title: Exposure to elevated Temperature affects the Expression of Piwi-interacting RNAs and Associated Transcripts in Mouse Testes [small RNA-seq]

city: guangzhou

first: wenbin

last: Chen

address: Industrial Avenue Central

department: zhujiang hospital

institute: Southern medical university

summary: Exposure to heat waves could result in adverse effects on human health, especially in male testicles. Piwi-interacting RNA (piRNA) is a novel type of small non-coding RNA, which can notably impact mRNA turnover and preserve germline maintenance in germline cells. In this study, a mouse testicular heat stress model was constructed and the testes were removed for piRNA-sequencing. Bioinformatics analysis was used to discover the differential expressed piRNAs, piRNA clusters, and enriched pathways.

overall_design: Twelve C57BL/6 mice were randomly divided into two groups:control groups and heat stress groups. The scrota of the control groups were put into a 36 °C water bath for 15 minutes, and the testicular heat stress groups utilized a 43 °C water bath instead for the same time. Small RNA sequencing was performed in the testicular tissues of control and testicular heat stress groups after 24 hours.

first: Wenbin

first: Zhang

first: Shengren

last: Cen

first: Xiangming

last: Mao


title: the anti lipid accumulation and anti liver cancer formation effect of CACF in CD36 overexpression transgenic zebrafish

status: Public on Jan 31 2023

city: Zhunan

first: Chiou Hwa

last: Yuh

address: 35, Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

type: Expression profiling by high throughput sequencing

summary: Carassius auratus complex formula (CACF) is composed of extracts from Carassius auratus, Rhizoma dioscoreae, Lycium chinense, and Rehmannia glutinosa Libosch. These ingredients are used to treat diabetes since ancient China. Previously, CACF elicits antidiabetic effects in streptozotocin-induced diabetic mouse models under high-fat diet treatment, reduces triglyceride levels, maintains blood sugar control, and enhances insulin sensitivity. However, the effects of CACF on anti-cancer and anti-inflammation and the underlying mechanism remain unknown. In this study, we revealed that CACF could be a promising therapeutic agent with multiple functions

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD36 zebrafish treat with or without CACF and use CD36 normal diet as control

first: He-Yun

last: Hsiao

first: Po-Jui

last: Hsu

first: Bonifasius

last: Putera Sampurna

first: Yu-Ju

last: Lin

first: Kuan-Hao

first: Horng-Dar

last: Wang

first: Chiou-Hwa


title: Bulk RNA sequecing  reveals the heterogeneity of fibroblasts in the diabetic heart

city: hangzhou

first: heyangzi

last: li

state: zhejiang

address: ZheJiang Unisversity yuhang tang road

department: basic medical school

country: China

institute: ZhejiangUniversity

summary: Diabetes mellitus is one of the most chronic diseases, of which diabetic cardiomyopathy is the major cause of morbidity and involves in multiple processes such as inflammation, oxidative stress, fibrosis, extracellular collagen deposition, apoptosis, mitochondria dysfunction.

overall_design:
We established diabetic mice by STZ injection and lead bulk RNA sequencing  to reveal the potential mechanisms in diabetic myocardium.
Real-time quantitative PCR, immunofluorescence and western blotting was used to verify the sequence data. In addition, cardiac function , fibrosis related indicators and morphological changes were performed to analyze the dysfunctions of diabetic cardiomyopathy.

first: Xiaoming

last: Zhang

first: Heyangzi

last: Li


title: A low-carbohydrate diet induces hepatic insulin resistance and metabolic-associated fatty liver disease

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: We demonstrate that the ketogenic diet a low carbohydrate diet can induce fibrosis and NASH regardless of body weight loss compared to high-fat diet (HFD) fed mice. KD-fed mice develop severe hepatic injury, inflammation, and steatosis. In addition, KD increases IL-6-JNK signaling and aggravates diet induced-glucose intolerance and hepatic insulin resistance compared to HFD. Notably, pharmacological inhibition of IL-6 and JNK reverses KD‐induced glucose intolerance and restores insulin sensitivity.

overall_design: Using metabolic, biochemical and omics approaches, we identified the effects of a KD on NASH and investigated the mechanisms by which KD induces hepatic insulin resistance, steatosis, and fibrosis

first: Tenagne

middle: D

last: Challa

first: Memoona

middle: R

last: Bhatti

first: Wenfei

last: Sun

first: Lennart

last: Opitz

first: Christian

last: Wolfrum


title: Single cell analysis reveals the heterogeneity of fibroblasts in the diabetic heart

summary: Diabetes mellitus is one of the most chronic diseases, of which diabetic cardiomyopathy is the major cause of morbidity and involves in multiple processes such as inflammation, oxidative stress, fibrosis, extracellular collagen deposition, apoptosis, mitochondria dysfunction. However, the exact mechanisms of fibroblasts concerning type Ⅰ diabetes remain unclear. To further understand the functional roles of fibroblasts of STZ-induced diabetic mice, we lead the single cell RNA sequence. Cells were comprised of endothelial, fibroblast, cardiomyocyte, smooth muscle cells, macrophage and other type cells. Single cell sequence illustrates novel fibroblast sub-clusters and highlight the role of Lox. Real-time quantitative PCR, western blotting, immunofluorescence was used to verify the sequence data. We validate the dysfunctions of diabetic cardiomyopathy by echocardiogram. Our study supports novel insights into the pathogenesis of diabetic cardiomyopathy.

overall_design: We lead the single cell RNA sequence. Cells were comprised of endothelial, fibroblast, cardiomyocyte, smooth muscle cells, macrophage and other type cells. Single cell sequence illustrates novel fibroblast sub-clusters and highlights the role of Lox. Real-time quantitative PCR, western blotting, immunofluorescence was used to verify the sequence data.


title: Characterization of mesenchymal stem cells in pre-B acute lymphoblastic leukemia

city: Nedlands

first: Anastasia

last: Hughes

state: WA

address: 15 Hospital Avenue

department: Cancer Centre

country: Australia

institute: Telethon Kids Institute

summary: The way in which leukemia develops, progresses and responds to treatment is mediated largely by components of the bone marrow microenvironment (BMM). Increasing evidence shows that leukemic cells hijack the BMM, altering its functioning and establishing leukemia-supportive interactions with stromal and immune cells. While previous work has highlighted functional defects in the mesenchymal stem cell (MSC) population from the BMM of acute leukemias, a thorough characterization and molecular profiling of MSCs of pre-B cell acute lymphoblastic leukemia (B-ALL), the most common cancer in children, has not been conducted. Here, we investigated the transcriptome profiles of MSCs isolated from the BMM of an immunocompetent BCR-ABL1+ model of B-ALL.

overall_design: MSCs were isolated from long bones of control or leukemia mice (4-7 mice pooled per sample). Two biological replicates were sequenced for both control and leukemia-associated MSCs.

middle: M


title: Characterisation of VDR signaling in prostate cancer health disparities (RNA-Seq; BAZ1A conditional)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

country: USA

institute: Cedars-Sinai Medical Center

summary: To investigate the effect of 1,25(OH)2D3 activation on RNA expression in prostate cell lines derived from European Americans and African Americans

overall_design:
GFP-BAZ1A was purchase from Addgene (plasmid # 65371)and cells were stable transducted by selection and maintenance in media supplemented with puromycin (2µg/mL).RNA was extracted from cells in the presence of 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq. Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA. Alignment of raw sequence reads to the human transcriptome (hg38) was performed via Rsubread and transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline.
Comparative RNA gene expression profiling analysis of RNA-seq data for prostate cell lines treated with 1α,25(OH)2D3 (100 nM, 8h), with stable expression of BAZ1A or vector control

first: Clayton

last: Yates


title: Effect of overexpression PBX1 on gene expression in HCT116 cells

city: Guangzhou

first: Yinan

last: Liu

state: Guangdong

address: no.58 Zhongshanerlu street

institute: The first affiliated hospital, Sun Yat-sen University

summary: To investigate the function of PBX1 in colorectal cancer (CRC). We overexpressed the PBX1 in CRC cell lines HCT116 with plasmids.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of PBX1 overexpression cells and negative control.

first: Jianhui

last: Chen


title: Transcriptomic alterations underlying metaplasia into specific metaplastic components in metaplastic breast carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: Metaplastic breast carcinoma (MpBC) typically consists of carcinoma of no special type (NST) with various metaplastic components. The intracase transcriptomic alterations between metaplastic components and paired NST components, which are critical for understanding the pathogenesis underlying the metaplastic processes, remain unclear. Herein, 59 NST components and paired metaplastic components (spindle sarcomatous [SPS], matrix-producing, rhabdomyoid [RHA], and squamous carcinomatous [SQC] components) were microdissected from specimens obtained from 27 patients with MpBC for gene expression profiling. Hierarchical clustering and principal component analysis revealed a heterogeneous gene expression profile (GEP) corresponding to the NST components, but the GEP of metaplastic components exhibited subtype dependence. Compared with the paired NST components, the SPS components demonstrated the upregulation of genes related to stem cells and epithelial–mesenchymal transition, and displayed enrichment in claudin-low and macrophage signatures. Despite certain overlap in the enriched functions and signatures between the RHA and SPS components, the specific differentially expressed genes differed. We observed the RHA-specific upregulation of genes associated with vascular endothelial growth factor signaling. The chondroid matrix-producing components demonstrated the upregulation of hypoxia-related genes and the downregulation of the immune-related MHC2 signature and the TIGIT gene. In the SQC components, TGF-β and genes associated with cell adhesion were upregulated. The differentially expressed genes among metaplastic components in the 22 MpBC cases with one or predominantly one metaplastic component clustered paired NST samples into clusters with correlation with their associated metaplastic types. These genes could be used to separate the 31 metaplastic components according to respective metaplastic types with an accuracy of 74.2%, suggesting that intrinsic signatures of NST may determine paired metaplastic type. The EMT activity and stem cell traits in the NST components were correlated with specimens displaying lymph node metastasis. In summary, we presented the distinct transcriptomic alterations underlying metaplasia into specific metaplastic components in MpBCs.

