title: The unexpected role of HBx in UC

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Ulcerative colitis is a chronic inflammatory disorder for which a definitive cure is still missing. This is characterized by an overwhelming inflammatory milieu in the colonic tract where a composite set of immune and non-immune cells orchestrate its pathogenesis. Over the last years, a growing body of evidence has been pinpointing gut virome dysbiosis as underlying its progression. Nonetheless, its role during the early phases of chronic inflammation is far from being fully defined. Here we show the gut virome-associated Hepatitis B virus protein X, most likely acquired after an event of zoonotic spillover, to be associated with the early stages of ulcerative colitis and to induce colonic inflammation in mice. It acts as a transcriptional regulator in epithelial cells, provoking barrier leakage and altering mucosal immunity at the level of both innate and adaptive immunity. This study paves the way to the comprehension of the aetiopathogenesis of intestinal inflammation and encourages further investigations of the virome as a trigger also in other scenarios. Moreover, it provides a brand-new standpoint that looks at the virome as a target for tailored treatments, blocking the early phases of chronic inflammation and possibly leading to better disease management.

overall_design:
3x HBx ChIP-Seq; 3x Caco-2 GFP RNA-Seq; 3x Caco-2 HBx RNA-Seq;
9x Ex-vivo biopsy GFP RNA-Seq; 9x Ex-vivo biopsy HBx RNA-Seq;
24x UC biopsy multiple cell sorting RNA-Seq

first: Federica

last: Ungaro

first: Luigi

last: Lamparelli

first: Silvio

last: Danese

first: Alessandra

last: Pirola

first: Rocco

last: Piazza


title: Isolation and Identification of Mammary Epithelial Cells from Goat Milk

status: Public on Feb 20 2023

city: Nanning

first: Sheng

last: Ye

address: No. 100 of Daxue East Road

country: China

institute: Guangxi University

type: Expression profiling by high throughput sequencing

summary: Mammary epithelial cells (MECs) have strong secretory function, which is an important target cell for studying mammary gland bioreactor. It is also a unique cell with lactation function in mammary gland. It can be used to study cell biological characteristics and molecular biological mechanism in the process of mammary gland growth, development and lactation. At present, mammary epithelial cells are obtained from mammary tissue, and the extraction of tissue block involves surgical anesthesia, which may lead to breast tissue injury and infection. This study aimed to describe the process of isolating and culturing goat mammary epithelial cells (GMECs) from goat milk, and to identify the biological characteristics of GMECs. Our study laid a foundation for the study of the regulation mechanism of mammary gland development and lactation, the improvement of milk quality, the increase of milk production and the establishment of mammary gland bioreactor.

overall_design: The five samples are analyzed. GEFs are control group with two replicates.  GMECs are treatment group with three replicates.

first: Ben

last: Huang


title: Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation rather than pre-mRNA splicing

status: Public on Feb 19 2023

city: Wuhan City

first: Liang

middle: an

last: min

state: Hubei Province

address: 299 Bayi Road

department: College of Life Sciences

institute: Wuhan University

summary: To investigate the functions of each singular copy of snRNA genes in Drosophila melanogaster, we focused on the U1 snRNA and systematically investigated all the five Drosophila U1 genes. We constructed two series of U1-gene strains, one is transgenic strains of U1 promoter-driven gfp that allows for detection of each U1-gene’s expression in various developmental stages and tissues, the other is the CRISPR/Cas9-mediated precise U1-gene deletion strains that allows for investigation of phenotypes and effects on multiple RNA processing steps, including transcription, splicing and 3'-end formation. Further in vitro pulldown assay reveal the Drosophila U1 variants have different activity in binding with Sm proteins.

overall_design: Comparatively analysis the differentially expressed genes, alternative polyadenylation events and alternative splicing events of RNA-Seq data for WT and detection of each U1-gene’s expression in Drosophila melanogaster.

first: Mei

last: Wang

first: An-Min

last: Liang

first: Yu-Jie

last: Fan

first: Yong-Zhen

last: Xu


title: The upregulation of miR-98-5p affects the glycosylation of IgA1 through cytokines in IgA nephropathy

city: Changsha

first: Hong

last: Liu

state: Hunan

address: Renmin Road 139#

department: Nephrology

institute: The Second Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Increases in galactose-deficient IgA1 (Gd-IgA1) play a crucial role in the pathogenesis of IgA nephropathy (IgAN), and several recent experiments have shown that microRNAs (miRNAs) are involved in regulating the development and physiological function of the kidney. The aims of this study were to identify miRNAs that can affect the pathogenesis of IgAN and reveal the underlying regulatory mechanism of IgA1 glycosylation in peripheral blood
Methods: The differentially expressed miRNAs in peripheral blood mononuclear cells (PBMCs) between IgAN patients and healthy controls were screened by high-throughput sequencing. The miRNA targets were predicted and verified by dual-luciferase reporter assays. We also explored the miRNA regulation of Gd-IgA1 through the transfection of miRNA mimics and related plasmids
Results: The high-throughput sequencing results showed that miR-98-5p was highly expressed in the PBMCs of IgAN patients compared with healthy controls, and the luciferase reporter gene system confirmed that miR-98-5p might target chemokine ligand 3 (CCL3). The transfection of si-CCL3 confirmed that a decrease in CCL3 can affect the expression of interleukin-6 (IL-6) and C1GALT1. The overexpression of miR-98-5p in PBMCs via the transfection of miR-98-5p mimic reduced the CCL3 and C1GALT1 levels and increased the IL-6 levels. However, these changes in PBMCs were attenuated by cotransfection with the CCL3 plasmid.
Conclusion: The results showed that miR-98-5p in PBMCs can target CCL3 to decrease its expression, which increased the IL-6 levels and the resulting increase in IL-6 can decrease C1GALT1 expression. Therefore, miR-98-5p might be involved in the development of IgAN.

overall_design: miRNA，mRNA and circRNA from IgAN patients and control subjects were generated by deep sequencing, in triplicate.

first: Di

first: Yexin

first: Liyu

last: He


title: Comparing alternative polyadenylation landscapes in highly and poorly metastatic breast cancer cells

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

summary: Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3’ UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo.

overall_design: 3'-end RNA sequencing to measure alternative polyA site selection in poorly and highly metastatic cancer cells, and HNRNPC knockdown cells

first: Navickas

last: Albertas

first: Asgharian

last: Hosseinali

first: Winkler

last: Juliane

first: Fish

last: Lisa

first: Garcia

last: Kristle

first: Goodarzi

last: Hani


title: Single-cell profiling and spatial transcriptome of primary tumors and paired metastatic lymph nodes in breast cancer patients

city: ShangHai

first: Ke-Da

last: Yu

address: No.270, Dongan Road

institute: ShangHai Cancer Center

summary: Metastasis remains the leading cause of death in breast cancer. However, little is known about the dynamic changes during the dissemination of breast cancer. Here, we generate single-cell RNA and spatial transcriptome of primary tumors and paired metastatic lymph nodes in 4 breast cancer patients. We identified a disseminated cancer cell cluster with high levels of oxidative phosphorylation (OXPHOS). We also noticed the transition between glycolysis and OXPHOS when dissemination initiates. Furthermore, this distinct cell cluster is distributed along the tumor’s leading edge.

overall_design: single-cell RNA and spatial transcriptome of  4 primary tumors and 4 paired metastatic lymph nodes in breast cancer

first: Yi-Ming

first: Jing-Yu

last: Ge

first: Yu-Fei

last: Chen


title: The oncogene-dependent resistance to reprogramming unveils cancer therapeutic targets

