title: Circulating PMN-MDSCs correlates with poor prognosis in metastatic hormone sensitive prostate cancer

status: Public on Jun 30 2022

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

country: Japan

institute: Tohoku Medicine and Pharmaceutical University

type: Expression profiling by high throughput sequencing

summary: Myeloid-derived suppressor cells are recognized as a immunosuppressive cells in cancer but the characteritics in prostate cancer have not yet been known. We analyzed MDSCs and immune cells by single cell RNA sequence to clarify their variationos in prostate cancer.

overall_design: Blood samples from a healthy control and a patient were collected and periperal white blood cells (pWBCs) were enriched. The pWBCs were analyzed in scRNAseq.

first: Yuki

last: Kohada

first: Akira

last: Nakamura

first: Makoto

last: Sato


title: Non-canonical imprinting ensures embryonic development   and restrains placental overgrowth

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Genomic imprinting regulates parental origin-dependent mono-allelic gene expression. It is mediated by either germline differential methylation of DNA (canonical imprinting) or oocyte-derived H3K27me3 (non-canonical imprinting) in mice. Depletion of Eed, an essential component of Polycomb repressive complex 2, results in genome-wide loss of H3K27me3 in oocytes, which causes loss of non-canonical imprinting (LOI) in embryos. Although Eed maternal KO (matKO) embryos show partial lethality after implantation, it is unknown whether LOI itself contributes to the developmental phenotypes of these embryos, which makes it unclear whether non-canonical imprinting is developmentally relevant. Here, by combinatorial matKO of Xist, a non-canonical imprinted gene whose LOI causes aberrant transient maternal X chromosome inactivation (XCI) at preimplantation, we show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Moreover, we find that the placentae of Eed matKO embryos are remarkably enlarged in a manner independent of Xist LOI. Heterozygous deletion screening of individual autosomal non-canonical imprinted genes suggests that LOI of the Sfmbt2 miRNA cluster-chromosome 2 miRNA cluster (C2MC), solute carrier family 38 member 4 (Slc38a4), and Gm32885 contributes to the placental enlargement. Taken together, our study provides evidence that Xist imprinting sustains embryonic development and autosomal non-canonical imprinting restrains placental overgrowth.

overall_design: RNA-seq was performed in Eed or Eed/Xist CTR and maternal KO/DKO morula embryos (xPWK sperm).

first: Shogo

last: Matoba

first: Chisayo

last: Kozuka

first: Kento

last: Miura

first: Kimiko

first: Mami

last: Kumon

first: Ryoya

last: Hayashi

first: Tatsuya

last: Ohhata

first: Atsuo

last: Ogura


title: Transcriptomic analysis of LN229 cell treated by unit of bortezomib and panobinostat

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

country: China

institute: Henan University

summary: We report the application of  unit of bortezomib and panobinostat on LN229 cell , and further explored the mechanism of drugs on GBM cells.

overall_design: Examination of transcriptome levels in LN229 cell treated by unit of bortezomib and panobinostat.

first: Yuanyuan

last: Liu

first: Bingyang

last: Shi

last: Wu


title: Transcriptome and N6-methyladenosine RNA methylome analysis of YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma

city: Nanjing

first: Zhen

last: Hua

state: Jiangsu

address: 138 Xianlin Avenue, Xianlin University Town, Nanjing

institute: Nanjing University of Chinese Medicine

summary: To identify the m6A methylome in Multiple Myeloma cells.MeRIP-seq and RNA-seq experiments was conducted to analyze changes in related signaling pathways and gene expression in colon cancer cells when YTHDF2 was knocked down.

overall_design: Examination of  two cell types


title: LncRNA SPRY4-IT1 Facilitates Cell Proliferation and Angiogenesis of Glioma by the miR-101-3p/EZH2/VEGFA Signaling Axis

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

institute: Soochow University

summary: SPRY4-IT1 (SPRY4 intronic transcript 1) is a long non-coding RNA (lncRNA) that was identified as a novel oncogene in various human cancers, including glioma. However, its function and the further mechanism in glioma remain largely unclear. Here, we aimed to investigate the role of SPRY4-IT1 in the development of glioma and its underlying molecular mechanism. We identify that SPRY4-IT1 is overexpressed in patients with glioma from the TCGA database and own cohort, and correlated with poor prognosis of patients. Then, loss of function and gain of function cell model were established by transfected with siRNA and pcDNA3.1 plasmid. SPRY4-IT1 promotes glioma cells proliferation by Cell Count Kit 8 assays and EdU assay in vitro, and xenograft tumor assays in vivo. RNA sequence was performed to compare the transcriptomes of U87 siSPRY4-IT1-NC and U87 siSPRY4-IT1 cells, and Gene Ontology (GO) enrichment analysis indicated angiogenesis is significantly enriched. HUVEC tube forming assays and Chick Embryo Chorioallantoic Membrane (CAM) assays confirmed that SPRY4-IT1 can induce angiogenesis of glioma in vitro and in vivo. Mechanistically, we identify that SPRY4-IT1 upregulates EZH2 expression by sponge miR-101-3p to induce VEGFA expression in glioma cells. Moreover, SPRY4-IT1 activates VEGFR2/AKT/ERK1/2 pathway in HUVECs by glioma cell-mediated. Rescue experiments were performed by co-transfected with SPRY4-IT1 and EZH2 overexpression plasmid in glioma cells, and confirmed that SPRY4-IT1 promotes cell proliferation and angiogenesis of glioma by miR-101-3p/EZH2/VEGFA signaling axis. Taken together, our studies clarify that SPRY4-IT1 upregulates EZH2 to induce VEGFA by sponge miR-101-3p to achieve cell proliferation and angiogenesis in glioma. Thus, these findings have provided insights into the prognosis prediction and therapeutic target of glioma.

overall_design: To test the effect of suppression of SPRY4-IT1 on the gene expression, U87 cells were transfected with SPRY4-IT1 Scramble siRNA (control) or SPRY4-IT1 siRNA. SPRY4-IT1-knockdown U87 cells were compared to control cells.

first: Yanming

last: Chen

first: Qing

last: Lan


title: Genetic Dissection of Photosynthetic Organs Contribution to Seed Oil Accumulation in Arabidopsis seeds

city: Wuhan

first: Chinedu

middle: Charles

last: Nwafor

state: Hubei

address: No. 1 shizeshan street

department: College of Plant Science and Technology

institute: Huazhong Agricultural University Wuhan

summary: We report the application of RNA-seq technology for highthroughput profiling of photosynthetic and non-photosynthetic seeds of Arabidopsis chlorophyll synthase mutant seeds. By generating over 21 GB of sequence data from these seeds, we showed that genes involved in oil accumulation in non-photosynthetic seeds were significantly induced compared to photosynthtic seeds. Additionally we found that genes involved in the plastidal oxidative pentos phosphate pathway were significantly upregulated in the non-photosynthetic seed opposite to photosynthetic seeds. Overall our RNA-seq analysis revealled the genes and pathway interaction underpinining oil accumulation in non-photosynthetic seeds.

overall_design: Examination of segregating green (photosynthetically-competent) and non-green (photosynthetically-non-competent) seeds in siliques of an Arabidopsis chlorophyll synthase mutant.

middle: C

first: Chunyu

last: Zhang


title: YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Analysis of transcriptome in mouse tissue following Mycobacterium avium subsp. paratuberculosis infection

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: Purpose : Comparative analysis of host transcriptomes according to infection route following MAP infection  Methods : Mice were infected with MAP by oral/intraperitoneal (IP) route. Total RNA were harvested from spleen and mesenteric lymph node after 6 weeks. RNA-seq was performed with total RNA of each sample.  Results : Canonical pathway analysis showed that LXR/RXR activation pathway had negative z-score in IP group, whereas positive in oral group.

overall_design: Gene expression analysis with animal model using RNA-seq analysis

first: Han Sang

last: Yoo

first: Jun Ho

last: Lee

first: Soojin

last: Shim

first: Suji

last: Kim


title: Donor Macrophages Modulate Rejection after Heart Transplantation

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

country: USA

institute: Washington University School of Medicine

summary: Cellular rejection after heart transplantation imparts significant morbidity and mortality. Current immunosuppressive strategies are imperfect, target recipient T-cells, and have adverse effects. The innate immune response plays an essential role in the recruitment and activation of T-cells. Targeting the donor innate immune response would represent the earliest interventional opportunity within the immune response cascade. There is limited knowledge regarding donor immune cell types and functions in the setting of cardiac transplantation and no current therapeutics exist for targeting these cell populations.  Distinct populations of donor and recipient macrophages co-exist within the transplanted heart. Donor CCR2+ macrophages are key mediators of allograft rejection and deletion of MYD88 signaling in donor macrophages is sufficient to suppress rejection and extend allograft survival. This highlights the therapeutic potential of donor heart-based interventions.

overall_design: Single cell n=

first: Benjamin

middle: J

last: Kopecky

first: Hao

last: Dun

first: Junedh

middle: M

last: Amrute

first: Chieh-Yu

last: Lin

first: Andrea

middle: L

last: Bredemeyer

first: Yuriko

last: Terada

first: Peter

middle: O

last: Bayguinov

first: Andrew

last: Koenig

first: C

last: Frye

first: James

last: Fitzpatrick

first: Daniel

last: Kreisel


title: Transcriptomics study of resistant and susceptible wheat lines to tan spot disease (Pyrenophora tritici-repentis)

city: Aberystwyth

first: Luis

middle: A J

last: Mur

address: Penglais Road

department: IBERS

country: United Kingdom

institute: Aberystwyth University

summary: Tan Spot (TS), causal agent Pyrenophora tritici-repentis (Ptr), is a major threat to wheat production due to the lack of resistant cultivars. In our previous work, we identified MAGIC population parental lines exhibiting TS resistance and susceptibility, namely Robigus and Hereward, respectively. To understand the mechanisms underlying these phenotypes, we performed RNA-seq analysis of leaves before and during Ptr interaction.  When comparing mock- and Ptr-inoculated samples, differentially expressed genes (DEGs) were identified with DESeq2, leading to the targeting of 15193 DEGs. Functional annotation showed the pathways enzyme classification, solute transport, RNA biosynthesis, protein modification and homeostasis represented 49.5% of DEGs in Robigus. Cellular metabolism pathways were induced, as well as vesicle trafficking, actin polymerization and cellulose. The upregulation of these cell wall related genes along with microscopic data suggested that barrier defence is a major feature of TS resistance in Robigus. Conversely, photosynthesis was the top fifth pathway in Hereward, totalling 389 repressed genes (12.63%). Photosynthesis collapse was linked to the activation of oligosaccharide metabolism and suppression of glycolysis, TCA cycle and amino acids degradation. This may reflect mobilization of host nutrients to Ptr. Our observations could inform wheat-breeding programmes targeting TS resistance.