overall_design: Gene expression profile

first: H

middle: C

last: Lien

first: C

middle: H


title: Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Alveolar Cell Death induced by LPS and Corona Virus [RNA-seq subset II]

city: New Haven

first: Barani Kumar

last: Rajendran

state: CT

address: 10 Amistad Street, New Haven, , Yale University

department: Pharmacology

institute: Yale University

summary: Pulmonary inflammation compromises lung barrier function and underlies many lung diseases including acute lung injury and acute respiratory distress syndrome (ARDS).  However, mechanisms by which lung cells respond to the damage caused by the inflammatory insults are not completely understood.  Here we show that Fzd6-deficiency in Foxj1+ ciliated cells reduces pulmonary permeability, lipid peroxidation, and alveolar cell death accompanied with an increase in alveolar number in lungs insulted by LPS or mouse coronavirus MHV-1.  Single cell RNA sequencing of lung cells indicates that the lack of Fzd6, which is primarily expressed in Foxj1+ ciliated cells, increases expression of the aldo-keto reductase Akr1b8. Intratracheal administration of the Akr1b8 protein phenocopies Fzd6-deficient lung phenotypes.  In addition, ferroptosis inhibitors also phenocopy Fzd6-deficient lung phenotypes and exert no further effects in Fzd6-deficient lungs. These results indicate that Fzd6-deficiency suppresses inflammation-induced ferroptotic death of alveolar cells via the release of Akr1b8, thus revealing a previously unknown mechanism by which Fzd6 signaling regulates ferroptosis via a paracrine pathway.  In addition, this study demonstrates the yet-to-be appreciated importance of ciliated cells in protecting alveolar cells during pulmonary inflammation.

overall_design: Compare gene expression at single cell level between TdTomato-positive cells isolated from WT and Fzd6 KO lungs after LPS treatment

first: Qingying

last: Yuan

first: Barani

middle: K

first: Dianqing

last: Wu


title: The oncogenic FOXL2 mutation C134W is the sole driver of granulosa cell tumors in mice

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

summary: We have generated a humanized Foxl2 mouse model by genome editing to evaluate in vivo the role of mutated FOXL2 in the development of murine Adult Granulosa Cell Tumors

overall_design: Comparative of genes dysregulated in mAGCTs compared to normal ovaries after RNAseq experiment

first: Elena

last: Llano

first: Anne-Laure

first: Natalia

last: Felipe-Medina

first: Xose

middle: S

last: Puente

first: Alberto

last: Pendas

first: Reiner

middle: A

last: Veitia


title: Genome wide expression from COVID-19 patients and controls' lung

city: Bern

first: Aref

last: Hosseini

address: Inselspital, INO-F

country: Swaziland

institute: university of Bern

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to coronavirus disease 2019 (Covid-19) which has caused worldwide pandemic infection. Yet due to unknown reason, certain COVID-19 patients exhibit severe inflammatory reactions associated with cytokine storm and neutrophil infiltration and neutrophil extracellular traps (NETs) in the lung, leading to further complications of SARS-CoV-2 infection. To find out whether the cause of lung injury in COVID-19 patients is due to increased reactive oxygen species and subsequently NET formation we have compared the post-mortem lung biopsies of deceased COVID-19 patients to normal lung tissues using RNA-Seq analysis.

overall_design: RNA expression profiling of formalin-fixed, paraffin-embedded (FFPE) lung tissues of seven patients and three non-covid infected individuals as control.

first: Hans-Uwe

last: Simon


title: EP300 promotes renal tubular epithelial cell fibrosis by accelerating HIF2α in diabetic nephropathy

city: Zhengzhou

first: Yanan

last: Gong

state: Henan

address: 1 Jianshe Road

institute: First Affiliated Hospital of Zhengzhou University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The target gene of EP300 action was detected in human renal tubular epithelial cells

overall_design: normal cell lines

first: Yanna

last: Dou

first: Zhanzheng

last: Zhao


title: Human derived and patient derived xenografts epigenome analysis of primary and metastasis colorectal cancer

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of primary (PR) and liver metastasis (LM) colorectal cancer (CRC).
The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in human and xenogratfs derived samples.
Raw data were processed using R minfi package. The main goal of this study is to develop a methylation-based classifier and predictor for metastatic CRC (mCRC),
in order to find specific patients stratification for anti-EGFR targeted therapy (cetuximab) and bring the promise to shed new light on the role of methylation in driving colorectal cancer progression in different groups of patients.

first: Marco

last: Viviani

last: Grassi

first: Andrea

last: Bertotti


title: Human MCF7 cells engineered to overexpress MYF6 vs. Control cells containing empty vector constructs [Rec2]

city: Odense

first: Sidsel

middle: Bering

last: Olsen

address: J.B. Winsløws Vej 25, 3

department: IMM

country: Denmark

institute: Syddansk Universitet

summary:
Background: Proliferation is an important hallmark of cancer development and progression. Tumor growth rate significantly influences the course of the disease, and patients with tumors that have a high proliferation rate have an increased risk (10-20%) of metastasis and death. The genomic region encoding the transcription factor MYF6 is often altered in breast cancer, and alterations in MYF6 methylation have been linked to several different cancer types. However, the functional role of MYF6 in cancer remain unknown. Here, we have dissected the functional role of MYF6 in ER+ breast cancer.
Methods: We analyzed cancer cell growth, proliferation, apoptosis, in vivo tumor formation, EMT phenotype and BCSC propagation in MCF7 and T47D ER+ breast cancer models with inducuble MYF6 overexpression or MYF6 knockdown. Additionally, we performed detailed molecular profiling and network analysis, and Western blot validation of identified targets.
Results: We show that MYF6 suppresses PI3K/Akt/mTOR and Wnt pathway signaling, two important pathways of cell proliferation, and suppression was accompanied by reduced cell growth in vitro and in vivo, and G0/G1 phase cell cycle arrest. MYF6 also induced an EMT phenotype and forced the cells into a cancer stem cell-like state, leading to resistance to -irradiation. Network analysis of molecular profiling data revealed that MYF6 activates hypoxia signaling and HIF1A was identified as a downstream target and an upstream regulator of MYF6.
Conclusion: Our results suggest both a tumor-suppressive and oncogenic role of MYF6 in ER+ breast cancer, and we theorize that, subject to the presence or absence of yet unidentified cellular factors, MYF6 can switch from a growth-inhibiting tumor suppressor to an oncogene state, associated with cancer stem cells and treatment resistance.

overall_design:
Transcriptional profiling of human ER+ MCF7 breast cancer cells modified by stable site-specific insertion of MYF6. Gene expression was induced for 48 h with Doxycycline and gene expression compared to control cell lines. Two MCF7-MYF6 cell lines were generated (MYF6 Rec1 and MYF6 Rec2). The goal was to determine the effects of MYF6 gene transfection on global gene expression and molecular phenotypes in ER+ breast cancer.
Two-condition experiment, MCF7-MYF6 Rec2 vs. MCF7-Ctrl cells. Biological replicates: 4 Ctrl replicates and 4 MYF6 Rec2 replicates. The data from MYF6 Rec2 is from the second generated MYF6-expressing MCF7 cell line, generated to validate the findings in Rec1.

middle: B

first: Mads

last: Thomassen

first: Henrik

middle: J

last: Ditzel


title: Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Alveolar Cell Death induced by LPS and Corona Virus [RNA-seq subset I]

first: Barani Kumar

last: Rajendran

overall_design: Compare gene expression at single cell level between WT and Fzd6 KO lungs after LPS treatment

first: Qingying

last: Yuan

first: BaraniKumar

first: Xiaofeng

last: Liao

first: Dianqing

last: Wu


title: RNA sequencing of midbrain regions from MPTP-treated mice with Irisin pre-treatment and delayed treatment

city: Shanghai

first: Xi

last: Zhang

address: No.1239 Siping Road

institute: Tongji University

summary:
Irisin, a recently identified myokine, is increased by exercise and plays pivotal roles in energy metabolism. However, it remains unknown whether irisin has any protective effects on Parkinson's disease.
To examine the role of irisin in PD, irisin was peripherally delivered before or after the establishment of PD models by MPTP to explore its effect.  We performed  mRNA analysis in the midbrain of MPTP treated mice with irisin pre-treatment or delayed-treatment through RNA-Sequencing. And bioinformatic analysis was done on the identified deregulated genes through gene ontology (GO) analysis, KEGG pathway analysis and Gene set enrichment analysis (GSEA).
Pathway analysis indicated that NAD(P)H activity and metabolism, PI3K-AKT pathway, MAPK pathway, inflammation-related signaling pathways played vital roles in the treatment of MPTP treated mice by  irisin pre-treatment and irisin delayed treatment.
This study provides a detailed analysis of the effects and underlying mechanisms of irisin treatment in MPTP treated mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT mice,  MPTP treated mice, and MPTP treated mice with Irisin pre-treatment or delayed treatment

first: Sutong

last: Xu

first: Yong

last: Hu

first: Qiulu

last: Liu

first: Chenming

first: Huazhen

last: Chai

first: Yuping

last: Luo

first: Lingjing

last: Jin

first: Siguang

last: Li


title: A Developmentally Prometastatic Niche in Neonatal Liver to Hepatoblastoma mediated by Cxcl1/Cxcr2 Axis

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: Hepatoblastoma (HB) is the most common pediatric liver cancer. Its exclusive occurrence in very young children leads us to investigating whether the immature liver provides a protumorigenic niche to HB development. We employed the single-cell RNA-sequencing (sc-RNAseq) to comprehensively profile the HB tumors and their microenvironment in the orthotopic transplantation models established in postnatal day 5 and 60. We demonstrated that the neonatal liver provides a prometastatic niche to HB development via Cxcl1/Cxcr2 axis-mediated HB-aHSC interaction.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We first established the orthotopic transplantation models of hepatoblastoma in postnatal day 5 and 60 mice (P5Tx and P60Tx models). Then we performed single-cell RNA-sequencing (sc-RNAseq) using tumor and liver tissues from both models. The top candidate cell type and gene identified by sc-RNAseq are investigated for their roles in HB cell growth, migration, and survival.

