 plays a crucial role in “healthy aging” by counteracting age-associated insulin resistance and hypertension.

overall_design: Comparative gene expression profiling of WT and CgA-KO mouse liver tissue by high throughput sequencing.

first: Matthew

last: Liu

first: Suborno

last: Jati

first: Kechun

last: Tang

first: Hong

last: Gao

first: Zhongmou

last: Jin

first: Wyatt

last: Miller

first: Frederic

last: Meunier

first: Wei

last: Ying

first: Geert

middle: D

last: Bogaart

first: Gourisankar

last: Ghosh

first: Sushil

last: Mahata


title: Redistribution of lamina-associated domains reshapes Foxa2 binding in development of NAFLD

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

summary: Non-alcoholic fatty liver disease (NAFLD) is highly prevalent in type 2 diabetes mellitus and the elderly, impacting 40% of individuals over 70.  Regulation of heterochromatin at the nuclear lamina has been associated with aging and age-dependent metabolic changes.  We have shown that changes at the lamina in aged hepatocytes and laminopathy models lead to redistribution of lamina-associated domains (LADs), opening of repressed chromatin, and upregulation of genes regulating lipid synthesis and storage, culminating in fatty liver. Here we test the hypothesis that change in expression of lamina-associated proteins and nuclear shape leads to redistribution of LADs, followed by altered binding of pioneer factor FOXA2, uprregulation of lipid synthesis and storage, and culminating in steatosis in younger NAFLD patients (aged 21-51). Changes in nuclear morphology alter LAD partitioning and reduced lamin B1 signal correlates with increased FOXA2 binding prior to severe steatosis in young mice placed on Western det.  Nuclear shape is also changed in younger NAFLD patients. LADs are redistrubted and Lamin B1 signal decreases similarly in mild and severe steatosis. In contrast, FOXA2  binding is similar in normal and NAFLD patients with moderate steatosis and is repositioned only in NAFLD patients with more severe lipid accumulation.  Hence, changes at the nuclear lamina reshape FOXA2 binding with progression of the disease. Our results suggest a role for nuclear lamina in etiology of NAFLD, irrespective of aging, with potential for improved stratification of patients and novel treatments aimed at restoring nuclear lamina function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptional analysis (RNA-Seq) of WT mice on Western diet with fatty liver and genome-wide location analysis (ChIP-Seq) of lamin B1 and Foxa2 in NAFLD patients.

first: Megan

last: Murphy

first: Nihal

last: Reddy


title: Differences in gene expression in CP-A cells treated with acid and deoxycholic acid (DCA) and those without acid

status: Public on Nov 07 2022

city: Saitama

first: Koichi

last: Suzuki

state: Saitama

address: 1-847 Amanuma

department: Department  of  Surgery

institute: Jichi  Medical  University, Saitama  Medical Center

summary: Gene expression arrays were performed to compare gene expression differences between the control and pH 6.4 and DCA-exposed groups in CP-A cells.

overall_design: Using Clariom™ S Array, Human, we compared the gene expression profiles when CP-A cells were exposed to acid and DCA.

first: Iku

last: Abe


title: Dopamine-inhibited POMCDrd2+ neurons in the ARC acutely regulate feeding and body temperature

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: Dopamine acts on neurons in the arcuate nucleus of the hypothalamus (ARC) which control homeostatic feeding responses. Here we demonstrate a differential enrichment of Drd1 expression in food intake-promoting AgRP/NPY neurons and a large proportion of Drd2-expressing anorexigenic POMC neurons. This translates into a predominant activation of AgRP/NPY neurons upon dopamine stimulation and a larger proportion of dopamine-inhibited POMC neurons. Employing intersectional targeting of Drd2-expressing POMC neurons, we reveal, that dopamine-mediated POMC neuron inhibition is Drd2-dependent and that POMCDrd2+ neurons exhibit differential expression of neuropeptide signaling mediators, which manifests in enhanced somatostatin responsiveness of these neurons compared to the global POMC neuron population. Retrograde pseudorabies mapping reveals predominant synaptic input onto these cells from within the ARC as well as characterized dopaminergic cell groups within the hypothalamus and subthalamic areas. Finally, selective chemogenetic activation of POMCDrd2+ neurons uncovers their ability to acutely suppress feeding and to preserve body temperature. Collectively, the present study provides the molecular and functional characterization of POMCDrd2+ neurons and aids to our understanding of dopamine-dependent control of homeostatic energy regulatory neurocircuits.

overall_design: In order to characterize the translational profile of POMCDrd2+ neuronal subpopulation, we crossed POMCDre Drd2Cre double transgenic mice with those allowing for restricted expression of a fusion protein of the ribosomal protein L10a and EGFP solely in presence of both Cre and Dre recombinases (R26-lx-rx-EGFP-L10a). Pull-down of EGFP-tagged ribosomes from POMCDrd2+ neurons and subsequent mRNA sequencing of ribosome-associated mRNAs allowed for enrichment of actively translated mRNAs originating from Drd2-expressing POMC neurons. Analogous, we also performed RNA sequencing of ribosome-associated mRNA from the global POMC neuronal population targeted by the POMCDre transgene. To this end, we crossed POMCDre mice with those expressing EGFP-L10a in a Dre-only dependent manner (R26-rx-EGFP-L10a) to obtain a translational profile of the entire POMC neuron population targeted in POMCDre mice.

first: Isabella

last: Gaziano