overall_design: Examination over time (0, 48 and 96 h) of two wheat lines (Robigus and Hereward) inoculated with Pyrenophora tritici-repentis or mock-inoculated

first: Larissa

last: Ferreira

first: Flavio

last: Santana

middle: A


title: Reduction of Cardiac Fibrosis by Interference With YAP-Dependent Transactivation

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary: Conversion of cardiospheres derived primitive cardiac stromal cells  into myofibroblasts is typically associated with hypoxia conditions, metabolic insults, and/or inflammation, all of which are predisposing factors to cardiac fibrosis and heart failure. We hypothesized that this conversion could be also mediated by response of these cells to mechanical cues through activation of the Hippo transcriptional pathway. The objective of the present study was to assess the role of cellular/nuclear straining forces acting in myofibroblast differentiation of cardiospheres derived primitive cardiac stromal cells  under the control of YAP transcription factor and to validate this finding using a pharmacological agent that interferes with the interactions of the YAP/TAZ complex with their cognate transcription factors TEADs, under high-strain and pro-fibrotic stimulation. We employed high content imaging, 2D/3D culture, atomic force microscopy mapping and molecular methods to prove the role of cell/nuclear straining in YAP-dependent fibrotic programming in a mouse model of ischemia-dependent cardiac fibrosis and in human-derived primitive cardiospheres derived primitive cardiac stromal cells . We also tested treatment of cells with Verteporfin, a drug known to prevent the association of the YAP/TAZ complex with their cognate transcription factors TEADs. Results suggested that pharmacologically targeting the YAP-dependent pathway overrides the pro-fibrotic activation of cardiospheres derived primitive cardiac stromal cells  by mechanical cues in vitro, and that this occurs even in the presence of pro-fibrotic signaling mediated by TGF-β1. In vivo administration of Verteporfin in mice with permanent cardiac ischemia reduced significantly fibrosis and morphometric remodeling but did not improve cardiac performance. Our study indicates that preventing molecular translation of mechanical cues in cardiospheres derived primitive cardiac stromal cells  reduces the impact of cardiac maladaptive remodeling with a positive effect on fibrosis.

overall_design: A total of 24 samples has been analyzed from 6 independent cultured cSt-Cs stimulated or not with TGF beta, verterporfin or a combination of the two. Samples were analysed for differentially expressed genes according to a paired-sample design between treated and untreated (control) cSt-Cs.

first: Mattia

last: Chiesa

first: Luca

last: Piacentini

first: Manzoni

last: Martina

first: Garoffolo

last: Gloria

middle: I

first: Maurizio

last: Pesce


title: The C-terminus of p53 Confers Liver-Specific Gene Regulation and Radio-Resistance in vivo [RNA-Seq]

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

summary: Thymus and spleen, in contrast to liver, are radiosensitive tissues in which p53-dependent apoptosis is triggered after whole body radiation in vivo. Combined RNA-seq and ChIP-seq analyses of radiation-treated mouse organs identifies both shared and tissue-specific p53 transcriptional responses. As expected, the p53 targets shared amongst thymus and spleen are enriched in apoptotic targets. Surprisingly, the inability to upregulate these genes in the liver is not due to reduced gene occupancy. Use of an engineered mouse model shows that deletion of the C-terminus of p53 can confer radiation-induced expression of p53 apoptotic targets in the liver with concomitant increased cell death. Global RNA-seq analysis reveals an additional role of the C-terminus being also needed for transcriptional activation of liver-specific p53 targets. It is hypothesized that both suppression of apoptotic gene expression combined with enhanced activation of liver-specific targets confers tissue-specific radio-resistance.

overall_design: Expression profiling by high throughput sequencing of spleen, liver and thymus in wt p53 mice and mice with a deletion of the C-terminus of p53. Organ pieces are immediately placed in RNAlater during dissection and stored at 4oC until RNA is extracted using RNeasy Mini Kit (Qiagen) and following manufacturer’s instructions.  The isolated RNA is quantitated and either stored at -80o in preparation for RNA-seq. Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

first: M

first: J

last: Manfredi


title: The C-terminus of p53 Confers Liver-Specific Gene Regulation and Radio-Resistance in vivo


title: The Role of Necroptosis-mediated Inflammation in Hepatocellular Carcinoma

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Non-alcoholic hepatosteatosis (NASH) due to metabolic syndrome or diabetes mellitus has been identified as the fastest growing cause of hepatocellular carcinoma (HCC), the fourth leading cause of cancer related deaths in the world. Therapeutic options for HCC are limited, and survival after diagnosis is poor (>10%). Thus, a better understanding of the mechanisms that drive the progression of NASH to HCC is critical in developing new strategies to prevent/treat HCC. Chronic inflammation is a key player in the pathogenesis of HCC, however, pathways that drive chronic hepatic inflammation in NASH-driven HCC is not known. Necroptosis is a regulated mode of cell death that causes inflammation and is activated in the livers of patients with NASH. Therefore, we tested whether necroptosis-mediated inflammation plays a role in the progression of NASH to HCC in a mouse model of NASH-induced HCC.

overall_design: For our study, we used wild type (WT) mice and mouse models where necroptosis is blocked (Ripk3 or Mlkl knockout mice). Mice were fed with normal chow diet (control diet) or choline deficient low or high fat diet (CD-LFD or CD-HFD) for 6 months. End point analyses was done for checking inflammation, tumor incidence and signalling pathway components. Transcriptomic analysis was done to understand the change in gene expression between the study groups. The results indicate that several genes invloved in HCC development are modulated in the WT group fed a CD-HFD , which gets reversed when necroptosis is blocked.

first: Sabira

last: Mohammed

first: Nidheesh

last: Thadathil

first: Haritha

middle: H

last: Nair

first: Albert

last: Tran

first: Michael

last: Van Der Veldt

first: Sangphil

last: Oh

first: Evan

last: Nicklas

first: Constantin

last: Georgescu

first: Benjamin

middle: F

last: Miller

first: Willard

last: Freeman

first: Ralf

last: Janknecht

first: Arlan

last: Richardson

first: Deepa

middle: S

last: Sathyaseelan


title: Comparison of NAT-lncRNA knockout effect by next-generation sequencing

city: Shenzhen

first: Shikuan

last: Zhang

state: Guangdong

address: Tsinghua Shenzhen International Graduate School, University Town of Shenzhen, Nanshan District

department: iBHE

institute: Tsinghua

summary: Analysis of different expression after lncRNA DHRS4-AS1 knockout with two strategies in immortalized human pancreatic duct epithelial cell line HPDE6-C7. The strategies include promoter-exon1 (PE) and branch point and 3‘ splicing site (BESST). The results provide transcriptome comparison between PE and BESST knockout approach, indicating the superior effect of BESST.

overall_design: The HPDE-C7 cell line was used in this study. CRISPR-based PE and BESST were applied to knockout DHRS4-RS1 lncRNA. Triplicates were done for each group.

first: Yue

last: Chen

first: Kunzhe

last: Dong

first: Yiwan

last: Zhao

first: Yanzhi

last: Wang

first: Songmao

first: Naihan

last: Xu

first: Weidong

last: Xie

first: Chunyu

last: Zeng

first: Qing

middle: R

last: Lyu

first: Yaou


title: MALINC1 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: The long-non-coding MALINC1 intergenic RNA (also known as LINC001024) was identified as significantly upregulated in breast ductal carcinoma in situ (DCIS). The aim of this study was to characterize the MALINC1 expression and localization, their phenotypic and molecular effects in non-invasive and invasive breast cancer models. We determined that MALINC1 is a E2-ER modulated lncRNA enriched in the cytoplasmic fraction of luminal A/B breast cancer cells that is associated with worse overall survival in patients with primary invasive breast carcinomas (p=0.027). Transcriptomic studies (RNA-seq) in normal and DCIS cells identified the main signaling pathways modulated by MALINC1 which include bioprocesses related to extracellular matrix remodeling, epithelial cell migration, adhesion, proliferation, and activation of AP1 signaling pathway. We conclude that MALINC1 over-expression behaves as an oncogenic lncRNA both in normal and DCIS breast cells involved with early-stage breast cancer progression.

overall_design: Transcriptomic studies (RNA-seq) in normal and DCIS cells transduced with empty vector or MALINC1 vector

first: C

last: Aldaz

first: Martín

first: María

last: Fabre


title: Transcriptomic characteristics underpin enhanced skeletal muscle mass, reduced fat accumulation and metabolically benign liver in human follistatin-344 transgenic pigs

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

summary:
Purpose:  The goal of this study was to compare the mRNA transcriptomes of transgenic pigs and wild-type pigs for five organs (liver,longissimus dorsi,psoas major,subcutaneous fat and retroperitoneal fat).
Methods: Total RNA was extracted from longissimus dorsi, psoas major, subcutaneous fat, retroperitoneal fat and liver using TRIZOL reagent (Life Technologies, Beijing, China), and each tissue has three biological replicates. For RNA sequencing, approximately 2 ug total RNA of each sample was used to construct transcriptome libraries following the manufacture’s standard procedures. Libraries were sequenced via Illumina HiSeqTM 4000, and 100 bp paired-end reads were generated.
Results: We detected 18,051 protein coding mRNA transcripts across 30 samples .
Conclusions:  Human FST induced transcriptome changes in liver,

overall_design: Five organs (liver, longissimus dorsi, psoas major, subcutaneous fat and retroperitoneal fat) mRNA profiles of transgenic pigs and wild type pigs were generated by deep sequencing, in triplicate using Illumina HiSeqTM 4000.


title: Transcriptional characterization of human and mouse choroidal neovascularization identifies fibroblast growth factor inducible-14 as a novel mediator of neo-vascular age-related macular degeneration