first: Li

last: Fan

first: Liqin

last: Zhu

first: Jiyang

last: Yu


title: Sensory nerve niche regulates mesenchymal stem cell homeostasis via FGF/mTOR/autophagy axis [RNA-seq]

city: Los Angeles

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

summary: The goal of this study is to compare transcriptome profiling (RNA-seq) of proximal end of incisor 1 week after TMX induction between control and Fgfr1 mutant mice

overall_design: mRNA profiles of control and Fgfr1 mutant mice were generated by deep sequencing, in triplicate, using NextSeq500 High Output. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer and all samples for sequencing had RNA integrity numbers >9.


title: Human MCF7 cells engineered to overexpress MYF6 vs. Control cells containing empty vector constructs [Rec1]

first: Sidsel

last: Olsen

overall_design:
Transcriptional profiling of human ER+ MCF7 breast cancer cells modified by stable site-specific insertion of MYF6. Gene expression was induced for 48 h with Doxycycline and gene expression compared to control cell lines. Two MCF7-MYF6 cell lines were generated (MYF6 Rec1 and MYF6 Rec2). The goal was to determine the effects of MYF6 gene transfection on global gene expression and molecular phenotypes in ER+ breast cancer.
Two-condition experiment, with dye-swaps:  MCF7-MYF6 Rec1 vs. MCF7-Ctrl cells. Biological replicates: 4 Ctrl replicates and 4 MYF6 Rec1 replicates.

first: Mads

last: Thomassen

first: Angela

last: Reidel

first: Henrik

last: Ditzel


title: Primary mesenchymal cells from the human fallopian tube infected with Chlamydia trachomatis

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

summary: We profiled metabolite changes upon C.trachomatis infection in primary human cells in order to identify rewiring of metabolite networks due to infection. In addition, gene expression micro array analyses were used to determine concurrent transcriptional regulation.

overall_design: Primary cells were isolated from healthy tissue of surgery specimen taken from patients undergoing resections for bening genecological disease and cultured as described in the accompanying publication. Cells in 2D were infected with C.trachomatis serovar L2 and harvested at 24h or 48h p.i. Total RNA was extracted from samples and hybridized on Agilent-8x60k Human custom arrays as single-color hybridizations.

first: Ana

middle: T

last: da Costa

first: Hans

last: Mollenkopf

first: Hilmar

last: Berger


title: Key circRNAs from goat: discovery, integrated regulatory network and their putative roles in the differentiation of intramuscular adipocytes

status: Public on Jan 30 2023

city: Chengdu

first: changsheng

last: he

address: No. 16, South Section, 1st Ring Roa

institute: southwest minzu university

type: Non-coding RNA profiling by high throughput sequencing

summary:
To find the differentially and highly expressed circRNAs between the early and late stages of intramuscular adipocytes differentiation. Explored their expression profiles and further predicted their possible interaction relationships.
To generated the final circRNA-miRNA interaction network that have valuable functions in adipocyte differentiation.

overall_design: Illumina HiSeq method was used to compare the whole transcriptomes of goat intramuscular adipocytes differentiation.

first: Yaqiu

last: Lin

first: Yu

last: Du


title: Genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multi-species single nucleotide polymorphism chip analysis

first: Huixiao

last: Yang

address: No 233 1st Guangshan Road

institute: Guangdong Academy of Forestry

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. High levels of genetic diversity were observed throughout the 19 E. urophylla populations based on genome-wide SNP data (HE=0.2677 to 0.3487). Analysis with STRUCTURE software, Principal component analysis (PCA) and a neighbor-joining (NJ) tree indicated that E. urophylla populations could be divided into three groups, and moderate and weak population structure was observed with pairwise genetic differentiation (FST) values ranging from −0.09 to 0.074. The low genetic diversity and shallow genetic differentiation found within the 19 populations may be a consequence of their pollination system and seed dispersal mechanism. In addition, 55 core germplasms of E. urophylla were constructed according to the genetic marker data. The genome-wide SNPs we identified will provide a valuable resource for further genetic improvement and effective use of the germplasm resources.

overall_design: In total, 382 samples were analyzed without replicates or control or/and reference samples.

first: Xiaohui

first: Fang

last: Xu

first: Huanqin

last: Liao

first: Wen

first: Weihua

last: Zhang

first: Bin

first: Baozhu

first: Yuxia

last: Wang

first: Xinyu

last: Chen


title: IL-13 stimulation of primary human bronchial epithelial cells in control individuals and patients with asthma.

city: Davos Wolfgang

first: Milena

last: Sokolowska

state: Graubünden

institute: Swiss Institute of Allergy and Asthma Research (SIAF)

summary:
We performed RNA sequencing of gene expression of differentiated primary human bronchial epithelial cells derived from control and asthmatic patients, stimulated with IL-13.
The Type 2 Asthma mediator IL-13 was described to induce airway hyperresponsiveness, goblet cell metaplasia, mucus hypersecretion and airway remoddeling including impairment of epithelial barrier integrity.
We investigated differential expression of SARS-CoV-2 related host gene expression as well as genes involved in N-linked glycosylation upon IL-13 in bronchial epithelial cells.
Top IL-13 affected pathways included ion- and transmembrane transport, lipid metabolic processed and protein glycosylation.

overall_design: RNA sequencing of gene expression in differentiated primary human bronchial epithelial cells upon IL-13 treatment in healthy controls and patients with asthma.

first: Wawrzyniak

last: Paulina

first: Tan

last: Ge


title: Investigation of MicroRNA Biomarkers in Equine Distal Interphalangeal Joint Osteoarthritis

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary:
Identify differentially expressed microRNAs in mild and severe equine distal interphalangeal joint osteoarthritis plasma and synovial fluid samples
Determine the effects of selected osteoarthritis-related miRNAs on equine chondrocytes in monolayer culture through the application of miRNA agomirs and antagomirs

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for mild osteoarthritis and severe osteoarthritis equine plasma and synovial fluid samples

first: Melissa

middle: E

last: Baker

first: Seungmee

last: Lee

first: Matthias

last: Hackl

first: Sarah

last: Taylor

first: Mike

last: Clinton

first: Mandy

last: Pfeffers

first: Catarina

last: Castanheira


title: MYF6 suppresses cell growth through inhibition of Akt and Wnt signaling in ER-positive breast cancer

first: Sidsel

last: Olsen

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

overall_design: Refer to individual Series


title: Induction and Reversal of beta-cell dysfunction

status: Public on Jan 29 2023

city: Waurn Ponds

first: Kathryn

last: Aston-Mourney

state: VIC

address: 75 Pigdons Rd

institute: Deakin University

summary: INTRODUCTION: Targeting β-cell failure could prevent, delay or even partially reverse Type 2 Diabetes. However, development of such drugs is limited as the molecular pathogenesis is complex and incompletely understood. Further, while β-cell failure can be modelled experimentally only some of the molecular changes will be pathogenic. Therefore, we used a novel approach  to identify molecular pathways that are not only changed in a diabetes-like state but are reversible and can be targeted by drugs.  METHODS: INS1E cells were cultured in high glucose (20 mM) for 72 hrs or high glucose for an initial 24 hrs followed by drug addition (exendin-4, metformin and sodium salicylate) for the remaining 48 hrs. RNAseq (Illumina TruSeq), Gene Set Enrichment and Pathway Analyses (using Broad Institute, Reactome, KEGG and Biocarta platforms) was used to identify changes in molecular pathways.   RESULTS: High glucose decreased function and increased apoptosis in INS1E cells with drugs partially reversing these effects. High glucose resulted in upregulation of 109 pathways while drug treatment downregulated 44 pathways with 21 pathways in common. Interestingly while hyperglycaemia extensively upregulated metabolic pathways, they were not altered with drug treatment, rather pathways involved in the cell cycle featured more heavily.  CONCLUSION: GSEA for hyperglycaemia identified many known pathways validating the applicability of our cell model to human disease. However, only a fraction of these pathways were downregulated with drug treatment, highlighting the importance of considering druggable pathways. Overall, this provides a powerful approach and resource for identifying appropriate targets for the development of β-cell drugs.

overall_design: INS-1E cells that were cultured in normal glucose (NG [or LG], 11.1 mM glucose) for 72 hours, high glucose (HG, 20mM glucose) for 72 hours or high glucose for an initial 24 hours followed by the addition of drugs (50 nM Exendin-4, 250 μM metformin and 250 μM sodium salicylate) for the remaining 48 hrs (HG+drugs).

first: K

first: S

last: Sithara

first: T

last: Crowley

last: Walder


title: RNA-seq during chondrocyte differentiation of iMSCs deived from iPSCs of healthy (AC-iPSCs) and OA chondrocytes (OA-iPSCs)

city: Atlanta

first: Mohd

middle: Nazir

last: Khan

state: GA

address: 21 Ortho Lane

department: Orthopaedics

institute: Emory University

summary: The global expression profile duirng chondrogenic differentiation of AC-iMSCs (#7) and OA-iMSCs (#5) was compared to determine the existance of memory of disease

overall_design: We performed pairwise differential gene expression analysis at day 0 and day 21 of chondrogenic differentiation and analyzed the effect of physiological state i.e. disease status of donor cells on chondrogenic potential of OA-iMSCs to demonstrate thr retention of OA-memory.

first: Nazir

first: Hicham

last: Drissi


title: Regulation of mouse chamber selective enhancers

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: High levels of NF-YAl drives EMT in Claudinlow tumors

status: Public on Jan 28 2023

city: Ceriano Laghetto

first: Alberto

last: Gallo

state: District Of Columbia

address: Via Marconi 11/B

institute: Università degli Studi di Milano

summary: NF-Y is a trimeric transcription factor whose binding site -the CCAAT box- is enriched in cancer-promoting genes. The regulatory subunit, the sequence-specificity conferring NF-YA, comes in two major isoforms, NF-YA long (NF-YAl) and short (NF-YAs). Extensive expression analysis in epithelial cancers determined two features: widespread overexpression and changes in NF-YAl/NF-Ys ratios (NF-YAr) in tumors with EMT features. We performed wet and in silico experiments to explore the role of the NF-YA isoforms in breast -BRCA- and gastric -STAD- cancers. We generated clones of two Claudinlow BRCA lines BT549 and SUM159PT ablated of exon-3, thus shifting expression from NF-YAl to NF-YAs. Edited clones show normal growth, but reduced migratory capacities in vitro, and ability to metastatize in vivo. Using TCGA, including upon deconvolution of scRNA-seq data, we formalize the clinical importance of high NF-YAr, associated to EMT genes and cell populations. We derive a novel, 158 genes signature common to BRCA and STAD Claudinlow tumors. Finally, we identify splicing factors associated to high NF-YAr, further validating RBFOX2 as promoting expression of NF-YAl with wet experiments. In conclusion, these data bring three relevant results: (i) concerning Claudinlow tumors, the definition and clinical implications of NF-YAr and the 158 genes signature; (ii) genetic evidence of a role of exon-3 28 aminoacids, empowering NF-YAl with EMT-driving features in BRCA. (iii) The definition of a set of splicing factors fine-tuning the levels of NF-YA isoforms.