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The resistance to transcription factor-mediated reprogramming into pluripotent stem cells is one of the distinctive features of cancer cells. Here, we dissect the profiles of the reprogramming factor binding and the subsequent transcriptional response in cancer cells to reveal the molecular mechanisms underlying this phenomenon. Using clear cell sarcomas (CCSs) as a model, we show that expression of the driver oncogene EWS/ATF1 misdirects the reprogramming factors to cancer-specific enhancer elements and thereby impairs the early transcriptional response toward pluripotency which is otherwise provoked. Consistently, sensitization to the reprogramming cue is also observed in other types of cancer when the corresponding oncogenic signals are pharmacologically inhibited. Exploiting this oncogene dependence of the transcriptional ‘stiffness’, we identify the mTOR signaling pathway downstream of EWS/ATF1, and discover inhibiting the mTOR activity substantially attenuates the propagation of CCS cells both in vitro and in vivo. Collectively, our results demonstrate that the early transcriptional response to cell fate perturbations can be a faithful readout to identify effective therapeutics in cancer cells. Moreover, the current study has implications for understanding how the cancer cell identity is robustly maintained.

overall_design: ChIP-seq was performed in a murine EWS/ATF1-induced sarcoma cell line G1297 in which HA-tagged EWS/ATF1 is induced in a Doxycycline (Dox) dependent manner.

first: Sho

last: Ohta


title: Single-cell RNA-seq of the esophagus of Keratin5CreERT2::Keap1 floxB/floxB and Keap1 floxB/floxB mice

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

institute: Tohoku University

summary: We analyzed the esophagus of Keap1 conditional knockout mice. In these mice, there were both Keap1-normal and Keap1-deleted cells in the esophageal epithelium. To compare the gene expression of these cells, we conducted single-cell RNA-seq for the mice esophagus.

overall_design: Esophagus tissue without muscle layer from Keatin5CreERT2::Keap1 floxB/floxB and control Keap1 floxB/floxB mice

first: Wataru

last: Hirose

first: Masayuki

last: Yamamoto


title: Reverse Transcription quantitative PCR (RT-q PCR) analysis of osteogenic-related markers for osteogenic differentiation from human periodontal ligamen  stem cells

city: Pathumwan

first: Medania

last: Purwaningrum

state: Bangkok

address: Henri Dunant

department: Pharmacology

country: Thailand

institute: Faculty of Veterinary Science

summary: We pre-treated human periodontal ligament stem cells (hPDLSCs) under Iinterleukin-6 (IL-6) in osteogenic inductive medium (OM) on osteogenic differentiation potential and investigate the specific signaling pathway by clarifying with several antagonists (Dkk-1, SP600125, SB431542, and DAPT) and siRNA (siWnt2B, siWnt10B, and siWnt5A) to identify the differences in the expression pattern of osteogenic related markers by reverse transcription quantitative polymerase chain reaction (RT-qPCR).

overall_design: qPCR gene expression profiling of differentiation cells compared to undifferentiated cells.

first: C

last: Sawangmake

first: M


title: Characterization of mouse cochlear macrophage enriched and age-dependent gene expression

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify genes with enriched expression in cochlear macrophages that were also regulated in an age-dependent manner

overall_design: Macrophages and nonmacrophages were isolated from young adult (1.5 month) and old adult (12-14 month) heterozygous CX3CR1 GFP knock-in mice (CX3CR1 GFP/+) whole cochlea or cochlea substructures. Cells were sorted for GFP expression using a dissociation and FACS protocol adapted from Panganiban et al., 2022.

first: Hainan

last: Lang

middle: L

first: Kenyaria

middle: V

last: Noble


title: HnRNP K regulates inflammatory gene expression by mediating splicing pattern of transcriptional factors

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: HnRNP K is a heterogeneous nuclear ribonucleoprotein and has been identified as an oncogene in most solid tumors via regulating gene expression or alternative splicing of genes by binding both DNA and pre-mRNA. However, how hnRNP K affects tumorigenesis and regulates the gene expression in cervical cancer (CESC) remains to be elucidated. In these data, higher expression of hnRNP K was observed in CESC and was negatively correlated with the patient survival time. We then overexpressed hnRNP K (hnRNP K-OE) and found that its overexpression promoted cell proliferation in HeLa cells (P = 0.0052). Next, global transcriptome sequencing (RNA-seq) experiments were conducted to explore gene expression and alternative splicing profiles regulated by hnRNP K. It is shown that upregulated genes by hnRNP K-OE were associated with inflammatory response and an apoptotic process of neuron cells, which involves in cancer. In addition, the alternative splicing of those genes regulated by hnRNP K-OE was associated with transcriptional regulation. Analysis of the binding features of dysregulated transcription factors (TFs) in the promoter region of the inflammatory response genes regulated by hnRNP K revealed that hnRNP K may modulate the expression level of genes related to inflammatory response by influencing the alternative splicing of TFs. Among these hnRNP K-TFs-inflammatory gene regulatory networks, quantitative reverse transcription polymerase chain reaction (RT-qPCR) experiments and gene silencing were conducted to verify the hnRNP K-IRF1-CCL5 axis. In conclusion, the hnRNP K-TFs-inflammatory gene regulatory axis provides a novel molecular mechanism for hnRNP K in promoting CESC and offers a new therapeutic target.

overall_design: Transcrptional analysis of hnRNP K overexpression and control in HeLa cells.

first: Siyi

last: Liu

first: Jinhai

last: Tan


summary: The resistance to transcription factor-mediated reprogramming into pluripotent stem cells is one of the distinctive features of cancer cells. Here, we dissect the profiles of the reprogramming factor binding and the subsequent transcriptional response in cancer cells to reveal the molecular mechanisms underlying this phenomenon. Using clear cell sarcomas (CCSs) as a model, we show that expression of the driver oncogene EWS/ATF1 misdirects the reprogramming factors to cancer-specific enhancer elements and thereby impairs the early transcriptional response toward pluripotency which is otherwise provoked. Consistently, sensitization to the reprogramming cue is also observed in other types of cancer when the corresponding oncogenic signals are pharmacologically inhibited. Exploiting this oncogene dependence of the transcriptional ?stiffness?, we identify the mTOR signaling pathway downstream of EWS/ATF1, and discover inhibiting the mTOR activity substantially attenuates the propagation of CCS cells both in vitro and in vivo. Collectively, our results demonstrate that the early transcriptional response to cell fate perturbations can be a faithful readout to identify effective therapeutics in cancer cells. Moreover, the current study has implications for understanding how the cancer cell identity is robustly maintained.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Analyzing transcriptional profiles by RNA-seq for cancer cell reprogramming

first: Mio

last: Kabata

first: Takuya


title: Diagnostic Utility and Pathogenic Implication of Circulating MicroRNAs in Reversible Cerebral Vasoconstriction Syndrome

city: HsinChu

first: Chih-Hung

last: Chou

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

summary: The pathophysiology of reversible cerebral vasoconstriction syndrome (RCVS) is elusive. We speculated that circulating miRNAs might participate in the pathogenesis of RCVS and could assist clinical diagnosis. We prospectively recruited 75 RCVS patients (including 20 in discovery cohort, 23 in validation cohort-1, and 32 in the validation cohort-2) together with 76 age- and sex-matched controls. Five miRNAs including miR-130a-3p, miR-130b-3p, let-7a-5p, let-7b-5p andlet-7f-5p were significantly upregulated in patients with RCVS during ictal stage in comparison with that in their remission stage or controls. The combined miRNA panel well differentiated patients from controls (area under curve of Receiver Operating Characteristic curve was 0.906, 0.890 and 0.867 in three different cohorts respectively.) The expression of miR-130a-3p was associated with disruption of blood-brain barrier. Target prediction and pathway enrichment analysis suggested that endothelin-1 (EDN1) and transforming growth factor-beta (TGF-β) signaling pathway might link these miRNAs to the pathogenesis of RCVS. In vitro functional validation in human umbilical vein endothelial cells (HUVEC), human blood-brain barrier cell line (hCMEC/D3 cells) and HEK 293 cells confirmed that EDN1 and genes (BMPR2, SMAD5 and TGFBR2) involved in TGF-β signaling pathway were downregulated by these miRNAs. These miRNAs were correlated with plasma endothelin-1 level in the controls but not patients, indicating a deregulated feedback loop in patients during the disease state. To conclude, we identified the miRNA signatures associated with RCVS, which revealed excellent diagnostic performance, clinical relevance, and were functionally relevant to the putative pathomechanisms.

