title: Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [RNA-seq II]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MOLM-13 cells treated with 1 μM MI-503, a combination of 1 μM MI-503 and 100nM PR-957 (ONX-0914) or diluent treated controls.

last: Zhang


title: Keloid fibroproliferative properties are dependent on stem cells modified by the HEDGEHOG-GLI1 pathway [EA1488]

status: Public on Dec 13 2023

city: Bunkyo-ku,

first: Mamiko

last: Tosa

state: Tokyo-to

address: 1-1-5, Sendagi

department: Plastic and Reconstructive Surgery

country: Japan

institute: Nippon Medical School Hospital

summary: Keloids are benign fibroproliferative skin tumors caused by aberrant wound healing, the etiology of which is unknown. Although keloids cause life inconveniences and cosmetic problems, the lack of animal models has yet to elucidate their pathogenesis or develop effective treatments. Here, we found that the characteristics of stem cells from keloid lesions and surrounding dermis differ from those of normal skin and that HEDGEHOG (HH) signal and its downstream transcription factor GLI1 were upregulated in keloid patient-derived stem cells. Inhibition of the HH-GLI1 pathway reduced the expression of genes involved in keloids and fibrosis-inducing cytokines, including osteopontin. Moreover, HH-signal inhibitor vismodegib reduced keloid reconstituted tumor size and the expression of keloid related genes in nude mouse, and the collagen bundle and the expression of cytokines characteristic for keloids in ex vivo culture of keloid tissues. These results implicate the HH-GLI1 pathway in keloid pathogenesis and suggest therapeutic target of keloids.

overall_design: In order to clarify the gene expression profile in keloids, we collected tissues from (1) central area of keloid, (2) marginal area of keloid, and (3) the normal skin surrounding the keloids, which were surgically resected. On the other hand, normal skin was collected from patients who underwent surgical treatment other than keloids and did not develop keloids, and was used as a normal control. Fibroblasts and stem cells derived from each were cultured and used as samples, and gene expression profile analysis was performed using Affymetrix microarray for comparison.

first: Yoshinori

last: Abe

first: Nobuyuki

last: Tanaka


title: Testis Transcriptome Profiles of Peripubertal and Adult Rodents exposed to an Acute dose of MEHP(Mono(2-ethylhexyl) phthalate)

city: Austin

first: Xin

last: Fang

state: Texas

address: 107 W Dean Keeton St, Austin, TX 78712

country: USA

institute: University of Texas at Austin

type: Expression profiling by high throughput sequencing

summary:
we used both young and adult age rodent animals (rats and mice) exposed to 700mg/kg MEHP
And performed differential gene experssion analysis using data obtained from Tag sequencing of 3 groups of animals from both treated and non-treated conditions

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Testis transcriptomic analysis of Tag seq data for peripubertal rats, adult rats and peripubertal mice with and without MEHP treatment

first: Richa

last: Tiwary


title: BPTF inhibitor increases gastric cancer response to Erlotinib by epigenetically regulating c-MYC/PLCG1/pErk axis.

city: Shanghai

first: Li

last: Fangyuan

state: Shanghai

address: Ruijin Er road

country: China

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [RNA-seq I]

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: Pharmacologic targeting of epigenetic protein complexes has shown significant in vitro responses in AML. Early clinical trials in MLL-rearranged leukemia indicate rather transient responses and development of resistance. In an effort to define functional dependencies of MLL-fusions in acute myeloid leukemia, we identify the catalytic immunoproteasome subunit PSMB8 as an oncogene-specific vulnerability. Genetic and pharmacologic inactivation of PSMB8 results in impaired proliferation of murine and human leukemic cells while normal hematopoietic cells remain unaffected. Disruption of immunoproteasome function results in cellular enrichment of transcription factor BASP1, and consecutive repression of MLL-target genes. Pharmacologic targeting of PSMB8 improves efficacy of Menin-inhibitors, eradicates leukemia in primary human xenografts and shows preserved activity against Menin-inhibitor resistance mutations. This identifies and validates a cell-intrinsic mechanism whereby selectivity of proteostasis results in altered transcription factor abundance and repression of oncogene-specific transcriptional networks. Therapeutic targeting of PSMB8-dependent transcription in combination with Menin-inhibition could thus eradicate AML harboring MLL-rearrangements.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MOLM-13 cells treated with 100nM PR-957 (ONX-0914) or diluent treated controls for 72hours.

first: Nuria

last: Tubío-Santamaría

first: Qirui

first: Florian

middle: H

last: Heidel


title: Keloid fibroproliferative properties are dependent on stem cells modified by the HEDGEHOG-GLI1 pathway [EA1874]

overall_design: 2×10^6 keloid fibroblasts from the marginal area (KMF) from 3 patients or normal fibroblasts from 2 donors were mixed with hydrogel, including synthesized extracellular matrix supplemented with recombinant human IL-6. The mixtures were immediately injected subcutaneously into the dorsal surface of 6- to 8-week-old male nude mice. KMF-transplanted mice were treated with vehicle or vismodegib by intraperitoneal injection once a day. Mice were killed three months after implantation. RNA was isolated from the transplant to perform qPCR analysis and microarray assay.


title: Keloid fibroproliferative properties are dependent on stem cells modified by the HEDGEHOG-GLI1 pathway


title: Robust Cardiac Reprogramming Systems with Selectivity to Cardiac Fibroblasts

city: Beijing

first: Yanmeng

last: Tao

state: Beijing

address: #5 Yiheyuan Road

department: Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies

institute: Peking University

summary: Direct cardiac reprogramming to induce cardiomyocyte-like cells, e.g. by GMT (Gata4, Mef2c and Tbx5), is a promising route for regenerating damaged heart in vivo and disease modeling in vitro. Supplementation with additional factors and chemical agents can enhance efficiency but raises concerns regarding selectivity to cardiac fibroblasts and complicates delivery for in situ cardiac reprogramming. Here, we screened 2000 chemicals with known biological activities and found that a combination of 2C (SB431542 and Baricitinib) significantly enhances cardiac reprogramming by GMT. Without Gata4, MT (Mef2c and Tbx5) plus 2C could selectively reprogram cardiac fibroblasts with enhanced efficiency, kinetics and cardiomyocyte function. More importantly, 2C+MYOCD selectively reprograms human cardiac fibroblasts into cardiomyocyte-like cells. 2C enhances cardiac reprogramming by inhibiting Alk5, Tyk2 and downregulating Oas2, Oas3, Serpina3n and Tgfbi. 2C thus enables selective and robust cardiac reprogramming that can greatly facilitate disease modeling in vitro and advance clinical therapeutic heart regeneration in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2-5 replicates for each condition were ran for Bulk RNAseq


title: Expression data changes induced by 3D conditions in T-ALL cells [CCRF-CEM cells]

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

country: Spain

institute: CIB-CSIC

summary: 3D constrained conditions promoted H3K4 methylation in ALL cells that altered the global chromatin configuration and transcriptional changes related to cell cycle and DNA replication.

overall_design: CCRF-CEM cells (T-ALL cell line) were used for RNA extraction and hybridization on Affymetrix microarrays. CCRF-CEM cells were cultured in suspension or 3D conditions (a type I collagen matrix of 1,7 mg/mL) for 1 hour. Cells were lised and mRNA was extracted to compare expression profiles. We used 2 replicates of each sample.

first: Raquel

last: González-Novo

first: África

last: González-Murillo

first: Elena

last: Madrazo

first: David

last: Acitores

first: Mario

last: García de Lacoba

first: Manuel

last: Ramírez


title: Microarray expression profile of exosomal circRNAs from high glucose stimulated human renal tubular epithelial cells

city: Guangzhou

first: Yanhua

last: Sha

address: 111 Dade Road

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine

summary: we used microarray technology to construct a comparative circRNA profiling of exosomes isolated from cell supernatant of high glucose stimulated human proximal tubular epithelial cell line (HK-2 cells)  and nomal controls, aimed to explore gene expression and the underlying molecular mechanism of exosomal circRNAs in DN development.

overall_design: High glucose induced gene expression in exosomes isolated from cell supernatant of human proximal tubular epithelial cell line (HK-2 cells) was measured at 30 hours after exposure to 30 mmol/L glucose. For the control group, HK2 cells were cultured in  5.5 mmol/L glucose for 30h.  Three duplicates of each group were performed.

first: Wenjin

last: Fu


title: Genomic changes of Peripheral Blood Neutrophils throughout Prostate Cancer Progression

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: Bulk RNA sequencing of peripheral blood neutrophils from prostate cancer at different stages of disease progression, including localized disease, hormone-sensitive- and castration-resistant metastatic prostate cancer

overall_design: Neutrophils were isolated from peripheral blood and sequenced

first: Leah

middle: M

last: Cook


title: miRNAs specifically bound by PrPc during C2C12 cell differentiation

city: Wuhan

first: Jing

state: Hubei Province

address: 299 Bayi Road, Wuchang District

institute: wuhan university

type: Non-coding RNA profiling by high throughput sequencing

summary: We used RIP-seq to sequenceWT C2C12 and the C2C12 cell line overexpressing WT PrPc to investigate the miRNAs that PrPc in them specifically binds at the fourth day of C2C12 cell differentiation

overall_design: To confirm the ability of PrPc to enrich miRNAs, and to analyze the reason why overexpression of PrPc inhibits C2C12 cell differentiation, we used a specific antibody capable of pulling down PrPc, 8H4,  against C2C12 cells (Control) and cells stably transfected with PrP (WT PrP) were subjected to formaldehyde cross-linking and RNA immunoprecipitation (RIP) at mid-differentiation Day4 induced with 2% horse serum.  By performing miRNA-seq on the enriched RNAs, we identified a large number of selectively enriched miRNAs based on sorted ratios of RIP to input. Displaying the small RNA-seq data for Control and small RNA-seq data for WT PrP and using a log2 fold-change cutoff of 0.5 and a P-value cutoff of 0.05, we defined 31 miRNAs bound by endogenous PrPc in Control, and 41 miRNAs bound by excess PrPc in WT PrP.


