title: Aerobic training induces physiological and cellular benefits in myotonic dystrophy type 1 patients

city: Hamilton

first: Mark

middle: A

last: Tarnopolsky

state: Ontario

address: 1200 Main St. West

department: Pediatrics and Medicine

country: Canada

institute: McMaster University Medical Center

summary: Myotonic dystrophy type 1 (DM1) is a progressive life-limiting neuromuscular disorder with no available cure. In the current study, we examined the extent to which 12-weeks of cycle ergometry can recuperate clinical and physiological metrics in DM1 patients. Furthermore, we studied the underlying mechanisms through which exercise elicits benefits in skeletal muscle. DM1 was associated with impaired muscle function, fitness, lung capacity, and mitochondrial function. Exercise training induced several clinical, physical, and metabolic advantages in DM1 patients. We highlight that exercise-induced molecular and cellular alterations in patients do not conform with previously published data in murine models and propose an alternative mechanism. Lastly, we briefly outline the involvement of small nucleolar RNAs as a novel component within the DM1 pathophysiology. Taken together, our data supports the efficacy of aerobic training to mitigate the relentless progression of DM1 in individuals affected.

overall_design: 11 DM1 replicates pre and post 12-weeks of cycle ergomety. 10 controls matched by age, weight, height, and body mass index.

first: Andrew

middle: I

last: Mikhail

first: Peter

middle: L

last: Nagy

first: Katherine

last: Manta

first: Nicholas

last: Rouse

first: Alexander

first: Sean

last: Ng

first: Jian-Qiang

last: Lu

first: Joshua

middle: P

last: Nederveen

first: Vladimir

last: Ljubicic

first: Michael

first: Paul

last: Smith


title: Genome-wide distribution of histone modification H3K36me3 in ECs during VEGF-signaling

status: Public on Apr 01 2022

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Vascular endothelial growth factor (VEGF) signaling serves a central role in vascular development as well as maintaining vascular homeostasis. In endothelial cells (ECs), VEGF activates gene expression of angiogenic transcription factors (TFs) followed by downstream induction of angiogenic responsive genes. Recent findings support histone modification dynamics contribute to transcriptional control of genes important for EC functions. Lysine demethylase 2B (KDM2B) demethylates histone H3K4me3 and H3K36me2/3 and also mediates monoubiquitylation of histone H2A119K. KDM2B functions as a transcriptional repressor in somatic cell reprograming and tumor development. However, the role of KDM2B during VEGF-signaling remains to be elucidated. Here, we show in cultured human ECs that knockdown of KDM2B enhances VEGF-induced angiogenesis via increased abilities of migration and proliferation. In contrast, ectopic expression of KDM2B has inhibitory effects on angiogenesis. The function of KDM2B is possibly dependent on its catalytic Jumondi C domain. Genome-wide analysis further reveal that KDM2B selectively controls transcription of VEGF-induced angiogenic TFs where increased H3K4me3/H3K36me3 and decreased of H2A119Kub are associated. These findings suggest an essential role of KDM2B during VEGF-signaling in ECs. Because dysregulation of VEGF signaling in ECs is involved in various diseases including cancer, KDM2B may be a potential therapeutic target in VEGF-mediated vasculopathic diseases.

overall_design: Total 4 samples were derived from VEGF-stimulated human cultured endothelial cells, H3K36me3 ChIP-seq profiling.

first: Yuji

last: Sasaki

first: Yasuharu

last: Kanki


title: Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (RNA-seq)

status: Public on Apr 02 2022

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

country: China

institute: Tongji University

type: Expression profiling by high throughput sequencing

summary: Chromatin remodeling is essential for the reprogramming process after fertilization. However, the detailed mechanism remains unclear to date. In this study, we reported the dynamic changes of nucleosome occupancy and positioning in pronuclear stages using low-input MNase-seq. We found distinct features of inheritance and reconstruction on nucleosome position can be observed in the male and female genome. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 hour after the injection of sperm. The nucleosome positioning pattern was further rebuilt continually to form nucleosome depletion regions (NDR) on promoter and transcription factor (TF) binding sites. The formation of promoter NDRs occurred faster on zygotic genome activation genes, which rely on the function of Brd4 but independent of transcription elongation or DNA replication. Importantly, we found the establishment of NDR on TF binding motifs might be associated with its potential pioneer function in zygotic genome activation (ZGA). Further verification suggested predicted factors Mlx and Rfx1 play important roles in minor and major ZGA, respectively. Our data do not only provided the first insight of nucleosome positioning dynamics in the very early stage of embryogenesis but also provided a way to identify key TF regulators in the developmental process.

overall_design: To investigate the function of Etv5, Rfx1 and Mlx in the zygotic genome activation, we generated RNA-seq dataset in mouse zygote and 2-cell embryo using siRNA to silence the expression of ctrl, Etv5, Mlx and Rfx1.

first: Chenfei

last: Wang

first: Chuan

last: Chen

first: Xiaoyu

last: Liu

first: Chong

last: Li

first: Qiu

last: Wu

first: Lingyue

last: Yang

first: Xiaolan

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

first: Yong

last: Zhang

first: Yawei


title: Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [scATAC-Seq]

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

country: USA

institute: Tulane University

summary: Background: Unraveling the dynamic accessibility of regulatory chromatin at single-cell resolution is key to understanding stem/progenitor cell fate choices in health and disease.  Nephron progenitor cells (NPCs) are a multipotent population giving rise to all cell types of the nephron, from the glomerular epithelium to the distal tubule. At any given time, the  NPC’s choice to self-renew or differentiate and gain a new identity is determined not only by its transcription factor repertoire but also by the genome accessibility of the cognate  cis-regulatory elements.  Methods: We performed singleome and multiome analysis of chromatin accessibility and gene expression in thousands of embryonic and neonatal NPCs toward defining the  regulatory landscape driving fate choices during nephrogenesis.  Results: We show that chromatin accessibility recovers the diverse states of NPCs and precursor states of proximal and distal nephron epithelial cells. We define the key cell  type-specific transcriptional regulators across pseudotime and NPC age. We find that chromatin accessibility in the podocyte lineage is established early in the trajectory and  identify a subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors. We also determined that strong linkages between cis-regulatory elements  and expression levels distinguish fate-determining TFs.  Conclusions: Single-cell mapping of accessible and active chromatin defines the regulatory landscape of nephrogenesis and provides a foundation for future studies in  disease states characterized by abnormal nephrogenesis.

overall_design: (1) Single cell ATAC sequencing and analysis of FACS-sorted Six2+ cells from E16.5 and P2 kidneys.

first: S


title: Pathogen size alters C-type lectin receptor signaling in dendritic cells to influence CD4 Th9 cell differentiation

city: Los Angeles

first: Seeun

last: Oh

state: CA

address: 8700 Beverly Blvd

department: Biomedical Science

institute: Cedars-Sinai Medical Center

summary: Dectin-1 recognizes β-glucan in fungal cell walls, and activation of Dectin-1 in dendritic cells (DCs) influences immune responses against fungi. Although many studies have shown that Dectin-1 activated DCs induce different subsets of T helper cells according to different cytokine milieus, the precise mechanisms underlying such differences remain unknown. By harnessing polymorphic Candida albicans and polystyrene beads of different sizes, we found that target size influences production of cytokine that control differentiation of T helper cell subsets. Hyphal C. albicans and large beads activate DCs but cannot be phagocytosed due to their size, which prolongs the duration of Dectin-1 signaling. Transcriptomic analysis revealed that the expression of Il33 was significantly increased by larger targets, and increased IL-33 expression promoted TH9 responses. Expression of IL-33 was regulated by Dectin-1-SYK-PLCγ-CARD9-ERK pathway. Altogether, our study demonstrates that size of fungi can be a determining factor in which DCs induce context-appropriate adaptive immune responses.

overall_design: Examination of mice bone marrow derived dendritic cell behavior with different physical forms of C.albicans and different size of beads

first: Kai

first: Alex

last: Prince

first: Matthew

last: Wheeler

first: Christopher

last: Nguyen

first: Hussein

last: Hamade

first: Kathrin

last: Michelsen

first: David

middle: M

last: Underhill


title: Temporal Changes in Transcripts of MITE Transposable Elements during Rice Endosperm Development

city: Yokohama

first: Hiroki

last: Nagata

state: Kanagawa

address: 641-12 Maioka, Totsuka

department: Kihara Institute for Biological Research

institute: Yokohama City University

summary: Repression of transposable elements (TEs) by DNA methylation is necessary for host plants to maintain genome integrity and prevent from harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and therefore activate their transcription. In A. thaliana and O. sativa, DNA demethylase targets to the sequence derived from TEs in the central cell, a progenitor cell of endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we survey transcripts generated from TEs during the rice endosperm development and some points of the embryo as a control using custom-made microarray. We found that TE transcripts are largely different in the embryo and endosperm. The expression patterns of TEs are dynamically up- and down-regulated during the endosperm development, especially for miniature inverted-repeat transposable elements (MITEs).

overall_design: Rice endosperm was harvested at 24 hr intervals from 2 to 7 days after pollination (DAP), and at 10 DAP. Rice embryo was dissected from the developing ovaries at 5, 7 and 10 DAP. These samples were used in this experiment.

first: Tetsu

last: Kinoshita


title: Expression of Arabidopsis WRI1 and DGAT1 during soybean embryo development alters oil and carbohydrate composition

city: Columbus

first: Tu

last: Huynh

state: OH

address: 2021 Coffey Rd

department: Horticulture and Crop Science

institute: Ohio State University

summary: Soybean (Glycine max [L.] Merr.) is the largest feedstock for protein and second largest source of vegetable oil in the world. In order to evaluate whether the expression of ATWRI1 and AtDGAT1 could direct carbon flow towards lipid accumulation, we generated three independent transformation events  (WD-1, -2, and -3). The transgenic events were evaluated in three field trials (2018, 2019, and 2020) as well as greenhouse conditions. RNAseq analysis was performed in immature embryos of both transgenic events grown under greenhouse conditions.  We discovered that Glycolysis and FA metabolism enzymes are enriched in WD differentially expressed genes during seed development.

overall_design: To check the response of the expression of Arabidopsis WRI1 and DGAT1 during soybean embryo development to alter oil and carbohydrate composition in seeds

first: Cintia

last: Arias

first: Truyen

last: Quach

first: Chi


title: Whole-genome DNA methylation landscapes of control and heat-stressed Linum usitatissimum seedlings.