overall_design: Comparison of gene- and isoform-level expression of RNA-seq data between SUM159PT and BT549 WT cell lines and two NF-YA ΔEx3 edited clones for each cell line. Samples for all the conditions were obtained by three independent biological replicates.

first: Michela

last: Londero

first: Diletta

last: Dolfini


title: RNA-seq for UBR5 and Cdc73-regulated genes in 4T1 cells treated with Dovitinib

status: Public on Jan 27 2023

city: New York

first: Ziqi

last: Yu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: In order to understand the molecular mechanisms underlying the regulatory activities of UBR5 and CDC73 in dovitinib-induced apoptosis in 4T1 tumor cells that were Dox-silenced for the expression of Ubr5, Cdc73, or both and treated with dovitinib.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4T1 cells and its KD derivatives (shUbr5, shCdc73, and shUbr5-Cdc73)

first: Xiaojing

last: Ma

first: Adrian

middle: Y

last: Tan


title: Trenscriptome analysis of TSLP stimulated regulatory T cells

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

summary: Regulatory T cells are indispensable for the immune homeostasis. Recent studies revealed the crucial roles of tissue factors; however, the roles of epithelial cell derived cytokine TSLP in the maturation of regulatory T cells are not adressed. Here, we report that TSLP activates mTOR signaling to mature regulatory T cells to maintain large intestine homeostasis.

overall_design: mRNA obtained from PBS or TSLP stimulated regulatory T cells

first: Tadamichi

last: Kasuya

first: Hiroshi

last: Nakajima


title: MicroRNA profile of breast cancer tissue samples

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

country: United Kingdom

institute: Imperial College London

summary:
RNA was isolated from FFPE tissue sections and expression profile of miRNAs determined by hybridization to Affymetrix GeneChip miRNA 4.0 Array
Both normal and cancer samples were used. Normal cases included cosmetic reduction mammoplasties (the only true normal tissue) and tissues with some morphological abnormalities. Some benign, non-cancer, cases were also included. Breast cancer cases included invaive ductal and lobullar carcinomas as well as metaplastic breast cancer

overall_design: RNA isolated from each tissue sample was hybridized to a single chip

first: E

first: U

last: Kumar

first: Y

last: Hu

last: Shousha


title: SOX11 promotes skin fibrosis by inducing fibrotic factors

city: SAGA

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

institute: Saga university

summary: In this study, we demonstrated that baseline SOX11 expression was significantly higher in dermal fibroblasts (DFs) isolated from patients with SSc than that in controls, and increased in response to TGF-b. We then showed that SOX11 is involved in the expression of periostin and some periostin-dependent fibrotic factors identified in lung fibroblasts previously. Moreover, we identified some fibrotic factors induced by SOX11 in DNA microarrays combining TGF-b induction and SOX11 knockdown. Finally, we showed that genetic deletion of SOX11 in Postn positive fibroblast cells protects from bleomycin (BLM)-induced skin fibrosis. Altogether, our data indicate that SOX11 and periostin forms a vicious circle and that TGF-b activates this circle specifically in SSc dermal fibroblasts.

overall_design: In order to clarify the mechanism of dermal fibrosis dependent on the SOX11/periostin pathway, we annotated the gene expression profiles of SSc dermal fibroblasts into TGF-b–dependent/independent genes and SOX11-dependent/independent genes using DNA microarray analysis

first: Kenji

last: Izuhara


title: Gene expression profile at single nucleus level of spinal cord  after treatment of hepatocyte growth factor(HGF)-releasing scaffold

city: Shinjukuku

first: Shogo

last: Hashimoto

state: Tokyo

address: 35 shinanomachi

department: Department of Orthopaedic Surgery

institute: Keio university

summary: To gain molecular insights into the ability of HGF-releasing scaffold to improve microenvironmental conditions, single-nucleus RNA-seq was conducted.

overall_design: Spinal cord tissue from the lesion epicenter was collected 49 days after spinal cord injury (7 days after implantation of scaffold)

first: Hideyuki

last: Okano

first: Narihito

last: Nagoshi

first: Aki

last: Minoda


title: Senescence rewires microenvironment sensing to facilitate anti-tumor immunity

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Senescence rewires microenvironment sensing to facilitate anti-tumor immunity (scRNA-Seq)

summary: Cellular senescence involves a stable cell cycle arrest coupled to a secretory program that, in some instances, stimulates the immune clearance of senescent cells. Using an immune competent tumor model in which senescence triggers CD8 T cell-mediated tumor rejection, we show that senescence also remodels cell surface proteome to alter how they sense environmental factors, as exemplified by Type II interferon gamma (IFN-γ). Compared to proliferating cells, senescent cells upregulate IFN-γ receptor, become hypersensitized to microenvironmental IFN-γ, and more robustly induce antigen presenting machinery -effects also recapitulated in human tumor cells treated with senescence-inducing drugs. Disruption of the IFN-γ sensing by senescent cells blunts their immune-mediated clearance without disabling their characteristic secretory program or immune cell recruitment. Our results demonstrate that senescent cells have an enhanced ability to both send and receive environmental signals, and imply that each process is required for their effective immune surveillance.

overall_design: Characterization of single-cell transcriptional profiles of immune cells (CD45+) isolated directly by FACS from p53 off and p53 On (day 8) liver tumor-bearing mice to assess the effects of p53-restoration induced senescence in tumor cells on the immune compartments. 2-3 biological replicates (independent mice) were used per experimental condition.

first: Hsuan-An

last: Chen

first: Direna

last: Alonso-Curbelo

first: Scott

middle: W

last: Lowe


title: Comprehensive transcriptome analysis of the heart in control, PAH and PAH/aKO mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: Pregnancy-associated hypertensive (PAH) mice were maintained by mating females carrying the human angiotensinogen (hAGT) gene with males expressing the human renin (hRN) gene, as previously described (Takimoto E., et al., Science, 1996). Angiotensin II (AngII) has critical roles in regulation of blood pressure. In late pregnancy of PAH mice, increased AngII causes acute and severe hypertension with proteinuria. Furthermore, PAH mice show cardiac hypertrophy, fibrosis and apoptosis. It is known that AngII downregulates mRNA of alpha 1a-adrenergic receptor (Adra1a) in neonatal rat cardiac myocytes (Li H.T., et al., Circ. Res., 1997). Interestingly, we found that Adra1a knock out PAH (PAH/aKO) mice display more severe phenotype of cardiac hypertrophy in comparison to PAH mice. In this study, to understand the molecular basis of cardiac hypertrophy via regulation of Adra1a expression with AngII in PAH mice, we performed a comprehensive analysis of gene expression changes in cardiac remodeling of PAH and PAH/aKO mice using the next-generation RNA sequencing (RNA-seq).

overall_design: mRNA profiles of mouse brain were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Chulwon

last: Kwon

first: Akiyoshi

last: Fukamizu


title: Single cell RNA-seq of human cornea organoids identifies cell fates of a developing immature cornea

status: Public on Jan 25 2023

first: Shukti

last: Chakravarti

state: NY

address: 435 E 30th Street

department: Department of Ophthalmology and Pathology, Department of Ophthalmology

institute: NYU Grossman School of Medicine

summary: The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly.  Here we elucidated the transcriptomic cell fate map of 4-month-old human cornea organoids and human donor corneas. The organoids harbor cell clusters that resemble cells of the corneal epithelium, stroma and endothelium with sub-populations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids contain large proportions of epithelial and endothelial-like cells. These corneal organoids offer a three-dimensional model to study corneal diseases and integrated responses of different cell types.

overall_design: scRNAseq profiling of human cornea organoids and human donor corneas.

first: George

last: Maiti

first: Maithê

last: Rocha Monteiro de Barros

first: Igor

last: Dolgalev

first: Mona

last: Roshan

first: James

last: Foster

first: Aristotelis

last: Tsirigos

first: Karl

last: Wahlin


title: Histone variant H3.3 facilitates open chromatin at promoters.