title: Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [RNA-seq]

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

summary: Despite ongoing attempts since the 1990s, no stable embryonic stem cell line has been established in pigs. Here, guided by insights from large-scale single-cell RNA-sequencing profiling of pig embryos from embryonic day (E) 0 to E14, we developed an in vitro culture system for establishing and maintaining stable pluripotent stem cell lines from pig E10 pre-gastrulation epiblasts (pgEpiSCs). Enabled by chemical inhibition of WNT-related signaling in culture, the pgEpiSCs maintain their pluripotency and normal karyotypes after more than 200 passages. Strikingly, ultra-deep in situ Hi-C analysis revealed functional impacts of 3D-spatial associations on the transcriptional regulation of pluripotency marker genes in the pgEpiSCs. Practically, we confirmed that the pgEpiSCs can readily tolerate at least three rounds of successive gene editing and generated cloned gene-edited live piglets. Our findings deliver on the long-anticipated promise of large model animal stem cells and open new avenues for biological research, animal husbandry, and biomedicine.

overall_design: We generated RNA sequencing (RNA-seq) data for pEpiSCs with 4 biological replicates and pEFs with 2 biological replicates.


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YF1B]

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from  chunk B of a 23 years old female.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

last: Behrens

first: Eran

middle: A

last: Mukamel


title: Differential diagnosis between uterine leiomyoma and leiomyosarcoma using transcriptome analysis

city: Pohang

first: Sarah

last: Kim

address: 558, Handong-ro, Buk-gu

country: South Korea

institute: Handong Global University

summary:
Objective: The objective of this study was to estimate the accuracy of transcriptome-based classifier in differential diagnosis of uterine leiomyoma and leiomyosarcoma.
Methods: We manually selected 114 normal uterine tissue and 31 leiomyosarcoma samples from publicly available transcriptome data in UCSC Xena as training/validation sets. We developed pre-processing procedure and gene selection method to sensitively find genes of larger variance in leiomyosarcoma than normal uterine tissues. Through our method, twenty genes were selected to build transcriptome-based classifier. The prediction accuracies of deep feedforward neural network (DNN), support vector machine (SVM), Random Forest (RF), and Gradient Boosting (GB) models were examined. We interpret the biological functionality of selected genes via network-based analysis using Gene-Mania. To validate the performance of trained model, we additionally collected 35 clinical samples of leiomyosarcoma and leiomyoma as a test set (18 + 17 as 1st and 2nd test sets).
Results: We discovered genes expressed in a highly variable way in leiomyosarcoma while these genes are expressed in a conserved way in normal uterine samples. These genes were mainly associated with DNA replication, cell cycle, and DNA damage checkpoint. Among evaluated machine learning classifiers, the DNN had the highest accuracy and average AUC value in training data set. As gene selection and model training were made in leiomyosarcoma and uterine normal tissue, proving discriminant of ability between leiomyosarcoma and leiomyoma is necessary. Thus, further validation of trained model was conducted in newly collected clinical samples of leiomyosarcoma and leiomyoma. The DNN classifier performed AUC of 0.917 and 0.914 supporting that the selected genes in conjunction with DNN classifier are well discriminating the difference between leiomyosarcoma and leiomyoma in clinical sample.
Conclusion: The transcriptome-based classifier accurately distinguished uterine leiomyoma from leiomyosarcoma.

overall_design: Transcriptome-based analysis and classification in the differential diagnosis of uterine leiomyoma and leiomyosarcoma

first: Kidong

first: TaeJin

last: Ahn

first: Hyojin

first: So-Jin

last: Shin

first: Chel

last: Choi

first: Sungmin

last: Park

first: Yong-Beom

first: Jae

last: No

first: Dong

last: Suh


title: Transcriptional profiles of liver from non-pregnant mice and pregnant mice at dpc8 and dpc16

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo


title: Transcriptional profiles of liver lobular zones from non-pregnant mice and pregnant mice at dpc8 and dpc16.

summary: We report transcriptional profiles of each liver lobular zone from non-pregnant mice and pregnant mice at dpc8 and dpc16. By RNA-sequencing of LCM-isolated each zonal cells, we revealed that  genes related to actin cytoskeleton, extracellular matrix organization and vascularization were enriched in the PA (zone2) and CV (zone3) zones at dpc8 and cell division related genes were enriched in the PV (zone1) zone at dpc8. At dpc16, genes related to metabolism, catabolism and xenobiotic process were enriched in all zones.

overall_design: LMD-RNAseq analyses of liver lobular zones (zone1,2, and 3) from non-pregnant mice and pregnant mice at dpc8 and dpc16.

first: Satoshi

last: Kozuki

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: Transcriptional profiles of liver in control and p21-AAV8 administered non-pregnant mice and pregnant mice at dpc8 and dpc16.

summary: We report transcriptional profiles of liver from control and p21-AAV8 administered no-pregnant mice and pregnant mice at dpc8 and dpc16. We revealed that genes related to carbohydrate transport and regulators of glucose and glycogen metabolism were down regulated in AAV-p21 administered liver at dpc16.

overall_design: Transcriptional profiles of liver from control AAV administered non-pregnant, dpc8 and dpc16 mice, and p21 AAV administered dpc8 and dpc16 mice.

first: Satoko

last: Sakurai


title: BPTF inhibitor increases gastric cancer response to Erlotinib by epigenetically regulating c-MYC/PLCG1/pErk axis [RNA-seq]

first: Li

last: Fangyuan

summary: To understand how BPTF conferred resistance to Erlotinib in GC cells, we performed transcriptome profiling (RNA-seq) in MGC803/BPTF-KO and MGC803/BPTF-NC cells.

overall_design: We knocked out BPTF by using CRISPR/Cas9 in MGC803 cells and explored the differentially expressing genes.

first: Fangyuan

last: Li

first: Junxian

last: Yu


title: Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines

first: Jianyong

last: Han


title: BPTF inhibitor increases gastric cancer response to Erlotinib by epigenetically regulating c-MYC/PLCG1/pErk axis [ChIP-seq]

summary: Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) was performed by using the anti-BPTF antibody in MGC803 cells to explore the downstream target genes of BPTF.

overall_design: We perfomred ChIP assay in MGC803 cells by using antibodies against BPTF, H3L4me3 and H3K27ac to explore the targets downstream BPTF.


title: Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [HiC]

overall_design: We separately constructed 4 in situ high-throughput chromatin conformation capture (Hi-C) libraries (as technical replicates) for each of 4 pig pre-gastrulation epiblast stem cell (pgEpiSC) biological replicates, and 8 Hi-C libraries (as technical replicates) for each of 2 pig embryonic fibroblast cell (pEF) biological replicates.


title: Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [single-cell RNA-seq]

overall_design: We collected pre-implantation porcine embryos (E0-E14) and pluripotent stem cell lines from porcine E10 pre-gastrulation epiblasts(pgEpiSCs) conducted single cell transcriptome sequencing.


title: Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [ChIP-seq]

overall_design: We generated H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) data for pEpiSCs and pEFs with 2 replicates, respectively.


title: Gene expression profiling of ipsilateral dorsal root ganglia of bone cancer pain in a rat model

status: Public on Dec 12 2023

city: Hangzhou

first: Shuxin

last: Tian

state: 浙江省

address: Binwen Road, Binjiang District

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary: Objectives: This study aimed to identify a set of differentially expressed genes (DEGs) in dorsal root ganglions (DRGs) between bone cancer pain (BCP) and sham BCP rats using RNA-sequencing (RNA-Seq).  Methods: We established a rat BCP model by implanting MRMT-1 cells into the bone marrow cavity of left tibia. RNA-Seq was used to screen related genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and protein-protein interaction (PPI) network analysis were conducted to investigate the bioinformatics functions of DEGs and possible potential pathological mechanisms of BCP. Results: RNA-Seq of ipsilateral DRGs from model rats identified a total of 152 DEGs compared to sBCP rats. The expression changes of four randomly selected DEGs were verified by qPCR. Four significant signaling pathways have been found for BCP including MAPK signaling pathway, calcium signaling pathway, apelin signaling pathway and oxytocin signaling pathway. Cxcl13 in DRGs was identified as a key player in the BCP model by comparing with published datasets in classic pain models. A core set of genes contributed to BCP mechanism were sorted out by PPI network analysis. Conclusions: These altered mRNAs and signaling pathways might be potential therapeutic targets for BCP treatment, which can guide future research on the molecular mechanism of BCP.

overall_design: Examination of 2 different groups mRNA profiles in DRG：sham bone cancer pain (sBCP) group and BCP group

first: Boxi

last: Zheng

first: Zhengyi

last: Lyu

first: Yi

last: Liang


title: Identification of MBL-1 target transcript through RIP-seq.

city: Helsinki

first: Jens

last: Verbeeren

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

summary: MBL-1 is an RNA-binding protein important for the differentiation and development of many animal tissues. Our aim was to identify the binding targets of the MBL-1 protein in C. elegans. RNA from a CRISPR/CAS9-generated strain expressing a 3xFLAG-tagged MBL-1 protein was immunopreciprecipitated with an anti-FLAG antibody. RNA-seq was then performed to identify binding targets of the RNA-binding protein MBL-1. Experiments were performed at the L4 stage.