city: Kolkata

first: Dipnarayan

last: Saha

state: West Bengal

address: Biotechnology Unit, Division of Crop Improvement, ICAR- Central Research Institute for Jute and Allied Fibres, Nilgunj, Barrackpore

country: India

institute: Indian Council of Agricultural Research - Central Research Institute for Jute and Allied Fibres

type: Methylation profiling by high throughput sequencing

summary: Whole-genome bisulfite sequencing (WGBS) was employed for identification of differential DNA methylation profiles among control and heat-stressed seedlings of a fibre flax (Linum usitatissimum L.) var., JRF-2. It was identified as a tolerant variety of heat stress-induced oxidative damage. High-quality genomic DNA from four samples comprised  3-week-old control and heat-stressed (40±2°C) seedlings, with or without treated with 5-Azacytidine (hypomethylating agent). High-quality and filtered paired-end Illumina reads were aligned to the flax reference genome, assembled in chromosomes, using bwa-meth tool, followed by methylation loci (5-mC) calling using the MethylDackel software. Differentially methylated regions (DMRs) between the control and other samples were identified using the methylKit and annotated using genomation package for their precedence in the promoter/exon/intron/intergenic regions. The DMRs comprised both hyper- and hypomethylated loci, but the latter found dominated due to heat stress in flax seedlings. The WGBS in flax for heat stress will provide a platform to identify epigenetic loci responsible for heat-stress adaptation in flax.

overall_design: Total genomic DNA of control and heat-stressed flax (cv. JRF-2) seedlings were quality checked and converted with bisulfite followed by size fractionated and paired-end library constructed. The libraries were sequenced on Illumina HiSeq 2500 using PE 2x150 chemistry. The raw reads were filtered and aligned to the reference genome for 5-mC loci calling using various bioinformatic softwares. A comparative analysis of the methylated loci between control and heat-stressed seedlings identified DMRs from the promoter, exons, introns, and intergenic regions.

first: Arun

middle: K

last: Shaw


title: Longitudinal analysis of pancreatic adenocarcinoma development reveals transient gene expression signatures

city: PORTLAND

first: JUNGSUN

last: KIM

state: OR

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

summary: We performed a transcriptome time-course analysis of genetically tagged human PDAC cells reprogrammed into a pluripotent stem cell-like line (10-22 cells) through the progression from PanINs to PDAC in mice. The results were validated using the Cancer Genome Atlas (TCGA) PDAC dataset, human clinical PanIN/PDAC tissues, and well-established murine PDAC model. Human normal pancreatic ductal epithelial cell line (H6C7) and PDAC cell lines (Miapaca2, Aspc1) are used for functional validation of HBP1. Pathways for extracellular vesicle transport pathways and neuronal cell differentiation were derepressed in the progression of PanINs to PDAC. Analysis of transcription factor (TF) motifs at dynamically expressed genes revealed roles for HBP1 and BACH during PDAC progression and their inverse correlations with PDAC patients' prognosis. Notably, we detected gene activity changes that were transient during PDAC progression.  Our longitudinal analysis provides insights into networks underlying PDAC progression and pathogenesis.

overall_design: Human normal pancreatic ductal epithelial cell line (H6C7) are used for functional validation of HBP1 overexpression

first: Jungsun

last: Kim

first: Taelor

last: Ekstrom

first: Wenli

last: Yang

first: Greg

last: Donahue

first: Dmytro

last: Grygoryev

first: Thuy

last: Ngo

first: John

last: Muschler

first: Terry

last: Morgan

first: Kenneth

last: Zaret


title: Longitudinal analysis of pancreatic adenocarcinoma development reveals transient gene expression signatures (I. 10-22 cell RNA-Seq)

summary: We performed a transcriptome time-course analysis of genetically tagged 10-22 cells through the progression from PanINs to PDAC in mice. The results were validated using the Cancer Genome Atlas (TCGA) PDAC dataset, human clinical PanIN/PDAC tissues, and well-established murine PDAC model.

overall_design: Each 10-22 cell tagged with KiR-EG was subcutaneously transplanted into 4-6 weeks old female NOD-SCID-IL2Rgc null (NSG) mice and harvested 1 week, 2 weeks, 3 months, 6 months, and 9 months. 10-22 KIR-EG clone 6 that was cultured in pluripotent ES culture condition were harvested as day 0 control.


title: Gene expression profile in DLBCL cases according to response to R-CHOP

city: Lisboa

first: Ivan

last: Dlouhy

address: Rua Prof Lima Basto

department: Hematology

country: Portugal

institute: IPO Lisboa

summary: Gene expression profile (GEP) was analyzed in DLBCL cases to compare early failure patients (10) vs. responding patients (29), to identify features associated to primary chemoresistance

overall_design: We used frozen samples of DLBCL cases to analyze GEP in 2 groups: early failure (EF) cases (10), defined as refractory to induction treatment or early relapsing  (<12 months from diagnosis); and responding patients (29). Data was then analyzed with GSEA program


title: Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]

first: Samir

last: El-Dahr

overall_design: (2) Single cell Multiome ATAC + Gene Expression Sequencing and anaylsis  of whole kidneys from E16.5.

first: S


title: Characterization of Richter Syndrome cell line U-RT1

city: Ulm

first: Julia

last: Maier

address: Albert-Einstein-Allee 23

country: Germany

institute: Institute of Pathology

summary: mRNA profiling of the Richter Syndrome cell line U-RT1. The expression profiles were compared to published expression profiles of different diffuse large B cell lymphoma cell lines (Array Express E MTAB-973 and GEO Accession Number GSM466597) to determine whether there are differences in expression that indicate differences on molecular grounds.

first: Kevin

last: Mellert


title: Understanding the nitrate responsive regulatory modules in Rice

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

institute: National Centre for Biological Sciences, TIFR

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression profile of murine proneural  glioblastoma

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: Murine proneural (PN) glioblastomas were induced by lentiviral vector expressing PDGFB and shRNA targeting p53. Tumor tissues were isolaed from mice reaching end point stage. RNA was isolated using RNAeasy kit according to manufacturer's protocol. cDNA libraries were preaped using TruSeq RNA sample Prep kit (Illumina). RNA sequencing was performed using

overall_design: Four PN glioblastoma samples and 2 controls by standard RNAseq method. Normalized against mesenchymal samples from GSE73127.

first: P

last: Magod

first: D

last: Friedmann-Morvinski

first: G


title: Next Generation Sequencing of transcript abundance in rice inoculated with Magnaporthe oryzae under 22℃ and 28℃

city: Hangzhou

first: Jiehua

last: Qiu

state: 省/直辖市

address: shuidaosuo 28 road,fuyang District, Hangzhou city

institute: CNRRI

summary: We report that rice inoculated with Magnaporthe oryzae at different temperatures and analysis of the whole genome expression to shed light on temperature-mediated rice disease resistance.

overall_design: Examination of four condition of rice inoculated with water or Magnaporthe oryzae at 22℃ and 28℃


title: Understanding the nitrate responsive regulatory modules in Rice [RNA-seq]

summary: To identify the differetially expressed genes under nitrate stress, RNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were mapped to rice (IRGSP-1) genome.

overall_design: Transcriptome profiles in Control (10 mM), low N stress (0 mM) and high N stress (100 mM)

last: Padubidri V

first: Anushree

last: Narjala

first: Kannan

last: Pachamuthu


title: Understanding the nitrate responsive regulatory modules in Rice [MADS27OE, RNA-seq]

summary: MADS27 was differetially expressed during nitrate stress in roots of rice plant. In order to further verify the effect of MADS27 overexpression in rice root development, RNA-seq analysis was performed on plants overexpressing MADS27.

overall_design: RNA-seq from roots of WT PB1 and MADS27OE seedlings.


title: Understanding the nitrate responsive regulatory modules in Rice [MADS27OE, ChIP-seq]

summary: To identify genome-wide binding sites of MADS27, we performed ChIP-seq experiment from 3xMyc-OsMADS27OE rice seedlings.

overall_design: Examination of genome-wide binding sites of MADS27

first: Vivek

middle: H

last: Sundar


title: Understanding the nitrate responsive regulatory modules in Rice [ncRNA-seq]

summary: To identify the differetially expressed sRNAs under nitrate stress, sRNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were processed and analysed using UEA sRNA workbench.

overall_design: sRNA profiles in Control (10 mM), low N stress (0 mM) and high N stress (100 mM)


title: Transcriptome Analysis of Tumor Associated High Endothelial Venules in Breast Cancer

status: Public on Mar 31 2022

city: St. Petersburg

first: Masanobu

last: Komatsu

state: FL

address: 600 5th Street S

institute: Johns Hopkins All Children's Hospital

summary: High endothelial venules (HEVs) are specialized post-capillary venules that recruit naïve lymphocytes to the lymph nodes and are essential for the development of adaptive immunity. HEVs can also develop in tumors. These specialized tumor vessels are thought to be important for recruiting naïve T cells and B cells into tumors and locally enhancing anti-tumor immunity by supporting the formation of tertiary lymphoid structures. By a comparative transcriptome analysis in human breast cancer, we investigated differentially expressed genes between tumor-associated HEVs and the rest of the tumor vasculature. Tumor vessels highly expressing HEV-upregulated genes, such as the homeobox gene MEOX2 and the tetraspanin gene TSPAN7, were associated with extensive infiltration of T and B lymphocytes and the occurrence of tertiary lymphoid structures, which is known to predict therapeutic responses to immune checkpoint inhibitors. Moreover, high transcript counts of these genes in clinical tumor specimens were associated with a significant survival benefit in advanced breast cancer. The molecular signature of HEVs identified here may be useful for guiding immunotherapies and provide a new direction for investigating tumor-associated HEVs and their clinical significance.

overall_design: mRNA profiles of tumor vessels and high endothelial venules in TLS-rich and TLS-free breast tumors

first: Junko

last: Sawada


title: Commonalities of Mycobacterium tuberculosis Transcriptomes in Response to Defined Persisting Macrophage Stresses

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

summary:
M. tuberculosis H37Rv was grown in vitro in five different conditions, including four stress conditions that could mimic what M. tuberculosis may experience in macrophages. The gene expression profiling was studied.
Methods: Mycobacterium tuberculosis H37Rv strain was grown under 5 different conditions, in duplicate. RNAseq was performed. The gene expression was compared and Differential Expression was analyzed.
Results: The gene expression profiling in microaerophilic and stationary phase conditions were the most similar while the profiling in acidic condition was the closest to exponential phase condition. An average 1050 genes were differentially transcribed in each stress condition except for the acidic stress, which had less than 200 genes differentially regulated.

overall_design: M. tuberculosis H37Rv was grown in vitro in five different conditions, in duplicate.