overall_design: We prospectively recruited patients with RCVS (during ictal and remission stage) and age- and sex-matched controls from the neurological clinics of Taipei Veterans General Hospital, Taipei, Taiwan. In the screening phase, we performed miRNA-sequencing on pooled samples of each group in the discovery cohort to identify differentially-expressed miRNAs, which were further confirmed in individual samples using quantitative PCR (qPCR) in the training phase. The candidate miRNAs were further investigated in two independent cohorts. The targeted genes and pathways were predicted using bioinformatics. The expression levels of the miRNAs were correlated with clinical parameters. The function of these miRNAs on the candidate target genes was further explored in human umbilical vein endothelial cells (HUVEC) via transfection of miRNA mimics.

first: S

middle: P

first: Y

middle: A

last: Chang

first: P

middle: C

last: Wu

first: H

last: Lee

last: Juan

middle: H

middle: F

last: Wang

first: J

last: Fuh

first: Huang

last: Hsien-Da

middle: J


title: Myostatin Increases Trophoblast Cell Invasion Through Regulating Epithelial Mesenchymal Transition Genes

status: Public on Feb 18 2023

city: Vancouver

first: Yuyin

last: Yi

address: 4500 Oak St

country: Canada

institute: University of British Columbia, BC Children’s Hospital Research Institute

summary: Myostatin (MSTN) is a TGF-β superfamily member and was recently shown to be secreted and functioning in the placenta. In this study, we perfomed mRNA sequencing on control and MSTN-treated primary trophoblast cells to decipher the underlying molecular mechanisms involved in MSTN-induced human trophoblast cell invasion.

overall_design:
Primary human trophoblasts from first-trimester placentas (n=5) were isolated and cultured with or without 50 ng/mL MSTN for 24 hours. Total RNA was extracted for transcriptomic analysis.
Please note that the samples have been analyzed with the control group previously deposited in GSE172040.

first: Peter

last: Leung

first: Faten

last: AbdelHafez


title: Combinational targeting CCL7 and Flt3L to promote the expansion and infiltration of cDC1 in tumors enhances T cell activation and anti-PD-1 therapy [CD8 T]

first: Hong-Peng

last: Dong

address: Donghu Road, No. 115, Wuchang District

summary: Immune checkpoint inhibitors (ICIs) represented by anti-PD-1/PD-L1 antibodies have been widely applied for various cancers and the response rate to ICIs is closely associated with the tumor immune microenvironment (TIME). Here, we show that combinational targeting CCL7 and Fms-like tyrosine kinase 3 ligand (Flt3L) increases the infiltration and expansion of conventional type 1 dendritic cells (cDC1s) in tumor sites and enhances the T cell antitumor responses and the efficacy of anti-PD-1 therapy in subcutaneous tumor models and spontaneous KrasG12D non-small cell lung cancer (NSCLC) models. We demonstrate that the fusion protein PD-1Ab7 in which CCL7 is fused with the single chain fragment variable region of anti-PD-1 antibody (PD-1Ab) exhibits superior antitumor activities compared to PD-1Ab. Mechanistically, PD-1Ab7 promotes antitumor immunity by increasing the infiltration of cDC1s and the activation of T cells, which is severely compromised by depletion of Zbtb46+ cDCs or inhibition of the CCL7 receptor CCR2. Furthermore, complementation of Flt3L sensitizes the ICI-resistant tumors to PD-1Ab7 and synergizes with PD-1Ab7 to inhibit tumor progression. These findings highlight the essential roles of PD-1Ab-based chemokine fusion strategy in targeting cDC1s and T cells for cancer prevention and provide therapeutic lead molecules for antitumor immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in cDC1s sorted from tumor-burdened lungs of  KrasLSL-G12D/+Tp53fl/fl NSCLC mouse treated with Flt3L plus PD-1Ab7,PD-1Ab7,PD-1Ab,and PBS.

first: Ying

last: Li

first: Qian

last: Chu

first: Bo

last: Zhong

first: Dandan

last: Lin


title: Combinational targeting CCL7 and Flt3L to promote the expansion and infiltration of cDC1 in tumors enhances T cell activation and anti-PD-1 therapy

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

overall_design: Refer to individual Series


title: Combinational targeting CCL7 and Flt3L to promote the expansion and infiltration of cDC1 in tumors enhances T cell activation and anti-PD-1 therapy [Dendritic Cell]


title: Mesenchymal stem cells reversibly dedifferentiate myofibroblasts to fibroblast-like cells by down-regulating the TGF-β-SMAD2/3 pathway

city: Guangzhou

first: Ruohao

last: Xu

state: Guangdong

address: Zhongshan Second Road, Guangzhou, China

department: Hematology

institute: Guangdong Provincial People's Hospital

summary: Bronchiolitis obliterans (BO) is a pulmonary chronic graft-versus-host disease (cGVHD), which is a noninfectious, irreversible, and poor prognostic complication after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Fibroblast-myofibroblast transition (FMT)-derived myofibroblasts (MFB) are the main effector cells involved in the development of BO. Through multiple regulations, the anti-fibrotic potential of mesenchymal stem cells (MSC) has been widely studied and was implied with potential clinical value. However, the MSC-mediated regulation of FMT and underlying mechanisms remained largely undefined. By identifying TGF-β1 hypertension as the pivotal landmark during the profibrotic FMT, TGF-β1-induced MFB and uMSC co-culture models were established and utilized to investigate regulations by uMSC on FMT in vitro. Methods including RNA sequencing (RNA-seq), Western blot, qPCR and flow cytometry were used. Our results revealed that uMSC reversibly dedifferentiated MFB into a group of FB-like cells by modulating the TGF-β-SMAD2/3 signaling. Importantly, these proliferation-boosted FB-like cells remained sensitive to TGF-β1 and could be re-induced into MFB. Our findings highlighted the reversibility of uMSC-mediated inhibitions on FMT through TGF-β-SMAD2/3 signaling, which may explain MSC's inconsistent clinical efficacies in treating BO and other fibrotic diseases. These dedifferentiated FB-like cells are still sensitive to TGF-β1 and may further deteriorate MFB phenotypes unless the profibrotic environment is corrected.

overall_design: RNA-sequencing data of untreated lung fibroblasts (FB), TGF-β1-induced myofibroblasts (MFB), and MFB co-cultured with MSCs (MFB-MSC).

first: Jianyu

last: Weng


title: Aging Decline of LEPR+ HSCs

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Leptin receptor (LEPR) identifies a subpopulation of hematopoietic stem cells (HSCs) with high repopulating potential. In this study, we demonstrated that LEPR-expressing HSCs while exhibiting significantly higher engrafting potential and self-renewing capacity in young mice showed early age-associated decline in these functions as compared to the LEPR- HSCs. LEPR+ HSCs have transcriptomic profiles significantly different from LEPR- HSCs in young mouse bone marrow, but middle-aged HSCs do not have distinct transcriptomic profiles based on LEPR status. The age-related phenotypes were associated with a proinflammatory transcriptomic profile at baseline in young LEPR+ HSCs, which was further exacerbated by age.  In contrast, LEPR- HSCs did not show age-associated functional impairment at the ages tested. This suggested that subsets of HSCs are susceptible to age-related decline in function at varying ages and that LEPR+ HSCs are a potential target for early cellular therapeutic interventions in delaying the detrimental effects of aging in hematopoiesis.