overall_design: RNA samples were collected from L4 stage 3xFLAG::MBL-1 animlas before (RNA input) and after immunoprecipitation with an anti-FLAG antibody (IP samples). Three replicates for each sample were made. Following RNA-seq, differentially expressed peaks (and thus MBL-1 binding targets) were identified by comparison of input and IP sample peaks.


title: MBL-1

overall_design: Refer to individual Series


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF2A]

first: Joseph

last: Ecker

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function. We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors (25 years old) and 2 young female donors (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.  This sample is from chunk A of a 74 years old female.

first: Jo-Fan

last: Chien

first: Hanqing

last: Liu

first: Bang-An

last: Wang

first: Chongyuan

last: Luo

first: Anna

last: Bartlett

first: Rosa

last: Castanon

first: Nicholas

middle: D

last: Johnson

last: Nery

first: Julia

last: Osteen

first: Junhao

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

first: Michelle

last: Liem

first: Naomi

last: Claffey

first: Caz

last: O'Connor

first: Luise

last: Seeker

first: M

last: Behrens

first: Eran

last: Mukamel


title: Acute irradiation induces a senescence-like chromatin structure in mammalian oocytes

city: Athens

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: College of Veterinary Medicine - Physiology and Pharmacology

institute: University of Georgia

summary: We used RNA-seq to investigate mechanisms leading to changes in epigenetics and chromatin organization during irradiation. Purpose: Use of next-generation sequencing (NGS) to investigate the changes in transcriptional (RNAseq) profiles in mouse oocyte after irradiation.

overall_design: Methods: Oocyte collection was carried out on non-primed day 16 female mice. Collected cells are maintained in minimal essential medium (MEM) supplemented with 3mg/ml bovine serum albumin (Sigma Aldrich, St. Louis, MO) and milrinone (Sigma; 1 μg/ml) to prevent meiotic resumption. These cells are either directly sequenced or treated with γ-irradiation before sequencing. Results: Transcriptomics analyses reveal that the effects of genotoxic stress induced by γ-irradiation in mammalian oocytes are mediated by signaling pathways associated with the activation of senescence and repair from DNA damage and provide the first evidence for a mechanistic link between the DNA damage response and the regulation of PCH structure in the oocyte genome.

first: Xiangyu

last: Zhang

first: Muthugapatti

middle: K

last: Kandasamy

first: Xiaohan

last: Mei

first: Shiyou

last: Chen

first: Kayvan

middle: F

last: Tehrani

first: Luke

middle: J

last: Mortensen

first: Wendy

last: Watford

first: Ashley

last: Lall

first: Rabindranath

last: De La Fuente


title: DKK1-SE promotes pancreatic cancer progression by recruiting AP1 to activate the target gene DKK1

city: Harbin

first: Shao

last: Lan

address: No.92, Xidazhi Street, Nangang District

institute: Harbin Institute of Technology

summary: Super Enhancers are a class of DNA Cis-regulatory elements that can regulate cell identity, cell fate, stem cell pluripotency, and even tumorigenesis.Increasing evidence shows that epigenetic modifications play an important role in the pathogenesis of various types of cancer. However, current research is far from sufficient to reveal the complex mechanisms behind epigenetic modifications.The aim of this study is to explore the function and mechanism of a new Super Enhancer in Pancreatic ductal adenocarcinoma (PDAC) tumors. By using epigenetic modification and chromatin interaction information, we found a new Super Enhancer enriched with abnormal active histone modifications in PDAC tumors and cells, called DKK1-super-enhancer (DKK1-SE).DKK1-SE was grouped according to the activity modification information, and the e1 component was identified as the main active unit by dual luciferase reporter gene system and dCas9-KRAB system.DNA motif analysis and core site deletion assay revealed that the e1 component possessed AP1 transcription factor family binding sites.Mechanically, AP1 activates DKK1 transcriptional activity by recruiting JUND and FOSL2 to induce enhancer chromatin remodeling.CRISPR/ Cas9-mediated deletion of DKK1-SE resulted in significant downregulation of its target gene DKK1.Analysis of TCGA data of PDAC tumors combined with immunohistochemical results of PDAC patients demonstrated that DKK1 was closely related to malignant clinical features of PDAC.Bioinformatics analysis of RNA-seq data showed that DKK1 was mainly related to tumor-related biological functions such as extracellular matrix, cell adhesion, angiogenesis, and cell proliferation.Cell malignant phenotype assay showed that deletion or interference of DKK1-SE significantly inhibited the proliferation, colony formation, migration and invasion of PANC-1, and these phenomena were partially alleviated after restoring DKK1 expression in DKK1-SE deficient cells.Experiments of Subcutaneous transplantation tumor in nude mice and Orthotopic transplantation tumor model showed that DKK1-SE deletion not only inhibited tumor proliferation, but also reduced the complexity of tumor microenvironment, resulting in less angiogenesis of tumor tissues and reduced fibrosis degree.In conclusion, DKK1-SE drives the expression of DKK1 by recruiting AP1 family transcription factors, which plays a carcinogenic role in PDAC tumors and enhances the complexity of the tumor microenvironment.

overall_design: To investigate the function of DKK1-SE in PANC-1, we used CRISPR/Cas9 gene editing technology to create a cell line with the deletion of DKK1-SE component enhancer e1.

first: Lan

last: Shao


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF1A]

first: Joseph

last: Ecker

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from chunk A of a 73 years old female.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen


title: Pien Tze Huang Targets Cancer Proliferation and Inhibits Growth of Patient-derived Organoid and Xenograft Tumors in Pancreatic Cancer

city: Fuzhou

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

institute: Fujian university

summary: We used RNA-sequencing (RNA-Seq) to analyze gene expression in PC cells treated with PZH. Next, we confirmed these findings on the protein level using Western blot and immunofluorescence. Finally, we analyzed the proliferative impact of PC cells treated with PZH using MTT and flow cytometric assays and verified it with PC patient-derived organoids (PDOs) and xenograft mice models.

overall_design: PC cell line AsPC1 was treated by PZH for 72 h and then performed RNA-Sequencing (RNA-Seq) by sequencing company.

first: Hong

last: Chen

first: Jian

last: Du

first: Hailan

last: Feng


title: Gene expression profile of single-cell level alterations in hippocampal tissue in a rat model of radiation-induced cognitive dysfunction

city: cahgnzhou

first: Wendong

last: Gu

address: NO.185, juqianjie road

institute: The Third Affiliated Hospital of Soochow University

summary: Radiotherapy is an important therapeutic option for the treatment of primary and metastatic brain tumors, and there is increasing concern about the side effects associated with it as survival time after treatment increases. By far, cognitive dysfunction is the most common radiation-induced central nervous system injury. Studies have shown that the hippocampus is involved in radiation-induced cognitive dysfunction. We constructed a model of radiation-induced cognitive dysfunction by irradiating the whole brain of one-month-old rats with 20 Gy, and analyzed the expression profiles in the hippocampus of rats with radiation-induced cognitive dysfunction using single-cell RNA sequencing (scRNA-seq).

overall_design: The hippocampus of rats was dissected two months after whole-brain 20Gy irradiation. A total of six samples were analyzed by scRNA sequencing, three in the control group and three in the irradiated group.

first: Rui

last: Sun

first: Kedi

last: Xi

first: Jingting

last: Jiang


title: Effect of deletion or isoform-specific expression of the C. elegans mbl-1 gene on miRNA expression.

first: Jens

last: Verbeeren

summary: MBL-1 is an RNA-binding protein important for the differentiation and development of many animal tissues. An evolutionarily conserved alternative splicing mechanism generates MBL-1 isoforms that are either expressed in the nucleus or show a more cytoplasmic distribution. We used small RNA-seq to investigate the individual contribution of evolutionarily conserved mbl-1 isoform expression of C. elegans miRNA expression. The analysis was done on L4 stage animals

overall_design: Whole organism RNA was isolated with the TRIzol method at the L4 stage and then analyzed using RNA-seq. Three biological replicates were used for each condition (wild-type, mbl-1 mutant, short MBL-1 protein isoform expressing mutant, and long MBL-1 protein expressing mutant). miRNA expression was compared to the N2 wild-type strain.


title: Dexamethasone treatment of immortalized and primary cancer associated fibroblasts (CAF)

city: Innsbruck

first: Florian

last: Handle

address: Müllerstrasse 44

department: Institute of Pathology, Neuropathology and Molecular Pathology

country: Austria

institute: Medical University of Innsbruck

summary: Glucocorticoids (GCs) are applied as concomitant medication in the course of ADT and chemotherapeutic treatment. therefore, it is essential to investigate specific effects on elevated stromal GR signaling and subsequently clarify a possible influence on tumor growth and disease progression.