first: Catherine

last: Vilcheze

first: Ettwiller

last: Laurence

first: Suzie

last: Hingley-Wilson

first: Rosalyn

last: Casey

first: William

middle: R

last: Jacobs


title: Identification of gene expression alteration in macrophage cells with oncolytic HSV

city: Okayama

first: Yoshihiro

last: Otani

address: 2-5-1, Shikata, Kita-ku

department: Neurological Surgery

institute: Okayama University Hospital

summary: To evaluate signaling changes in macrophages upon oHSV treatment, we performed RNA-Seq from co-cultures of human GBM cells with murine macrophages

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 4 samples in each group

first: Yuanqing

first: Balveen

last: Kaur


title: WT versus Girk3-/- Chondrocytes

city: Rochester

first: Samantha

last: Weaver

state: MN

address: 200 1st Street SW

department: Orthopedic Surgery

institute: Mayo Clinic

summary: Long bones are formed and repaired through the process of endochondral ossification. Activation of G protein coupled receptor (GPCR) signaling regulates skeletal development and long bone growth. G protein-coupled Inward-Rectifying potassium (K+) channel (GIRK) genes are key functional components of the GPCR in excitable tissues (e.g., neurons and cardiomyocytes) but their roles in the non-excitable cells that directly contribute to endochondral bone formation have not been studied. In this study we analyzed skeletal phenotypes of Girk2-/-, Girk3-/- and Girk2/3-/- mice. Bones from 12-week-old Girk2-/- mice were normal in length, but femurs and tibiae from Girk3-/- and Girk2/3-/- mice were longer. Epiphyseal chondrocytes from five-day-old Girk3-/- mice expressed higher levels of genes involved in collagen chain trimerization and collagen fibril assembly and lower levels of VEGF receptors and produced larger micromasses than wildtype chondrocytes in vitro. Girk3-/- chondrocytes were also more responsive to the GPCR ligand, dynorphin, as evidenced by greater cAMP and pCREB expression, greater GAG production, and upregulation of Col2a1 and Sox9 transcripts. Imaging studies showed that Kdr (Vegfr2) and endomucin expression was dramatically reduced in bones from young Girk3-/- mice, supporting a role for delayed vasculogenesis during postnatal growth. Together these data identify Girk3 as a GPCR effector that controls bone lengthening.

overall_design: Six samples of total RNA, n=3 biological replicates of wildtype (WT) mice and n=3 biological replicates of Girk3-null (Girk3-/-) five-day-old mouse chondrocytes

first: Jennifer

middle: J

last: Westendorf

first: Earnest

last: Taylor


title: A Positive Regulatory Feedback Loop Between EKLF/ KLF1 and TAL1/SCL Sustaining the Erythropoiesis

city: Taipei

first: Chun-Hao

middle: James

last: Hung

state: TAIWAN

address: 128 Academia Road, Section 2, Nankang, Taipei, Taiwan

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

type: Genome binding/occupancy profiling by genome tiling array


title: PCSK9 knockdown in EndoC-bH1 cells at 72 hours

city: Paris

first: Raphael

last: Scharfmann

address: 123 boulevard Port Royal

department: Endocrinology, Métabolism et Diabetes

country: France

institute: Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104

summary: The aim of the study was to characterize the role of PCSK9 in human beta cells. We performed siRNA-mediated knockdown of PCSK9 in human beta cell line EndoC-bH1 and compared the expression profiles against control siRNA-treated cells.

overall_design: Triplicate per condition. EndoC-bH1 cells were classified as human biological material, and FASTQ files were not deposited. FASTQ files can be obtained from the senior author upon reasonable request.


title: Differential expression and correlation analysis of global transcriptome for hemorrhagic transformation after acute ischemic stroke

status: Public on Mar 30 2022

city: Jining

first: Daojing

last: Li

state: Shandong

address: No.89 Guhuai Road

department: Department of Neurology

institute: Affiliated Hospital of Jining Medical University

summary: In order to explore the epigenetic characteristics of hemorrhagic transformation(HT) after acute ischemic stroke, we used transcriptome sequencing technology to analyze the global transcriptome expression profile of patients with and without HT after acute ischemic stroke and to study the differential expression of messenger RNA (mRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) between HT group and non-HT group.

overall_design: RNA sequencing was performed with patients with and without HT after acute ischemic stroke(n = 3 for each group) to identify the differently expressed genes and related pathway.

first: Rongrong

last: Han

first: Peng

last: Zhang

first: Hongfang

first: Yun

last: Chen

first: Yongnan

last: Hao

first: Qiang

last: Guo

first: Aimei


title: Microarray expression level comparison between WT and KO fetal liver cells

summary: The erythroid Krüppel-like factor EKLF/KLF1 is a hematopoietic transcription factor binding to CACCC DNA motif and participating in the regulation of erythroid differentiation. With combined use of microarray-based gene expression profiling and promoter-based ChIP-chip assay of E14.5 fetal liver cells from wild type (WT) and EKLF-knockout (Eklf-/-) mouse embryos, we have identified the pathways and direct target genes activated or repressed by EKLF. This genome-wide study together with molecular/ cellular analysis of mouse erythroleukemic cells (MEL) indicate that among the downstream direct target genes of EKLF is Tal1/Scl. Tal1/Scl encodes another DNA-binding hematopoietic transcription factor TAL1/SCL known to be an Eklf activator and essential for definitive erythroid differentiation. Further identification of the authentic Tall gene promoter in combination with in vivo genomic footprinting approach and DNA reporter assay demonstrate that EKLF activates Tall gene through binding to a specific CACCC motif located in its promoter. These data establish the existence of a previously unknow positive regulatory feedback loop between two DNA-binding hematopoietic transcription factors that sustains the mammalian erythropoiesis.

overall_design: Novel gene regulation throught EKLF manipulation.  Comparison between WT and KO fetal liver cells.

first: Tung-Liang

last: Lee

first: Yu-Chiau

last: Shyu

first: Kang-Chung

last: Yang

first: Shinsheng

last: Yuan


title: ChIP-Chip data from WT E14.5 fetal liver

overall_design:
AEK antibody pull down chromtatin analysis for identifying promoter regions which had been targeted by KLF factor and also defined the unknow genes' promoters
The home-made antibody pulls down the novel regions that should be identified and validated.
WT fetal livers only


title: Closed chromatin of the CXCR5 gene due to DNA hypermethylation limits trafficking potential of CD8+ T cells into B cell follicles during HIV-1 clade C infection

city: Umbilo

first: Werner

last: Smidt

state: KZN

address: 719 Umbilo Rd

country: South Africa

institute: African Health Research Insititute

summary: CD8+ T cells play an important role in HIV control. However, in human lymph nodes (LNs), only a small subset of CD8+ T cells expresses CXCR5, the chemokine receptor required for cell migration into B cell follicles, which are major sanctuaries for HIV persistence in individuals on therapy. Here, we investigate the impact of HIV infection on follicular CD8+ T cells (fCD8s) frequencies, trafficking pattern and CXCR5 regulation. We show that, although HIV infection results in a marginal increase of fCD8s in LN, the majority of HIV-specific CD8+ T cells are CXCR5 negative (non-fCD8s) (p<0.003). Mechanistic investigations using ATAC-seq showed that non-fCD8s have closed chromatin at the CXCR5 transcriptional start site (TSS). DNA bisulfite sequencing identified DNA hypermethylation at the CXCR5 TSS as the most probable cause of closed chromatin. Transcriptional factor footprints analysis revealed enrichment of transforming growth factors (TGFs) at the TSS of fCD8s. In40 vitro stimulation of non-fCD8s with recombinant TGF-β resulted in significant increase in CXCR5 expression (fCD8s). Thus, this study identifies TGF-β signaling as a viable strategy for increasing fCD8s frequencies in follicular areas of the LN where they are needed to eliminate HIV infected cells, with implications for HIV cure strategies. ~

overall_design: ATAC-Seq data from six fCD8, six non-fCD8, eight Naive CD8+, Six GCTfh and Four non-Tfh cells from lymphnodes were compared.  RNA-Seq from five fCD8, five non-fCD8, five GCTfh, four Naive CD8+ and four non-Tfh cells from the lymph node were compared.

first: Funsho

last: Ogunshola

first: Zaza

last: Ndhlovu


title: Effect of bacteriocin NC8 on human intestinal flora

first: Jiaqian

last: Pu

address: Xuezheng Str.

institute: Zhejiang Gongshang University

summary: Herein, we evaluated the regulation of plantaricin NC8 on gut microbiota by in vitro simulation system, and assessed their modulation on different intestinal types, namely enterotype 1 (ET B) and enterotype 2 (ET P), for the first time. Plantaricin NC8 could not significantly promote or inhibit the production short chain fatty acids (SCFAs) by the gut flora in the fecal samples from eight subjects to produce through Gas chromatography (GC) determining, neither ET B nor ET P. 16S rDNA sequencing showed that plantaricin NC8 shortened the Shannon index of ET B and the Simpson index of ET P, but their β diversity change was not statistically significant. In addition, plantaricin NC8 could promote the growth of beneficial bacteria. Results showed that plantaricin NC8 mainly increased the abundance of Actinobacterias, Bacteroides, Bifidobacterium, Megamonas, Escherichia-Shigella, and decreased the abundance of Streptococcus in ET B. And it also increased the abundance of Prevotella_9, Bifidobacterium, Escherichia-Shigella, Mitsuokella and others in ET P. Plantaricin NC8 can influence intestinal microorganisms, but the influence were different for different enterotypes.

overall_design: Examination of the effect of different concentrations of bacteriocins on intestinal flora


title: Single-cell transcriptional changes of spinal cord immune cells associated with Reg1-MO treatment during EAE neuroinflammation

status: Public on Mar 28 2022

city: Kyoto

first: Ka Man Carman

last: Tse

state: Kyoto

address: Yoshidakonoecho, Sakyo-ku

department: Graduate School of Medicine, Department of Medical Chemistry

institute: Kyoto University

summary: Regnase-1 plays essential roles in restricting inflammation by acting as a RNase degrading mRNAs involved in immune reactions via the recognition of stem-loop structures in the 3'UTRs. Here we developed a novel therapeutic strategy to suppress inflammatory responses by upregulating Regnase-1 expression, which was enabled by the simultaneous use of two antisense morpholino oligonucleotides (MOs) to alter the stem-loop structures present in the Regnase-1 3'UTR and inhibit its auto-regulation. Intracranial Reg1-MO treatment successfully altenuated the disease severity of EAE, with significant delay in disease onset and lower incidence of paralysis. To clarify the cell types responsible for the suppression of autoimmune responses by Reg1-MOs in the CNS, we performed single-cell RNA sequencing (scRNA-seq) using the 10X Chromium platform using the spinal cord CD45+ cells derived from control and Reg1-MO groups collected at the peak of disease (D16). We found that Reg1-MO treatment not only stalled the microglial activation, but also increased the suppressive fucntion of regulatory T cells.