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center


title: piR-36249 and DHX36 together inhibit testicular cancer cell progression by upregulating OAS2

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: PIWI-interacting RNAs (piRNAs) have been identified in mammalian germline initially and later also found to be aberrantly expressed in various cancers. However, their functions in cancer is not very clear. Here, we studied the role of piR-36249, a member of the piRNA family, in testicular cancer. We show that piR-36249 is significantly downregulated in testicular cancer tissues comparing to tumor-adjacent tissues. Functional studies demonstrate that piR-36249 inhibits testicular cancer cell proliferation, migration and invasion. Mass Spectrometry (MS) analysis of piR-36249 pull-downed proteins reveals that piR-36249 interacts with ATP-dependent DNA/RNA helicase (DHX36). Dual-luciferase assays shows that piR-36249 binds to the 3'UTR of 2'-5'-oligoadenylate synthetase 2 (OAS2) mRNA. OAS2 has been shown in literature as a tumor suppressor modulating the occurrence and development of some tumors, such as colorectal cancer and breast cancer. In this study, OAS2 knockdown also promotes testicular cancer cell proliferation and migration. Furthermore, RNA immunoprecipitation assay reveals that DHX36 can also bind to OAS2 mRNA, and knockdown of DHX36 increases OAS2 mRNA yet downregulates its protein, indicating the enhancing OAS2 protein expression level effect of DHX36. All these data suggest that piR-36249, together with DHX36, functions in inhibiting testicular cancer cells proliferation, migration and invasion by upregulating OAS2 protein, and piR-36249 may serve as a potential predictor for the prognosis of testicular cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for piR-36249 KD and its control in NT-2 cells

first: Qianqian

last: Wang

first: Peize

first: Xiaorong

first: Yueming

last: Wu

first: Kaiguo

last: Xia

first: Xiangyu

last: Mu

first: Qiang

last: Xuan

first: Jun

last: Xiao

first: Yaohui

last: He

first: Wen

last: Liu

first: Xiaoyuan

last: Song

first: Fei

last: Sun


title: Histone variant H3.3 facilitates open chromatin at promoters [ChIP-seq]

summary: We analyze the contribution of H3.3 to chromatin accessibility, post-translational modification states, and transcription in mouse embryonic stem cells (mESC).

overall_design:
Crosslinking ChIP analysis of Brd4 in mouse embryonic stem cell lines (H33WT and H33KO). All inputs sequenced.
Native ChIP of H3K4me3 in mouse embryonic stem cell lines (H33WT and H33KO).

first: Amanuel

last: Tafessu


title: A single-cell transcriptomic atlas of fruitless-expressing neurons in the Drosophila pupal central nervous system

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

summary: To examine the repertoires of genes expressed in individual fru P1-expressing neurons, we performed single cell sequencing. The analysis was performed on male and female central nervous system tissues (48-hour pupal stage), from flies that expressed membrane-bound GFP in fru P1 neurons. We chose this developmental stage to gain further insight into how genes direct development of fru P1 neurons, as this is the stage where FruM has peak expression (in ~2,000 neurons).

overall_design: scRNA-seq using 10x Genomics CHROMIUM Single Cell 3’ Solution V3 Chemistry of 48hr after puparium formation (APF) fru P1-expressing cells from the male and female Drosophila Central Nervous System (CNS).

first: Colleen

last: Palmateer


title: Genome binding/occupancy profiling of HIF and AHR in RCC4 cells under co-activating conditions

status: Public on Jan 24 2023

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

summary: ChIP-seq analysis of HIF-1, HIF-2 and AHR DNA binding under single and combined activating conditions

overall_design: ChIP-seq analysis of HIF-1α, HIF-2α, HIF-1β and AHR DNA binding in RCC4/VHL and RCC4/VA cells under various single and combined stimuli: normoxia, hypoxia (0.5% oxygen, 6h), DMSO (0.1%, 0.5h), ITE (100nM, 0.5h) and/or FICZ (10nM, 0.5h) treatments. 2 replicates per condition.

first: Véronique

last: Lafleur

first: Silvia

last: Halim

middle: R


title: Short Chain Fatty Acid Independent Hepatic Histone Acetylation Patterns, Induced by Microbiota Exposure, are Irreversible

city: Philadelphia

first: Gary

middle: D

state: PA

address: 915 Biomedical Research Building, 421 Curie Blvd

department: Department of Medicine, Division of Gastroenterology

institute: University of Pennsylvania

summary: Germ-free mice are an indispensable tool in studying the gut microbiome and its effects on host physiology, though they are phenotypically different than their conventional counterparts. While antibiotic mediated microbiota depletion in conventional mice mimics the germ-free state, the scope of these reversible changes is unknown. We demonstrate robust hepatic transcriptomic alterations after antibiotic-mediated microbiota depletion together with depletion of luminal and portal vein levels of SCFAs though hepatic histone acetylation states remained largely unchanged.

overall_design: Liver RNA from mice treated with non-absorbable antibiotics to deplete gut microbiota were was analyzed by RNAseq (N=4-5/group). To assess the differential gene expression between conventional and microbiota depleted mice, we performed RNAseq.

first: Yedidya

last: Saiman

first: Peder

last: Lund

first: Victoria

middle: M

last: Gershuni

first: Cholsoon

last: Jang

first: Emma

last: Furth

first: Elliot

last: Friedman

first: Lillian

last: Chau

first: Joshua

last: Rabinowitz

first: Benjamin

last: Garcia


title: RCC4/VHL cells under HIF and AHR co-activating conditions

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

overall_design: Refer to individual Series


title: PolyA RNA sequencing of gastrocnemius and soleus muscles of WT and LSD1-mKO mice under dexamethasone administration

city: Kumamoto

first: Hirotaka

last: Araki

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: To understand the role of LSD1 in transcriptional regulation in muscle under glucocorticoid stress, RNA-seq analyses of gastrocnemius and soleus muscles of  skeletal muscle-specific LSD1 KO mice (LSD1-mKO mice) and WT mice after dexamethasone were carried out. We found that LSD1 inhibition led to increased expression of muscle atrophy associated genes and slow fiber genes in gastrocnemius muscle but not in soleus muscle.

overall_design: Dexamethasone was administerd to LSD1-mKO and WT mice.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: polyA RNA-seq of WT and LSD1-mKO mice under two different environmental stresses

status: Public on Jan 23 2023


title: Expression profiling in RCC4/VHL cells under HIF and AHR co-activating conditions

summary: Pan-genomic analysis of poly-adenylated transcript levels under HIF and AHR single and combined activating conditions

overall_design: PolyA RNA-seq analysis of gene expression in RCC4/VHL cells under various single and combined stimuli: normoxia, hypoxia (0.5% oxygen, 6h), DMSO (0.1%, 6h) or ITE (100nM, 6h) treatments. 6 replicates per condition.


title: Single cell sequencing reveals sex bias in autism associated cells and genes

city: Kaifeng

first: Yijie

last: Zhang

address: Jinming Avenue

institute: Henan University

summary: Here we performed single-cell RNA sequencing to examine the transcriptomes of over 45,000 cells isolated from the hippocampus of an autistic mouse model. Each cell was assigned to one of twelve major cell types based on distinct expression profiles. Differential expression analysis identified cell type specific genes with altered expression after prenatal valproic acid exposure. The largest number of differentially expressed genes was detected in neurons, choroid plexus epithelial cells, and microglia. In microglia, there were more male-specific than female-specific inflammation-related pathways that were important to induce autistic-like behavior. Meanwhile, there were several X-linked genes among the male-specific DEGs of neurons, and the changes of those genes after prenatal VPA exposure may be another key reason why more male than female ASD patients are seen in clinic.

overall_design: Examination of 4 control and 4 prenatally VPA exposed mice hippocampi samples

first: Ruixue

last: Xia

first: Yongjie

last: Wang

first: Qian


title: Characterization of the minimal residual disease state reveals distinct evlutionary trajectories of human glioblastoma [single-cell RNA-seq]

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: Recurrence of solid tumors renders patients vulnerable to a distinctly advanced, highly treatment-refractory disease state that has an increased mutational burden and novel oncogenic drivers not detected at initial diagnosis. Improving outcomes for recurrent cancers requires a better understanding of cancer cell populations that expand from the post-therapy, minimal residual disease (MRD) state. We profiled barcoded tumor cell populations through therapy at tumor initiation/engraftment, MRD and recurrence in our therapy-adapted, patient-derived xenograft models of glioblastoma (GBM). Tumors showed distinct patterns of recurrence in which clonal populations exhibited either an a priori, pre-existing fitness advantage, or a priori equipotency fitness acquired through therapy. Characterization of the MRD state by single-cell and bulk RNA sequencing revealed a tumor-intrinsic immunomodulatory signature with strong prognostic significance at the transcriptomic level and in proteomic analysis of cerebrospinal fluid (CSF) collected from GBM patients at all stages of disease. Our results provide insight into the innate and therapy-driven dynamics of human GBM, and the prognostic value of interrogating the MRD state in solid cancers.

overall_design: Assessing clonal distribution patterns in human GBM specimens through treatment using cellular DNA barcoding

first: Maleeha

last: Qazi

first: Sabra

middle: K

last: Salim

first: Kevin

last: Brown

first: Nicholas

last: Mikolajewicz

first: Neil

last: Savage

first: Hong

last: Han

first: Minomi

last: Subapanditha

first: David

last: Bakhshinyan

first: Allison

last: Nixon

first: Parvez

last: Vora

first: Kimberly

last: Desmond

first: Chirayu

last: Chokshi

first: Mohini

first: Amanda

last: Khoo

first: Andrew

last: Macklin

first: Shahbaz

last: Khan

first: Nazanin

last: Tatari

last: Winegarden

first: Laura

last: Richards

first: Trevor

last: Pugh

last: Bock

first: Alireza

last: Mansouri

first: Chitra

last: Venugopal

first: Thomas

last: Kislinger

first: Sidartha

last: Goyal

first: Jason

last: Moffat


title: Characterization of the minimal residual disease state reveals distinct evlutionary trajectories of human glioblastoma [Bulk RNA-seq]

first: Sheila

last: Singh

overall_design: Cell lines were engrafted intracranially in NSG mice, and treated with an adapted standard-of-care protocol (TR) or control (CON) until tumors regressed.  Tumors from control mice were harvested when there was no radiographic evidence of disease in treated mice, and profiled by RNA sequencing.

first: Maleeha

last: Qazi

first: Sabra

last: Salim

first: Kevin

last: Brown

first: Nicholas

last: Mikolajewicz

first: Neil

last: Savage

first: Hong

last: Han

first: Minomi

last: Subapanditha

first: David

last: Bakhshinyan

last: Nixon

first: Sidhartha


title: Characterization of the minimal residual disease state reveals distinct evlutionary trajectories of human glioblastoma


title: Direct correction of haemoglobin E / beta-thalassaemia using base editors

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, Oxford University

summary: Haemoglobin E (HbE)/β-thalassaemia causes approximately 50% of all severe thalassaemia worldwide; equating to around 30,000 births per year. HbE/β-thalassaemia is due to a point mutation in codon 26 of the human HBB gene on one allele (GAG; glutamate → GAA; lysine, E26K), and any mutation causing severe β-thalassaemia on the other. When inherited together in compound heterozygosity these mutations can cause a severe thalassaemic phenotype. However, if only one allele is mutated individuals are carriers for the respective mutation and have an asymptomatic phenotype (β-thalassaemia trait). Here we describe a base editing strategy which corrects the HbE mutation either to wildtype (WT) or a normal variant haemoglobin (E26G) known as Hb Aubenas and thereby recreates the asymptomatic trait phenotype. We have achieved editing efficiencies in excess of 85% in primary human CD34+ cells. We demonstrate editing of long-term repopulating haematopoietic stem cells (LT-HSCs) using serial xenotransplantation in NSG mice. We have profiled the off-target effects using a combination of CIRCLE-seq and deep targeted capture and have developed machine-learning based methods to predict functional effects of candidate off-target mutations.