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years as a result of anti-VEGF therapy. However, some patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF injections, indicating a role of other proangiogenic mediators. The present study applied transcriptional profiling of human and mouse CNV membranes each with reference to healthy control tissue to identify novel mediators of CNV. Following this approach, the study identifies Fibroblast growth factor induci-ble-14 (FN14) as a novel phylogenetically conserved mediator of CNV. Blocking the pathway by intravitreal injection of an FN14 decoy receptor modulates the cytokine profile - most notably IL-6 - and leads to a significant and IL-6 mediated reduction of CNV size in vivo. These results identify FN14 as a promising new therapeutic target for neovascular AMD, which may potentially be beneficial in patients with exudative AMD with special regard to anti-VEGF resistant cases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MACE RNA sequencing of 6 mouse CNV and 6 mouse RPE/choroid control samples as well as 4 human CNV membranes and 4 human control RPE/choroid samples.

first: Julian

last: Wolf

first: Anja

last: Schlecht

first: Dennis-Dominik

last: Rosmus

first: Stefaniya

last: Boneva

first: Peter

last: Wieghofer

first: Hansjürgen

last: Agostini

first: Guenther

last: Schlunck


title: MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [bulk RNA-Seq]

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary:
Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3’ untranslated region of the dystrophia myotonica-protein kinase (DMPK) gene. Despite its prominence as the most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms of DM1 can present with debilitating neurocognitive symptoms along the autism spectrum, characteristic of possible in utero   cortical defects. However, the molecular mechanism by which CTG MREs lead to these developmental central nervous system (CNS) manifestations is unknown. Here, we showed that CUG foci discovered early in maturation of three-dimensional cortical organoids from DM1 patient-derived induced pluripotent stem cells, cause hyperphosphorylation of CUGBP Elav-Like Family Member 2 (CELF2 ) protein. Integrative single-cell RNA-seq and enhanced crosslinking and immunoprecipitation (eCLIP ) analysis revealed reduced CELF2 protein-RNA substrate interactions resulting in mis-regulation of genes critical for excitatory synaptic signaling in glutamatergic neurons, including key components of the Methyl-CpG binding protein 2 (MECP2) pathway. Comparisons to MECP2(-/-) cortical organoids revealed convergent molecular and cellular defects such as glutamate toxicity and neuronal loss. Our findings provide evidence suggesting that early-onset DM1 might involve neurodevelopmental disorder-associated pathways and identify N-Methyl-D-aspartic acid (NMDA ) antagonists as potential treatment avenues for neuronal defects in DM1.
To determine if CUG expansions in DMPK alter cellular RNA composition during differentiation, we performed transcriptomic analyses using RNA-seq at four consecutive developmental stages, ranging from iPSCs to 6-month-old cortical organoids from two independent differentiations. mine We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different  time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of 4 cortical organoid lines  differentiated from 2 DM1 iPSC lines (DM1200 and DM600) and 2 Neurotypical Control Lines (CSO and Kin).

first: Shashank

last: Shathe

first: Kathryn

last: Morelli


title: The C-terminus of p53 Confers Liver-Specific Gene Regulation and Radio-Resistance in vivo [ChIP-seq]

first: Moray

last: Campbell

overall_design: Dissected mouse organs are placed in 6-well plates contain chilled PBS. The DNA fragments are purified the following day using the Qiagen Qiaquick PCR purification Kit Protocol. The sample and input DNA can be used for PCR or measured using the Qubit reader and used for ChIP-seq.

first: M

first: J

last: Manfredi


title: Genome-wide maps of chromatin state in YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma

first: Zhen

last: Hua

summary: We found that the experssion of STAT5A was upregulated when the YTHDF2 was knocked down. To identify the function of STAT5A protein as a Transcription factor in YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma. CHIP-seq was conducted to analyze changes in related signaling pathways and gene expression in Multiple Myeloma  cells when YTHDF2 was knocked down.

overall_design: Examination of 2 different histone modifications in 2 cell types.


title: Differentially expressed genes (DEGs) analysis in control and melatonin treated human coronary artery endothilial cells (HCAECs).

city: Shanghai

first: yuanzheng

last: Zheng

address: Dongan road 130

institute: Fudan University

summary: To explore the detailed mechanism by which melatonin allivates TNF-α induced HCAECs damage, we performed RNA-seq in control and melatonin treated HCAECs, and identified 213 upregualted and 103 downregulated genes with the criterion of |FC|≥2 and p≤0.05.

overall_design: We prepared 3 replicates for control and melatonin group, respectively, to perform the RNA-seq analysis.

first: Yuanzheng

first: Yonghao

last: Gui


title: Next Generation Sequencing Facilitates Quantitative Analysis of SPS and Control Rats Model

city: Shenyang

first: Fang

last: Han

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

summary: In the present study, we used the single prolonged stress (SPS) model to mimic  posttraumatic stress disorder. High-throughput sequencing were utilized to analyze differentially  expressed genes (DEGs) in the hippocampus of control and SPS rats. RNA-seq analysis revealed 230 significantly DEGs between  the control and SPS groups.

overall_design: mRNA profiles of single prolonged stress (SPS) and control rats model


title: m6A-SAC-seq for quantitative whole transcriptome m6A profiling

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

summary: This protocol describes a method for base-resolution, quantitative m6A sequencing in the whole transcriptome. The method generates highly reproducible results containing 31,233-129,263 sites using as low as 2 ng of poly-A RNA.

overall_design: The RNA is treated with recombinant MjDim1 enzyme with allylic-SAM cofactor under optimized conditions to selectively convert m6A residues to a6m6A, followed by adding I2 to convert am6A to EA. Reverse transcription induces mutations at EA sites, enabling identification of the sites labeled with a6m6A.

first: Ruiqi

last: Ge

first: Yong

last: Peng

first: Qing

last: Dai

first: Shun

last: Liu

first: Lulu

last: Hu

first: Chuan

last: He


title: NMT inhibition in the context of MYC levels

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

summary: Characterisation of the impact of 24 hours of NMT inhibition (100 nM IMP1088) on the P493-6 cell line with medium levels of MYC and high levels of MYC.

overall_design: The different levels of MYC were induced 24 hours prior to the experiment, according to literature procedure (high: normal DMEM media; medium: DMEM with 0.1 ug/mL doxycycline and 1 uM of beta-estradiol). Subsequently 100 nM of the NMT inhibitor IMP1088 or a DMSO control were added to the cells for 24 hours and then cells were lysed for further RNA extraction.

first: Gregor

last: Lueg


title: Transcriptome  analysis of YTHDF2 kockdown(KD) and wildtype(WT) cells in Multiple Myeloma

city: Nanjing

institute: Nanjing University of Chinese Medicine

summary: RNA-seq experiments was conducted to analyze changes in related signaling pathways and gene expression in colon cancer cells when YTHDF2 was knocked down.

overall_design: Examination of  two cell types


title: Nanopore sequencing reveals isoform-specific alterations in human bronchial epithelial cells with U2AF1 S34F mutations

city: Santa Cruz

first: Angela

middle: N

last: Brooks

address: 1156 High Street

department: Biomolecular Engineering

institute: University California Santa Cruz

summary: U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associated splicing alterations have been described, the fate of affected mRNA isoforms remains largely unexplored. To better understand the impact U2AF1 S34F has on isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without U2AF1 S34F mutation. We find that nearly 75% (49,366) of our long-read constructed multi-exon isoforms do not overlap GENCODE or short-read assembled isoforms, a large proportion of which (12,397) are due to novel junction connectivity rather than novel splice site usage. We find 198 transcript isoforms with significant expression and usage changes relative to wild-type, some of which were not assembled by short-reads. We find an enrichment of isoforms from immune related genes are down regulated in the presence of U2Af1 S34F, none of which are observed to have splicing changes detected from long-read data. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are largely downregulated in U2AF1 S34F cells, suggesting that the impact of observed isoform changes may alter the translational output of affected genes. Altogether, our data builds on previous work by providing a higher resolution transcriptome snapshot of full-length isoform alterations associated with U2AF1 S34F in HBEC3kt cells.

overall_design: Examination of RNA processing changes due to mutations in splicing factor protein U2AF1.

first: Soulette

last: Cameron

first: Brooks

last: Angela


title: Bulk sequencing of MYCN-overexpressing chicken retinal cell lines

city: Uppsala

first: Finn

last: Hallböök

address: Dag Hammarskjölds v 20

department: Dept Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary:
Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer.
Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression.
Methods: MYCN-overexpressing cells were taken from MYCN electroporated E14 chicken retina and kept in culture for over 4 weeks. Unelectroporated E14 chicken retina central region was dissected as a control. Total RNA was extracted and sequenced on Illumina NovaSeq 6000. The data were used for differential expression analysis and GO/Pathway enrichment analysis.
Results: Genes related to proliferation were upregulated in MYCN-overexpressing cells, while genes related to neural differentiation were downregulated. GO/Pathway enrichment analysis showed that upregulated genes were enriched for pathways associated with cell proliferation and downregulated genes for neural differentiation.

overall_design: RNA sequencing of three biological replicates of MYCN-overexpressing cell lines in long-term culture and with three replicates of E14 dissected chicken retinas as control

first: Dardan

last: Konjusha

first: Hanzhao

last: Zhang

first: Nima

last: Rafati


title: The role of microglial cells in the development of retinal angiomatous proliferation in the Vldlr knockout mouse

first: Clemens

last: Lange

summary: Objective:   Retinal angiomatous proliferation (RAP) represents a special form of neovascular age-related macular degeneration. Immune cells accumulate at RAP, but so far it is unclear whether these cells are resident retinal microglial cells (MG) or blood infiltrating monocytes (MO) and whether these cells can influence RAP formation. The aim of this study is to determine the relative contribution of MG and MO to RAP and to define the transcriptional profile of the dominant cell population.   Methods:   Vldlr -/- Knockout mice were crossed with MG-specific Cx3cr1CreER/+:Rosa26-Tomfl/+ re-porter mice (MG-Tom). The resulting Vldlr-/-:MG-Tom mice received tamoxifen injection at day 1 after birth (P1), leading to expression of Tomato fluorochrome (Tom) in myeloid cells. Myeloid cells were examined at P17, P31, and P42 by immunohistochemical Iba1 staining and retinal Tom expression. In addition, Tom-positive MG were isolated at P17 by fluorescence-activated cell sorting, and the transcriptional profile of MG was analyzed by RNA sequencing. MG Tom mice, also injected at P1 with tamoxifen, served as controls for RNA-Seq.   Results:   Our data show that at the beginning of RAP formation (P17), hardly any MO migrates from blood into tissues (0.2±0.5 MO/RAP, 2.0±0.8 MG/RAP). During the course of RAP formation, this changes only slightly (P31: 0.6±2.2 MO/RAP, 10.3±12.8 MG/RAP; P42: 0.6±2.4 MO/RAP, 14.3±9.4 MG/RAP). RNA sequencing of the isolated MG identified 140 differentially expressed genes (DEG), of which 67 were upregulated and 73 were downregulated upon RAP formation. Gene ontology enrichment analysis of the 140 DEGs revealed that they contribute primarily to immune-associated processes, such as leukocyte migration and chemotaxis, regulation of the immune system and immune response, and wound responses. Retinal MG thereby express the pro-angiogenic soluble factor Spp1 (log2FC 1.8) in addition to Ccl2 and Cxcl14 during RAP formation.  Conclusion:   Our data indicate that resident MG represent the dominant immune cell population during retinal angiomatous proliferation in the Vldlr knockout mouse. RNA sequencing of MG reveals upregulation of immune-associated processes and of pro-angiogenic factors, such as Spp1. Cell-specific modulation of MG may thus form the basis of a future therapeutic option for the treatment of RAP.