overall_design: Sorted mouse spinal cord CD45+ immune cells (D16) from animals received intracranial administration of Ctrl MO or Reg1-MOs on D9 post EAE immunization.

first: Ka Man

first: Alexis

last: Vandenbon

first: Takuya

last: Uehata

first: Keiko

last: Yasuda

first: Osamu

last: Takeuchi


title: The transition from G0 to GAlert is regulated by GLI3 processing by the primary cilia

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Satellite stem cells are required for the growth, maintenance, and regeneration of skeletal muscle. Quiescent satellite stem cells possess a primary cilium, a structure that regulates the processing of the GLI-family of transcription factors. We find that GLI3, specifically, plays a critical role in satellite cell activation. Strikingly, primary cilia-mediated processing of GLI3, independent of canonical Hedgehog signaling, is required to maintain satellite cells in a G0 dormant state, as satellite cells lacking GLI3 enter GAlert in absence of injury. Furthermore, GLI3 depletion or inhibition of its processing stimulates symmetrical division in satellite cells and expansion of the stem cell pool. As a result, satellite cells lacking GLI3 display rapid cell-cycle entry, increased proliferation and augmented self-renewal, and markedly enhanced long-term regenerative capacity. Therefore, our results reveal an essential role for primary cilia processing of GLI3 in regulating muscle stem cell activation.

overall_design: Muscle stem cells were isolated from hindlimb muscles of 3-4 month old Pax7-CreERT2/+;Gli3+/+;R26R-YFP (control) and Pax7-CreERT2/+;Gli3fl/fl;R26R-YFP (Gli3-cKO) mice. Quiescent muscle stem cells (alpha7-Integrin+, CD34+ sorting) were obtained from uninjured hindlimb muscles, while activated muscle stem cells (alpha7-Integrin+, VCAM1+ sorting) were obtained from cardiotoxin-injured muscles 3 days after the induced-injury.

first: Caroline

middle: E

last: Brun

first: Marie-Claude

last: Sincennes

first: Michael

last: Rudnicki


title: Transcriptomic alterations in fibroblast from parkinson's disease patients at high and low glucose levels

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

summary: In this study, we evaluate the hypothesis that molecular pathways in a cell model of Parkinson’s disease (PD) could be altered depending of glucose levels. We cultured fibroblasts from sporadic PD (sPD; n=4), PD patients carrying LRRK2 mutations (LRRK2-PD; n=3) and healthy controls (HC; n=4) at high (25 mM) and low (5 mM) glucose and analysed the transcriptome profile by using whole RNA sequencing.   We found 1439 differentially expressed transcripts (DET) comparing HC with overall PD cases. These genes are related with THE gene ontology terms cytosqueleton, cell adhesion, protein translation and ribosomes, mitochondrial electron transport between others, when cultured at 25 mM of glucose. However, at 5 mM there are virtually no gene expression changes in PD compared to controls. When compared between 5 and 25 mM condition separately for each group HC and PD, we found 1482 DET in controls, and 3381 in PD cases, but only found altered significant gene ontology terms in PD.  These findings suggest that high glucose levels cause specific molecular changes in fibroblasts which is exacerbated in PD, potentially leading to non adaptive changes. This work emphasizes the importance of energetic balance in PD and the need of further research about the role of glucose levels in clinical studies.  .

overall_design:
Examination of fibroblast expression by RNA seq at low (5 mM) and high (25 mM) glucose levels

Batch 2 and 3 samples have been re-analyzed from GSE82340 and are also included here.

first: Ruben

last: Fernandez-Santiago


title: Diversity of V(D)J repertoire of germinal center (GC) and non-germinal center (NGC) B cells following W614A-3S peptide-KLH vaccination using Squalene emulsion and Alum formulation

status: Public on Mar 24 2022

first: Olivia

last: Bonduelle

address: 91 bd de l'Hopital

institute: INSERM U1135

summary: We compared the efficacy of W614A-3S peptide formulated in either squalene emulsion (SQE) or in aluminum hydroxide (Alum) in BCR repertoire of peptide-specific B cells after 4 immunizations (at week 11 after the first intramuscular injection). The V(D)J sequencing of W614A-3S-specific BCR showed significant differences in BCR sequences and validates the dichotomy between adjuvant formulations.

overall_design: Four samples (one per condition) were analyzed. A pool of 25 mice per condition was use for B cell sorting.


title: Effect of Pou2af1 on activated T cell transcriptome

city: Montreal

first: Sylvie

last: Lesage

address: 2900 Bd Édouard-Montpetit

institute: Universite de Montreal

summary: Pou2af1 encodes for OCA-B, a coactivator of OCT-1/2. Although primarily studied in B cells, Pou2af1 mRNA expression is induced in activated T cells and T cells from B6.129S-Pou2af1-/- mice, bearing a mixed genetic background, show impaired T cell functions, such as cytokine production and Tfh differentiation. To revisit the impact of Pou2af1 in T cells, we generated Pou2af1fl/fl mice with specific genetic disruption of Pou2af1 in hematopoietic cells, Vav-Cre, or T cells, CD4-Cre, on the B6 background. Surprisingly, T cell cytokine production was not impaired in these models, and Tfh differentiation was influenced by T cell extrinsic deletion of Pou2af1. To determine the role of Pou2af1 induction in T cells, we performed RNA-Seq on activated T cells from CD4-Cre-.Pou2af1fl/fl and CD4-Cre+.Pou2af1fl/fl mice. Apart from Pou2af1 mRNA expression, the transcriptomic profiles were remarkably comparable. Overall, this study provides strong evidence that Pou2af1 does not act as transcriptional coactivator in T cells.

overall_design: 4 samples per cell type (CD4 and CD8 T cells) and genotype (WT, Het, KO) are analyzed. Pou2af1+/+ cell samples serve as control.

first: Felix

last: Lombard-Vadnais


title: Transcriptome analysis of LPS-stimulated BMDMs pretreated with Ctrl MO or Regnase-1-targeting MOs (Reg1-MOs)

summary: Regnase-1 plays essential roles in restricting inflammation by acting as a RNase degrading mRNAs involved in immune reactions via the recognition of stem-loop structures in the 3’untranslated regions (UTRs). Dysregulated expression of Regnase-1 is implicated in the pathogenesis of inflammatory and autoimmune diseases in mice and humans. Here we developed a novel therapeutic strategy to suppress inflammatory responses by blocking Regnase-1 self-regulation, which was enabled by the simultaneous use of two antisense phosphorodiamidate morpholino oligonucleotides (MOs) to alter the binding affinity of Regnase-1 towards the stem-loop structures present in its 3’UTR. The Regnase-1-targeting MOs successfully stabilized Regnase-1 mRNA expression. Furthermore, increasing the abundance of Regnase-1 by MO treatment effectively reduced multiple pro-inflammatory transcripts that were controlled by Regnase-1 in BMDMs. Collectively, these data suggested that MO-mediated disruption of the Regnase-1 self-regulation pathway is an attractive therapeutic strategy to enhance Regnase-1 abundance, which could provide clinical benefits for treating inflammatory diseases through the suppression of inflammation.

overall_design: Bome marrow cells were isolated from wild-type B6 animals, and were cultured in macrophage growth medium for 7 days (exchange with fresh macrophage growth medium on D4). BMDMs were transfected with Ctrl MO (2 µM) or Reg1-MOs (2 µM) together with Endoporter for 24 hours, followed by stimulation with LPS for 4 hours.

first: Masonori

last: Yoshinaga

first: Fabian

last: Hia


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Sdhaf4-/- Cardiac Transcriptomes

city: Xi'an

first: Zhihui

last: Feng

address: 28# West Xianning Road

institute: Xi'an Jiaotong University

summary: Cardiac mRNA profiles of 2-month-old wild-type (WT) and muscle Sdhaf4 knockout (Sdhaf4−/−) mice were generated by deep sequencing, in 6 repeats, usingIllumina HiSeqTM. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.

overall_design: Cardiac mRNA profiles of 2-month-old wild type (WT) and Sdhaf4-/- mice

first: Jiankang

last: Liu


title: FAT atypical cadherin 1 upregulates in oral squamous cell carcinoma (OSCC) and promotes cell proliferation via cell cycle and DNA repair

status: Public on Mar 25 2022

city: Fuzhou

first: Ting

last: Lan

state: Fujian

address: NO.88,Jiaotong Road,Fuzhou City,Fujian Prov

institute: Fujian Medical University

summary: Previous studies have revealed FAT atypical cadherin 1 (FAT1) played a tumor suppressive or oncogenic role in a context-dependent manner in various cancers. However, the functions of FAT1 are ambiguous in tumorigenesis owing to inconsistent research in oral squamous cell carcinoma (OSCC). The present study aimed to gain an insight into the role of FAT1 in the tumor genesis and development by comprehensive bioinformatics, in vitro experiments and analysis of RNA-seq after FAT1 silencing. The expression and survival data analysis were done using data from the Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) database, verified with clinical samples via real-time polymerase chain reaction (qRT-PCR), Western blot (WB) and immunohistochemical (IHC). Overall, FAT1 significantly raised in OSCC with a poor prognosis outcome. Some work on FAT1 mutant implied that 404, 614, 1662 and 3554 may be four SNP loci. The in vitro experiment showed the promoting effect of FAT1 in the proliferation and migration of OSCC cells. FAT1 can also inhibit both the early and late apoptosis of OSCC cells. Bioinformatics analysis of FAT1 silencing revealed that the cell cycle, DNA replication, and some core genes (MCM2, MCM5, CCNE1 SPC24, MYBL2, KIF2C) may be the potential mechanism in OSCC. Taken together, these findings demonstrated that FAT1 may act as oncogenesis in OSCC with potential mechanism influencing the cell cycle and DNA repair.

overall_design: Examination of 2 FAT1 knockdown and corresponding negative control cells in HN6 and HN30. Repeated at another separate time.