first: Mohsin

last: Badat

first: Peng

last: Hua


title: Characterization of the minimal residual disease state reveals distinct evlutionary trajectories of human glioblastoma [DNA barcoding]

middle: A

first: Allison

first: Parvez

last: Vora

first: Kimberly

last: Desmond

first: Chirayu

last: Chokshi

first: Mohini

first: Amanda

last: Khoo

first: Andrew

last: Macklin

first: Shahbaz

last: Khan

first: Nazanin

last: Tatari

last: Winegarden

first: Laura

last: Richards

first: Trevor

last: Pugh

last: Bock

first: Alireza

last: Mansouri

first: Chitra

last: Venugopal


title: Gene expression profile at single cell level of tumor infiltrating myeloid antigen presenting cells from tonsillar cancer patients

status: Public on Jan 19 2023

city: Lund

first: David

last: Gomez Jimenez

state: Skane

address: Scheelevägen 2

department: Immunotechnology

country: Sweden

institute: Lund University

summary: Myeloid antigen presenting cells are a heterogeneous population, and their identity is greatly influenced by niche specific cues. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of myeloid antigen presenting cells in tonsillar cancer tissue and paired contralateral healthy tissue.

overall_design: Myeloid antigen presenting cells from tonsillar cancer patients were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of CD13 and HLA-DR and analyzed using scRNAseq.

middle: G

last: Jimenez

first: Malin

last: Lindstedt


title: Differential gene expression profile between WT and FAM21 cKO bone marrow derived dendritic cells (BMDC).

city: Taipei

first: Wen

last: Chang

address: 128 Sec 2 Academia Rd, Nankang

institute: Institute of Molecular Biology, Academia Sinica

summary: We isolated and cultured BMDC from WT and FAM21 cKO mice and analyzed transcriptional profiling of the cellular genes between WT and FAM21 cKO mice.

overall_design: Differential gene expression profile between WT and FAM21 cKO BMDC,  Biological replicates: 3 replicates per genotype.

first: RAKESH

last: KULKARNI

first: WEN

last: CHANG


title: Chronic lymphocytic leukemia skews antigen-specific CD8 T cells leading to dysfunctional memory response

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

summary: In a murine, adoptive transfer model of chronic lymphocytic leukemia we injected OT-I cells followed by infection with mCMV-OVA. On day 7 post-infection, OT-I cells from the spleen were FACS sorted and studied with ATAC sequencing and RNA sequencing. In additition to flow cytometry data demonstrating a skewing towards short-lived effector cells and a lower proportion of memory-precursor cells of OT-I cells from CLL mice compared to  WT, we also found effector and memory genes epigenetically and transcriptionally altered.

overall_design: Splenic OT-I cells from CLL mice vs splenic OT-I cells from WT mice on day 7 post-infection

middle: S

first: Anne

last: Martens

first: Arnon

middle: P

last: Kater


title: Comparative transcriptomics reveal highly conserved regional programs between porcine and human colonic enteric nervous system

status: Public on Jan 22 2023

city: Los Angeles

first: Tao

last: Li

state: California

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary: The enteric nerve system (ENS) coordinates diverse gastrointestinal functions. The porcine gastrointestinal tract is increasingly regarded as a useful translational model. However, porcine ENS molecular profiling and its similarity to that of human are lacking. Bulk RNA sequencing (RNA-seq) coupled with laser-capture microdissection and single-cell RNA-seq on myenteric ganglia (MG) addressed that discrepant transcriptional programs explained the functional characteristics between inner submucosal and/or MG in porcine proximal or/and distal colon (p-pC, p-dC). Comparative bulk transcriptomics of MG in corresponding colonic regions of porcine and human revealed highly conserved programs existing in p-pC and p-dC, which interpreted >90% of their transcriptomic responses to vagal nerve stimulation (VNS), suggesting that p-pC and p-dC could serve as predictors in translational studies. At bulk and single-cell resolution, we highlighted specific conserved programs, executing inflammatory modulation in porcine with VNS. This study offers rich foundations to understand human colonic functions and neuromodulation using porcine model.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: The colonic specimens with full thickness from three castrated male and three intact female naïve Yucatan minipigs and three castrated male Yucatan minipigs undergoing vagal nerve stimulation (VNS) were removed from the proximal colon (p-pC) and distal colon (p-dC). The full thickness of colonic specimens were dissected from healthy margin of the post-operative ascending and descending colon (h-aC, h-dC, 4 of each) from 12 patients (4 males and 8 females) with colonic adenocarcinoma. A range of 25-40 ganglia/subject were harvested from inner submucosal ganglia (ISG) and myenteric ganglia (MG) respectively of p-pC and p-dC and from MG of h-aC and h-dC using LMD-6000 Laser Micro-dissection System. Total 46 samples were sequenced on an Illumina HiSeq 3000 sequencer. In addition, the muscularis externa containing myenteric ganglia from each p-pC and p-dC of 4 naïve porcine (2 of each sex) were processed for cell suspension preparation, which were loaded on the 10x Genomics Chromium platform and sequenced on an Illumina NextSeq 500 Sequencer.

first: Pu-Qing

last: Yuan


title: Pollen tube emergence is mediated by ovary-expressed ALCATRAZ in cucumber

status: Public on Jan 20 2023

city: Beijing

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

summary: Cucumber is an important vegetable crop worldwide, which is mainly propagated by seed. The successful occurrence of double fertilization is the premise of seed production in angiosperms. Cucumber ALC homolog (CsALC) displayed a novel and positive function in pollen tube emergence process, and regulated female fertility by promoting CsRALF4/19 function during pollen tube guidance in cucumber.

overall_design: Ovaries of wild type and Csalc mutant at 32 h after pollination were collected for RNA-seq analysis. Three biological replicates were performed.

first: Zhihua

last: Cheng

first: Xiaofeng

last: Liu

first: Shuangshuang

last: Yan

first: Bin

first: Yanting

last: Zhong

first: Weiyuan

last: Song

first: Jiacai

last: Chen

first: Zhongyi

last: Wang

first: Gen

last: Che

first: Liu

first: Ao

last: Ying

first: Hanli

last: Lv

first: Lijie

last: Han

first: Min

first: Jianyu

last: Zhao

first: Junqiang

last: Xu

first: Zhengan

last: Yang

first: Zhaoyang

last: Zhou

first: Xiaolan

last: Zhang


title: RNA-Sequencing of young and aged satellite cells before and after transplantation into the young niche

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

institute: McGill University

summary: The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. Using an in vivo allogeneic stem cell transplantation model, we show that exposure of MuSCs from old mice to a youthful niche environment significantly restores the gene expression of genes that are altered in aging. We show that age-related changes in the MuSC transcriptome are mainly driven by alterations in chromatin and transcription but are not due to posttranscriptional mechanisms affecting RNA stability. Furthermore, our data indicates that the portion of the genome that is activated in aging is significantly more responsive to restoration by niche factors compared to the repressed counterpart. Taken together, our data reveals that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs.

overall_design: Satellite cells were isolated by Fluorescence-Activated Cell Sorting (FACS) from either young or aged Pax7-eGFP mice. 10 000-20 000 of these freshly-sorted cells were subsequently injected into the TA muscle of young NCG (NOD-Prkdcem26Cd52Il2rgem26Cd22/NjuCrl) immunocompromised mice that had their hindlimb irradiated 24 hours prior to injection. 21 days post-engraftment, donor satellite cells were re-isolated by FACS. RNA-Seq libraries were created from young or aged cells at T0 (before transplantation) and at T21 (after transplantation into young NCG mice) using SMART-Seq HT for conversion into cDNA followed by Nextera XT for the addition of Illumina sequencing adapters.

first: Hamed

last: Najafabadi


title: Transcriptional profiling of hepatic macrophages isolated from mice with high-fat diet -induced non-alcoholic fatty liver disease

status: Public on Jan 17 2023

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

summary:
Purpose: The goals of this study were to identify preferential gene expression signatures that are unique to hepatic macrophages in high-fat diet -induced non-alcoholic fatty liver disease.
Methods and results: Wild-type and Casp11-/- mice were treated with high fat and normal chow diet for a period of 12 weeks. Hepatic macrophages from liver were isolated to generate mRNA transcription.
Conclusion: Our study represents detailed analysis of caspase-11 in regulating hepatic macrophages in high-fat diet -induced non-alcoholic fatty liver disease.

overall_design: Hepatic macrophages from Wild-type and Casp11-/- mice with high-fat diet -induced non-alcoholic fatty liver disease.

first: Xiaofeng

first: Fatma

last: Saaoud


title: T follicular helper 17 (Tfh17) cells are superior for immunological memory maintenance

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

department: Immunology

institute: The Australian National University

summary: A defining feature of successful vaccination is the ability to induce long-lived antigen-specific memory cells. T follicular helper (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+ memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) mouse cells in vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended resting in vivo to mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+ central memory Tfh cells with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.