overall_design: RNA-seq

first: Anja

last: Schlecht

first: Julian

last: Wolf

first: Stefaniya

last: Boneva

first: Guenther

last: Schlunck

first: Hansjürgen

last: Agostini


title: Transcriptome analysis of Newly Diagnosed Type 2 Diabetes Subjects identifies genes to predict Metformin drug Response

city: Manipal

first: Padmalatha

last: Rai

state: Karnataka

address: Manipal

department: Biotechnology

country: India

institute: Manipal School of Life Sciences, Manipal Academy of Higher Education

summary:
Aims: Metformin is a widely used, primary drug of choice to treat individuals with type 2 diabetes (T2D). Clinically, inter-individual variability of drug response is of significant  concern. The targets and precise mechanisms of action for metformin is still under interrogation. In the present study, a whole transcriptome analysis was performed with an  intent to identify predictive biomarkers of metformin response in T2D individuals.
Methods: Twenty drug naïve individuals with T2D and ten healthy controls were enrolled. T2D individuals were administrated with metformin monotherapy and were defined as responders and non-responders based on the changes in their glycated haemoglobin (HbA1c) over a period of three months. Poly(A) RNA Seq was performed using Ion Torrent Proton platform and differentially expressed genes were identified from the transcriptome profiles. The gene prioritization, enrichment analysis, drug-gene interactions, disease gene association analysis were performed using various tools and databases. A correlation analysis was also performed between gene expression and change in HbA1c levels after 3 months of metformin therapy.
Results: The expression analysis highlighted differentially expressed genes in metformin responders, non-responders and healthy individuals. The gene prioritization and enrichment analysis highlighted potential targets for predicting metformin response (n=35) as well as T2D disease (n=14). The drug-gene interactions did not show any direct association with diabetes drugs. However, the expression of GDF15, TWISTNB and RPL36A genes showed maximum correlation with change in HbA1c levels after 3 months of metformin therapy. The disease gene association analysis highlighted rs113805659 in MAGI2 gene to be linked with T2D in African Americans.
Conclusion: The results of the present study provide evidence for the perturbed transcriptome and pathways associated with metformin drug response in T2D individuals.

overall_design: Whole transcriptome profile of 20 drug naïve individuals with T2D and 10 healthy controls was generated for total RNA isolated from whole blood using Ion Torrent Proton

first: Manik

last: Vohra

first: Anu

last: Sharma

first: Sandeep

last: Mallya

first: Shivashankar

middle: K

last: Nagri

first: Shashikiran

last: Umakanth

first: Kapaettu

last: Satyamoorthy


title: mRNA expression profile of regulatory neutrophil induced by sodiumtaurodeoxycholate

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

summary: Conventional strategies for the development of new drugs have used chemical compounds or large molecules that act as an agonist, antagonist, inhibitor (enzyme or signal transducer), enzyme cofactor or supplement for normal constituents in the body. Recently, the field of cell therapeutics has received much attention. Ex vivo expansion and/or manipulation is essential in cell therapy, which might limit the entrance of pharmaceutical companies into the cell therapy market. In this paper, we show that we can expand a specific subtype of cells, regulatory neutrophils, in vivo by i.v. injection of a compound which stimulate GPCR19 pathway. The in vivo - expanded cells showed therapeutic efficacy in mice with systemic inflammatory diseases, which was not shown by parental cells. The results of this study demonstrate an innovative novel achievement in developing a new drug, using a strategy similar to cell therapy combined with a small molecule.

overall_design: We injected sodiumtaurodeoxycholate (HY209; or PBS as a negative control for HY209) to C57BL/6 mice intravenously after the inducing sepsis by injecting LPS (or PBS as a negative control for sepsis) i.p.. Two to three biological replicates each containing MACS-soreted Gr1+ cells from 30-40 pooled spleen of C57BL/6 mice were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips

first: S

middle: Y


title: pICln, an spliceosome assembly chaperone, controls alternative splicing, flowering time and stress responses in Arabidopsis

city: Buenos Aires

first: Julieta

middle: Lisa

last: Mateos

address: Av. Patricias Argentinas 435

institute: Fundacion Instituto Leloir

summary: RNA-Seq from picln-1 mutant, prmt5-5 mutant and wt grown at 22°C for 9 days in a 12h light 12h dark photoperiod

overall_design: Examination of cold treatment in picln and wt seedlings

first: Sabrina

last: Sanchez

first: Marcelo

last: Yanovsky


title: Activating Parkin-dependent mitophagy alleviates oxidative stress, apoptosis, and promotes random-pattern skin flaps survival

status: Public on Jun 29 2022

city: Wenzhou

first: Weiyang

last: Gao

address: West Xueyuan Road, Wenzhou

institute: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University

summary: The random-pattern skin flap is a crucial technique in reconstructive surgery and flap necrosis caused by ischemia/reperfusion injury is a major postoperative complication. Herein, we investigated the mechanism of mitophagy induced by Melatonin (ML) and its effect on the survival of skin flaps. Our results demonstrated that ML could activate mitophagy, ameliorate oxidative stress and alleviate apoptosis in TBHP-stimulated human umbilical vein endothelial cells in vitro. Inhibiting ML-induced mitophagy considerably abolished its protective effects. Moreover, knockdown of Parkin by siRNA inhibited ML-induced mitophagy, and subsequently exacerbated oxidative stress and apoptosis. Further study demonstrated that inhibition of AMPK reversed these protective effects of ML and downregulated the expression of TFEB. In the vivo study, ML effectively promoted flap survival by activating mitophagy and subsequently ameliorating oxidative stress and mitigating apoptosis. These results established that ML is a potent agent capable for increasing random-pattern skin flap survival by activating Parkin-dependent mitophagy through the AMPK-TFEB signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVEC cells.

first: Zhengtai

last: Chen

first: Hongqiang

last: Wu

first: Jianxin

last: Yang

first: Baolong

last: Li


title: eEF1A1 mediates the mechanosensation of NSC differentiation

city: Berkeley

first: Paola

last: Lopez

address: Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

summary: We report a transcriptome sequencing to identify mechanosensitive genes 12-36 hours after initiating differentiation of adult rat neural stem cells on 2D soft and stiff laminin-coated polyacrylamide gels.

overall_design: Identification of stiffness-dependent genes in neural stem cells

first: Phillip

last: Kang

first: Sanjay

last: Kumar


title: Hoxb5 reprograms murine multipotent blood progenitors into hematopoietic stem cell-like cells

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

summary: We performed the single cell RNA-seq for the Hoxb5 Mac-1+CD48+ SK cells, bone marrow HSC, bone marrow MPP, and fetal liver HSC by Smart-Seq2.

first: Qitong

last: Weng


title: Tongue immune compartment analysis reveals spatial macrophage heterogeneity [bulk RNA-Seq]

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

institute: Max Delbrück Center

summary: The tongue is a unique muscular organ situated in the oral cavity where it is involved in taste sensation, mastication and articulation. As a barrier organ, which is constantly exposed to environmental pathogens,the tongue isexpected to host animmune cell network ensuringlocal immune defence. However, the composition and the transcriptional landscape of the tongue immune system are currently not completely defined. Here we characterised the tissue-resident immune compartment of the murine tongue during development, health anddisease, combining single cell RNA-sequencing with in situ immunophenotyping. We identified distinct local immune cell populations and described two specific subsets of tongue-resident macrophages occupying discrete anatomical niches. Cx3cr1+macrophages were located specifically in the highly innervated lamina propria beneath the tongue epidermis and at times in close proximity to fungiform papillae.Folr2+ macrophages were detected in deeper muscular tissue. The two macrophage subsets originate from a common proliferative precursor during early postnatal development and responded differently to systemic LPSin vivo. Our description of the under-investigated tongue immune system sets a starting point to facilitate research on tongue immune-physiology and pathology including cancer and taste disorders.

overall_design: 38 samples

first: Ekaterini

last: Lyras

first: Karin

last: Zimmermann

first: Lisa

last: Wagner

first: Dorothea

last: Dörr

first: Cornelius

last: Fischer

first: Steffen

last: Jung

first: Alexander

last: Mildner


title: Whole-blood transcriptional profiles early predict the presence of coronary atherosclerosis and high-risk plaque features at coronary CT angiography

city: Milano

first: Gualtiero

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

summary: This study aims at identifying gene expression patterns in the whole blood that could differentiate patients with severe coronary atherosclerosis from subjects without detectable coronary artery disease (CAD), and assess associations of gene expression patterns with plaque features at coronary CT angiography (CCTA). Patients undergoing CCTA for suspected CAD, with no cardiovascular history, were enrolled. Coronary stenosis was quantified and CCTA plaque features were assessed. The whole-blood transcriptome was analyzed by RNA-Sequencing. We detected highly significant differences in the circulating transcriptome between patients with high-degree coronary stenosis (> 70%) at CCTA and subjects with the absence of coronary plaques. Noteworthy, regression analysis revealed expression signatures associated with Leaman score, segment involved score, segment-stenosis score, and plaque volume with density <150 HU at CCTA. This pilot study shows that patients with significant coronary stenosis are characterized by whole blood transcriptome profiles that may discriminate them from patients without CAD. Furthermore, our results suggest that whole blood transcriptional profiles may predict plaque characteristics.

overall_design: Whole blood poly(A)+ RNA profiles of 27 CAD and 25 noCAD patients were generated through RNA-Seq using Ion S5 system.