first: DaLi

last: Zheng


title: Bulk RNA-seq on unstimulated and LPS-stimulated human macrophages

city: Frankfurt

first: Nadine

last: Biesemann

state: Hessen

address: Industriepark Hoechst H824

institute: Sanofi

summary: The goal of this experiment is to profile LPS-stimulated transcriptome changes in human macrophages. Human whole blood was from the Sanofi in-house blood donor service that is approved by the local ethics committee and all blood donors signed informed consent. Human peripheral blood monocytes were isolated from anonymous donors’ prefinal blood using Ficoll density centrifugation, followed by magnetic separation with positive selection (CD14 MicroBeads, Miltenyi Biotec). Monocytes were differentiated into macrophages by culturing in macrophage serum-free medium (Life Technologies) containing 50 ng/ml recombinant human macrophage colony-stimulating factor (Immunotools) for 5 days. Following differentiation, cells were cultured in RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum (Thermo Fisher) and maintained at 37°C in a 5% CO2/air environment. Macrophages were stimulated with 50 ng/ml lipopolysaccharides from Escherichia coli O111:B4 (Sigma) for 24 hours.

overall_design: RNA isolated from unstimulated and LPS-stimulated human macrophages from 4 blood donors (n = 4 for unstimulated, n = 4 for LPS-stimulated)

first: Lingzi

last: Li

first: Ekaterina

last: Zezina

first: Michel

last: Didier


title: Sirtuin 5 levels are limiting in preserving cardiac function and suppressing fibrosis in response to pressure overload

status: Public on Mar 23 2022

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

summary: Heart failure (HF) is defined as an inability of the heart to pump blood sufficiently to meet the metabolic demands of the body. HF with reduced systolic function is characterized by cardiac hypertrophy, ventricular fibrosis and remodeling, and decreased cardiac contractility, leading to cardiac functional impairment and death. Transverse aortic constriction (TAC) is a well-established model for inducing hypertrophy and HF in rodents. Mice globally deficient in sirtuin 5 (SIRT5), a NAD+-dependent deacylase, are hypersensitive to cardiac stress and display increased mortality after TAC. Prior studies assessing SIRT5 functions in the heart have all employed loss-of-function approaches. In this study, we generated SIRT5 overexpressing (SIRT5OE) mice, and evaluated their response to chronic pressure overload using TAC. Compared to littermate controls, SIRT5OE mice were protected against adverse functional consequences of TAC, left ventricular dilation, and impaired ejection fraction. Transcriptomic analyses revealed that SIRT5 suppresses key HF sequelae, including the metabolic switch from fatty acid oxidation to glycolysis, immune activation, and fibrotic signaling pathways. We conclude that SIRT5 is a limiting factor in the preservation of cardiac function in response to experimental pressure overload.

overall_design: RNA-seq was performed on mouse whole heart tissue from either control or TAC mice on an Illumina HiSeq4000. The transcriptome was analyzed using Kallisto, counted using Tximport, and differential expression was determined using DESeq2.

first: Angela

last: Guo

first: Rachael

last: Baliira

first: Mary

last: Skinner

first: Surinder

last: Kumar

first: Anthony

last: Andren

first: Li

last: Zhang

first: Robert

last: Goldsmith

first: Shaday

last: Michan

first: Norma

last: Davis

first: Merissa

middle: W

last: Maccani

first: Sharlene

last: Day

last: Sinclair

first: Matthew

last: Brody

first: Costas

last: Lyssiotis

first: Adam

last: Stein


title: Nuclear GSK-3β and Oncogenic KRas Promote Aqp5+ Pancreatic Duct Stem Cell Expansion

status: Public on Mar 22 2022

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

summary: Intraductal papillary mucinous neoplasm (IPMN) represents the most commonly diagnosed precursor lesion of pancreatic ductal adenocarcinoma (PDA), however the cell-of-origin remains unclear. Herein, we show that pancreas-specific activation in mice of nuclear-targeted glycogen synthase kinase-3β and oncogenic KRasG12D leads to the loss of acinar cells, the expansion of ductal cells, and the rapid development of IPMN with low-grade dysplasia. RNA-sequencing identified the expression of several ductal stem cell lineage genes including the water channel AQP5. The Aqp5+ pancreatic ductal cell pool was proliferative, phenotypically distinct from mature pancreatic ductal cells, and deletion of AQP5 limited IPMN development. Significantly, Aqp5 is highly expressed in human IPMN along with GSK-3b suggesting that human preneoplastic lesions likely arise from the expansion of an Aqp5+ pancreatic ductal stem cell. Altogether, these data identify Aqp5+ ductal cells in the mouse and human pancreas as the likely cell-of-origin for IPMN.

overall_design: Pancreas from three 4-week old mice were dissociated into single-cell suspension and equal amount of cells from three were then mixed into one sample.

last: Ding

first: Cheng

first: Daniel

middle: D

last: Billadeau


title: Base editing in bovine embryos reveals a species-specific role of SOX2 in regulation of pluripotency

city: Hangzhou

first: Kun

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Proper lineage specification is extremely important for the embryo's implantation and development. Numerous findings of lineage specification emerged in the mouse embryo but remain unclear in the bovine embryo due to the limited techniques. Here, our study is the first to demonstrate that the single base editor (ABE7.10 and BE3) can be applied to bovine embryos for base conversion, which contributes us to further exploring the lineage specification of the bovine embryo. We further show SOX2 is not necessary for blastocyst formation but is required for ICM maintenance in bovine early embryo development. The underlying mechanism may be that SOX2 promoted the differentiation of ICM by maintaining the expression levels of OCT4 and NANOG. Meanwhile, the disappearance of SOX2 in TE of bovine late blastocyst depended on the expression of CDX2.

overall_design: PolyA RNA profiles of mouse and bovine embryos

first: Lei

last: Luo

first: Yan

last: Shi

first: Yanna

last: Dang


title: Transcriptomics identified mechanisms responsible for similarity and differences in effects  2 of nanomaterials across species

status: Public on Mar 21 2022

city: Milwaukee

first: Rebecca

middle: D.

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

summary: Impacts of engineered nanomaterial (ENM) exposure is known to be dependent upon physico-chemical characteristics of the material but is also significantly dependent upon the organism exposed, with unclear reasons for these differences. Although studies have identified some common mechanistic impacts across species (e.g., oxidative stress), these do not necessarily correlate to adverse outcomes, which may differ by orders of magnitude across species. Differences in toxicological response could potentially be due to species-specific biochemical mechanisms, magnitude of response of common pathways across species, or differences in the exposure and uptake of nanomaterials. In-depth analysis across studies is made difficult as multiple species are not often included in the same study, nanomaterials from multiple sources differ in their characteristics, and variation in exposure duration and media confounds the ability to draw synthetic conclusions from existing cross-species data. The current study examines mechanisms of response across model species Danio rerio, Daphnia magna, and Chironomus riparius to a single-source complex metal oxide, lithium cobalt oxide nanosheets. Each species has previously been shown to have differing sensitivities to NM exposure. RNA-sequencing was used to identify impacted pathways and physiological functions, revealing nanomaterial-specific biochemical responses not replicated by ion exposures, as has also been shown by standard toxicology tests, and importantly that nanomaterial uptake does not fully explain cross-species differences. Significant variation in biochemical response may explain differences, both in the magnitude of response of unifying mechanisms across species and novel pathways impacted in a sensitive or tolerant species. Analysis indicates both commonly identified responses to ENM, including stress, changes in energy metabolism, apoptosis, and immune functions and lesser-explored or novel responses involved in cardiovascular system, hormone, and central nervous system impacts. This comparison demonstrates new universal mechanisms of toxicity for this model ENM and provides insight into how biomolecular responses across species can play a role in varying sensitivity to nanomaterials in general.

overall_design: We made a cross species comparison of global transcriptomic responses to lithium cobalt oxide (LCO) nanosheets. RNA-sequencing samples were generated by collecting 6 replicates of daphnids (10 individuals/replicate), 6 replicates of zebrafish (20 individuals/replicate), and 5 replicates of chironomids (5 individuals/replicate). Samples were chosen for RNA sequencing based on quality control parameters: OD260/OD280 ratio 1.8-2.0 and OD260/OD230 ratio 2.0-2.2 and a RIN >7.

first: Becky

last: Curtis

first: Nicholas

last: Niemuth

first: Evan

last: Bennett

first: Angela

last: Schmoldt

first: Olaf

last: Mueller

first: Aurash

last: Mohaimani

first: Elizabeth

last: Laudadio

first: Yu

last: Shen

first: Jason

middle: C

last: White

last: Hamers


title: Bulk RNA-seq on paws of collagen-induced arthritis (CIA) mouse model at different disease stages

first: Nadine

last: Biesemann

summary: The goal of this experiment is to profile longitudinal transcriptome changes during the development of murine arthritis in CIA mouse model. Male DBA1 mice (age between 10 to 12 weeks) were used in this study. CIA was induced by two immunizations with Type II collagen in Complete Freund’s adjuvant (CFA) at day 0, and with Type II collagen in Incomplete Freund’s adjuvant (IFA) at day 21. Bulk RNA-seq were done on right hind paws from control (non-immunized DBA1 mice) and CIA mice at different disease stages (up to 10 weeks after 1st immunization).

overall_design: Sacrifice at 2 days after 1st immunization: CIA 18, control 6  2 weeks: CIA 15, control 6  3 weeks: CIA 14, control 6  4 weeks: CIA 16, control 5  6 weeks: CIA 17, control 5  7 weeks: CIA 17, control 5  8 weeks: CIA 16, control 5  10 weeks: CIA 15, control 5

first: Lingzi

last: Li

first: Christian

last: Asbrand


title: Differential gain-of-function activity of three p53 hotspot mutants in vivo

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: To identify mutant p53 gain-of-function, primary murine osteosarcomas expressing p53 heterozygous mutants were compared to p53 heterozygous tumors. Transcriptomes regulated by different p53 hotspots were used to identify their mechanisms of action. Validation was done in cell line expressing mutant p53, to confirm its binding to transcription factors Stat3 and Egr1.

overall_design: Primary murine osteosarcomas from all genotypes were collected during necropsy, snap frozen using liquid nitrogen, crushed, and used for RNA-isolation and subsequent sequencing. QC was performed using FastQC. The reads were aligned to GRCm38 reference genome using STAR, and DEGs were identified using DESeq2, and further used for pathway analyses using IPA. Differentially upregulated genes were used to perform promoter analysis to identify enriched motifs of transcription factors using Enrichr, oPOSSUM, and IPA. Cell lines were established from primary murine osteosarcomas at the time of necropsy, and siRNA against p53 was used to knockdown mutant p53 in cell line 14.