overall_design: Differential gene expression of young and middle-aged murine HSCs based on LEPR status. Comparisons performed were: young LEPR+ HSCs vs young LEPR- HSCS; middle-aged LEPR+ HSCs vs middle-aged LEPR- HSCs; young LEPR+ HSCs vs middle-aged LEPR+ HSCs; young LEPR- HSCs vs middle-aged LEPR- HSCs.

first: Thao

last: Trinh

first: Mark

last: Kaplan


title: N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing

city: guangzhou

first: xiaomei

last: yu

address: Harbour Road

institute: The Fifth Affiliated Hospital of Guangzhou Medical University

summary: To investigate the key gene in metastatic cancer, we established highly metastatic ESCC  cell lines. We then performed gene expression profiling analysis using data obtained from lncRNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of lncRNA-seq data for KYSE150-Luc cells and KYSE150-Luc-LM3 cells.

first: Xiao-Mei

last: Yu

first: Shu-Jun

first: Zi-Ting

last: Yao

first: Jiao-Jiao


title: Characterization of molecular changes associated with aging in the mouse cochlear lateral wall

first: Jeremy

last: Barth

summary: Overall goal of the study is to identify key molecular regulators that change in the cochlear lateral wall as a function of aging

overall_design: Three experimental replicates of lateral wall (LW) from young (2 months) and old (2.5 years) CBA/CaJ mice were compared by RNAseq analysis

first: Hainan

last: Lang

first: Clarisse

last: Paganiban

first: Kenyaria

last: Noble


title: Next generation sequencing for quantitative transcriptomic analysis of subpopulations of BM cells from young Hopx-wildtype and Hopx-knockout mice.

city: Taipei City

first: Chi-Yuan

address: No.7, Chung Shan S. Rd.

institute: National Taiwan University Hospital

summary: Hopx conditional knockout mouse (Hopx-/-) was generated. We then studied the biological effects of Hopx knockout on the hematopoietic system of young mice, via whole-transcriptome RNA-seq.

overall_design: Gene expression profiling of subpopulations of bone marrow cells, including long-term HSC (LT-HSCs), type 2 multipotent progenitors (MPP2), type 3 multipotent progenitors (MPP3), of young Hopx-wildtype and Hopx-knockout mice, was generated by RNA sequencing.

first: Chien-Chin

first: Wen-Chien

last: Chou


title: Next generation sequencing for quantitative transcriptomic analysis of Hopx-wildtype and Hopx-knockout murine bone marrow cells.

summary: We generated Hopx conditional knockout mouse (Hopx-/-) and studied the biological effects of Hopx knockout on the hematopoietic system, via whole-transcriptome RNA-seq. The findigns of our studies support crucial roles of Hopx in physiological and malignant hematopoiesis.

overall_design: Gene expression profiling of bone marrow cells of aged Hopx-wildtype and Hopx-knockout mice, with and without MN1 overexpression, were generated by RNA sequencing


title: Nucleotide variation in histone H2BL promotes cell proliferation by upregulating c-Myc

city: Shanghai

first: Dade

last: Song

address: No.1239,Siping Road

institute: Advanced Institute of Qingdao,Tongji University

summary: We found a histone H2B mutation, H2BL-T11C (leading to L3P amino acid variation) from tissue samples. Cells overexpressing H2BL-L3P showed stronger proliferation, colony formation and tumorigenic abilities. We further demonstrated that overexpressing H2BL-L3P made the cell cycle distribution changed via upregulation of c-Myc expression level. Furthermore, cell cycle studies based on EdU staining revealed the importance of c-Myc in promoting cell cycle progression through the G1/S checkpoint. As expected, treatment with 10058-F4, an inhibitor of the c-Myc-MAX interaction, alleviated the cell proliferation and cell cycle distribution phenotypes in the H2BL-L3P group and partially inhibited tumour growth. Overall, the amino acid mutation L3P, resulting from a SNP at a histone H2B locus, is associated with tumorigenesis and tumour progression. Additionally, the mechanisms and inhibitors involved in this study may provide a theoretical basis for targeted treatment of cancers with the same mutation.

overall_design: Three independent replacations  from each group of samples of SMMC-7721 cell lines (H2BG,H2BL and H2BL-L3P) with stable expression were collected and used for high-throughput RNA sequencing.

first: Jin

last: Sun

first: Lei

last: Zhang


title: Integrated analysis of physiology, transcriptomics and metabonomics revealed the mechanisms of high pH mitigating copper toxicity in Citrus sinensis roots

status: Public on Feb 17 2023

city: FuZhou

first: Jiang

state: FuJian

address: ShangXiaDian Street No.15

department: College of Resources and Environment

institute: Fujian Agriculture and Forestry University

summary: Limited data are available on the impacts of copper (Cu)-pH-interaction-responsive genes in roots. Citrus sinensis seedlings were treated with 300 (Cu-toxicity) or 0.5 uM (control) CuCl2 x pH 3.0 or 4.8 for 17 weeks. Thereafter, we investigated the impacts of Cu-pH interactions on transcriptomics in roots.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pH 4.8 and pH 3 at different Cu concentration（0.5 μM Cu- and 300 μM Cu-treated）in Citrus sinensis roots

first: Wenshu

last: Chen

first: Rongyu

last: Rao

first: Ningwei

last: Lai

first: Zengrong

last: Huang

first: Lintong

last: Yang

first: Lisong


title: Exon- expression data of Human hepatocellular carcinoma cells ( CD90 + HSP90 + HCC cells )

city: beijing

first: Xiong

last: Shu

address: No.31, Xinjiekou East Street, Xicheng District, Beijing

institute: Beijing Research Institute of Traumatology and Orthopaedics, Beijing JiShuiTan Hospital

summary:
Identification of surface antigens that exhibited cancer-specific expression is a crucial step in the development of novel antibody-targeted therapies. We here aimed to investigate the anti-tumor activity of a novel monoclonal antibody (mAb) 11C9 and identify the antibody tractable target in the hepatocellular cancer stem cells (HCSCs).
This research has studied differentially expressed genes (DEGs) between CD90+HSP90+ cells and 11C9-treated CD90+HSP90+ cells. We collected those two types cells for RNA extraction and hybridization on Affymetrix microarrays.

overall_design: 2 samples from  CD90+HSP90+ cells, 1 sample treated by 11C9, 1 sample is normal  CD90+HSP90+ cells.

first: Hui-Qi

last: Liu

first: Li-Xin


title: Effects of short distance transportation on physiological indexes, intestinal morphology, microbial community and transcriptome of jejunum in Weaned Piglets

city: Harbin

first: Honggui

address: changjiang street num 600

institute: Northeast Agricultural University

summary: To investigate the effect of short distance transport on jejunal tissueof weaned piglets, We then performed gene expression profiling analysis using data obtained from RNA-seq in jejunal tissues of weaned piglets after transport and without transport

overall_design: Comparative gene expression profile analysis of RNA-seq data from jejunum of weaned piglets after transport and without transport.

first: Qin

last: Fu

first: Xuesong

first: Sitong

last: Zhou


title: Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi [scRNA-seq]

city: Bonn

first: Amir Hossein

last: Kayvanjoo

address: Carl-Troll-Straße 31

country: Germany

institute: LIMES Institute

summary: We investigate the heterogeneity of macrophage populations in the fetal liver to define their specific roles during hematopoiesis.

overall_design: CD11b+,F4/80+ cells were sorted from WT fetal livers at E14.5 using FACS and analyzed using scRNAseq.