overall_design:
Differential gene expression analysis of RNA-seq data from immortalized PF179T CAF and primary isolated CAFs upon dex and abi treatment.
*** Raw data files are not available for the primary patient samples due to privacy concerns. ***

first: Martin

last: Puhr


title: Hypoxia inducible microRNA-155 negatively regulates epithelial barrier in Eosinophilic Esophagitis by suppressing Tight Junction Claudin-7

city: Maynooth

first: Joanne

middle: Carol

last: Masterson

address: Biomedical Sciences Building, Maynooth University

department: Biology

country: Ireland

institute: Maynooth University

summary: MicroRNA (miRNA)-mediated mRNA regulation directs many homeostatic and pathological processes, but how miRNAs coordinate aberrant esophageal inflammation during eosinophilic esophagitis (EoE) is poorly understood. Here, we report a deregulatory axis where microRNA-155 (miR-155) regulates epithelial barrier dysfunction by selectively constraining tight junction CLDN7 (claudin-7). MiR-155 is elevated in the esophageal epithelium of biopsies from patients with active EoE and in cell culture models. miR-155 localisation using in situ hybridisation (ISH) in patient biopsies, and intra-epithelial compartmentalisation of miR-155 shows expression predominantly within the basal epithelia. Epithelial miR-155 activity was evident through diminished target gene expression in 3D organotypic cultures, particularly in relatively undifferentiated basal cell states. Mechanistically, generation of a novel cell line with enhanced epithelial miR-155 stable overexpression induced a functionally deficient epithelial barrier in 3D air-liquid interface epithelial cultures measured by transepithelial electrical resistance (TEER). Histological assessment of 3D esophageal organoid cultures overexpressing miR-155 showed notable dilated intra-epithelial spaces. Unbiased RNA-sequencing analysis and immunofluorescence determined a defect in epithelial barrier tight junctions and revealed a selective reduction in the expression of critical esophageal tight junction molecule, claudin-7. Together, our data reveal a previously unappreciated role for miR-155 in mediating epithelial barrier dysfunction in esophageal inflammation.

overall_design:
Esophageal epithelial cells (EPC2-hTERTs) were transfected via lentiviral-mediated overexpression of miR-155-5p to genrated a stable overexpressing miR-155-5p cell line.
miR-155-5p overexpressing (miR-155OE) and control (CTRL) cells were cultured in physiologically relevant 3D-ALI cultures to investigate the function of miR-155-5p overexpression on epithelial barrier and overall epithelial biology.
RNA-seq was carried out using these miR-155OE and CTRL cells. Comparative gene expression profiling of RNA-seq data for miR-155OE and CTRL cells was conducted.

first: Gary

middle: E

last: Markey

middle: C


title: Adipo-glial signaling mediates metabolic adaptation in peripheral nerve regeneration

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The peripheral nervous system harbours a remarkable potential to regenerate after acute nerve trauma. Full functional recovery, however, is rare and critically depends on peripheral nerve Schwann cells that orchestrate break down and resynthesis of myelin and, at the same time, support axonal regrowth. How Schwann cells meet the high metabolic demand required for nerve repair remains poorly understood. We here report that nerve injury induces adipocyte to glial signaling, and identify the adipokine leptin as an upstream regulator of glial metabolic adaptation in regeneration. Signal integration by leptin receptors in Schwann cells ensures efficient peripheral nerve repair by adjusting injury-specific catabolic processes in regenerating nerves, including myelin autophagy and mitochondrial respiration. Our findings propose a model according to which acute nerve injury triggers a therapeutically targetable intercellular crosstalk that modulates glial metabolism, to provide sufficient energy for successful nerve repair.

overall_design: sciatic nerve crush was performed on control mice and mice with conditional ablation of the leptin receptor in Schwann cells. After two and four weeks post crush, injured and healthy nerves (endoneuria) were sampled and subjected for bulk RNA sequencing.

first: Robert

last: Fledrich

first: Ruth

last: Stassart


title: A convenient platform of in vivo functional studies reveals the roles of TGFBR2 in ESCC progression and distal metastases

city: Chengdu, Cihna

first: Xiangmeng

last: Luo

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Genomics studies have detected numerous genetic alterations in esophageal squamous-cell carcinoma (ESCC), a highly malignant and leading mortal cancer. However, the functions of these mutations in the formation and progression of ESCC largely remain elusive, partially due to lack of feasible animal models. Here, we report a convenient platform with normal esophageal organoids, CRISPR/cas9-mediated introduction of ESCC-associated genetic alterations, and orthotopic transplantation to generate a serial of primary ESCC models in mice. With this platform, we validated that multiple frequently mutated genes, including FAT1/2/4, NOTCH2, KMT2D, EP300, and TGFBR2, as bona fide tumor suppressor genes in ESCC. Among them, TGFBR2 loss dramatically promoted tumorigenesis and multi-organ metastasis. Paradoxically, TGFBR2 deficiency led to Smad3 activation and disruption of Smad3 could partially restrain the progression of Tgfbr2 mutated tumors. Drug screening with tumor organoids revealed that pinaverium bromide, a calcium channel blocker used for irritable bowel syndrome, could repress Smad3 activity and restrain Tgfbr2 deficient ESCC in vitro and in vivo. Our studies provide a highly efficient platform to investigate the in vivo functional of ESCC-associated mutations and develop potential treatment for this miserable malignancy.

overall_design: We provide a highly efficient platform called OPCM. Various mouse models of esophageal cancer were applied using OPCM to investigate the vivo functional of ESCC-associated mutations. Among them, we fonud that TGFBR2 loss dramatically promoted tumorigenesis and multi-organ metastasis. Thus we conducted bulk RNA-seq on organoids with or without Tgfbr2 knockout, revealing Tgfbr2 deficiency led to Smad3 activation.  Pinaverium bromide, a calcium channel blocker could re-press Smad3 activity and restrain Tgfbr2 deficient ESCC in vitro and in vivo.Thus, our studies provide a highly efficient platform to investigate the in vivo functional of ESCC-associated mutations and develop potential treatment for this miserable malignancy.

last: Wang

first: Jiajia

first: Yu

last: Liu

first: Chong


title: Effect of deletion or isoform-specific expression of the C. elegans mbl-1 gene on gene expression.

summary: MBL-1 is an RNA-binding protein important for the differentiation and development of many animal tissues. An evolutionarily conserved alternative splicing mechanism generates MBL-1 isoforms that are either expressed in the nucleus or show a more cytoplasmic distribution. We used RNA-seq to investigate the individual contribution of evolutionarily conserved mbl-1 isoform expression of C. elegans gene expression and to identify pathways associated with isoform expression. The analysis was done on L4 stage animals

overall_design: Whole organism RNA was isolated with the TRIzol method at the L4 stage and then analyzed using RNA-seq. Three biological replicates were used for each condition (wild-type, mbl-1 mutant, short MBL-1 protein isoform expressing mutant, and long MBL-1 protein expressing isoform).


title: Effect of subchronic ototoxicity on the vestibular ganglion in rodents

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

institute: Universitat de Barcelona

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


title: Effect of subchronic ototoxic (3,3'-iminodipropionitrile - IDPN) exposure on the vestibular ganglion of the rat.

summary: The response of the vestibular ganglion neurons to the stress or loss of their presynaptic hair cells (HC) is not understood. This understanding is necessary because the survival and functional competence of these neurons will determine the outcome of any intervention aiming at repair or regeneration of the HC. One existing observation is that of uncoupling of the synapse between the HCs and ganglion neurons following subchronic ototoxic exposure in rodent models. We here studied the expression response of the vestibular ganglion associated with this synaptic uncoupling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular ganglia of control rats and rats after subchronic ototoxic exposure.

first: Erin

last: Greguske

first: Alberto

last: Maroto

first: Marta

last: Gut

first: Anna

last: Esteve-Codina

first: Alejandro

last: Barrallo-Gimeno


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM2A]

first: Joseph

last: Ecker

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors (25 years old) and 2 young female donors (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.  This sample is from chunk A of a 25 years old male.

first: Jo-Fan

last: Chien

first: Hanqing

first: Bang-An

first: Chongyuan

last: Bartlett

first: Rosa

last: Castanon

first: Nicholas

last: Johnson

last: Nery

first: Julia

last: Osteen

first: Junhao

last: Li

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

first: Michelle

last: Liem

first: Naomi

last: Claffey

first: Caz

last: O'Connor

first: Luise

last: Seeker

first: M

last: Behrens

first: Eran

last: Mukamel


title: Skeletal muscle-specific DJ-1 ablation-induced atrogenes expression and mitochondrial dysfunction contributing to muscular atrophy

city: Shanghai

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

summary: DJ-1 is a causative gene for a familial form of Parkinson disease. DJ-1 deficient mice develop progressive behavioral abnormalities in gaits and forearm grip strength are hypoactive. The mechanisms under the activity are not fully known. Here we show that DJ-1 is critical for disuse- induced skeletal muscle atrophy. Firstly, DJ-1 expression is positively correlated with muscle mass in human, and is decreased in atrophy muscle of immobilization mice and aged human. Secondly, DJ-1-deficient muscles are dystrophic, as well as impaired in activities and oxidative capacity. In disuse-atrophic condition, skeletal muscle specific-DJ-1 knockout mice show less cross section area (CSA) and more central nuclei than control mice. Thirdly, biochemical analysis indicates that these changes are due to enhanced activation of FoxO1, and subsequent upregulation of atrogenes. Finally, the inhibitor of DJ-1, compound 23, can mimic the effects of DJ-1 ablation in vivo. Our results illuminate that skeletal muscle DJ-1 has an unexpected role in the regulation of catabolic signals from mechanical stimulation, providing a therapeutic target for muscle-wasting diseases.

overall_design: Gastrocnemius（gas） muscle tissues from immobilized muscle-specific DJ-1 knockout (MPARK7KO) mice and flox mice were extracted for RNA sequencing. The sequencing was conducted using Illumina BGIseq500 platform (BGI-Shenzhen, China). The transcriptomics data processing was addressed as previous article described. The clean reads were mapped to the reference genome (mm10) using STAR (2.7.10a). Quantification of gene expression was calculated using RSEM (v1.2.28). Subsequently, differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expression genes.