first: Dhruv

last: Chachad

first: Xiaoping

last: Su


title: Nuclear GSK-3β and Oncogenic KRas Promote Expansion of Terminal Duct Cells and the Development of Intraductal Papillary Mucinous Neoplasm

first: Hu

institute: Mayo Clinic

summary:
Intraductal papillary mucinous neoplasm (IPMN) represents one precursor lesion of pancreatic ductal adenocarcinoma (PDA), but the cell-of-origin remains unclear.
Here we describe a new mouse model in which pancreas-specific Cre activation of a nuclear glycogen synthase kinase-3β transgene is combined with oncogenic KRas (referred to as KNGC). KNGC mice show accumulation of neoplastic ductal cells at 4-weeks that progressively develop into IPMN with low-grade dysplasia in advanced age.
RNA-sequencing identified expression of several genes found in the terminal duct cell lineage including Agr2 and Aqp5. Interestingly, Aqp5, a water channel, was found to be required for the development of IPMN lesions in KNGC mice. Staining of human IPMN samples indicates that these preneoplastic lesions also arise from expansion of the terminal duct population.
Altogether, these data highlight the utility of the KNGC model for understanding the biology of IPMN and potential utility in defining predictive biomarkers of IPMN – PDA development.

overall_design: Pancreas mRNA profiles of 4-weeks age littlermates Pdx1-cre (WT), Pdx1-cre/LSL-KRasG12D (KC), Pdx1-cre/LSL-nuclear GSK-3β (NGC), Pdx1-cre/LSL-KRasG12D/LSL-nuclear GSK-3β (KNGC) were generated by deep sequencing, in triplicate, using Illumina TruSeq v2 kit.

first: Li

last: Ding

first: Daniel

last: Billadeau


title: A multimodal assay identifies optimized binders for a bicistronic CAR against GPC2 OR CD276 to overcome heterogeneity in Neuroblastoma

status: Public on Mar 18 2022

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Neuroblastoma (NB) is the most common extra-cranial solid tumor in children and remains deadly in patients with high-risk disease. Single chimeric antigen receptor T-cell therapies (CAR-T) for solid tumor have shown poor efficacy in clinical trials due, in part, to T cell exhaustion and uneven expression of target antigens in tumors. Here, we attempted to target Glypican-2(GPC2) and CD276(B7-H3), both highly but heterogeneously expressed on NB cell surface, to overcome these challenges in single CAR T- therapies. First, to identify optimal binders for CAR T- cell targeting each antigen, we made individual CAR constructs using multiple binders against these antigens and utilized a multimodal approach including simultaneous protein and transcriptome measurement at single cell level to characterize each individual CAR T- cell in a pooled strategy. Combined with cell expansion and cytotoxicity assays, we identified the most effective CAR construct for each target.

overall_design: To identify individual CAR T- cells and parallel characterize their functions in the CAR T- competition assay, we designed a multimodal single cell profiling approach(surface protein staining (Biolegend TotalSeq-C lyophilized panel), mRNA and CAR T- binders) using 10x Genomics Chromium system. This assay simultaneously identify CARs by sequencing the binding domain of CARs and assess T cell functions using simultaneous 28 protein markers (plus 3 isotype control anitibodies) and transcriptome measurement at the single cell level (CITE-seq).

first: Tian

last: Meijie

first: Wen

last: Xinyu

first: Wei

last: Jun

first: Khan

last: Javed


title: Differential gene expression in W614A-3S peptide-specific B cell populations following W614A-3S peptide-KLH vaccination using Squalene emulsion and Alum formulation

status: Public on Mar 19 2022

first: Olivia

last: Bonduelle

summary:
W614A-3S peptide is a modified 3S motif of the HIV-gp41 (mutation W614A). We previously detected the presence of natural neutralizing antibodies directed against W614A-3S peptide (NAbs) in long-term non-progressor HIV+ patients. Here, we compared the efficacy of W614A-3S peptide formulated in either squalene emulsion (SQE) or in aluminum hydroxide (Alum) in inducing broadly-NAbs (bNAbs). Rabbit and mouse models were used to screen the induction of bNAbs following 4 immunizations. SQE was more efficient than Alum formulation in inducing W614A-3S-specific bNAbs with up to 67-93% of HIV strains neutralized. We then analyzed the quality of peptide-specific murine B cells by single-cell gene expression by quantitative Reverse Transcription-PCR and single-cell V(D)J sequencing. We found more frequent germinal center B cells in SQE than in Alum, albeit with a different gene expression profile. The V(D)J sequencing of W614A-3S-specific BCR showed significant differences in BCR sequences and validates the dichotomy between adjuvant formulations. All sixteen BCR sequences which were cloned were specific of peptide. Adjuvant formulations of W614A-3S-peptide-conjugated immunogen impact the quantity and quality of B cell immune responses at both the gene expression level and BCR sequence.
We used a single-cell quantitative Reverse Transcription-PCR (qRT-PCR) approach to compare between the two formulations the quality of W614A-3S-specific B cell populations isolated from draining lymph nodes, one week after 2nd and 3rd immunizations (W3 and W5, respectively).

overall_design: Draining lymph nodes (dLNs; n=pool of 5 mice/condition - two independent experiments) were harvested at W3 and W5 after immunization, and used to isolate peptide-specific B cells and to perform single-cell gene expression analysis.


title: Vaccine Induces Dual T cell plus NK cell Attack against Resistant Tumors

city: Boston

first: Soumya

last: Badrinath

address: 1 jimmy fund way

department: Cancer Immunology and Virology

institute: DFCI

summary: Here we report a cancer vaccine that induced a coordinated attack by diverse T cell and NK cell populations.  The vaccine targeted the MICA and MICB (MICA/B) stress proteins expressed by many human cancers due to DNA damage.  MICA/B serve as ligands for the activating NKG2D receptor on T cells and NK cells, but tumors evade immune recognition by proteolytic MICA/B cleavage.  Vaccine-induced antibodies increased the density of MICA/B proteins on the surface of tumor cells by inhibiting proteolytic shedding, increased presentation of tumor antigens by dendritic cells to T cells, and enhanced the cytotoxic function of NK cells.  Importantly, this vaccine maintained efficacy against MHC-I deficient tumors resistant to cytotoxic T cells through the coordinated action of NK cells and CD4 T cells.  The vaccine was also efficacious in a clinically important setting: immunization following surgical removal of primary, highly metastatic tumors inhibited the later outgrowth of metastases.  This vaccine design enables protective immunity even against tumors with common escape mutations.

overall_design:
Single cell RNA-seq on tumor-infiltrating immune cells between the experimental group (MICB-vax + dox) versus the three control groups (control-vax +/- dox, MICB-vax -dox).

Bulk RNA-seq of migratory DCs and NK cells between the experimental group (MICB-iso) versus the three control groups (Ferritin-iso, Ferritin-aCD4, MICB-aCD4)

first: Badrinath

last: Soumya

first: Zheng

last: Shiwei


title: Differentially expressed lncRNAs profile between ischemic stroke patients and non-stroke patients in South China

status: Public on Mar 20 2022

city: Guangzhou

last: Jiang

state: Guangdong

address: 111 Dade Road

department: Department of Second Institute of Clinical Medicine

institute: Guangzhou University of Traditional Chinese Medicine

summary: To evaluate lncRNA expression and changes in whole blood samples of patients during the acute cerebral ischemia phase, we have employed whole genome microarray expression profiling as a discovery platform to identify dysregulated genes to put forth predicted connections and functions of the differentially expressed lncRNAs.There were 1123 differentially expressed lncRNAs (Fold change ≥2.0, p<0.05) between stroke patients and the control group. Among these, 371 lncRNAs were upregulated, and 752 lncRNAs were downregulated. Expression of nine lncRNAs (ENST00000452599, ENST00000527450, ENST00000608826, T013651, T029143, T131416, T294865, ENST00000530525 and T058035) from this signature was quantified in the same RNA samples by real-time PCR, confirming our gene chip performance.

overall_design: For five stroke patients, it was performed after symptom onset, with times varying from a few hours to two weeks. For five control samples, this time point was recorded as zero.

first: Xiao

last: Cheng


title: Hypothalamic Microglia Activation is Associated with High Fat Diet-Induced Obesity and Metabolic Dysfunction in Mice

status: Public on Mar 14 2022

city: Hershey

first: Anirban

last: Paul

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

summary: Comparing the effect of high-fat diet and minocycline in mouse PVN.

overall_design: PVN bulk RNA profile from adult mouse.

first: Yuval

last: Silberman

first: Amy

last: Arnold


title: CD8+ T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

institute: Institut Curie

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

overall_design: Refer to individual Series


title: CD8+ T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas [ATAC-seq]

summary: Purpose: We show that genetic ablation or pharmacological inhibition of H3K9-methyl transferase Suv39h1 delays tumor growth and potentiates tumor rejection by anti-PD-1.

overall_design: Suv39h1-KO and littermate WT mice were injected with B16-OVA tumor cells. On day 20, tumors were processed with Liberase and DNase I, stained with DAPI,  CD45.2, TCRb, CD8, CD19, NK1.1, F4/80 and sorted on an Aria (BD) by gating on live,  CD45.2+, (CD19, NK1.1, F4/80 negative cells) and CD8+ on PBS 0.04% BSA. Chromatin profiling was performed by ATAC-seq as described in Buenrostro et al. In brief,  50,000 cells per sample were washed in cold PBS and lysed. Transposition reaction was  performed at 37°C for 30 minutes and DNA was purified with MinElute PCR purification kit  (Qiagen). Transposed DNA was amplified for 5 cycles and additional PCR cycles were  evaluated by real time PCR. Libraries were sequenced on Novaseq 6000 using 1xSp-Flow  (Illumina). A total of 130 to 210x106 paired reads were generated per sample.

first: Leticia

last: Niborski

first: Mengliang

last: Ye


title: profile of exosomal microRNA in ovarian cancer cell line culture media

status: Public on Mar 08 2022

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

institute: Hirosaki university

summary: Exosomes endogenous microRNAs (miRNAs) play critical roles in many biological processes.to obtain profiles of the miRNAs of exosomal and cell lysates in ovarian cancer cell lines.

overall_design: We used five ovarian cancer cell lines of different histological types and as a control is Ovarian Surface Epithelial Cell. Next, isolate the exosomes and extract the miRNAs. And then, to quality check and quantitation of miRNA and microarray to analyzed the exosomal and cell lysate miRNAs.