first: Chiara

last: Vavassori

first: Mattia

last: Chiesa

first: Luca

last: Piacentini

first: Martina

last: Manzoni

first: Eleonora

last: Cipriani


title: RNA sequencing on EphrinB2 overexpression cardiac fibroblasts and vector cardiac fibroblasts within or without induction of osteogenic differentiation in the 7th day.

city: hangzhou

first: wudi

last: li

address: 88 Jiefang Road

institute: Second Affiliated Hospital of Zhejiang University

summary: Purpose: To investigate the function of EphrinB2 in the regulation of osteogenic differentiation of cardiac fibroblasts, we established EphrinB2-overexpressing cardiac fibroblasts and corresponding control group by lentivirus.Methods:Adult cardiac fibroblasts were isolated from 6 to 8-week-aged C57BL/6 mice, passage 1 cardiac fibroblasts plated at a density of 2.5 x 104 cells/cm2 were infected with the EphrinB2-overexpressing or vector lentivirus at an MOI of 20 for 12h, after 48 hours’ infection, osteogenesis was induced using differentiation medium (α-MEM supplied with 10% FBS, 10 mM β-glycerophosphate, 100nM dexamethasone and 50 µg/mL L-ascorbic acid). Cardiac fibroblasts harvested at Day7 were used for RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EphrinB2-overexpressing cardiac fibroblasts and vector cardiac fibroblasts within or without induction of osteogenic differentiation

first: Wudi

last: Li

first: Sheng-an

last: Su


title: Exploring the microbiota pecularity in stool and biopsies of Eosinophilic Granulomatosis with Polyangiitis (EGPA) patients

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: Comparing bacteriota between EGPA patients and healthy subjects

overall_design: Total DNA was extracted from feces of 29 EGPA patients and 9 healthy controls and from biopsies of 7 EGPA patients. The DNA has been amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x250bp) Illumina platform.


title: Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress

first: Yujie

last: Wang

address: No. 1, Weigang, Xuanwu District

institute: Nanjing Agricultural University

summary: Fg infection induces host alkalinization, and the pH-dependent transcription factor FgPacC undergoes a proteolytic cleavage into the functional isoform named FgPacC30 under alkaline host environment. Subsequently FgPacC30 binds to a GCCAR(R=A/G)G element at the promoters of the genes involved in iron uptake and inhibits their expression, leading to adaption of Fg to high-iron stress. Mechanistically, FgPacC30 binds to FgGcn5 protein, a catalytic subunit of Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, leading to deregulation of histone acetylation at H3K18 and H2BK11, and repression of iron uptake genes.

overall_design: It was proved by RNA-seq and ChIP-seq data that the transcription factor FgPacC affects the expression of iron uptake genes by mediating the deregulation of histone acetylation at H3K18 and H2BK11

first: Qin

last: Gu

first: Bingqin

last: Yuan


title: Glucose supply and glycolysis inhibition shape the clinical fate of preterm newborns infected with Staphylococcus epidermidis [whole blood]

city: Copenhagen

first: tik

last: muk

state: copenhagen

address: Dyrlægevej 68,1870 Frederiksberg C, Dyrlægevej 68, 1870 Frederiksberg C

country: Denmark

institute: University of Copenhagen

summary:
To investigate if appropriately adjusted parenteral glucose supply and/or temporary glycolysis inhibition by administration may help to prevent sepsis or improve sepsis outcomes of preterm newborns, we using a preterm pig model inoculated with Staphylococcus epidermidis to mimic the inflammation condition of preterm newborns at birth and treated them with different parenteral nutrition glucose supplyment and glycolysis inhibitor administration.
We then performed gene expression profiling analysis using data obtained from RNA-seq of preterm pigs` whole blood, which collected at 12 hours after SE infection, treated with different parenteral glucose supply and glycolysis inhibitor administration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for whole blood samples from preterm pigs with/without S. epidermidis (5×10^5 CFU/ml) infection and DCA administration, pigs received either high or standard parenteral glucose supply.

first: Tik

last: Muk

first: Anders

last: Brunse

first: Nicole

middle: L

last: Henriksen

first: Karoline

last: Aasmul-Olsen

first: Duc

last: Nguyen


title: GPER/β-alanine Positive Interaction in the Dorsal Root Ganglion Uncovers Potential Mechanisms: Mediating Continuous Neuronal Sensitization and Neuroinflammation Responses in Neuropathic Pain

city: Wuhan

first: Zhen

middle: Zhen

last: Xu

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Background: The pathogenesis of neuropathic pain and the reasons for the prolonged unhealing are still unknown. Increasing evidence suggests that oestrogen sex differences play a role in pain sensitivity, but few studies focused on the role of oestrogen receptor which maybe an important molecular component contributing to peripheral pain transduction. We aimed to investigate the impact of ooestrogen receptors in nociceptive neuronal response in the dorsal root ganglion (DRG) and spinal dorsal horn using a spared nerve injury (SNI) rat model of chronic pain.   Methods: We used a class of oestrogen receptors antagonists and agonists intrathecal (i.t.) administrated to male rats with SNI or normal rats to identify the main receptor. Moreover, we applied genes identified through genomic metabolic analysis to determine the key metabolism point and elucidate potential mechanisms mediating continuous neuronal sensitisation and neuroinflammation responses in neuropathic pain. The excitability of DRG neurons was detected using the patch clamp technique. Primary culture was used to extract microglia and DRG neurons, and siRNA transfection was used to silence receptor protein expression. Immunofluorescence, Western blotting, qPCR and behavioral testing were used to assess the expressions, cellular distributions, and actions of main receptor and its related signaling molecules.  Results: Increasing the expression and function of G protein-coupled oestrogen receptor (GPER), but not oestrogen receptor-α (ERα) and oestrogen receptor-β (ERβ), in the DRG neuron and microglia, but not the dorsal spinal cord, contributed to SNI-induced neuronal sensitisation. Inhibiting GPER expression in the DRG alleviated SNI-induced pain behaviours and neuroinflammation by downregulating iNOS, IL-1β and IL-6 expression as well as restoring GABAα2 expression simultaneously. Additionally, the positive interaction between GPER and β-alanine, β-alanine accumulation enhances pain sensation and promotes chronic pain development.   Conclusion: GPER activation in the DRG causes a positive interaction of β-alanine with iNOS, IL-1β and IL-6 expression and represses GABAα2 involved in post-SNI neuropathic pain development. Blocking GPER and eliminating β-alanine in the DRG neuron and microglia may prevent neuropathic pain development.

first: Zhenzhen

first: Wanli

last: Xie


title: Glucose supply and glycolysis inhibition shape the clinical fate of preterm newborns infected with Staphylococcus epidermidis [cord blood]

summary:
To investigate the glycolysis inhibition effect on the inflammation responses of preterm newborns infected with Staphylococcus epidermidis, we used preterm pigs` cord blood to mimic the inflammation condition of preterm newborns at birth and stimulated with S. epidermidis and glycolysis inhibior.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the cord blood, which were stimulated with S. epidermidis and DCA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cord blood samples with/without S. epidermidis (5×10^5 CFU/ml) and DCA incubation.


title: Differential translatome in the DRG of mice treated with normal chow vs Western diet

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: We show differences in translatome of the DRG from ribo tagged mice fed normal chow or western diet.

overall_design: Evaluation of changes in translatome in the DRG of mice with diet

first: Chaitanya

last: Gavini

first: Nadia

last: Elshareif


title: Glucose supply and glycolysis inhibition shape the clinical fate of preterm newborns infected with Staphylococcus epidermidis [liver]

summary:
To investigate if appropriately adjusted parenteral glucose supply may help to shift liver metabolism profiling to further prevent sepsis or improve sepsis outcomes of preterm newborns, we using a preterm pig model inoculated with Staphylococcus epidermidis to mimic the inflammation condition of preterm newborns at birth and treated them with different parenteral nutrition glucose supplyment.
We then performed gene expression profiling analysis using data obtained from RNA-seq of preterm pigs` liver tissue, which collected at 22 hours after SE infection, treated with different parenteral glucose supply.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissue samples from preterm pigs with/without S. epidermidis (5×10^5 CFU/ml) infection, pigs received either high or standard parenteral glucose supply.


title: Melatonin alters the transcriptome of human granulosa cells and improves fertilization and blastocyst formation

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

institute: Yamaguchi university

summary: Granulosa cells in the ART cycle before and during melatonin treatment from the three patients and analyzed the transcriptome changes by RNA-sequence. The other four patients had good ART outcomes. Their GCs were also subjected to RNA-sequence as controls of good ART outcomes.

overall_design: mRNA profiles of human granulosa cells in the ART cycle

first: Isao

last: Tamura


title: Single-cell analysis of gene networks in trophoectoderm and inner cell mass during human, monkey and mouse preimplantation development

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. Gene network preservation analysis reveals that genetic programs in monkey embryos more closely resemble human embryos compared to mouse, supporting the notion that preimplantation development in primate species are divergent from rodent species. For example, primate blastocysts show differential expression of ICM and TE genes such as X and Y, whereas mouse show differences in A and B expression. Interestingly, the overall conservation of TE gene networks is higher than ICM across three species, suggesting a more conserved developmental program in TE lineage differentiation. Additionally, TE-specific gene networks are exclusively activated at the blastocyst stage with low or no expression in morula or earlier embryos. In contrast, a majority of ICM-specific genes are strongly activated during the first major wave of EGA, which are further fine-tuned during late morula and blastocyst stages. Taken together, our study provides new insight into mammalian preimplantation development and sequential activation of lineage-specific genetic programs of TE versus ICM.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design:
single-cell RNA-seq of monkey, human, and mouse embryos

Please note that the raw data for GSM1977282 is not provided.