first: Amir

first: Iva

last: Splichalova

first: David

last: Bejarano

first: Hao

first: Katharina

last: Mauel

first: Nikola

last: Makdissi

last: Heider

first: Nora

middle: R

last: Balzer

first: Collins

last: Osei-Sarpong

first: Kevin

last: Bassler

first: Joachim

last: Schultze

first: Stefan

last: Uderhardt

first: Eva

last: Kiermaier

first: Marc

last: Beyer

first: Andreas

last: Schlitzer


title: YAP1 is essential for self-organized differentiation of pluripotent stem cells [RNAseq]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: The Yes-associated protein 1 (YAP1) is a downstream effector of the Hippo pathway and essential mechanotransducer. It has been suggested to play a crucial role for early embryo development, but the relevance for early germ layer commitment of human induced pluripotent stem cells (iPSCs) remains largely unclear. To gain better insight into the functional relevance of YAP1 in these early cell-fate decisions, we generated iPSC lines with YAP1 knockout (YAP-/-) with CRISPR/Cas9 technology and analyzed transcriptomic and epigenetic modifications. In YAP-/- iPSCs the expression of several YAP1 targets changed and NODAL, which is an important regulator of cell differentiation, was upregulated. Furthermore, YAP1 deficiency evoked global DNA methylation changes. Directed differentiation of adherent iPSC colonies toward endoderm, mesoderm, and ectoderm could be induced, albeit endodermal and ectodermal differentiation showed transcriptomic and epigenetic changes in YAP-/- lines. Notably, in self-organized embryoid bodies (EBs) germ layer specification was clearly impaired. This phenotype was rescued via lentiviral overexpression of YAP1 and in tendency also by NODAL inhibitors. Our results demonstrate that YAP1 plays an important role during early germ layer specification of iPSCs, particularly for the non-directed self-organization of EBs, and this is at least partly attributed to activation of the NODAL pathway.

overall_design: 2 YAP1 knockout (YAP-/-) iPSC lines were differentiated into the three germ layer with directed differentiation. Additionally, 5 cell lines (3 wildtype (WT) and 2 YAP-/-) were also used to generate embryoid bodies (EBs) for undirected multilineage differentiation (5 days). DNA and RNA was isolated for Illumina Methylation BeadChips and RNA-seq.

first: Kira

last: Zeevaert

first: Roman

last: Goetzke

first: Mohamed

last: Elsafi Mabrouk

first: Marco

last: Schmidt

first: Catharina

last: Maaßen

first: Ann-Christine

last: Henneke

first: Chao

last: He

first: Arnold

last: Gillner

first: Martin

last: Zenke


title: YAP1 is essential for self-organized differentiation of pluripotent stem cells [DNAm]

type: Methylation profiling by genome tiling array

overall_design: 2 YAP1 knockout (YAP-/-) iPSC lines were differentiated into the three germ layers with directed differentiation. Additionally, 5 cell lines (3 wildtype (WT) and 2 YAP-/-) were also used to generate embryoid bodies (EBs) for undirected multilineage differentiation (5 days). DNA and RNA was isolated for Illumina Methylation BeadChips and RNA-seq.


title: YAP1 is essential for self-organized differentiation of pluripotent stem cells


city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: Ballan wrasse (Labrus bergylta) is used as a cleaner fish in Norwegian aquaculture to control sea lice. Thus, knowledge on the digestive physiology and nutrient requirements, as well as the ontogeny of the immune system is important. In this study, two different diets were tested; diet 1 was used as control diet consisting of artemia and rotifers cultivated and enriched in the in-house facility at IMR, Austevoll, Bergen (Norway). Diet 2 consists in plankton which has successfully been used before in cod larvae generating more robust individuals. Sampling was done according to the standard length of the larvae rather than age (dph). Sampling point 0 (BW0) (4 mm), sampling point 2 (BW2)  (4,5 mm), sampling point 3 (BW3)  (5,7 to 6 mm), sampling 4 (BW4) (7 to 7,5 mm), sampling point 5 (BW5) (10 to 10,5 mm), sampling point 6 (BW6)  (16 to 16,5 mm), and sampling point 7 (BW7)  (25 to 30 mm). Ontogeny of lymphoid organs and mucosal associated lymphoid tissues in ballan wrasse and the effect of different diets were investigated.

overall_design: Brood stock ballan wrasse (30 females and 6 males) were kept in tanks for a year under optimal conditions before the spawning season (beginning of April 2020). After spawning, eggs were collected and placed in incubators until hatching. At 4 dph, 30 000 to 34 000 individuals were transferred into 6 different tanks (B5 – B10) for the feeding trial were three tanks (B6, B8, and B 10) were fed with control diet (rotifers and artemia) and three tanks (B5, B7, and B9) were fed with plankton (2 diets in experimental triplicates). Formulated feed (dry feed) was given at 40 dph for first time in a co-feeding regime until 56 dph were only dry feed was supplied to all the tanks.  A total of 6 sampling points was undergone according to the 6 developmental stages in ballan wrasse. Sampling was done according to the standard length of the larvae rather than age (dph). Sampling point 0 (BW0) (4 mm), sampling point 2 (BW2)  (4,5 mm), sampling point 3 (BW3)  (5,7 to 6 mm), sampling 4 (BW4) (7 to 7,5 mm), sampling point 5 (BW5) (10 to 10,5 mm), sampling point 6 (BW6)  (16 to 16,5 mm), and sampling point 7 (BW7)  (25 to 30 mm). At each sampling point a series of pooled larvae were collected from the tank, rinsed with distilled water and immersed in RNA later at 4°C overnight and further kept at -20°C until further extraction.

first: Angela

last: Etayo

middle: K

first: Øystein

last: Sæle


title: Immunotoxin-αCD40 therapy activates innate and adaptive immunity and generates a durable antitumor response in glioblastoma models

city: Durham

first: Vidyalakshmi

last: Chandramohan

state: NC

address: 181c MSRB1, 203 Research Drive

department: Neurosurgery

institute: Duke University

summary: D2C7-immunotoxin (IT), a dual-specific IT targeting wild-type epidermal growth factor receptor (EGFR) and mutant EGFR variant III (EGFRvIII) proteins, demonstrates encouraging survival outcomes in a subset of patients with glioblastoma. We hypothesized that immunosuppression in glioblastoma limits D2C7-IT efficacy. To improve the response rate and reverse immunosuppression, we combined D2C7-IT tumor cell killing with αCD40 costimulation of antigen-presenting cells. In murine glioma models, a single intratumoral injection of D2C7-IT+αCD40 treatment activated a proinflammatory phenotype in microglia and macrophages, promoted long-term tumor-specific CD8+ T cell immunity, and generated cures. D2C7-IT+αCD40 treatment increased intratumoral Slamf6+CD8+ T cells with a progenitor phenotype and decreased terminally exhausted CD8+ T cells. D2C7-IT+αCD40 treatment stimulated intratumoral CD8+ T cell proliferation and generated cures in glioma-bearing mice despite FTY720-induced peripheral T cell sequestration. Tumor transcriptome profiling established CD40 upregulation, pattern recognition receptor, cell senescence, and immune response pathway activation as the drivers of D2C7-IT+αCD40 antitumor responses. In order to determine potential translation, immunohistochemistry staining confirmed CD40 expression in human GBM tissue sections. These promising preclinical data allowed us to initiate a phase I study with D2C7-IT+αhCD40 in patients with malignant glioma (NCT04547777) to further evaluate this treatment in humans.

overall_design: Comparative gene expression analysis of RNA-seq data of post-treatment day 0 and day 3 of CT-2A-dmEGFRvIII-Firefly Luciferase (CT-vIII) brain tumors treated in vivo by convection-enhanced delivery with control, D2C7-IT, αCD40, and D2C7-IT+αCD40.


title: AGO4 slicer activity reveals the passenger strand function of plant 23 nt siRNAs and the post-slicing retention of target RNAs mediating RNA-directed DNA methylation [WGBS]

city: Bloomington

first: Craig

middle: S.