title: Lineage factor functions in renal carcinoma [II]

status: Public on Mar 11 2022

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: The oncogenic potential of cancer-associated genetic alterations displays strong tissue-selectivity, the origins of which remain poorly understood. Here, we demonstrate that the lineage transcription factor PAX8 is essential for oncogenic signaling downstream of the most common genetic alterations causing clear cell renal cell carcinoma (ccRCC). Through interaction at a distal enhancer element PAX8 facilitates CCND1 expression by HIF2A, an oncogenic driver that is genetically activated due to VHL loss in ~90% of ccRCCs. PAX8 binding at this enhancer which mediates HIF2A-dependent ccRCC formation is inhibited by the common ccRCC protective allele C at rs7948643. In addition, PAX8 supports MYC expression in ccRCC through HNF1B, another renal lineage factor. Transcriptional lineage factors are thus critical determinants of the tissue-specific cancer risk associated with somatic and inherited genetic variants. Our data also suggest that lineage factors could be targeted for therapeutic inhibition of canonical oncogenic drivers such as MYC and CCND1.

overall_design: mRNA profiling in experimental models of renal carcinoma.

first: Saroor

middle: A

last: Patel


title: RNA seq of mouse CD3 T cells

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary:
Purpose: To gain more mechanistic insights into the effects of SDHB deletion in T cells, we performed RNAseq in activated WT and SDHB cKO T cells.
Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA).
Results: RNA-seq revealed an enriched pro-inflammatory gene signature in SDHB cKO T cells after activation
Conclusions: SDH inactivation results in a pro-inflammatory gene signature in T cells after activation

overall_design: mRNA profiles of activated WT and SDHB KO T cells were generated by deep sequencing, using Illumina GAIIx.

first: Jun

last: Yang

first: Ruoning

last: Wang


title: CD8+ T cell responsiveness to anti-PD-1 is epigenetically regulated by Suv39h1 in melanomas [scRNA-seq]

overall_design: Suv39h1-KO and littermate WT mice were injected with B16-OVA tumor cells. On day 20, tumors were processed with Liberase and DNase I, stained with DAPI,  CD45.2, TCRb, CD8, CD19, NK1.1, F4/80 and sorted on an Aria (BD) by gating on live,  CD45.2+, (CD19, NK1.1, F4/80 negative cells) and CD8+ on PBS 0.04% BSA.  Cells were loaded on a 10x Chromium instrument (10x Genomics) and libraries were  prepared using a Single Cell 3′ Reagent Kit (V2 chemistry) (10x Genomics) according to  manufacturer’s protocol. Sequencing reads were aligned to the mm10 transcriptome using the Cell Ranger suite with default parameters


title: Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress

status: Public on Mar 07 2022

city: Liberec

first: Alena

last: Sevcu

state: Liberec

address: Bendlova 1409/7

department: Applied Biology

country: Czech Republic

institute: Technical University of Liberec

summary:
Objective: We aimed to decipher how the transcriptome of P.putida would regulate in the presence of 100 mg/L nZVI and its surplus iron released from nZVI, (44.5 μg/L of dissolved iron obtained from nZVI suspension over 24 h in environmental-sourced reservoir) using Next-Seq RAN-sequencing on an Illumina Next-Seq platform
Results: Transcriptomic analysis revealed more pronounced differentially expressed genes (DEGs) caused by dissolved iron (3,839 DEGs) against nZVI (945 DEGs). Dissolved iron (but not nZVI) triggered mostly hypothetical genes, and genes which dual-regulating the oxidative stress-antioxidant response, carbohydrate metabolism, and energy metabolism, a cascade effect which demands high ATP and NADPH energy fuels, but downregulated genes associated with flagellar assembly and two-component systems. The results compare and deepen our understanding of iron particle and ionic stressors effect which triggered different transcriptomic trajectories on soil bacterium, and uncovers the underlying energy-fueled mechanism to resolve oxidative insults due to the iron-exchanging activity within cells.

overall_design: Transcriptomic profile of Pseudomonas putida exposed to nZVI after 0 h, 6 h, 24 h and 24-h exposed to dissolved iron

first: Cheryl

last: Yeap

first: Vladimir

last: Benes

first: Roman

last: Spanek

first: Jan

last: Provaznik


title: Astronauts plasma-derived exosomes induced gene expression in AC16 cells

status: Public on Mar 12 2022

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

summary: There are unique stressors in the spaceflight environment. Exposure to such stressors is associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. Human adult ventricular cardiomyocyte cells (AC16) were treated with L-10 and R+3 astronauts-derived exosomes for 24 hours. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Transcription factor enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes c by promoting the activation of the PRC2 complex and H3K27me3 levels.

overall_design: Gene expression was measured in untreated (n = 3) and exosome-treated (n = 6) AC16 human cardiomyocyte cell line. Cell were treated with exosomes isolated from 3 austonauts at two different time points: 10 days before mission (n = 3) and 3 days upon return from mission (n = 3).

first: Malik

last: Bisserier

first: Agnieszka

last: Brojakowska

first: Nathaniel

last: Saffran

first: Amit

last: Rai

first: Matthew

last: Coleman

first: Aimy

last: Sebastian

first: Angela

last: Evans

last: Mills

first: Sankar

last: Addya

first: Venkata

last: Garikipati

first: Lahouaria

last: Hadri

first: David

last: Goukassian


title: PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production -- DATA HAVE BEEN MOVED TO GSE193942

status: Public on Mar 06 2022

city: Singapore

first: Anand

last: Jeyasekharan

state: Outside US/Canada

address: 14 Medical Drive,  Centre for Translational Medicine, 13-02 Bench 13

country: Singapore

institute: Cancer Science Institute of Singapore

summary: See GSE193942

overall_design: See GSE193942


title: Gene expression based profiling of tumor and mediastinal and hilar lymph nodes in NSCLC

status: Public on Mar 05 2022

city: München

first: Laura

last: Sellmer

address: Ziemssenstrasse 1

institute: Department of Medicine V

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 770 genes in 16 surgically-trested non-small cell lung cancer (NSCLC) cases with a focus on immune exhaustion

overall_design: In the study presented here, an operated well-defined cohort of 16 NSCLC cases, was used to acquire expression profiles of a total of 770 unique genes, leading to the analysis of immune suppressive environments and immune exhaustion in NSCLC

first: Julia

last: Kovacs

last: Walter

first: Jörg

last: Kumbrink

first: Jens

last: Neumann

first: Diego

last: Kauffmann-Guerrero

first: Rosemarie

last: Kiefl

first: Christian

last: Schneider

first: Andreas

last: Jung

first: Jürgen

last: Behr

first: Amanda

last: Tufman


title: Real-time quantitative PCR analysis of human serum

city: Salamanca

first: Luis

middle: Miguel

last: Rincon

state: Salamanca

address: Paseo de San Vicente 58-182

department: Cardiology

institute: Hospital Universitario de Salamanca

summary: Blood samples for determination of serum miRNAs in acute myocardial infarction

overall_design: qPCR miRNA expression profiling. 200 ul of Serum samples from 10 healthy individuals distributed in two pools of 5 individuals each and 3 patients per test group (STEMI/NSTEMI) were used for quantitative PCR Array screening of 752 miRNAs using the  miRCURY LNA Universal RT microRNA PCR, 4x Human panel I+II in 384well PCR plates (type R),  (Exiqon 203616).

last: Rincón


title: Lineage factor functions in renal carcinoma - ChIP-seq

first: Sakari

last: Vanharanta

overall_design: ChIP-seq profiling in experimental models of renal carcinoma.

first: Saroor

last: Patel

first: Shoko

last: Hirosue

first: Paulo

last: Rodrigues


title: Bulk single nuclear sequencing in the ventral medial preoptic area

status: Public on Mar 02 2022

city: Cambridge

first: Catherine

last: Dulac

state: MA

address: 16 Divinity Ave

institute: Harvard

summary: Single nuclear RNA-sequencing from tissue dissected from the ventral medial preoptic area (VMPO) of the hypothalamus in saline and LPS injected mice

overall_design: The saline and LPS samples were composed of a pool of 5 VMPO dissections each

first: Jessica

last: Osterhout

first: Eric

last: Vaughn


title: Lineage factor functions in renal carcinoma [I]

first: Erika

last: Vojtasova


title: Functional study on the mutations of HBV X gene

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University


title: mRNA vaccination in octogenarian nuns 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron

status: Public on Mar 09 2022

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Knowledge about the impact of prior SARS-CoV-2 infection of the elderly on mRNA vaccination response is needed to appropriately address the demand for additional vaccinations in this vulnerable population. Here we show that octogenarians, a high-risk population, mount a sustained SARS-CoV-2 spike-specific IgG antibody response for 15 months following infection. This response boosts antibody levels 35-fold upon receiving a single dose of BNT162b2 mRNA vaccine 15 months after recovery from COVID-19.  In contrast, antibody responses in naïve individuals boost only 6-fold after a second vaccine. Spike-specific ACE2 antibody binding responses in the previously infected octogenarians following two vaccine doses exceed those found in a naïve cohort after two doses. RNA-seq demonstrates activation of interferon-induced genetic programs, which persist only in the previously infected. A preferential increase of specific IGHV clonal transcripts that are the basis of neutralizing antibodies is observed only in the previously infected nuns.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from recovered COVID-19 patients and naïve individuals who had received the BNT162b mRNA vaccine.

first: Hye

first: Ludwig

last: Knabl


title: Lineage factor functions in renal carcinoma - ATAC-seq

overall_design: ATAC-seq profiling in experimental models of renal carcinoma.


title: Expression data from sheroids cultured in medium that promotes myoepithelial or proacinar differentiation

city: Albany

first: Susan

middle: Ellen

last: LaFlamme

state: New York

address: 47 New Scotland Ave

department: Regenerative and Cancer Cell Biology

institute: Albany Medical Center

summary:
We identifiied culture conditions that promoted the differentiation of the murine salivary gland epithelial cell line, mSG-PAC1 towards myoepithelial or proacinar cell fates, which were characterized by the expression of known cell type markers.
Differentiation gene expression was analyzed and GSEA was performed comparing the resulting transcirptomes and published sc_RNA seq data for murine salivary gland myoepithleial and acinar cells

overall_design: Cells were cultured in Matriget for 5 days in either medium that  promoted myoepithelial or proacinar differentiaiton. RNA was extracted and processed for microarray analysis

first: Renee

last: Thiemann

first: Scott

last: Varney

first: Nicholas

last: Moskwa

first: John

last: Lamar

first: Melinda

last: Larsen


title: The transcriptomic landscape of the photoperiodic stress response in Arabidopsis thaliana resembles the response to pathogen infection

status: Public on Feb 28 2022

city: Berlin

first: Anne

last: Cortleven

address: Albrecht-Thaer-Weg 5

department: Institut fur Biologie

institute: FU Berlin

summary: Plants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signaling and clock mutants. Transcriptomic changes induced by photoperiod stress included numerous changes in reactive oxygen species (ROS)-related transcripts and showed a strong overlap with alterations occurring in response to ozone stress and pathogen attack, which have in common the induction of an apoplastic oxidative burst. A core set of photoperiod stress-responsive genes has been identified, including salicylic acid (SA)-biosynthesis and -signaling genes. Genetic analysis revealed a central role for NPR1 in the photoperiod stress response as npr1-1 mutants were stress-insensitive. Photoperiod stress treatment led to a strong increase in camalexin levels which is also observed in response to pathogen infections. Photoperiod stress induced the resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae pv. tomato DC3000 indicating priming of the defence response. Together, photoperiod stress causes transcriptional reprogramming resembling plant pathogen defence responses and induces systemic acquired resistance in the absence of a pathogen.

overall_design: 5-weeks-old short day-grown Arabidopsis plants (WT, ahk2 ahk3, cca1 lhy) were exposed to a 24 h-extended light period (32 h light in total). Sampling for RNAseq analysis was done at 0 h, 4 h, 6 h and 12 h after the end of the prolonged light period. Control plants were sampled on the same moment. For each sampling point, three biological and three technical replicates were taken.

first: Venja

last: Roeber

first: Manuel

last: Frank

first: Jonas

last: Bertels

first: Gerrit

last: Beemster

first: Thomas

last: Schmülling


title: Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression.