title: Microglia adopt longitudinal transcriptional changes after traumatic brain injury

status: Public on Dec 11 2023

city: Chicago

first: Deborah

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: Traumatic brain injury (TBI) is an under-recognizedpublic healththreat. Even mild brain injuries can lead to long-term neurologic impairment.Microgliaplay a fundamental role in the development and progression of this ensuing neurologic impairment. Despite this, a microglia-specific injury signature has yet to be identified. We hypothesized that TBI would lead to long-term changes in the transcriptional profile of microglial pathways associated with the development of subsequent neurologic impairment.

overall_design: Bone marrow chimeras (BMC) were generated by transplanting male B6.CD45.1 donor bone marrow into male B6.CD45.2 recipient mice irradiated with head shielding.  BMC then underwent TBI via a controlled cortical impact and were followed longitudinally. CD45.2 microglia were sorted and subjected to bulk RNA-seqat 7, 30, and 90d after TBI.

first: Steven

last: Schwulst


title: Gene expression data of formalin-fixed-paraffin-embedded (FFPE) renal biopsy tissue assessed with Banff Human Organ Transplant (B-HOT) gene panel assay on NanoString nCounter®

city: Brisbane

first: Hao

last: Zhang

address: 3260 Bayshore Blvd

department: Research and Development

institute: CareDx, Inc.

summary: Development and validation of a multi-class molecular model for differential diagnosis of renal allograft rejection, built upon gene expression data from the B-HOT gene panel in a large and diverse cohort of diagnostic FFPE renal biopsies.

overall_design: In this study, gene expression profiling analysis of 770 genes, including 12 housekeeping genes and 758 target genes, was performed for the FFPE renal biopsy tissue of totally 1395 samples, retrieved from clinical pathology archive, with the B-HOT gene panel assays on NanoString nCounter® platform.  All 1395 samples are divided into 4 different groups based on the clincial histology diagnosis related to kidney transplant rejection status: antibody-mediated rejection, T cell-mediated rejection, mixed rejection, and no rejection controls.

first: Randy

last: Haun

first: Francois

last: Collin

first: Clarissa

last: Cassol

first: Johnathan

last: Napier

first: Jon

last: Wilson

first: Samar

last: Hassen

first: Kerime

last: Ararat

first: Christie

last: Boils

first: Nidia

last: Messias

first: Tiffany

last: Caza

last: Cossey

first: Shree

last: Sharma

first: Josephine

last: Ambruzs

first: Nikhil

last: Agrawal

first: Grigoriy

last: Shekhtman

first: Titte

last: Srinivas

first: Wenlan

last: Tian

first: Kruti

last: Calcuttawala

first: Kunbin

last: Qu

first: Robert

last: Woodward

first: Sham

last: Dholakia

first: Christopher

last: Larsen

last: Stone

first: Shana

last: Coley


title: Asymmetric bending of lateral petals, a novel trait originated within Delphinium (Ranunculaceae), reinforces their mirrored helical rotation during flower opening

city: Yangling

first: Liping

last: Guo

address: Taicheng Road

institute: Northwest A&F University

summary: During the process of flower opening, most petals move downward in the direction of pedicel (i.e., epinastic movement). In most Delphinium flowers, however, their two lateral petals display a very peculiar movement, the mirrored helical rotation. Such a distinctive petal movement requires the twist of the stalk. However, in some lineages, their lateral petals also exhibit asymmetric bending that increases the degree of mirrored helical rotation, facilitating the formation of a 3D final shape. Notably, the petal asymmetric bending is a novel trait that has not been noticed yet so that its morphological nature, developmental process and molecular mechanisms remain largely unknown. Here, by using D. anthriscifolium as a model, we determined that the petal asymmetric bending was caused by localized expansion of cell width, accompanied with specialized arrangement of surface ornamentation, on the adaxial epidermis. Digital gene analyses, gene expression and functional studies revealed that a class I homeodomain-leucine zipper family transcription factor gene, DeanLATE MERISTEM IDENTITY1 (DeanLMI1), contributes to the petal asymmetric bending; knockdown of it led to the formation of explanate 2D petals. Specifically, DeanLMI1 promotes cell expansion in width and influences the arrangement of surface ornamentation, through regulating the auxin distribution, on the localized adaxial epidermis. These results not only provide a comprehensive portrait of petal asymmetric bending for the first time, but also shed some new insight into the mechanisms of flower opening and helical movement in plants.

overall_design: The dorsal spurred and lateral non-spurred petals at four developmental stages (S9, S10, S12 and S16) were sampled for RNA-sequencing. For comparison, the three sub-types of sepals (i.e., dorsal spurred, lateral and ventrally non-spurred), stamens and carpels at corresponding stages, as well as leaves and bracts that are just underneath the S9 floral buds were also included. For the VIGS-treated plants, the mock and ans-lmi1 strongly silenced petals at stage 12 of floral development, were separately subjected to toRNA-sequencing.

first: Rui

last: Zhang

first: Hanghang

first: Fang

last: Xue


title: Obese Skeletal Muscle-Expressed Interferon Regulatory Factor 4 Transcriptionally Regulates Mitochondrial Branched-Chain Aminotransferase Reprogramming Metabolome

first: Kong

last: Xingxing

summary: It is well established that obese animals and humans show deficiencies in skeletal muscle content and metabolism. However, the mechanisms under how skeletal muscle metabolism affects systemic energy homeostasis is not well-defined. Here, we compared the skeletal muscle transcriptome from obese and lean controls in different species. We found an immune-responsive transcription factor interferon regulatory factor 4 (IRF4) was conserved to be increased in obese subjects from the three species (humans, non-human primates and mice). Thus, we demonstrated that loss of IRF4 specifically in skeletal muscle of mice showed protection against the metabolic effects of high-fat diet, with unexpected increased plasma and muscle branched-chain amino acid (BCAA) levels. Conversely, overexpression of skeletal muscle IRF4 caused obesity and insulin resistance, with decreased BCAA contents. Mechanistically, IRF4 can transcriptionally regulate branched-chain aminotransferase isozyme (BCATm) expression, and that overexpression of BCATm can reverse the effects of IRF4 depletion regarding to metabolic phenotypes. Further, we demonstrated ablation of IRF4 in skeletal muscle increased mitochondrial activity and glycogen synthesis in a BCATm- dependent manner. These studies establish IRF4 as a novel driver of BCAA metabolism via BCATm in skeletal muscle and may interpret the BCAAs paradox in obesity.

overall_design: Examination of different gene expression in skeletal muscle of lean and obesity Macaca fascicularis.

first: Xingxing

last: Kong

first: Tiemin

last: Liu


title: Transcriptomics dissection of the calorie restriction and/or exeTranscriptomics dissection of the calorie restriction and/or exercise training in BAT and skeletal muscle

summary: Calorie restriction (CR) and exercise training (EX) are two critical lifestyles for the prevention and treatment of metabolic diseases, such as obesity and diabetes. Brown adipose tissue (BAT) and skeletal muscle (SkM) are two important organs to generate heat. Here we provide detailed transcriptional profiling of these two thermogenic tissues from mice treated with CR and/or EX. We demonstrate the transcriptional reprogramming of BAT and SkM according to CR, but little to EX. Consistent with this, CR induces genes encoding adipokines or myokines alteration in BAT and SkM, respectively. Deconvolution analysis implies differences of subpopulations of myogenic cells, mesothelial cells and endogenic cells in BAT, and demonstrates differences of subpopulations of satellite cells, immune cells and endothelial cells in SkM according to CR or EX. NicheNet analysis, exploring potential inter-organ communication, indicates that BAT and SkM can mutually regulate their fatty acid metabolism and thermogenesis by ligands and receptors. These data comprise an extensive resource for thermogenic tissues molecular responses to CR and/or EX in healthy state. Calorie restriction (CR) and exercise training (EX) are two critical lifestyles for the prevention and treatment of metabolic diseases, such as obesity and diabetes. Brown adipose tissue (BAT) and skeletal muscle (SkM) are two important organs to generate heat. Here we provide detailed transcriptional profiling of these two thermogenic tissues from mice treated with CR and/or EX. We demonstrate the transcriptional reprogramming of BAT and SkM according to CR, but little to EX. Consistent with this, CR induces genes encoding adipokines or myokines alteration in BAT and SkM, respectively. Deconvolution analysis implies differences of subpopulations of myogenic cells, mesothelial cells and endogenic cells in BAT, and demonstrates differences of subpopulations of satellite cells, immune cells and endothelial cells in SkM according to CR or EX. NicheNet analysis, exploring potential inter-organ communication, indicates that BAT and SkM can mutually regulate their fatty acid metabolism and thermogenesis by ligands and receptors. These data comprise an extensive resource for thermogenic tissues molecular responses to CR and/or EX in healthy state.

overall_design: 5 BAT samples, including 3 in sedentary group (control), 4 in CR group, 4 in EX group (EX) and 4 in CR+ EX group (CREX), and 14 gastrocnemius (GAS) muscle tissue samples, including, 4 in control group, 4 in CR group, 4 in EX group and 4 in CREX group, were used to perform transcriptome analysis.


title: Transcriptomic analysis of resistant and wild-type Botrytis ci-nerea isolates revealed fludioxonil-resistant mechanisms