last: Pikaard

state: Indiana

address: 915 E. Third Street

department: Department of Biology and Department of Molecular and Cellular Biochemistry

institute: Howard Hughes Medical Institute, Indiana University

type: Methylation profiling by high throughput sequencing

summary: In plants, transcriptional silencing by RNA-directed DNA methylation (RdDM) is mediated by ARGONAUTE 4 (AGO4) and 24 nt short-interfering RNAs (siRNAs) that are generated in parallel with 23 nt RNAs of unknown function. We show that 23 nt RNAs serve as the passenger strands of 23/24 nt duplexes loaded into AGO4. The 24 nt siRNAs then guide AGO4 slicing of the passenger strands, generating 11 and 12 nt cleavage products. Unexpectedly, we find that the 12 nt products remain associated with the guide strand-AGO4 complexes. Long noncoding RNAs generated at RdDM loci are similarly sliced and retained by AGO4.  These results suggest a model in which RNA POLYMERASE V transcripts at target loci are sliced repeatedly as transcription elongation proceeds, sequentially releasing AGO4-siRNA-scaffold RNA complexes that independently recruit the RdDM machinery. Consistent with this hypothesis, plant lines expressing wild-type versus slicing-defective AGO4 show quantitative variation in cytosine methylation and siRNA levels within RdDM loci.

overall_design: Whole-genome bisulfite sequencing of wild-type Arabidopsis thaliana ecotype/strain Wassilewskija, ago4-4 null-mutant plants, and ago4-4 plants that stably express transgenes expressing either wild-type or slicing-defective AGO4.

first: Feng

last: Wang

first: Hsiao-Yun

last: Huang


title: AGO4 slicer activity reveals the passenger strand function of plant 23 nt siRNAs and the post-slicing retention of target RNAs mediating RNA-directed DNA methylation [smallRNA-seq]

overall_design: Small RNA sequencing of RNAs copurifying with wild-type or slicing-defective AGO4 proteins stably expressed in ago4-4 null-mutant Arabidopsis plants.


title: Streamlined DNA-encoded small molecule library screening and validation for the discovery of novel chemotypes targeting BET proteins (RNA-seq)

status: Public on Feb 16 2023

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Targeting aberrant epigenetic programs that drive tumorigenesis is a promising approach to cancer therapy. DNA-encoded small-molecule library (DEL) screening is a core platform technology increasingly used to identify drugs that bind to protein targets. Here, we use DEL screening against bromodomain and extra-terminal motif (BET) proteins to identify inhibitors with new chemotypes, and successfully identified BBC1115 as a selective BET inhibitor. While BBC1115 does not structurally resemble OTX-015, a clinically active pan-BET inhibitor, our intensive computational modeling and biological characterization revealed that BBC1115 binds to BET protein BRD4 and suppresses aberrant cell fate programs. Phenotypically, BBC1115-mediated BET inhibition impaired proliferation in acute myeloid leukemia, pancreatic, and colorectal cancer cells in vitro. Moreover, intravenous administration of BBC1115 inhibited subcutaneous pancreatic and colorectal cancer xenograft growth with minimal toxicity and favorable pharmacokinetic properties in vivo. Since epigenetic regulations are ubiquitously employed across normal and malignant cells, it will be critical to evaluate whether BBC1115 interferes with normal cellular functions. Nonetheless, our study implicates that integrating DEL-based small-molecule compound screening and multi-step biological validation represents a reliable strategy to discover new chemotypes with selectivity, efficacy, and safety profiles for targeting proteins involved in epigenetic regulation in human malignancies.

overall_design: RNA-seq of murine leukemia cells (RN2) treated with indicated drugs

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Streamlined DNA-encoded small molecule library screening and validation for the discovery of novel chemotypes targeting BET proteins (ChIP-seq)

overall_design: H3K27ac, BRD4, and RNA Polymerase II (phosphorylated Ser 5) ChIP-seq of murine leukemia cells (RN2) treated with indicated drugs


title: A key residue in the precursor region of M protein contributes to the neurovirulence and neuroinvasiveness of the African lineage of Zika virus

city: Beijing

first: He

middle: Meng

last: Jiao

state: Beijing

address: No.20 Dongda Street

institute: Academy of Military Medical Sciences

summary: The Zika virus (ZIKV) represents an important global health threat due to its unusual association with congenital Zika syndrome. ZIKV strains are phylogenetically grouped into the African and Asian lineages. However, the viral determinants underlying the phenotypic differences between the lineages remain unknown. Here, multiple sequence alignment revealed a highly conserved residue at position 21 of the pre-membrane (prM) protein, which is glutamic acid and lysine in the Asian and African lineages, respectively. Using reverse genetics, we generated a recombinant virus carrying an E21K mutation based on the genomic backbone of the Asian lineage strain FSS13025 (termed E21K). The E21K mutation significantly increased viral replication in multiple neural cells lines with a higher ratio of M to prM production. Animal studies showed E21K exhibited increased neurovirulence in suckling mice, leading to more severe defects in mouse brains through causing more neural cell death and destruction of the hippocampus integrity. Moreover, the E21K substitution enhanced neuroinvasiveness in interferon (IFN) α/β receptor knockout mice, as indicated by the increased mortality, enhanced replication in mouse brains. The global transcriptional analysis showed E21K infection profoundly altered neuron development networks and induced stronger antiviral immune response than WT in both neural cells and mouse brains. More importantly, the reverse K21E mutation based on the genomic backbone of the African strain MR766 caused less mouse neurovirulence. Overall, our findings support the 21st residue of prM functions as a determinant for neurovirulence and neuroinvasiveness of the African lineage of ZIKV.

overall_design: Retinal mRNA profiles of infected WT or E21K mutant virus U87 cells (72 h.p.i.) were generated by deep sequencing ,in triplicate, using Illumina NovaSeq 6000.

first: Xiao-Feng

last: Li

first: Cheng-Feng

last: Qin

first: Meng-Jiao


title: RNA-seq analysis of GCBC and NBC that had been stimulated for either 2h or 4h with IL-21, CD40 ligation, BCR ligation, or combinations of these.

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose: To gain insight into both similarities and differences in the gene expression programs induced  by IL-21R, BCR and CD40 signals, we performed RNA-seq on both GCBC and NBC that had been stimulated for either 2h or 4h with IL-21, CD40 ligation, BCR ligation, or combinations of these.
Methods : Purified GCBC from d14 NP-CGG immunized MEG mice and NBC from naïve MEG mice were warmed at 37C for 30 minutes and then stimulated with 10ng/mL IL-21, 20μg/ml ⍺-IgM or 2.5μg/mL ⍺-CD40 (prepared as tetramer) alone or combined IL21/⍺-CD40 or ⍺-IgM/⍺-CD40 for 2 and 4 hours. After stimulation, cells were processed for RNA isolation using QIAshredder columns (Qiagen) and the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.  Samples were sequenced using Illumina NextSeq 500 with 75 bp paired-end reads and aligned to the mm10 genome using the STAR aligner (Dobin et al., 2013). Gene-level counts were determined using featureCounts (Liao et al., 2014), and raw counts were quantile normalized to each other for differential expression using the voom method (Law et al., 2014) in the Limma R package (Ritchie et al., 2015). For normalization of the datasets, the Quantile method was used.
Results: Like BCR and CD40 signals, IL-21R plus CD40 signals also synergize to induce c-Myc in GCBC. However, IL-21R plus CD40 stimulation differentially affects GCBC fate compared to BCR plus CD40 ligation—engaging unique molecular mechanisms

overall_design: Bulk RNA-seq of GCBC cultures with either of these two stimuli or with the combination of IL-21R/CD40 and BCR/CD40 stimulation.

first: Wei

last: Luo

first: Shuchi

last: Smita

first: Florian

last: Weisel


title: IL-21 from high-affinity CD4 T cells drives differentiation of brain-resident CD8 T cells during persistent viral infection

city: Hershey

first: Aron

last: Lukacher

address: 500 University Dr.