first: Youjin

last: Hu

first: Guoping

last: Fan


title: Glucose supply and glycolysis inhibition shape the clinical fate of preterm newborns infected with Staphylococcus epidermidis

first: tik

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

overall_design: Refer to individual Series


title: Tongue immune compartment analysis reveals spatial macrophage heterogeneity

first: Achim

last: Leutz


title: Delayed maturation of Fragile X Syndrome GABAergic neurogenesis revealed by functional and single-cell gene expression analysis

city: La Jolla

first: Alain

last: Domissy

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

summary:
FXS (Fragile X Syndrome), a leading monogenic cause of intellectual disability and autism spectrum disorder, is caused by an expansion of a CGG repeat in the 5′-UTR of the FMR1 (Fragile X Mental Retardation-1) gene.
While current studies of FXS have focused on the effects of Fragile X Mental Retardation Protein (FMRP) loss in excitatory neurons, evidence suggests that GABAergic inhibitory networks are also affected in FXS.
In this study, we developed a method to reproducibly derive GABAergic inhibitory neurons from multiple FXS and control human pluripotent stem cell lines (PSCs).
We found that compared to control, functional assays with microelectrode arrays and immunocytochemistry suggested a developmental delay in the maturing FXS inhibitory network that involves the GABA function switch.
The GABA function switch converts the GABAA channel’s role from depolarization to hyperpolarization and has profound effects on the developing brain.
To investigate the cause of this delay, we analyzed 14,400 single-cell transcriptomes from FXS and control PSC-derived GABAergic neuron cultures at early and late stages of neurogenesis.
Genes related to neuroblast proliferation were upregulated in FXS cells, while neuron-specific differentially expressed genes (DEGs) associated with action potential regulation, synaptic processes, and mitochondria function were downregulated in FXS cells.
In addition, autism-associated genes were overrepresented in the DEGs. Our analysis of inhibitory neuron development suggests that loss of FMRP is associated with delays in the GABAergic neurogenesis and maturation.
This observation suggests a novel direction for understanding the underlying disease mechanisms and may help to guide development of therapeutic interventions.

overall_design: single cell RNAseq profiling from 3 FXS and 3 Control hPSC-derived GABAergic inhibitory neurons at 2 timepoints: day 22 and day 42-48 of differentiation

first: Ai

last: Zhang


title: RNA-seq IU10991 vs IU1781

city: Bloomington

first: David

last: Giedroc

state: IN

address: 800 E. Kirkwood Ave

department: Chemistry

institute: Indiana University

summary: Here we analyze the transcriptomic profile of Streptococcus pneumoniae D39 Dspd_1448::KanrpsL (IU10991) vs Streptcococcus penumoiae D39 wt  (IU1781) under anaerobic growth condition in BHI growth media

overall_design: Transcriptomic profle of IU10991 vs IU1781 by RNA-seq

first: Julia

middle: E

last: Martin

middle: P


title: Real-time quantitative PCR analysis of human astrocytes exposed to pressure-driven flow and/or Direct Current Stimulation in vitro

city: New York

first: Limary

last: Cancel

state: NY

address: 160 Convent Ave

department: Biomedical Engineering

institute: The City College of New York

summary: The objective of this study was to investigate the effect of Direct Current Stimulation (DCS) on the gene expression of human astrocytes (HA). DCS at 0.1 or 1mA was applied to monolayers of HA for 10 minutes. Expression of a set of neuroactive genes was assessed immediately of 1 hour after DCS using RT-qPCR. Because DCS can produce electroosmotic flow and fluid shear stress known to influence cell function, we compared three interventions: pressure-driven flow across the monolayer alone (conP), pressure-driven flow plus DCS (DCS P), and DCS alone with flow blocked (DCS S).

overall_design: HA were obtained from Cell Applications. DCS was applied with (DCS P) or without (DCS S) a pressure differential that induced fluid flow across the cell monolayer. Monolayers exposed only to convective flow (conP) were also examined. A static control (conS) kept in an incubator for the duration of the experiment was used as the calibrator sample for gene expression analysis. Total RNA was collected either immediately after DCS, or 1 hour after DCS using the RNeasy Mini kit from Qiagen, and reversed transcribed using the High-capacity cDNA Reverse Transcription kit from Thermo Scientific. Real time RT-qPCR was performed on the 7300 Real Time PCR System from Applied Biosystems. Samples were run in duplicates.

middle: M

first: John

last: Tarbell


title: Comparative expression among organs between upland cotton species upland cotton CKG (Coker312-gland) and CKN (Coker312-glandless)

city: Beijing

first: Chengyu

last: Ye

address: 67 North Forth Ring Road

institute: BGI Genomics

summary:
To investigate the gossypol synthasis between distinct cotton species CKG and CKN
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 organs betweeen two species

overall_design: Comparative gene expression profiling analysis of RNA-seq data for organs between upland cotton species upland cotton CKG (Coker312-gland) and CKN (Coker312-glandless)

first: Lei

last: Mei

first: Sanjie

last: Jiang


title: Transcriptional profiles in human milk and whole blood after live attenuated and inactivated influenza vaccination

first: Pia

last: Pannaraj

state: California

address: 4650 Sunset Blvd, MS#51

department: Infectious Diseases

institute: Children's Hospital of Los Angeles

summary: Breastfeeding protects against mucosal infections in infants. The underlying mechanisms through which immunity develops in human milk following maternal infection with mucosal pathogens are not well understood. We simulate mucosal influenza infection through live attenuated influenza vaccination (LAIV) and compared milk and blood immune responses to inactivated influenza vaccination (IIV). Transcriptomic analysis was performed on RNA extracted from human milk and whole blood. Differentially expressed genes (DEGs) and gene set enrichment analysis (GSEA) on days 1 and 7 post-vaccination were compared to pre-vaccination.

overall_design: We enrolled 78 (361 samples) lactating women during the months of influenza vaccine availability from 2011 to 2016. The mothers were post-partum for a median of 7.5 days at the time of influenza vaccination. None had received a prenatal influenza vaccine during the influenza season of participation until study enrollment. Gene expression profiles from blood (132 samples) and human milk (229 samples) were performed before (day 0) and day 1 and day 7 after vaccination. Influenza HA-specific HAI titers (sera) and IgA (milk) were evaluated at days 0, 30, 90, and 180.

first: André

middle: G

last: Costa-Martins

first: Chiara

last: Cerini

first: Fan

last: Li

first: Sook-San

last: Wong

first: Richard

middle: J

last: Webby

first: Youvika

last: Singh

first: Alysson

middle: H

last: Urbanski

first: Patrícia

last: Gonzalez-Dias

first: Juliana

last: Yang

first: Helder

last: Nakaya

first: Grac

last: Aldrovandi


title: Tongue immune compartment analysis reveals spatial macrophage heterogeneity [bulk RNA-Seq]

first: Achim

last: Leutz

summary: The tongue is a unique muscular organ situated in the oral cavity where it is involved in taste sensation, mastication and articulation. As a barrier organ, which is constantly exposed to environmental pathogens,the tongue isexpected to host animmune cell network ensuringlocal immune defence. However, the composition and the transcriptional landscape of the tongue immune system are currently not completely defined. Here we characterised the tissue-resident immune compartment of the murine tongue during development, health anddisease, combining single cell RNA-sequencing with in situ immunophenotyping. We identified distinct local immune cell populations and described two specific subsets of tongue-resident macrophages occupying discrete anatomical niches. Cx3cr1+macrophages were located specifically in the highly innervated lamina propria beneath the tongue epidermis and at times in close proximity to fungiform papillae.Folr2+ macrophages were detected in deeper muscular tissue. The two macrophage subsets originate from a common proliferative precursor during early postnatal development and responded differently to systemic LPSin vivo. Our description of the under-investigated tongue immune system sets a starting point to facilitate research on tongue immune-physiology and pathology including cancer and taste disorders.

overall_design: 4 samples

first: Ekaterini

last: Lyras

first: Karin

last: Zimmermann

first: Lisa

last: Wagner

first: Dorothea

last: Dörr

first: Cornelius

last: Fischer

first: Steffen

last: Jung

first: Alexander

last: Mildner


title: Differential translatome in the sensory neurons of the DRG treated with LXR agonist

first: Matthew

last: Schipma

summary: We show differences in translatome of the sensory neurons of the DRG primary neurons treated with LXR agonist GW3965.

overall_design: Evaluation of changes in translatome of the sensory neurons in the DRG with LXR activation

first: Chaitanya

last: Gavini


title: Differential expression of genes involved in salt-treated iU1 seedlings

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia sinica

summary: To help understanding the mechanisms involved in the development of salt hypersenstivitivy phenotype of iU1 seedlings.

overall_design: Salt stress induced gene expressions of Arabidopsis seedlings were measured. 3 independent experiments were performed for each genotype and each treatment.

first: Ya-Huei

last: Chen


title: Transcriptomic analysis of sturgeon embryos in response to chemically induced DNA damage

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: In this study we show that the exposure to genotoxicants (10 nM camptothecin and 20 µM Olaparib) affects embryo development in a stage-dependent manner with early stages being the most sensitive to DNA damage. The transcriptomic and proteomic patterns changed significantly after exposure to genotoxicants compared to the control. Camptothecin and Olaparib downregulated metabolic pathways and developmental processes. Additionally, the exposure to genotoxicants led to upregulation of cell proliferation, neural precursor cell proliferation, generation of neurons, taxis and locomotion. Protein patterns were altered as well by DNA damage. The results of this study indicate that there is a strong correlation between phenotype formation and changes in transcriptomic and proteomic profiles.

overall_design: We analyzed the effect of the genotoxins, CPT (camptothecin) and Ola (olaparib) on the transcriptome of the Acipenser ruthenus embryos during the sxposure period from 2 to 24 hpf (blastula); 24 to 48 hpf (gastrulation) and 48 to 72 hpf (neurulation).

first: Levgeniia

last: Gazo

last: Sindelka

first: Martin

last: Psenicka

first: Pavel

last: Abaffy

first: Ravindra

last: Naraine


title: Poly(A)-capture full-length double-strand cDNA sequencing for transcriptome analysis

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

summary: We tried two methods which are the DNase I treated full-length double-strand cDNA sequencing and the poly(A) capture full-length double-strand cDNA sequencing to avoid the non-specific genomic DNA amplification.

overall_design: Transcriptome analysis by Total RNA, DNaseI-treated and Poly(A) capture Sequencing.

first: Yo

last: Niida


title: Recombinant FGF10-induced de novo alveologenesis in neonatal mice after hyperoxia exposure is associated with enhanced AT2’s resident mesenchymal cell niche activity

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Recombinant FGF10 improved hemodynamic measurements and alveologenesis. Alveolosphere assays indicate that the activity of rMC-Sca1Pos is negatively impacted by HYX and partially rescued by FGF10 treatment. scRNAseq results identified clusters expressing Fgf10, Fgf7, Pdgfra, Axin2 which could represent the rMC niche cells for the AT2 stem cells. In this syudy, we demonstrate that FGF10 administration is curative for BPD and identified a subpopulation of rMC-Sca1Pos niche cells which could represent its cellular target.