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Botrytis cinerea (gray mold) is one of the most destructive pathogens of cherry tomatoes, causing fruit decay and economic loss. Fludioxonil is an effective fungicide widely used for crop protec-tion and is essential for controlling tomato gray mold. The emergence of fungicide-resistant strains has made the control of Botrytis cinerea more difficult. While the genome of Botrytis cinerea is available, there are few reports regarding the large-scale functional annotation of the genome using expressed genes derived from transcriptomes, and the mechanism(s) underlying such flu-dioxonil resistance remain unclear. The present study prepared RNA-sequencing (RNA-seq) li-braries for three Botrytis cinerea strains [two highly resistant (LR and FR) versus one highly sen-sitive (S) to fludioxonil], with and without fludioxonil treatment, to identify fludioxonil responsive genes that facilitate fungicide resistance. Functional enrichment analysis identified nine resistant related DEGs in the fludioxonil-induced LR and FR transcriptome that were simultaneously up regulated, and seven resistant related DEGs down regulated. These included adenosine tri-phosphate (ATP)-binding cassette (ABC) transporter-encoding genes, major facilitator super-family (MFS) transporter-encoding genes, and the high-osmolarity glycerol (HOG) pathway homologues or related genes. The expression patterns of twelve out of the sixteen fludioxo-nil-responsive genes, obtained from the RNA-sequence data sets were validated using quantita-tive real-time PCR (qRT-PCR). Based on RNA-sequence analysis it was found that fugal HHKs, like BOS1, BcHHK2, and Bchhk17, were in some way involved in the fludioxonil resistance of B. cinerea, in addition, a number of ABC and MFS transporter genes that were not reported before, such as BcATRO, BMR1, BMR3, BcNMT1, BcAMF1, BcTOP1, BcVBA2, and BcYHK8 were differen-tially expressed in the fludioxonil-resistant strains, indicating that overexpression of these efflux transporters located in the plasma membranes played a crucial role in the fludioxonil resistant mechanism of B. cinerea. These lines of evidence together allowed us to draw a general portrait of the anti-fludioxonil mechanisms for Botrytis cinerea, and the assembled and annotated transcrip-tome data provide valuable genomic resources for further study of the molecular mechanisms of B. cinerea resistance to fludioxonil.

overall_design: Mycelium of the parent fludioxonil-sensitive strain (S), laboratory fludioxo-nil-resistant strain (LR), and field fludioxonil-resistant strains were obtained as de-scribed above. All of the isolates were grown at the same time for the same amount of time (three days) under the same conditions (shaking at 23°C and 180 rpm) in PDB. The mycelium were then collected at the same time.  RNA was extracted from samples using the TRIzol method (Invitro Corp., Carlsbad, CA, USA).The RNA concentration and quality were assessed using a nanodrop and gelelectrophoresis. The samples were stored at ?80°C. RNA sequencing was conducted by Novogene using an Illumina? (San Diego, CA, USA) based method to generate 20 million 150-bp paired-end reads per sample. The sequencing library was prepared with the NEBNext? Ultra?RNA Library Prep Kit for Illumina?, and sequencing was performed on the NovaSeq PE150.

first: Mei

first: Liusheng

last: Duan


title: Effect of subchronic ototoxic (3,3'-iminodipropionitrile - IDPN) exposure on the vestibular ganglion of the mouse.

first: Jordi

last: Llorens

overall_design: Comparative gene expression profiling analysis of RNA-seq data from vestibular ganglia of control mice and mice after subchronic ototoxic exposure.

first: Erin

last: Greguske

first: Alberto

last: Maroto

first: Marta

last: Gut

first: Anna

last: Esteve-Codina

first: Alejandro

last: Barrallo-Gimeno


title: Radium 223 induces transient functional bone marrow toxicity

city: Houston

first: FENG

last: WANG

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

summary: Radium 223 (Rad223) is a bone-seeking, alpha-particle-emitting radionuclide approved for the treatment of patients with metastatic castration resistant prostate cancer and is currently being tested in a variety of clinical trials for primary and metastatic cancers to bone. Clinical evaluation of Rad223 hematologic safety showed a significantly increased rate of neutropenia and thrombocytopenia in patients, hinting at myelosuppression as side effect. In this study we present a preclinical approach to investigate the consequences of Rad223 treatment on bone marrow biology. Rad223 accumulated in bones and induced confined radiation damage, followed by progressive replacement of the impaired areas with adipocyte infiltration, as monitored by three-dimensional multiphoton microscopy, ex vivo. Flow cytometry and single cell transcriptomic analyses on bone marrow hematopoietic populations revealed transient, non-specific Rad223-mediated cytotoxicity on resident populations, including stem, progenitor and mature leukocytes. This was paralleled by a significant decrease of white blood cells and platelets in peripheral blood, which was overcome within 40 days post-treatment. Rad223 exposure did not impair full hematopoietic reconstitution, suggesting that the bone marrow function is not permanently hampered. Our results provide a comprehensive explanation of Rad223 reversible effects on bone marrow cells and exclude long-term myelotoxicity, supporting its safety during treatment of patients at both early and late disease stages.

overall_design: Bone marrow was collected at d0, d4, d11, d40 from Rad223 treatment. After sorting for CD117+ cells from 3 mice/timepoint, each timepoint was tagged with oligo-tagged antibodies to uniquely label cells from distinct samples (https://cite-seq.com/cell-hashing/). Samples were pooled and single-cell RNA-seq libraries were prepared using Single Cell 3′ Reagent Kits v.2: Chromium Single Cell 3′ Library & Gel Bead Kit v.2, PN-120237; Single Cell 3′ Chip Kit v.2 PN-120236; and i7 Multiplex Kit PN-120262 (10x Genomics) following the Single Cell 3′ Reagent Kits v.2 User Guide (Manual Part no. CG00052 Rev A). Libraries were run on an Illumina NovaSeq 6000 system as 150-bp paired-end reads, one full lane per sample.

first: Maria

last: Parlani

first: Francesco

last: Boccalatte

last: Yeaton

first: Feng

first: Jianhua

first: Iannis

last: Aifantis

first: Eleonora

last: Dondossola


title: Glioblastoma Molecular Characteristics and Immune Microenvironment Associated with Survival Outcomes in Patients Treated with Dendritic Cell Vaccination

city: bethesda

first: Aiguo

last: Li

state: MD

address: 37 CONVENT DR

department: nci

institute: nih

summary: Purpose:  Autologous tumor lysate-pulsed dendritic cell (DC) vaccination has shown promising long-term survival in a cohort of patients with newly diagnosed glioblastoma.  The purpose of this study was to better understand the mechanisms and modulation of the immune microenvironment underlying the clinical efficacy of DC-based vaccine therapy.  Experimental Design:  We performed bulk RNA sequencing on tumor samples from patients with newly diagnosed glioblastoma obtained prior to treatment with dendritic cell vaccination.  We characterized the molecular mechanisms and immune microenvironments of long-term survivors (LTS, n= 8), medium-term survivors (MTS, n= 13), and short-term survivors (STS, n = 17). Results:  There was an enrichment of the mesenchymal subtype of glioblastoma in the long-term survival group.  Additionally, decreased tumor cell density, upregulation of cell surface markers, and increased neuronal activity were associated with the longer survival cohorts. Two microglia populations, one associated with increased survival and one associated with decreased survival in the DC-treated cohorts, but not standard of care (SOC) cohorts, are also potentially implicated in response to DC immunotherapy. There were increases in functional activity of the immune environment in longer survivor cohorts. Conclusions:  These analyses suggest the potential to identify tumor-based predictive factors that may be associated with favorable responses to DC vaccination in glioblastoma patients; and if validated, these findings may enable better patient selection for future clinical trials.

overall_design: The study was designed to understand the molecular characteristics and immune microenvironments of dendric cell vaccine treated patients. Long term survivors of newly diagnosed IDH wild type glioblastoma patients treated with DC vaccine with survival >5year, compared with medium term survivors (3-5 year) and short term survivors to understand the molecular mechanisms and immune microenvironments.

first: Kunal

last: Patel

first: Bharati

last: Mehani

first: Nicole

last: Briceno

first: Kun

first: Kenneth

last: Aldape

first: Eytan

last: Ruppin

first: Emma

last: Billingslea-Yoon

first: Robert

last: Prins

first: Mark

last: Gilbert

first: Linda

last: Liau


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM3A]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from chunk A of a 25 years old male.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

last: Behrens

first: Eran

last: Mukamel


title: Inhibition of ADAM9 mediates KRAS-related pathways in pancreatic cancer cells

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

summary: Kirsten rat sarcoma virus (KRAS) signaling drives pancreatic ductal adenocarcinoma (PDAC) malignancy, which is an unmet clinical need. Here we identify a disintegrin and metalloproteinase domain 9 (ADAM9) as a modulator of PDAC progression via stabilization of wild-type and mutant KRAS proteins. Mechanistically, ADAM9 loss increases the interaction of KRAS with plasminogen activator inhibitor-1 (PAI-1), which functions as a selective autophagy receptor in conjunction with LC3, triggering the lysosomal degradation of KRAS. Suppression of ADAM9 by a small molecule inhibitor restricts disease progression in spontaneous models, and the combination with gemcitabine elicits dramatic regression of patient-derived tumors. Our findings provide a promising strategy to target the KRAS signaling cascade and demonstrate a potential modality to enhance sensitivity to chemotherapy in PDAC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ADAM9i-treated PDAC103P cells and its vehicle control (Vehicle and ADAM9i).