department: Microbiology & Immunology

institute: Penn State College of Medicine

summary: To investigate IL-21 producing CD4 T cells, we infected IL21-VFP reporter mice with mouse polyomavirus and compared VFP+ (IL-21+) CD4 T cells to VFP- (IL-21-) CD4 T cells in the brains and spleens.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VFP+ and VFP- CD4 T cells derived from the brains or spleens of IL21-VFP reporter mice at 15 day post Mouse Polyomavirus infection (dpi).

first: Lukacher

last: Aron

first: Ren

last: Heather

last: Mingqiang


title: Caspase-11 promotes inflammation and thrombosis  in SARS-CoV-2 infection

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: SARS-CoV-2 infections are a worldwide health concern, and new treatment strategies are needed for decreasing virus-induced inflammatory tissue damage. Targeting inflammatory innate immunity pathways holds therapeutic promise, but effective molecular targets remain elusive. Here, we show that the innate immunity proteins, human caspase-4 (CASP4), and its mouse homologue, caspase-11 (CASP11), are upregulated in SARS-CoV-2 infections, and that CASP4 expression correlates with severity of SARS-CoV-2 infection in humans. SARS-CoV-2-infected Casp11-/- mice experienced less severe infections in terms of weight loss and lung damage than WT mice. Notably, these phenotypes were not recapitulated in mice lacking the CASP11 downstream effector gasdermin D (Gsdmd-/-), though viral titers were similar in all groups. Global transcriptomics of infected WT and Casp11-/- lungs identified decreased inflammation and neutrophil gene signatures. We confirmed that protein levels of inflammatory mediators IL-1β and CXCL1, and neutrophil infiltration, were decreased in Casp11-/- lungs. Additionally, Casp11-/- lungs expressed less von Willebrand factor, a marker for endothelial dysfunction and more Kruppel-Like Factor 2 (KLF2), a transcription factor with anti-thrombotic functions. Thus, CASP11 is established as an upstream regulator of blood coagulopathy in SARS-CoV-2 infection. Overall, our results demonstrate that CASP11, promotes detrimental SARS-CoV-2-associated inflammation and coagulopathy, identifying CASP11 as a promising drug target for treatment and prevention of tissue damage in COVID-19.

overall_design: We sequenced 2 types of mouse knockout models and 1 wild-type, each with 3 replicates

last: Webb

first: Amal

middle: O

last: Amer

first: Mostafa

last: Eltobgy


last: Mengjiao

overall_design: Retinal mRNA profiles of infected WT or E21K mutant virus mice (3, and 7 d.p.i.)were generated by deep sequencing ,in triplicate.

last: He


title: Chromatin remodeling in bovine oocytes and preimplantation embryos

city: Davis

first: Chuan

last: Zhou

address: Meyer Hall, 450 Bioletti Way

department: Animal Science

institute: University of California, Davis

summary: Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.

overall_design: H3K4me3, H3K27ac, H3K27me3 and H3K9me3 were profiled with CUT&Tag technique in bovine GV oocytes (GV), 2-cell embryos (2C), 4-cell embryos (4C), 8-cell embryos (8C), morula (MO), blastocyst (BL), inner cell mass (ICM) and trophectoderm (TE). To investigate the relationship between embryonic transcription and chromatin remodeling, embryos were concurrently cultured in the presence of a transcriptional inhibitor (α-amanitin) and α-amanitin-treated 8-cell embryos (8A) were collected for library construction of H3K4me3, H3K27ac, H3K27me3 and H3K9me3. ATAC-seq libraries were prepared from bovine blastocyst, inner cell mass and trophectoderm.

first: Richard

middle: M

last: Schultz

first: Pablo

last: Ross


title: Higher intelligence is genetically linked with longevity

city: Jeonju

first: Mousumee

last: Khan

address: 20 Geonji-ro

institute: Jeonbuk National University

summary: We report the application of mRNA sequencing technology for identifying that the genetic linkage of higher intelligence with longevity in Drosophilla melanogaster. a transcriptome analysis was performed by sequencing the total mRNA. The differentially expressed gene analysis by a negative binomial test showed that a subset of genes displayed remarkably altered expression where 56, 152, and 26 genes were significantly upregulated (adjusted P value <0.01), and 30, 397, and 10 genes were downregulated (adjusted P value < 0.01) in INT compared to F0, NINT compared to F0, and INT compared to NINT each. The functions of the differentially expressed genes were analyzed at high levels by using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment program. Compared to F0, the pathways of ribosome and autophagy were up-regulated in INT while the pathways related to metabolisms were down-regulated. Meanwhile, the pathways associated with genome stability and immune reaction was upregulated and the pathway of oxidative phosphorylation responsible for ATP generation was down regulated in NINT. The KEGG comparison of INT with NINT, which eliminates genes associated with the environmental factors during the selection process, visualized more precise pathways associated with higher intelligence and longevity. The pathways related to genome stability (Fanconi anemia pathway, Mismatch repair, DNA replication, Homologous recombination, and Nucleotide excision repair) and immune reaction (Toll and lmd signaling pathway) were up-regulated in NINT, and these pathways were down-regulated in INT.

overall_design: Total mRNA from 5-days-old INT and NINT D. melanogaster at the F12 generation and F0 flies

first: Enkhchimeg

last: Lkhagva

first: Sharif

last: Siddiqui

first: Seong-Tshool

last: Hong


title: Translational control by microRNAs is essential for protein homeostatsis in the mouse brain

status: Public on Feb 15 2023

city: Boston

first: Serkan

last: Erdin

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: MicroRNAs (miRNAs) are important regulators of gene expression; however, their contribution to protein homeostasis remains unclear. Impaired protein homeostasis could contribute to brain aging and neurodegeneration; however, the underlying mechanisms are not well understood. Here, we show that conditional inactivation of Dicer in the adult mouse brain postnatal forebrain causes age-dependent accumulation of lipofuscin and polyubiquitinated protein aggregates. Impaired protein turnover in the cerebral cortex of Dicer conditional knockout (cKO) mice is associated with protein misfolding and endoplasmic reticulum stress. Conditional Drosha inactivation using the same Cre driver results in similar phenotypes, suggesting that the phenotypes may be due to the loss of canonical miRNAs. RNA-sequencing analysis revealed increased expression of target genes of neocortical neuron-enriched miRNAs in the Dicer cKO neocortex and dysregulated expression of genes involved in protein homeostasis maintenance. Further analysis revealed a similar gene expression profile in the hippocampal CA1 region of Dicer cKO mice as in the aging brain. Moreover, translational inhibition using anisomycin or rapamycin ameliorated the protein aggregation and neurodegeneration in Dicer-deficient brains. Thus, protein translational control by miRNAs is an essential component of the protein homeostasis network controlling neuronal survival in the adult brain. Our results show that excessive translation can produce key features of human neurodegenerative diseases, and suggest that translational suppression may be a therapeutic strategy to restore protein homeostasis and combat neurodegeneration.

overall_design: Bulk RNAseq based transcriptomic analyses of mouse necortex and mouse hipocampal CA1 region samples with Dicer conditional knockout and control samples

first: Hiroo

last: Yamaguchi

first: Mark

last: Chong

first: Dan

last: Littman

first: Matthias

last: Merkenschlager

first: Michael

middle: E

last: Talkowski

first: Jie

last: Shen

first: Raymond

last: Kelleher III


title: Effect of short-term high fat diet consumption on hippocampal and amygdalar gene expression in adult and aged male rats

last: Butler

state: OH

address: 460 Medical Center Drive

institute: Ohio State University

summary: It is known that short-term high fat diet consumption leads to significant memory impairments and an exaggerated proinflammatory phenotype in the aged rat brain. To gain a better understanding of the underlying mechanisms driving this cognitive and proinflammatory response, we conducted bulk RNAseq analysis of the hippocampus and amygdala from young adult and aged male rats.

overall_design: This was a 2x2 (Young vs old x chow control vs HFD) design with an n=3 per group for each brain region (hippocampus and amygdala).