overall_design: In this study, we used a well-established mouse BPD model.C57BL/6J mice were maintained in two groups in NOX (21% O2) and HYX (85% O2) from P0 to P8. Next, We used FGF10 recombinant protein intraperitoneally at three different time intervals (P8-P14, P22-P28 and P36-P42) following HYX. We carried out hemodynamic measurements, morphometry analysis and IF at day 45. scRNAseq between rMC-Sca1Pos isolated from NOX and HYX were also carried out to analyze transcriptional changes in NOX vs. HYX in terms of resident mesenchymal niche activity after injury.

first: Harald

last: Ehrhardt

first: Christos

last: Samakovlis

first: Janine

last: Koepke

last: Guenther

first: Sara

last: Taghizadeh


title: m6A-mRNA&lncRNA Epitranscriptomic Microarray

city: Cleveland

first: Chengfeng

last: Yang

state: OHIO

address: 2500 MetroHealth Drive

department: Medicine

institute: Case Western Reserve University

summary: Total RNA samples from human bronchial epithelial BEAS-2B passage-matched control cells and Cr(VI)-transofmred BEAS-2B cells were submitted to ArraySatr for total RNA m6A epitranscriptomic microarray analysis

overall_design: Total RNAs were extracted from three biological samples of each group


title: The expression profile of miRNA in response to IFN-γ-driven ferroptosis in melanoma

city: Xi'an

first: Weinan

last: Guo

address: No.127, Changle Xi Road

institute: Xijing Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Anti-PD-1 immunotherapy has been established to be greatly effective in melanoma treatment, but the low response rate and occurrence of treatment resistance significantly hinder its efficacy. Recent studies have demonstrated that IFN-γ secreted by tumor-infiltrating CD8+T cells suppresses the expression of Xc- system to induce ferroptosis of tumor cells. However, whether the escape of tumor cells from ferroptosis facilitates the resistance to immunotherapy and the upstream regulatory mechanism remain elusive. MiRNAs participate in ferroptosis execution and can be delivered systemically by nanoparticle or alternative carriers, through which obvious therapeutic effect on cancer has been obtained. Herein, through RNA sequencing, we first obtained miRNAs expression profile of melanoma cells in IFN-γ-potentiated ferroptosis.

overall_design: Examination of miRNAs expression profile in A2058 melanoma cells in response to RSL3 treatment with or without the combination of IFN-γ

first: Chunying

last: Li


title: β-cell-specific deletion of Zfp148 improves nutrient-stimulated β-cell Ca2+ responses

city: Madison

first: Alan

last: Attie

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Insulin secretion from pancreatic β-cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β-cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. These RNA sequencing data show pathways altered in the β-Zfp148KO consistent with altered PEP cycling and improved insulin secretion responses.

overall_design: Details of generating the β-Zfp148KO and their control littermates is provided by Keller et al. JCI 2019 (https://doi.org/10.1172/JCI129143). 5 female littermate control (floxed Zfp148), 6 female β-Zfp148KO, 5 male control, and 4 male β-Zfp148KO mice were placed on a high-fat, high-sucrose diet (TD.08811) for 20 weeks. They were then sacrificed. RNA extracts and cDNA were prepared from whole islets harvested from these mice. RNA sequencing was performed by the UW-Madison Biotechnology Center. Processed sequencing data were analyzed by EBSeq (for EBSeq method, see Leng et al. https://doi.org/10.1093/bioinformatics/btt087).

first: Christopher

last: Emfinger

middle: D

first: Mark

last: Keller


title: Extracellular vesicles microRNA cargo in porcine follicular fluids: the potential association with oocyte quality

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The objective of this study was to identify miRNA expression profiles of extracellular vesicles (EVs) from porcine  follicular fluids (FFs) in association with oocyte quality. Antral follicles were aspirated individually and oocytes were stained with 0.5% Lissamine Green B stain (LB), a vital stain for oocyte quality. Each oocyte was classified separately according to the stain into high-quality (unstained; HQ) and low-quality (stained; LQ). Oocyte corresponding FFs were pooled together into HQ and LQ groups and their EV-miRNAs were isolated and sequenced. Sequencing analysis revealed that a total of 295 known miRNAs were commonly detected in both groups. MiR-27b-3p, miR-140-3p, miR-29a-3p, miR-202-5p, and miR-16 were the top highly abundant miRNAs in both groups. Differentially expression (DE) analysis exhibited that 19 miRNAs (including miR-193a-5p, miR-125b, and miR-320) were up- while 22 (including miR-9, miR-6516, and miR-206) were down-regulated in the HQ compared to the LQ group.

overall_design: Six small-RNA libraries were prepared from two different groups of follicular fluid-extracellular vesicles (FF-Evs) corresponding to oocyte quality (High vs. Low) and sequenced on an Illumina NovaSeq 6000.

first: Matej

last: Murin

first: Alexandra

last: Bartkova

first: Veronika

last: Kinterova

first: Kateřina

last: Marcollová

first: Jozef

last: Laurincik

first: Radek

last: Prochazka


title: Identification of large offspring syndrome during pregnancy through maternal blood transcriptome analyses

city: Columbia

first: Rocio

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

summary: In vitro production of bovine embryos can result in large/abnormal offspring syndrome (LOS), a condition characterized by macrosomia, macroglossia, exomphalos and placental abnormalities.  LOS can lead to the death of dam and calf.  Currently, no test exists to identify LOS pregnancies.  We hypothesized that maternal blood markers are useful to identify LOS.  Bovine fetuses were generated by artificial insemination (control) or produced in vitro.  Surgical fetal collections performed on d56 or d105. Maternal blood was collected on gestation d55 and d105.  On d56 and d105, fetuses produced in vitro weighing greater than 97th percentile of the AI weight were considered as LOS. To determine whether maternal blood may be used to identify LOS on d55 and/or d105 of gestation, leukocyte mRNA from 23 pregnant females was isolated and sequenced using a short-read platform.  Unsupervised clustering grouped 20 samples by animal (n=10 heifers) rather than by stage of pregnancy.  Leukocyte gene expression analyses revealed >3,500 differentially expressed genes in females carrying the two largest LOS fetuses.  In summary, our study suggests that transcript amount of ATF7IP from d105 maternal leukocytes may be useful to identify extreme cases of LOS.

overall_design: Comparision of day 55 and day 105 maternal blood transcriptome analyses of females carrying day 105 the AI, ART-normal and ART-LOS fetuses.

first: Bhaumik

last: Patel


title: Estrogen Receptor Regulated Gene Signatures in Invasive Breast Cancer Cells and Aggressive Breast Tumors

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: When co-activated with IKKβ, estrogen receptor regulates a subset of genes in invasive cells, which are associated with proliferation, vesicle and intracellular trafficking. These genes are associated with poor survival in patients and are enriched in metastatic tumors in PDX models.

overall_design: scRNA-seq (OneCellBio) and bulk RNA-seq

first: Emily

last: Smart

first: Svetlana

last: Semina

first: Luis

last: Alejo

first: Jonna

last: Frasor


title: RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients

city: Bandung

first: Miftahul

last: Faridl

state: Jawa barat

address: Jalan Ganeca No. 12, Dago, Coblong, Bandung, Jawa Barat, Indonesia

department: School of Life Sciences and Technology

country: Indonesia

institute: Bandung Institute of Technology

summary: We used total RNA of nasopharyngeal swabs from COVID-19 patients to identify their gene expression profile. Multiple biological process were significantly enriched in either asymptomatic or mildly symptomatic patients. These significantly expressed genes were suggested to contribute to the severity of the disease. We also performed metagenomics analysis to identify differences in the microbiome profile of the two groups of patients.

overall_design: Gene expression and metagenomic profile of nasopharynx tissue from 2 asymptomatic and 2 mildly symptomatic COVID-19 patients

first: Karlina

last: Mellyani

first: Karimatu

last: Khoirunnisa

first: Popi

last: Septiani

first: Ernawati

middle: A

last: Giri-Rachman

first: Husna

last: Nugrahapraja

first: Ema

last: Rahmawati

first: Cut Nur

middle: C

last: Alamanda

first: Ryan

middle: B

last: Ristandi

first: Rifky

middle: W

last: Rachman

first: Rini

last: Robiani

first: Azzania

last: Fibriani


title: Identification of eIF4A1-binding RNAs in human prostate cancer cell line DU145

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: We screened the translational targets of eIF4A1 in DU145 cells using the Native RNA immunoprecipitation (RIP) assay with RNA-seq (RIP-seq). The eIF4A1-binding peaks and RNA fractions were normally distributed around the ATG translation start site. A total of 197 coding genes with eFI4A1-binding peaks in mRNAs, including 5' UTR, exon, and 3' UTR regions.  were identified in the eIF4A1-RIP sample. The most enriched eFI4A1-binding motifs (MAGGTA, CCASCYC, and GARGA) were identified by aligning the sequences of all eFI4A1-binding RNA fractions to a reference genome.

overall_design: RNA immunoprecipitation (RIP) assay with RNA-seq (RIP-seq) was performed in paired sets with eIF4A1- and IgG-derived IPs, respectively, using human prostate cancer cell line DU145.

first: Runhua

last: Liu


title: Gene expression profile chqnge of intestinal stem cells after VSG bariatric surgery

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

summary: To investigate the effect of vertical sleeve gastrectomy (VSG) on intestinal stem cell (ISC)/progenitor cells, we performed VSG on a dietary-induced obese mouse models that expresses eGFP fluorescence tag in its Lgr5 gene, a specific marker of ISCs. We then performed RNAseq on the GFP-positive ISCs sorted from the duodenal, jejunal, and ileal epithelia. We pre-sorted immune cells (CD45 positive), endothelial cells (CD31 positive), apoptotic (Annexin5 positive), and dead cells (stained with Sytox blue). By performing differential expression analysis (P < 0.05, adjusted P <0.2, log2 fold change > 0.5, normalized count > 50 by DESeq2), we found that VSG altered 467 genes (259 up; 208 down) in the duodenum, 510 genes (348 up; 162 down) in the jejunum, and 955 genes (600 up; 355 down) in the ileum. Of note, some of the VSG-increased genes are region-specific. Overall, our data suggest that VSG induces ISC fate toward enteroendocrine cell differentiation and that there are critical regional differences among ISCs in the duodenum, jejunum, and ileum.

overall_design: mRNA profiles of sorted ISC/progenitor cells from VSG vs. sham-treated dietary-induced obese mice.