overall_design: Naïve, TCM, TEM, TfhCM, TfhEM CD4 subsets were FACS purified from 2 healthy blood donors to perform total RNA extraction and RNA-Seq

first: Kaiming

last: Luo

first: Diya

first: Yunbo

last: Wei

first: Yin

last: Yao

first: Jun

last: Deng

first: Yang

first: Qunxiong

last: Zeng

first: Xiaoru

last: Dong

first: Le

last: Xiong

first: Dongcheng

last: Gong

first: Lin

last: Lin

first: Kai

last: Pohl

first: Shaoling

last: Liu

first: Yu

first: Lu

first: Thi HO

last: Nguyen

first: Lilith

middle: F

last: Allen

first: Katherine

last: Kedzierska

first: Yanliang

last: Jin

first: Mei-Rong

last: Du

first: Wanping

first: Liangjing

last: Lu

last: Shen

first: Zheng

first: Ian

last: Cockburn

first: Wenjing

first: Di

last: Yu


title: PolyA RNA sequencing of soleus muscles of WT and LSD1-mKO mice after voluntary wheel running

first: Hirotaka

last: Araki

summary: To understand the role of LSD1 in transcriptional regulation in muscle under voluntary wheel running (VWR) training, RNA-seq analyses of soleus muscles of  skeletal muscle-specific LSD1 KO mice (LSD1-mKO mice) and WT mice after VWR were carried out. We found that loss of LSD1 led to increased expression of oxidative metabolism genes in soleus muscle.

overall_design: LSD1-mKO and WT mice were trained by voluntary wheel running.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: TCDD-mediated multigenerational effects in mice

status: Public on Jan 18 2023

city: Columbia

first: Narendra

last: Singh

state: South Carolina

address: 6439 Garners Ferry Road,

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina

summary: TCDD exposure cauuses multigenerational effect in mice.

overall_design: Pregnanat (GD14) mice (C57BL6) were exposed to 10 µg/kg body weight and thymic cells of three generations were processes for microRNA analysis.

first: Xiaoming

last: Yang

first: Marpe

last: Bam

first: Mitzi

last: Nagarkatti

first: Prakash


title: Zebrafish her3 knockout impacts developmental and cancer-related gene signatures

status: Public on Jan 16 2023

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

summary: HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3’s role in neurogenesis. To further investigate how HES3 functions during development, we generated a zebrafish CRISPR/Cas9 knockout of her3, the zebrafish ortholog of HES3. Zebrafish her3 mutants are not embryonic lethal and as adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants are significantly smaller than wildtype and present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 knockout embryos are enriched for HOX and sox10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts.

overall_design: 6 different conditions were analyzed, each with 3 biological replicates, from zebrafish (Danio rerio). Each sample was a pool of 20-25 embryos at either 24 hour post-fertilization (hpf) or 72hpf. Wildtype WIK zebrafish were used as a control at both 24hpf and 72hpf. Wildtype WIK embryos were used for the her3-morpholino (MO) and mismatch(mm)-MO injections. Morpholino injections were only analyzed at 24hpf. mm-MO injected samples were used as an additional control for her3-MO injected samples. her3-knockout (her3_38aa samples) were analyzed at both 24hpf and 72hpf.

first: Matthew

last: Kent

first: Delia

last: Calderon

first: Katherine

last: Silvius

first: Jack

last: Kucinski

first: Collette

last: LaVigne

middle: V

last: Cannon

middle: C


title: Single-cell RNA-Sequencing of young and aged satellite cells, macrophages and fibro-adipogenic progenitor cells

first: Vahab

last: Soleimani

overall_design: An aimed total of 2500 cells per mouse, composed of satellite cells, fibro-adipogenic progenitor cells and macrophages were isolated from 3 young and 4 aged male C57BL/6J mice by Fluorescence-Activated Cell Sorting. They were then processed for single-cell RNA-Sequencing using Chromium Single Cell 3' Reagent Kits (v3 Chemistry) using 10x genomics technology.

first: Hamed

last: Najafabadi


title: Characterisation of VDR signaling in prostate cancer health disparities

status: Public on Jan 21 2023

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

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

overall_design: Refer to individual Series


title: INFLAMMATION OF THE RETINAL PIGMENT EPITHELIUM DRIVES EARLY-ONSET PHOTORECEPTOR DEGENERATION IN MERTK-ASSOCIATED RETINITIS PIGMENTOSA

city: New Haven

first: Maria

middle: Elisa

last: Mercau

address: 300 Cedar st

department: Immunobiology

institute: Yale University

summary: Severe, early-onset photoreceptor (PR) degeneration associated with MERTK mutations is thought to result from failed phagocytosis by retinal pigment epithelium (RPE). Notwithstanding, the severity and onset of PR degeneration in mouse models of Mertk ablation is determined by the hypomorphic expression or the loss of the Mertk paralog Tyro3. Here we find that loss of Mertk and reduced expression/loss of Tyro3 led to RPE inflammation, even before eye-opening. Incipient RPE inflammation cascaded to involve microglia activation and PR degeneration with monocyte infiltration. Inhibition of RPE inflammation with the JAK1/2 inhibitor ruxolitinib mitigated PR degeneration in Mertk -/- mice. Neither inflammation nor severe, early-onset PR degeneration were observed in mice with defective phagocytosis alone. Thus, inflammation drives severe, early-onset PR degeneration-associated with Mertk loss of function.

overall_design: (C57BL/6, Tyro3-/-V1 and Mertk-/-V2Tyro3-/-V2 ) and (WT129 and Itgb5-/-) RPE were collected at post-natal day 25 (1 hour after light onset) and processed for RNA sequencing

middle: E

first: Yemsratch

middle: T

last: Akalu

first: S

last: Finnemann

first: C

last: Rothlin

last: Ghosh


title: Unravelling HRDness and therapeutic opportunities in soft tissue and bone sarcoma

city: Zurich

first: Alicia

last: Pliego Mendieta

address: Schmelzbergstrasse 12

institute: University Hospital Zurich

summary: Genomic instability is a hallmark of many cancers. Aberrant proliferation in cancer cells leads to the accumulation of alterations in genes that belong to the homologous recombination (HR) DNA double-strand break (DSB) repair pathway. Deficiency in HR-mediated repair (HRR) exacerbates genomic instability and correlates with poor prognosis and development of metastases. Determining HRR deficiency (HRD) in a given tumour is of major clinical relevance as it is associated with therapeutic vulnerabilities. HRD has been widely investigated in certain tumor types such as ovarian and breast cancer but remains greatly unexplored in sarcoma, a rare and heterogeneous group of mesenchymal cancer. Here, we show that specific sarcoma entities are characterized by high levels of genomic instability signatures and a wide range of molecular alterations in HRR genes, while exhibiting a complex pattern of chromosomal instability features. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signatures that predicts PARP inhibitor sensitivity in patient-derived ex vivo sarcoma models. Concomitantly, HRDhigh sarcoma cell models lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HR-mediated DNA repair. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness traits and demonstrate clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways in patient-derived ex vivo cell models and in a leiomyosarcoma patient. In summary, we provide the most comprehensive analysis of HRDness in sarcoma to date and support a bench-to-bedside personalized oncological approach to successfully treat sarcoma patients.

overall_design: RNA from patient-derived sarcoma cell models was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega AS1340). The extracted RNA was quantified with a Nanodrop (ThermoFisher Scientific) and the High Sensitivity RNA ScreenTape Assay for TapeStation systems (Agilent 5067). RNA-sequencing libraries were prepared using the Illumina Stranded mRNA sample preparation protocol following the manufacturer’s instructions. Each library was sequenced in paired-end mode using the NovaSeq 6000 platform and resulting reads were mapped to the human transcriptome.  Differential gene expression between HRDhigh and HRDlow sarcoma samples from the TCGA cohort was investigated by downstream processing of raw counts using the R package DESeq2 26.

last: Pliego-Mendieta

first: Lara

last: Planas-Paz


title: Effects of FOXP3Δ2Δ7 exogenous expression on gene expression in a non-tumorigenic keratinocyte model

city: Guadalajara

first: Natalia

last: García

state: Jalisco

address: Sierra Mojada 800

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

summary: Cervical cancer (CC) is the fourth most common type of cancer among women. FOXP3, a critical transcription factor involved in the biology of regulatory T cells, has been detected as highly expressed in the tumor cells of CC patients. However, its biological role in CC, particularly in the keratinocytes, remained unclarified. Therefore, this work aimed to uncover the effects of FOXP3 on the biology of the tumoral cells. For this purpose, a model with constitutively expression of FOXP3Δ2Δ7was established to evaluate its role in proliferation, migration, and cell division. As well, RNAseq was performed to identify differentially expressed genes and enriched pathways modulated by FOXP3Δ2. The exogenous expression of FOXP3Δ2Δ7 promotes cell division, proliferation, and migration. The transcriptomic analyses highlight the upregulation of multiple genes with protumor activities. Moreover, immunological and oncogenic pathways were detected as highly enriched. These data support that FOXP3Δ2Δ7 in epithelial cells induces cancer-related hallmarks and provides information about the molecular events triggered by this isoform, which could be important for developing CC.

overall_design: Total RNA extraction was performed by duplicate from cell models obtained from HaCaT transduced with viral particles containing the FOXP3Δ2Δ7 gene, HaCaT cells transduced with the empty vector were used as controls. RNA-seq was performed to obtain the differentially expressed genes and the enriched pathways modulated by FOXP3Δ2Δ7. Next-generation RNA sequencing with Nova Seq 6000 Illumina platform was conducted by Novogen Bioinformatics Technology Co., Ltd (Beijing, China); independent sample duplicates of total RNA from HaCaT-LVX and HaCaT-FOXP3Δ2Δ7 were sent preserved in RNAstable (Cat. No. 93221-001, Biomatrica, San Diego, CA).  Retrieved data was analyzed in both open-source platforms, RStudio (Version 1.4.1717) and Galaxy (Version 22.05.1) (https://www.usegalaxy.org).  The sequencing quality of the returned data (FASTQ archives) was analyzed with FASTQC (Version 0.11.9). Subsequently, alignment to the Homo sapiens genome (Version 42) (GRCh38.p13) was performed with Subjunc aligner (Version 2.0.0) from the Rsubread package (Version 3.14). Afterwards, BAM files were processed with featureCounts (Version 2.0.1). Normalization of reads counts as FPKM (Frag-ments per Kilobase of exon per Million Mapped Fragments) was achieved using DESeq2 tool (Version 1.36.0).

first: L

last: Jave-Suarez

first: A

last: Aguilar-Lemarroy

first: N

last: Garcia-Becerra


title: The Aryl Hydrocarbon Receptor Repressor Prevents Oxidative Stress and Ferroptosis of Intestinal Intraepithelial Lymphocytes