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences III

institute: UC Irvine

summary: The complement system is part of the innate immune system that works to clear pathogens and cellular debris. In the central nervous system (CNS)  complement activation can promote synaptic pruning  clearance of neuronal blebs  recruitment of phagocytes  and protection from pathogens. However  in a neuropathologic environment  complement activation may contribute to inflammatory pathways  neuronal dysfunction  and  in the Alzheimer’s disease (AD) brain  cognitive decline. If complement activation proceeds to the cleavage of C5 and thus generation of C5a  engagement of C5a with the receptor C5aR1 can instigate a feed-forward loop of inflammation  injury  and neuronal death  thus making this molecule a potential target for modulation in AD therapeutics. The Arctic (Arc) AD mouse model  known to rapidly accumulate fibrillar amyloid plaques  was crossed to a model that lacks the receptor for C5a (ArcC5aR1KO) or to a transgenic mouse that generates C5a under the GFAP promoter (ArcC5a+). ArcticC5a+ mice showed accelerated loss of spatial memory compared to Arc mice. While eliminating C5aR1 did not alter amyloid plaque accumulation in this AD model  C5aR1KO delayed or prevented the expression of important AD-associated genes in the hippocampus  indicating a separation between those genes induced by amyloid plaques and those influenced by C5a-C5aR1 signaling. C5ar1 deletion also reduced/delayed the expression of select pan-reactive and A1 reactive astrocyte genes. ArcC5aR1KO showed delayed expression of genes enriched for biological processes that are significant in the AD context  such as regulation of inflammatory signaling  microglial cell activation  astrocyte migration  and lysosome pathway. Interestingly  overexpression of C5a also delayed the increase of some AD-  complement  and astrocyte-associated genes perhaps mediated by C5aR2  and emphasizing the importance of selectively suppressing C5aR1. Immunohistochemical investigation further confirmed that modulation of C5a-C5aR1 either delayed or reduced some reactive microglial markers in the Arc hippocampus  including CD11b and CD11c.  These results suggest that C5a-C5aR1 signaling in the context of AD largely exerts its effects by suppressing those microglial activation pathways that accelerate disease enhancing pathways. Given the highly focused modulation of a common driver of neurotoxicity  pharmacological inhibition of this C5aR1 signaling pathway is a promising therapeutic strategy to treat AD.

overall_design: Bulk RNA-seq libraries of 6 distinct mice genotypes

first: Klebea

last: Carvalho

first: Nicole

last: Schartz

first: Andrea

last: Tenner


title: Lineage factor functions in renal carcinoma

first: Sakari

last: Vanharanta

overall_design: Refer to individual Series


title: MicroRNA-21 is immunosuppressive and pro-metastatic via separate mechanisms

status: Public on Mar 01 2022

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: MiR-21 was identified as a gene whose expression correlated with the extent of metastasis of murine mammary tumours. Since miR-21 is recognized as being associated with poor prognosis in cancer, we investigated its contribution to mammary tumour growth and metastasis in tumours with capacity for spontaneous metastasis. Unexpectedly, we found that suppression of miR-21 activity in highly metastatic tumours resulted in regression of primary tumour growth in immunocompetent mice but did not impede growth in immunocompromised mice. Analysis of the immune infiltrate of the primary tumours at the time when the tumours started to regress revealed an influx of both CD4+ and CD8+ activated T cells and a reduction in PD-L1+ infiltrating monocytes, providing an explanation for the observed tumour regression. Loss of anti-tumour immune suppression caused by decreased miR-21 activity was confirmed by transcriptomic analysis of primary tumours.  This analysis also revealed reduced expression of genes associated with cell cycle progression upon loss of miR-21 activity. A second activity of miR-21 was the promotion of metastasis as shown by the loss of metastatic capacity of miR-21 knockdown tumours established in immunocompromised mice, despite no impact on primary tumour growth.  A proteomic analysis of tumour cells with altered miR-21 activity revealed deregulation of proteins known to be associated with tumour progression. The development of therapies targeting miR-21, possibly via targeted delivery to tumour cells, could be an effective therapy to combat primary tumour growth and suppress the development of metastatic disease.

overall_design: Comparison of the transcriptomic profiles of control tumours and miR-21-knockdown tumours (n=4/group).

first: Soroor

last: Hediyeh-zadeh

first: Laphing

last: Chi


title: Gene expression of microdissected colon epithelium

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

summary: RNA-seq analysis of total RNA isolated from laser capture microdissected intestinal epithelium. The analysis aimed at characterizing the epithelial gene expression changes in IBD patients vs. healthy controls.

overall_design:
Microdissected epithelial monolayer from five patients with active Crohn's disease (CD), five patients with inactive CD, seven patients with active ulcerative colitis (UC), six patients with inactive UC and six healthy controls were included in the final analysis. 29 samples in total; active IBD (12), uninflamed IBD (11), healthy controls (6)

>>>Submitter states: raw data not provided as Norwegian law does not allow public access to human sequences raw data<<<

first: Siri

last: Sæterstad

first: Ann

last: Østvik

first: Elin

last: Røyset

first: Ingunn

last: Bakke

first: Arne

last: Sandvik


title: Dynamic lncRNA expression pattern during ESC-derived cardiac differentiation

city: nanjing

first: liu

middle: xiao

last: min

state: jiangsu

address: longmiandadao

department: College of life science and technology

institute: China Pharmaceutical University

summary: Long noncoding RNAs (lncRNAs) have emerged as crucial regulators of gene expression during embryonic stem cell (ESC) self-renewal and differentiation. Here, we systemically analyzed the differentially regulated lncRNAs during ESC-derived cardiomyocyte (CM) differentiation. We established a perspicuous profile of lncRNA expression at four critical developmental stages and found that the differentially expressed lncRNAs were grouped into six distinct clusters. The cluster with specific expression in ESC enriches the largest number of lncRNAs. Investigation of lncRNA-protein interaction network revealed that they are not only controlled by classic key transcription factors, but also modulated by epigenetic and epitranscriptomic factors including N6-methyladenosine (m6A) effector machineries.

overall_design: Examination of lncRNA expression among different stages of mESC-derived cardiac differentiation.

first: Xiaomin

last: Liu

first: Jun

last: Zhang

first: Shen

last: Wang


title: Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module

status: Public on Feb 23 2022

city: Bethesda

first: Hye Kyung

last: Lee

summary: Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. While viral infections elicit a conserved immune response, it is not known whether SARS-CoV-2 variants, which display reduced neutralizing activity by vaccine-elicited antibodies, prompt specific genomic immune responses. To test this, we generated and investigated the transcriptomes in PBMCs from hospitalized patients infected with either the Alpha variant (n=36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n=13). We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Alpha (n=9) and Gamma (n=3) variants that also carry by the E484K escape mutation. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. However, both cohorts had undergone similar treatments and no differences in disease severity were reported suggesting that this signature reflects a variant response and does not necessarily associate with disease outcome. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. While the OAS1 Neanderthal mutation has been linked to a milder COVID-19 pathology, we did not identify significant immune transcriptomes differences in the 25 patients homozygous for this mutation. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Alpha varient with or without the escape mutation.

first: Hye

first: Ludwig

last: Knabl


title: Arabidopsis: 3OC8-HSL-treated  vs Control

city: Shijiazhuang

first: Fang

state: HeBei

address: 46th, South Street of Friendship

department: Biology Institute

institute: Biology Institute, Hebei Academy of Sciences

summary:
Transcriptional profiling of Arabidopsis comparing 10 μM 3OC8-HSL-treated Arabidopsis wild-type Col-0 with control untreated Col-0.
A transcriptomic analysis for Arabidopsis responses to bacterial quorum sensing molecule N-3oxo-octanoyl-homoserine lactone (3OC8-HSL).

overall_design: Two-condition experiment, 3OC8-HSL-treated Arabidopsis vs untreated Arabisopsis. One replicate per array

first: Shuishan

last: Song

first: Qian

last: Zhao


title: Heterogeneity and Clonality of Kidney-infiltrating T cells in Murine Lupus Nephritis.

status: Public on Feb 24 2022

city: Pittsburgh

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose:We previously found that kidney-infiltrating T cells (KITs) in murine lupus nephritis (LN) resembled dysfunctional T cells that infiltrate tumors. This unexpected finding raised the question of how to reconcile the “exhausted” phenotype of KITs with ongoing tissue destruction in LN.
Methods: we performed scRNA-seq and TCR-seq of KITs in murine lupus models using 10X Genomics Chromium system .
Results: We found that CD8 KITs exist first in a transitional state, before clonally expanding and evolving toward exhaustion. On the other hand, CD4 KITs did not fit into current differentiation paradigms, but included both hypoxic and cytotoxic subsets with a pervasive exhaustion signature. Thus, autoimmune nephritis is unlike acute pathogen immunity; rather the kidney microenvironment suppresses T cells by progressively inducing exhausted states. Our findings suggest that lupus nephritis, a chronic condition, results from slow evolution of damage caused by dysfunctional T cells and their precursors on the way to exhaustion. These findings have implications for both autoimmunity and tumor immunology.

overall_design: mRNA profiles of CD4 and CD8 T cells from spleen and kidney of murnine lupus nephritis models were generated in triplicate by sequencing using Illumina NextSeq 500

first: Shuchi

last: Smita

first: Jeremy

middle: S

last: Tilstra