first: Yu-Kai

last: Huang

first: Yuh-Pyng

last: Sher


title: Development of gene expression signatures of liver in a primary Sjögren's syndrome mouse model

city: Tokushima

first: Takaaki

last: Tsunematsu

address: 3-18-15 Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University

summary: To elucidate gene expression signatures of liver induced by Sjögren's syndrome, we have employed whole genome microarray expression profiling as a discovery platform.

overall_design: To establish a primary Sjögren's syndrome mouse model, neonatal thymectomy (Tx) was performed to female NFS/sld mice on day 3 after birth.  The gene expression of liver was measured by using liver tissue of female NFS/sld mice at 8 weeks after the Tx surgery. The control mice used in this study were non-thymectomized (nonTx) female NFS/sld mice. Four independent replicate were utilized.

first: Naozumi

last: Ishimaru


title: EPAS1-mutated paragangliomas are associated with hemoglobin disorders

city: Paris

first: Thierno Abdoulaye

last: BALDE

address: 15 rue de l’École de Médecine

department: INSERM UMR-S1138

country: France

institute: INSERM

summary: This study reports a large series patients presenting EPAS1-mutated paraganglioma in whom we investigated a cause underlying chronic hypoxia. Four patients (10%) suffered from hypoxemic heart disease. In patients with available hemoglobin electrophoresis results, 59% presented a hemoglobin disorder. Histological and transcriptomic characterization of EPAS1-tumors revealed increased angiogenesis and high similarities with pseudohypoxic paragangliomas caused by VHL gene mutations.

overall_design: To investigate the transcriptomic characterization of EPAS1-related paragangliomas we performed gene expression profiling analysis using data obtained from RNA sequencing for 52 paragangliomas with various genotypes including 19 EPAS1 (including one tumor in duplicate), 6 SDHx, 2 SLC25A11, 6 VHL, 3 RET, 3 NF1, 1 MAX, 1 MAML3 and 11 unmutated paragangliomas.

first: N

last: Burnichon

first: J

last: Favier

first: A

last: Buffet


title: A paradigm for post-embryonic Oct4 re-expression: E7-induced hydroxymethylation regulates Oct4 expression in cervical cancer

city: Aglantzia

first: Vasilis

last: Promponas

state: Nicosia

address: 1 Panepistimiou Avenue

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

summary: The Octamer-binding transcription factor-4 (Oct4) is upregulated in different malignancies, yet a paradigm for mechanisms of Oct4 post-embryonic re-expression is inadequately understood. In cervical cancer, Oct4 expression is higher in HPV-related than HPV-unrelated cervical cancers and this upregulation correlates with the expression of the E7 oncogene. We have reported that E7 affects the Oct4-transcriptional output and Oct4-related phenotypes in cervical cancer, however, the underlying mechanism remains elusive. Here, we characterize the Oct4-protein interactions in cervical cancer cells and reveal that Methyl-binding proteins (MBD2 and MBD3), are determinants of Oct4 driven transcription. E7 triggers MBD2 downregulation and TET1 upregulation, thereby disrupting the methylation status of the Oct4 gene. This coincides with an increase in the total DNA hydroxymethylation leading to the re-expression of Oct4 in cervical cancer and likely affecting broader transcriptional patterns. Our findings reveal a previously unreported mechanism by which the E7 oncogene can regulate transcription by increasing DNA hydroxymethylation and lowering the barrier to cellular plasticity during carcinogenesis.

overall_design: To assess whether E7 (main oncogene of HPV) has an impact on DNA methylation/demethylation in C33A cells, we isolated RNA from Oct4-expressing and Oct4+E7-expressing C33A cells. We performed Gene Experession Profile using the data generated from this experiment

first: Theofano

last: Panayiotou

first: Katerina

last: Strati


title: Identification of Messenger RNA Signatures in Age-Dependent Renal Impairment

city: Saitama City

first: Katsunori

last: Yanai

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

institute: Jichi Medical University, Saitama Medical Center

summary: In general populations, age-dependent renal impairment contributes to the progression of renal dysfunction. It has not been known which molecules are involved in age-dependent renal im-pairment. Messenger RNA (mRNA) has been reported to modulate various renal diseases, and we therefore investigated mRNA signatures in age-dependent renal impairment. We performed an initial microarray-profiling analysis to screen mRNAs, the expression levels of which changed in the kidneys of 50-week-old senescence-accelerated prone (SAMP1) mice (which have accelerated age-dependentd renal impairments) compared with those of 50 -wk- old senes-cence-accelerated-resistant (SAMR1) mice (which have normal aged kidneys) and with younger (10 -wk- old) SAMP1 and SAMR1 mice. We next assessed the expressions of mRNAs that were differentially expressed in the kidneys of SAMP1-50wk mice by conducting a quantitative real-time polymerase chain reaction (qRT-PCR) and compared the expressions among the SAMP1-10wk, SAMR1-10wk, and SAMR1-50wk mice. The results of the microarray together with the qRT-PCR analysis revealed five mRNAs whose expression levels were significantly altered in SAMP1-50wk mouse kidneys versus the control mice. The expression levels of the five mRNAs’ expression levels were increased in the kidneys of the mice with age-dependent renal impairment. Our findings in-dicate that the five mRNAs might be related and could become therapeutic targets for age-dependent renal impairment.

overall_design: 10-week-old SAMR1 mice (n=2), 50-week-old SAMR1 mice (n=2), 10-week-old SAMP1 mice (n=2), 50-week-old SAMP1 mice (n=2)


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM1B]

first: Joseph

last: Ecker

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from chunk B of a 25 years old male.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

last: Ecmer


title: Epigenome analysis of de novo replication repair deficient glioblastoma, IDH-wildtype in adults

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

summary: Genome-wide DNA methylation profiling of 7 de novo replication repair deficient glioblastoma, IDH-wildtype in adult patients. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 7 glioblastomas.

overall_design: Bisulfite converted genomic DNA extracted from the 7 glioblastoma tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YF2A]

department: Genomic Analysis Laboratory

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function. We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors (25 years old) and 2 young female donors (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.  This sample is from chunk A of a 30 years old female.

first: Jo-Fan

first: Chongyuan

last: Luo

first: Nicholas

first: Julia

last: Osteen

first: Junhao

last: Li

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

first: Michelle

last: Liem

first: Naomi

last: Claffey

first: Caz

last: O'Connor

first: Luise

last: Seeker

first: M

last: Behrens

first: Eran

last: Mukamel


title: Dual-hit strategy for therapeutic targeting of pancreatic cancer in patient-derived xenograft tumors

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

summary: Paracrine activation of pro-fibrotic sonic hedgehog (sHH) signaling in pancreatic ductal adenocarcinoma (PDAC) results in stromal amplification that compromises tumor drug delivery, efficacy, and patient survival. Interdiction of sHH-mediated tumor-stroma crosstalk with smoothened inhibitors transiently increases tumor permeability and macromolecule delivery. Using diffusion-weighted magnetic resonance (DW-MR) imaging, we demonstrate in multiple patient-derived xenografts (PDX) that responders to short-term sHH inhibitor exposure show increased permeability with proportionate increases in tumor diffusivity. However, a subset of PDXs fails to respond. Responders show co-induction of epithelial-mesenchymal transition (EMT), elevated FGF drive, and distinctly higher nuclear localization of fibroblast growth factor receptor (FGFR1). A pan-FGFR inhibitor (NVP-BGJ398) reverses EMT and nuclear FGFR1 accumulation without compromising the tumor priming effect. This dual-hit strategy of SMO and FGFR inhibition provides a clinically-translatable approach to compromise the profound impermeability of PDAC tumors. Furthermore, clinical deployment of DW-MR imaging could fulfill the essential clinical requirement for patient stratification

overall_design: Total RNA was extracted using RNeasy Minikit (Qiagen, Germantown, MD) according to the manufacturer’s instructions, and included RNase inhibitor (N808-0119, Applied Biosystems, Waltham, MA). RNA-seq libraries from 1μg RNA/sample (low-sample protocol of TruSeq Stranded mRNA Library Prep Kit, Illumina, San Diego, CA) were indexed using an automated IP-Star Compact Liquid Handler (Diagenode, Belgium) amplified, quantified, pooled, and sequenced to yield 25-30M single-end 80BP reads per sample on an Nextseq 500 (Illumina). FASTQ files were de-multiplexed and aligned to pre-compiled reference human (Hg19) and mouse (Mm10) genomes (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html) using outFilterMultimapNmax= 1 to identify only unique reads. Using the R package Xenofilter, reads were then filtered to generate bam files and mapped to genes with HTSeq to generate gene counts (https://github.com/simon-anders/htseq).

first: Gerard

last: Quinn

first: Tista

last: Chaudhuri

first: Robert

last: Straubinger


title: A Molecular Switch for Neuroprotective Astrocyte Reactivity

city: Palo alto

first: Jeffrey

last: Goldberg

state: Ca

address: 1651 page mill rd rm 2200

department: Ophthalmology

institute: Stanford University

summary: The intrinsic mechanisms that regulate neurotoxic versus neuroprotective astrocyte phenotypes and their effects on central nervous system (CNS) degeneration and repair remain poorly understood. Here, we show injured white matter astrocytes differentiate into two distinct C3-positive and C3-negative reactive populations, previously simplified as neurotoxic (A1) and neuroprotective (A2)1,2, which can be further subdivided into unique subpopulations defined by proliferation and differential gene expression signatures. We find the balance of neurotoxic versus neuroprotective astrocytes is regulated by discrete pools of compartmented cAMP derived from soluble adenylyl cyclase (sAC) and show proliferating neuroprotective astrocytes inhibit microglial activation and downstream neurotoxic astrocyte differentiation to promote retinal ganglion cell (RGC) survival. Finally, we report a new, therapeutically tractable viral vector to specifically target optic nerve head astrocytes and show elevating nuclear or depleting cytoplasmic cAMP in reactive astrocytes inhibits deleterious immune cell infiltration and promotes RGC survival after optic nerve injury. Thus, soluble adenylyl cyclase and compartmented, nuclear- and cytoplasmic-localized cAMP in reactive astrocytes act as a molecular switch for neuroprotective astrocyte reactivity that can be targeted to inhibit microglial activation and neurotoxic astrocyte differentiation to therapeutic effect. These data expand upon and define new reactive astrocyte subtypes and represents a novel step towards the development of gliotherapeutics for the treatment of glaucoma and other optic neuropathies.