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

summary: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that buoys intestinal immune responses. AHR induces its own negative regulator, the AHR repressor (AHRR). Here we show that AHRR is vital to sustain intestinal intraepithelial lymphocytes (IEL). Fewer IEL of all types were present in the absence of AHRR. Single cell RNA sequencing (scRNAseq) revealed an oxidative cell stress profile in Ahrr–/– IEL. Ahrr deficiency unleashed AHR-induced expression of CYP1A1, an oxidative enzyme that generates reactive oxygen species; this resulted in elevated intracellular content of reactive oxygen species, lipid peroxidation and ferroptosis in Ahrr–/– IEL. Dietary supplementation with selenium or Vitamin-E (Vit-E) to restore redox homeostasis rescued Ahrr–/– IEL. Loss of IEL in Ahrr deficient mice caused susceptibility to Clostridium difficile infection and dextran sodium sulfate-induced colitis. We conclude that AHR signaling must be tightly regulated to prevent oxidative stress and ferroptosis of IEL to preserve intestinal immune responses.

overall_design: CD3+ small intestinal IEL were sorted from two Ahrr KO mice and two WT littermate controls.

first: Santosh

last: Panda

first: Marco

last: Colonna


title: Global transcriptome and targeted metabolite analyses of roots reveal different defense mechanisms against Ralstonia solanacearum infection in two resistant potato cultivars

city: Gödöllő

first: Zsófia

last: Bánfalvi

address: Szent-Györgyi Albert u. 4.

department: Genetics and Biotechnology Institute

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: The causal agent of bacterial wilt is Ralstonia solanacearum (Rs) with an unusually wide host range including potato. Bacterial wilt is the most destructive bacterial disease of plants that seriously reduce crop yield word-wide. Control of Rs through resistance breeding and biotechnology is considered to be very important and necessary. Rs resistance has been reported in a few potato cultivars and hybrids. Identification of defense mechanism underlying resistance is a prerequisite of biotechnological approaches. In this study, two resistant cultivars, ‘Calalo Gaspar’ (CG) and ‘Cruza 148’ (CR), and a sensitive cultivar, ‘Désirée’, were analysed and compared to each other at molecular level before-, and a few days after Rs infection. The transcriptome analysis of roots revealed up-regulation of chitin interaction and cell wall related genes in CR and DES. The phenylpropanoid biosynthesis and glutathione metabolism pathways were induced only CR. Microscopic analysis detected lignification over the whole stele in CR roots. In CG roots, concentrations of chlorogenic acid and quercetin derivatives were highly increased upon Rs infection. A characteristic increase at the transcript level of MAP kinase signalling pathway genes and concentrations of jasmonic-, salicylic-, abscisic and indoleacetic acid was detected in DES roots. These results indicate a different mechanism of defence both in the two tested resistant and the sensitive potato cultivar.

overall_design: RNA-seq of Ralstonia solanacearum (Rs) infected and control plants of 2 Rs resistant and 1 Rs sensitive cultivar

first: Jeny

last: Jose

first: Csaba

last: Éva

first: Zoltán

last: Bozsó

first: Áron

middle: H

last: Kamirán

last: Fekete

first: Attila

last: Fábián

first: László

last: Sági


title: Bacterial lifestyle switch in response to algal metabolites

city: Rehovot

first: Noa

last: Barak-Gavish

address: POB 26

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly understood that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during interactions with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. The interaction displays two distinct phases: first, there is a coexisting phase in which the alga grows exponentially and the bacterium grows as well. The interaction shifts to pathogenic when the virulence of Sulfitobacter D7 towards E. huxleyi is invoked upon exposure to high concentrations of algal dimethylsulfoniopropionate (DMSP), which occurs when the algae reach stationary growth or when DMSP is applied exogenously to algae in exponential growth. We aimed to unravel the response of Sulfitobacter D7 to the pathogenicity-inducing compound, DMSP, and to different algae-derived infochemicals that affect the lifestyle of the bacterium. We grew Sulfitobacter D7 in conditioned media (CM) derived from algal cultures at the different growth phases, exponential and stationary (Exp-CM and Stat-CM, respectively), in which DMSP concentration is low and high, respectively. This enabled us to separate between different phases of the interaction with E. huxleyi, i.e., Exp-CM representing the coexisting phase, and Stat-CM representing the pathogenic phase. An additional pathogenicity-inducing treatment was Exp-CM supplemented with 100 µM DMSP (herein Exp-CM+DMSP). This condition mimicked co-cultures to which we added DMSP exogenously and thus induced Sulfitobacter D7 pathogenicity, which lead to death of exponentially growing E. huxleyi. In order to identify bacterial genes that are specifically responsive to DMSP, and are not affected by other algae-derived factors, we grew Sulfitobacter D7 in defined minimal medium (MM), lacking algal metabolites, supplemented with 100 µM DMSP (herein MM+DMSP), and examined the transcriptional response. After 24 h of Sulfitobacter D7 growth in all 5 media, triplicates were taken for transcriptomic analysis. Altogether, this experimental design allowed to expand our understanding on the bacterial response to DMSP, algal infochemicals and which of these are essential for coexistence and pathogenicity.

overall_design: Total of 15 samples were analyzed, which include triplicates of the 5 following treatments: Exp-CM, Exp-CM+DMSP, Stat-CM, MM, MM+DMSP.

first: Bareket

last: Dassa

first: Constanze

last: Kuhlisch

first: Inbal

last: Nussbaum

first: Gili

last: Rosenberg

first: Roi

last: Avraham

first: Assaf

last: Vardi


title: Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Human]

status: Public on Jan 15 2023

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Most pre-messenger RNA (pre-mRNA) undergo extensive processing to create distinct transcripts from the same gene. One of these processes, alternative polyadenylation, involves over twenty proteins to bind and cleave the pre-mRNA at poly(A) sites that can lie within the 3' UTR, introns, or exons; this can modulate protein function, but the effect of choosing a site internal to the gene vs. within the 3' UTR remains unclear. Here we show that reduced expression of CPSF6, one of the proteins involved in site selection, derails development in both humans and zebrafish by causing a bidirectional shift in poly(A) site usage. CPSF6 insufficiency favors the use of intronic poly(A) sites in neuronal genes, reducing mRNA and protein abundance, but promotes 3' UTR site usage in cardiovascular and skeletal genes, upregulating mRNA and protein.These data thus provide a long-sought link between APA and gene expression and shows that poly(A) site selection influences development.

overall_design: Comparative analysis of alternative polyadenylation using polyA-click seq (PAC-seq) on CPSF6 patient derived fibroblasts carrying CPSF6 heterozygous deletion  or CPSF6 de novo missense mutation (D535V), compared to fibrobrasts from healthy donors (ATCC CRL-2097, CRL-2091, CRL-2076)

first: Nicola

last: de Prisco

first: Vincenzo

last: Gennarino

first: Hari

last: Yamalanchili

first: Eric

middle: J

last: Wagner

first: Nathan

last: Elrod

first: Kai-Lieh

last: Huang

first: Ai

last: Lin

first: Ping

last: Ji


title: Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression [Zebrafish]

summary: Most pre-messenger RNA (pre-mRNA) undergo extensive processing to create distinct transcripts from the same gene. One of these processes, alternative polyadenylation, involves over twenty proteins to bind and cleave the pre-mRNA at poly(A) sites that can lie within the 3' UTR, introns, or exons; this can modulate protein function, but the effect of choosing a site internal to the gene vs. within the 3' UTR remains unclear. Here we show that reduced expression of CPSF6, one of the proteins involved in site selection, derails development in both humans and zebrafish by causing a bidirectional shift in poly(A) site usage. CPSF6 insufficiency favors the use of intronic poly(A) sites in neuronal genes, reducing mRNA and protein abundance, but promotes 3' UTR site usage in cardiovascular and skeletal genes, upregulating mRNA and protein.These data thus provides a long-sought link between APA and gene expression and shows that poly(A) site selection influences development.

overall_design: Comparative analysis of alternative polyadenylation using polyA-click seq (PAC-seq) on whole larva and head of cpsf6-/- Danio rerio compared to stage-matched wt controls.


title: Loss of CPSF6 causes developmental disease via bimodal changes in polyadenylation site usage and protein expression

status: Public on Jan 13 2023

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens


title: TMT-based quantitative proteomic analysis of spheroid cells of endometrial cancer possessing cancer stem cell properties

status: Public on Jan 14 2023

city: Guangzhou

first: Qingyan

last: Zhang

state: Guangdong

address: hongshan 2nd Road, Number 58

country: China

institute: the First Affiliated Hospital of Sun Yat-sen University

summary: RNA-seq of HK2-siRNA  transfected to Ishikawa and HEC1A cells to investigate the molecular mechanism of HK2 in endometrial cancer.

overall_design: Total RNA extraction in four groups (Ishikawa-NC V.S Ishikawa-HK2-siRNA, HEC1A-NC V.S HEC1A-HK2-siRNA) was used by Trizol for library preparation, and the sequencing platform was Illumina sequencing, which was completed in Sangon Biotech (Shanghai, China). DESeq2 software (version 1.16.1) was applied to investigte differential expressions between two comparative combinations (Ishikawa-NC V.S. Ishikawa-HK2-siRNA, HEC1A-NC V.S. HEC1A-HK2-siRNA).

first: Mingzhu

last: Cao


title: Single-cell discovery and multi-omic characterization of therapeutic targets in multiple myeloma [bulk RNA-seq]

first: Ravi

last: Vij

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

summary: Multiple myeloma (MM) is a highly refractory hematological cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which are previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA-sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA-sequencing reiterated top candidates, further affirming the ability of single cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.

overall_design:
We utilized bulk RNAseq from 33 patient samples to cross-validate single-cell based discovery of myeloma markers.

Submitter states: raw data will be submitted to dbGaP due to patient privacy concerns.
Raw data files for patients in WU cohort 1 are being submitted via dbGaP
Raw data files for patients in MMRF cohort are available via dbGaP Accession: phs000748

first: Li

last: Ding

first: John

last: DiPersio