first: Ki-Suk

last: Kim

first: Yu-Han

last: Hung

first: Darleen

last: Sandoval


title: Transcriptional responses in SIX2 nephron progenitor cells following mitochondrial complex III subunit 7 (Qpc) inactivation

city: Nashville

first: Volker

middle: Hans

last: Haase

state: TN

institute: Vanderbilt University Medical Center

summary: To identify novel transcriptional targets following Qpc inactivation. We deleteted Qpc in SIX2 nephron progenitor cells using a Six2-eGFP/cre BAC transgene. We compared SIX2-expressing progenitors from Six2-Qpc-/- kidneys with control (Six2-Qpc+/-) embryonic kidneys at E18.5.

overall_design: 4 control samples were compared with 5 mutant samples

last: Guan


title: Ebag9 defines a regulatory checkpoint for CD8+ T cell memory formation responding to non-infectious stimuli

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: We examined the role of cytolytic strength on T cell fate decisions made by functionally competent CTLs under non-inflammatory priming conditions.  Employing the HY-specific miHAg system in conjunction with non-inflammatory priming conditions, we demonstrate a higher cytolytic efficacy despite unchanged effector frequencies in the primary response. In Ebag9-/- mice, an expanded memory population was obtained for anti HY- and anti SV40 T antigen-specific CD8+ T cells.

overall_design: CD8+ memory commitment was analyzed by single-cell RNA-seq in Ebag9-deficient mice that exhibit an amplified secretion of granzyme A and an augmented allogeneic and tumor cell lysis.

first: Armin

last: Rehm

first: Anthea

last: Wirges

first: Dana

last: Hoser

first: Stefanie

last: Herda

first: Kerstin

last: Gerlach

first: Christof

last: Bauer

first: Sascha

last: Sauer

first: Isabela

last: Schmitt-Knosalla

first: Gerald

last: Willimsky

first: Uta

last: Höpken


title: Culturing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnosis and genome sequencing

city: Guangzhou

first: Wenda

state: Guangdong

address: No. 151, Yan Jiang Xi Road

institute: Guangzhou Institute of Respiratory Health

summary: The effectiveness of virus culturing in 24 hours for the sequencing of SARS-CoV-2

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: The cultured and non-cultured samples of 1 x 50% tissue culture infectious dose (TCID50) were sequenced using metagenomics next-generation sequencing. The depth and coverage of SARS-CoV-2 genome were measured.

first: Zhiqi

last: Zeng

first: Hua

last: Guo

first: Liping

last: Chen

first: Yutao

last: Wang

first: Haiming

last: Jiang

first: Xiao

last: Wu

first: Yong

last: Yin

first: Zelong

last: Gao

first: Canxiong

first: Zhengshi

last: Lin

first: Zifeng

last: Yang


title: Transient inhibition of JNK pathway improves hematopoietic stem cell engraftment

first: Ligong

state: China

address: No.1, Qinghuayuan, Haidian District

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: We found that transient inhibition of JNK pathway increased short term-HSC frequency in cord blood CD34+ cells by 12.56 folds. Transcriptome analysis shows that inhibition of JNK pathway upregulated HSC-specific and anti-oxidative gene expression, prevented upregulation of cell cycle entry, oxidative phosphorylation and glycolysis related gene expression, and downregulated reactive oxygen species (ROS) active gene expression. Consistently, cell cycle and metabolic analysis show that inhibition of JNK pathway prevented HSC from cell cycle entry, glucose uptake increase and ROS accumulation. Accordingly, transient inhibition of JNK pathway also enhanced long term-HSC recovery during cord blood CD34+ cell collection. Collectively, these findings suggest that transient inhibition of JNK pathway could promote quiescent state of HSCs by preventing cell cycle entry and metabolic activation, thus improving HSC recovery and engraftment ability.

overall_design: RNA-seq analysis of 3 different cell samples: uncultured cord blood CD34+ cells, cord blood CD34+ cells cultured with DMSO for 24 h, and cord blood CD34+ cells cultured with JNK-IN-8 for 24 h

first: Huangfan

last: Xie


title: Consticted migration is associated with stable 3D genome structure differences in cancer cells (ATAC-Seq)

city: Knoxville

first: Rosela

last: Golloshi

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary: We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

overall_design: ATAC-Seq was performed to investigate chromatin accessibility state. This experiment was performed on Control, Top-5 and Bottom-5 cells and only one biological replicates was performed for each condition.

first: Christopher

last: Playter

first: Trevor

middle: F

last: Freeman

first: Priyojit

last: Das

first: Thomas

middle: I

last: Raines

first: Joshua

last: Garretson

first: Delaney

last: Thurston

first: Rachel

last: McCord


title: Biological effect of azacitidine (CC-486) on diffuse large B-cell lymphoma

city: New York

first: Maria

middle: Victoria

last: Revuelta

address: 1300 York Avenue

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Biomarker study for a phase 1, Open-Label, multicenter trial of azacitidine (CC-486) plus R-CHOP in subjects with high-risk previously untreated diffuse large B-cell lymphoma

overall_design: RNA and DNA methylation profiles of DLBCL tissue samples and CD3+ circulating cells methylation profiles pre and post CC486 treatment were generated by Illumina sequencing. *Please note that authors has not provided the 'pre and post CC486 treatment' status for each Sample record.

first: Leandro

last: Cerchietti

first: John

last: Leonard

first: Peter

last: Martin

middle: V


title: RNA Immunoprecipitation and high-throughput sequencing of  wild-type HEK293 cells upon HSV-1 infection.

city: Beijing

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

summary: SAFA showed stronger binding with HSV-1 RNA than with human RNA

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: For RNA immunoprecipitation sequencing (RIP-Seq), six 10-cm2 dishes (1×107 cells/dish) of HEK293 cells were infected with HSV-1 for 8 hours and the total RNAs were immunoprecipited by anti-SAFA antibody,then co-precipitated RNAs were isolated according to manufacturer’s instructions and sequenced on Illumina .

first: Lili

last: Cao

first: Fuping

last: You


title: Ripk3 signaling regulates the number and function of HSCs during stress and represses radiation-induced leukemia in mice

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

summary: We found that Ripk3 signaling selectively regulates both the number and function of hematopoietic stem cells (HSCs) during stress conditions and inhibits ionizing radiation (IR)-induced leukemia development in mice.  During serial transplantation, which stimulates a chronic Ripk3 activation in HSCs, Ripk3 promotes the loss of HSCs via Mlkl-mediated necroptosis and impairs HSC function by inducing ROS-p38-p16 mediated senescence.  In response to 6Gy of IR, which induces the activation of p53-p21-mediated cell cycle arrest/senescence in HSCs, Ripk3 is required for the activation of NF-κB and permits the survival of the senescent cells.  However, in response to multiple low doses of IR (1.75 × 4), Ripk3 signaling inhibits leukemia development by inducing ROS-p38-p16-mediated senescence and repressing Ire1α-Xbp1-Dnajb8 UPR fitness in pre-leukemic stem cells (pre-LSCs) and also inducing Mlkl-dependent clearance of pre-LSCs.  Mlkl deletion prevents IR-induced loss of HSCs and slightly accelerates leukemia development in mice, while Ripk3 deletion represses both necroptotic and senescence signals in pre-LSCs and significantly accelerates IR-induced leukemia development.  Our study suggests that immediately after high dose IR, temporal inhibition of Ripk3-NF-κB signaling might help to prevent long-term residual damage (LT-RDs) in bone marrow by eliminating the IR-induced senescent HSCs.  However, in response to low dose radiation, induced activation of Ripk3 signaling at the pre-leukemia stage might help to prevent the accumulation of mutant HSCs and the development of leukemia.

overall_design: We have finished the RNA-SEQ to investigate the role of Ripk3 signaling in  LSK cells (Lin- Sca1+ Kit+) and LK  (Lin- Kit+) cells from bone marrow.

first: Suming

last: Huang

first: Jiwang

last: Zhang


title: VIROME OF PEACH TREES IDENTIFIED BY SMALL RNA HTS IN HUNGARY

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

summary: Virus elimination is indispensable for the maintenance of stone fruit plantations, because these pathogens can cause serious crop damage and crop losses. Currently we do not possess efficient plant protection methods against viruses therefore prevention has a prominent role. In order to prevent infections, pathogen-free propagation material production and application of effective diagnostic methods have essential role. Our examined peach samples derived from isolator houses and stock nurseries of Fruitculture Research Institute of NARIC. With the help of highly sensitive metagenomic diagnostic methods: such as next generation sequencing of small RNAs, we are able to detect all of the presenting pathogens within our samples. During preparation steps, total RNA was isolated from leaf samples, RNA pools were made from the varieties, and then small RNA libraries were prepared. Sequencing was performed on Illumina platform and we used CLC Genomics Workbench for the bioinformatics evaluation. Results were verified by RT-PCR and Northern-blot. PCR products were cloned into pJET vector and Sanger sequenced. As a result, we detected nectarine stem pitting-associated virus (NSPaV), peach associated luteovirus (PaLV) and also peach latent mosaic viroid (PLMVd) which presence has to be checked regularly. Moreover we proved the incidence of PLMVd and PaLV first time in Hungary. We suspect, that the source of the viral infection might be the propagation material, which was used as a base for the variety collection in this isolator house.

overall_design: Virus diagnostics of 2 peach varieties in isolator house (2 libraries), open air stock nurseries (2 libraries) and 10 different peach variety in isolator house (1 library) by Illumina sequencing of the small RNAs

first: Dániel

last: Baráth

first: Nikoletta

last: Jaksa-Czotter

first: Tünde

last: Varga


title: Genome-wide maps of chromatin state in iBMDM (immortalized bone-marrow-derived macrophages) cells without or with virus infection.

summary:
iBMDM cells were infected with VSV (Vesicular Stomatitis Virus) or HSV-1 (Herpes Simplex Virus 1)  for 8 hours, followed by CHIP-seq analysis with H3K27AC antibody (Abcam, ab4729).  We find that chromatin state changed with virus infection, some enhacer and superenhancer were induced to promote anti-viral gene expression.
Conclusions: virus infection induce enhancer and superenhancer activation.

overall_design: iBMDM cells were infected with VSV or HSV-1 for 8 hours, then cells were fixed and lysed, chromatin DNA were immunoprecipitated with H3K27AC antibody, followed by CHIP-seq analysis. Input was a pool of total DNA from uninfected iBMDM cells.