overall_design: To investigate the function of soluble adenylyl cyclase (sAC) in astrocyte proliferation.

first: Evan

middle: G

last: Cameron

first: Michael

last: Nahmou

first: Bogdan

last: Tanasa

middle: L


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM2B]

first: Joseph

last: Ecker

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. This sample is from chunk A of a 73 years old female.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen


title: Real-time quantitative PCR analysis of Nrf2, HO-1, IL-6 and VEGF-A genes in human retinal pigment epithelium (RPE-19) cells

city: Bundoora

first: Dao

last: Nguyen

state: Victoria

address: 289 McKimmies Rd

department: School of Science and Health and Biomedical Science

country: Australia

institute: Royal Melbourne Institute of Technology

summary: Human RPE-19 cells were treated with either Trolox (50 µg/mL), lutein (10 µg/mL) or gac peel extracts (0-200 µg/mL) for 12, 24, 48 or 72 h before being exposed to 500 µM H2O2 for 24 h prior to RNA collection. Results were presented as the fold change compared to untreated controls ± SEM (n=3), different letters indicated statistical significance at p≤0.05 between different treatments (Analysis by One-way ANOVA with Turkey’s LSD test).

overall_design: RNA was extracted using TRIzol™ Reagent (Life Technologies, Melbourne, Australia) as per the manufacturer’s protocol. RNA was quantified spectrophotometrically at 260 nm (Nanodrop ND1000), and its purity checked using the ratios of absorbance at 260/280 nm and 260/230 nm. cDNA was synthesized from 1 μg total RNA using SuperScript III reverse transcriptase (Thermo Fisher Scientific) with oligo (dT) primers according to the manufacturer’s instructions. Each transcript quantification was carried out in triplicate. Subsequently, 4 µL (10 ng/µL) cDNA was added to 10 µL SYBR mix, 0.8 µL of each (10 µM) forward and reverse primer, and 4.4 µL DEPC H2O. The qPCR was performed on a Qiagen Rotor-Gene Q (Qiagen, Germany) and analysed with inbuilt software (version 2.3.1.49). The thermal cycling conditions were as follows: initial activation at 95°C for 2 min, 39 cycles of 95°C 5 s, 60°C for 10 s, 72°C for 15 s, and melting curve from 65°C to 95°C. Relative quantitative analysis of Nrf2, HO-1, IL-6 and VEGF-A mRNAs were performed using the 2−ΔΔCq method which was normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA. The expression was calculated as n-fold induction of the gene of interest in treated cells relative to that of untreated control cells.


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YF2B]

first: M

last: Behrens

first: Eran

last: Mukamel


title: ADAM9 deficiency mediates KRAS related pathways in pancreatic cancer cells

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pan18 cells and its ADAM9 KO derivatives (ADAM9 WT and ADAM9 KO).

first: Yu-Kai

last: Huang

first: Yuh-Pyng

last: Sher


title: Characterization of macrophages influence in human melanoma cells

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages, one of the more abundant cell types in the tumor microenvironment, to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the mechanisms governing their protumoral activity are not completely understood. Thus, identifying molecular pathways promoted by macrophages that could be responsible for immune evasion and tumor malignicity may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: BLM human melanoma cell line was coculture for 24h with in vitro differentiated macrophages, obtained from CD14+ monocytes isolated from human PBMCs in the presence of GM-CSF or M-CSF for seven days. All samples have been processed in triplicates.

first: Celia

last: Barrio-Alonso

first: Alicia

last: Nieto-Valle

first: Paloma

last: Sánchez-Mateos

first: Elena

last: García-Martínez


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OM1B]

first: Joseph

last: Ecker

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors (25 years old) and 2 young female donors (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.  This sample is from chunk B of a 70 years old male.

first: Jo-Fan

last: Chien

last: Liu

first: Chongyuan

last: Luo

first: Anna

last: Bartlett

first: Nicholas

first: Junhao

last: Li

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

first: Michelle

last: Liem

first: Naomi

last: Claffey

first: Caz

last: O'Connor

first: Luise

last: Seeker


title: Gene expression profiling of Ralstonia solanacearum in unexplored environmental niches reveals essential genes to complete its life cycle

city: Cerdanyola del Valles

first: Marc

last: Valls

email: marcvalls@ub.edu, mercerf93@gmail.com

state: Barcelona

address: CRAG Building - Campus UAB

institute: CRAG

summary: Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between environments is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate the bacterial transcriptomic adaptation to two environments, water and soil, and compare it with the well-studied in planta gene expression. We identified extensive transcriptional reprogramming in response to each environment. Strikingly, gene expression in water resembled expression during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). We reveal that basic pH and also to nutrient scarcity - conditions also encountered in planta during late infection stages - trigger the T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and alternate carbon source metabolism genes, mostly phenylacetate metabolism and glyoxylate cycle and downregulated virulence-associated genes. Furthermore, we proved through gain- and loss-of-function that genes encoding proteins associated with oxidative stress, such as the oxidative stress regulator OxyR and the catalase KatG, are key for survival of the bacterium in soil. This work identifies essential factors necessary for R. solanacearum to complete its life cycle and provides valuable insights into the biological processes driving pathogen adaptation to unexplored environments out of their hosts.

overall_design: Soil samples inoculated with R. solanacearum for 3 days at 28C. Water samples inoculated with R. solanacearum for 6 hours at 28C.

first: Roger

last: de Pedro-Jové

first: Jordi

last: Corral

first: Mercedes

last: Rocafort

first: Marina

last: Puigvert

first: Fàtima

last: Latif Azam

first: Cristina

last: Vandecaveye

first: Alberto

middle: P

last: Macho

first: Carlos

last: Balsalobre

first: Núria

last: Coll

last: Orellano


title: NUDT2 loss-of-function variants are associated with a recessive neurodevelopmental disease with mental retardation, movement disorder and peripheral neuropathy

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: We present cases of a neurological disorder in children characterized by developmental delays in mental and motor skills, gait disturbances, and peripheral neuropathy. The disorder is associated with rare variants in the NUDT2 gene, which encodes a Nudix family mRNA decapping enzyme. The spectrum of variants includes two previously reported truncating variants and two novel variants, namely the missense c.174G>T and the in-frame deletion c.410_412del. We report that these new variants result in a marked reduction in enzymatic hydrolase activity of the encoded protein, strongly suggesting loss of function of NUDT2 as the cause of the disorder. Morover, we document that loss of function may be due to reduced enzymatic activity or impaired protein stability of NUDT2 variants. Consistent with its function in mRNA decapping, NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, likely due at least in part to changes in mRNA stability. Our results confirm that a reduction or loss of NUDT2-dependent mRNA decapping activity is associated with recessive neurological disease in pediatric patients. Taken together, these findings underscore the importance of a physiologically balanced mRNA processing for neuronal development and homeostasis.

overall_design: RNA-Seq was used to identify results of Nudt2 mutations found in patient fibroblasts

first: Xinfu

last: Jiao

first: Megarditch

last: Kiledjian


title: Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Preclinical evaluation of a long acting GLP1R/GlucagonR agonist (NN1177) in GAN DIO mouse

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

institute: Novo Nordisk Research Centre Oxford

summary: Mouse were fed either a CHOW diet or an AMLN diet for 36 weeks and subsequently treated by various compounds for 8 weeks.

overall_design: RNA-sequencing data. CHOW diet: Vehicle n=7 (one sample excluded during quality control); AMLN diet: Vehicle, NN1177 low dose, medium dose, high dose; Semaglutide: n = 8 for each group

first: Jenny

last: Norlin

first: Anne

last: Bugge

first: Elisabeth

last: Galsgaard

first: Cesar

last: Prada-Medina

first: Markus

last: Latta

first: Sanne

last: Veidal

first: Pia

last: Petersen

first: Michael

last: Feigh

first: Dorte

last: Holst


title: Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells [BulkRNA-seq]

summary: We have applied a novel and unique strategy to validate the annotation of cell cluster identified from scRNA-seq. Bulk RNA-seq data were generated for osteoblast and fibroblast samples and  from bulk RNA-seq data. Signature Scores were computed based on the signature genes that were differentially expressed between osteoblasts and fibroblasts to infer the concordance between cell clusters identified in scRNA-seq data and osteoblasts and fibroblasts.

overall_design: We generated the bulk RNASeq data from osteoblasts and fibroblasts, two main differentiated cell types from DPSC and PDLSC, for validating the clustering results from scRNA-seq

first: Di

last: Wu

first: Alpdogan

last: Kantarci


title: Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis (using MARS-seq) in Xenoturbella bockii adult specimens.

overall_design: Adult specimens were dissociated and pooled before sorting single-cells for scRNAseq.

first: Helen

last: Robertson

first: Max

last: Telford

first: Heather

last: Marlow