first: Rebecca

last: Biltz

first: Sabrina

last: Mackey-Alfonso

first: Jonathan

last: Godbout

first: Ruth

last: Barrientos


title: Fluorescence detection of FAO activity with a chemical probe in cultured cells and mouse liver tissue

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

summary: Fatty acid beta oxidation (FAO) pathway is an important metabolic pathway for energy generation and is deeply associated with various diseases such as cancer and NAFLD/NASH. Therefore, development of detection methods of FAO activity change would contribute to understanding of disease mechanism and drug discovery. In this study, we newly developed a fluorescent probe for fluorescence detection of FAO activity in cultured cells and mouse liver tissue and applied this probe for investigation of the heterogeneity of FAO activity in mouse liver tissue by FACS and mRNA sequence.

overall_design: Hepatocytes in the liver of the mice administrated with our fluorescent probe were separated by FACS and mRNAs expressing in the hepatocytes were investigated for understanding of heterogeneity of FAO activity.

first: Naoya

last: Matsunaga

first: Akio

last: Ojida

first: Shohei

last: Uchinomya

first: Hiroko

last: Hagiwara

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: Geometric Framework for nutrition on Sucrose Taste Sensitization in Drosophila

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

institute: School of Pharmaceutical Sciences (Shenzhen)

summary: Numerous studies show dietary carbohydrates (C) affect the sensation of sweetness. However, protein (P) is one of the most critical macronutrients in the diet as well. It is still unclear how carbohydrates and proteins interact to influence sweet taste sensitivity. Here, we use the nutritional geometry framework (NGF) to tackle this problem in Drosophila melanogaster. Our results showed that the combination of high protein and low carbohydrates caused higher taste responses to sucrose stimuli in both sexes. Additionally, transcriptome analysis revealed that the gene expression of glycine, serine, and threonine pathway in the high-protein, low-carbohydrate diet was significantly upregulated, compared to a diet with low protein, and high carbohydrate. We confirmed that serine and threonine supplementation in the high-carbohydrate, low-protein diet enhanced the sucrose sensitivity of flies. Our results demonstrate that sucrose taste sensitivity is affected by the dietary balance of protein and carbohydrates possibly mediated by the change in serine, and threonine. The high protein, low carbohydrate diets enhanced sucrose taste sensitivity.

overall_design: Brain mRNA profiles of 4-7-day old flies treated with low protein and high carbohydrates diet（P:C=0:1,360g/L) that caused lower taste responses to sucrose stimuli and high protein and low carbohydrates diet（P:C=1:2,360g/L) that induced higher taste responses to sucrose stimuli.

first: An-Qi

last: Li

first: Sha-Sha

first: Ruo-Xin

last: Zhang

first: Zhi-Ying

last: Liu

first: Yun

last: Hu

first: Stephen

last: Simpson

first: Qiao-Ping

last: Wang


title: Vemurafenib, BRAF inhibitor, Resistance in BRAFV600E Positive Thyroid Cancer cell lines

city: Houston

first: Irene

last: Min

state: TX

address: 6565 Fannin Street

department: Radiology

institute: Houston Methodist Research Institute

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNAs in BRAFV600E+ thyroid cancer cell lines 8505C and WRO. We generated genome-wide transcriptome maps of 8505C and WRO cells after vemurafenib, BRAF inhibitor, treatment. In addition, we generated genome-wide transcriptome maps of clonally selected vemurafenib-resistant 8505C and WRO cells with or without vemurafenib treatment. Negative control treatment was 0.1% of dimethy solfoxide (DMSO), the diluent used to resuspend vemurafenib. The treatment regine of vemurafenib was 2 µM concentration for 24 hours. We find that both inducible response to BRAFi and acquired BRAFi resistance in thyroid cancer cells showed significant activation of the JAK/STAT pathway. Our study demonstrates that the JAK/STAT-signaling pathway is activated as thyroid cancer cells develop resistance to BRAFi and that this pathway is a potential target for anticancer activity and to overcome drug resistance that commonly develops to treatment with BRAFi in thyroid cancer and potentially in other malignancies.

overall_design: Examination of Vemurafenib response in 2 different BRAFV600E+ thyroid cancer cell lines, 8505C and WRO

first: Tuo


title: Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites

city: Montreal

first: Georgios

last: Mitsis

state: Quebec

address: McConnell Engineering Building, 3480 University Street, Room 350

department: Bioengineering

institute: McGill University

summary: Cell sedimentation in 3D culture environments refers to the vertical migration of cells towards the bottom of the space. This occurs despite the use of hydrogel materials in 3D cell cultures, which would be expected to prevent this behavior. To better understand and explain these experimental observations, we conducted a multiscale experimental and mathematical examination of 3D cancer growth and sedimentation in triple negative breast cancer cells. The migration of cells towards the bottom was examined in the presence and absence of the migrastatic drug Paclitaxel, as well as in a low adhesion environment and the presence of fibroblasts. The observed behaviour was modeled mathematically by hypothesizing self-generated chemotactic gradients. Our results reveal that active migration mechanisms, specifically collective migration regulated by the MAPK and TGF-β pathways, play an important role in sedimentation. The mathematical model was able to describe the experimental data in the absence and presence of Paclitaxel, suggesting the inhibition of random motion and advection mechanism in the latter case. Low adhesion environment and multiple cell type experiments resulted in an inhibition of sedimentation. Overall, our results suggest that cells, initially uniformly distributed in the 3D space, actively migrate towards the bottom due to the presence of signals produced by cells already attached to it, providing mechanistic insights into this unexpected behavior.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Triple Negative Breast Cancer (TNBC) cells from the MDA-MB-231 cell line, non-treated and treated with Paclitaxel, grown in 3D Matrigel scaffold. The doses for the treated are: 0.5μΜ, 0.05μΜ, 0.005μM and 0.0005μΜ. Samples were collected on days 2 and 4. Paclitaxel was administered on Day 2.

first: Nikolaos

last: Dimitriou

first: Salvador

last: Torres

first: Maria

last: Kyriakidou

first: Joseph

last: Kinsella

middle: D


title: Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages.

city: yangzhou

first: Z

last: LL

address: shuangqiaojiedao

institute: yangzhouaxue

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

overall_design: Refer to individual Series


title: Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages [rRNA-depleted RNA-seq]

summary: Alveolar macrophages (AMs) form the first defense line against a variety of respiratory pathogens, and their immune response has profound impact on the outcome of respiratory infection. It is of critical importance to clarify the immune regulation in AMs. Enhancer of Zeste Homolog 2 (EZH2), which catalyzes the trimethylation of H3K27 for epigenetic repression, has gained increasing attentions about their roles in immune regulation. However, the molecular mechanism underlying the immune regulation role of EZH2 in AMs remains largely unclear. Using porcine 3D4/21 alveolar macrophage cells as model, this study combined transcriptomic and epigenomic techniques to decipher the molecular function of EZH2 in AMs. Transcriptomic comparison revealed that inhibition of EZH2 in AMs causes transcriptional activation of dozens of immune genes which indicates an enhanced antiviral state, and as expected, we found that the infection of influenza A viruses can be remarkably affected. Interestingly, about one hundred families of transposable elements, particularly LTRs/ERVs and LINEs which belong to retrotransposons, get derepressed after EZH2 inhibition. Given that derepression of ERVs promotes innate immune activation in many tumors through the “viral mimicry” mechanism, the derepression of retrotransposon in AMs may also contribute to the coincided immune activation after EZH2 inhibition. Overall, this study improves the mechanistical understanding on the EZH2-dependent immune regulation in AMs and provides novel insights for the epigenetic regulation of retrotransposons in pigs.

overall_design: ChIP-Seq (H3K27ac) and RNA-Seq data are generated for porcine 3D4/21 alveolar macrophages with or without the treatment of the EZH2 inhibitor GSK126

first: Liangliang

first: Ming-an

last: Sun


title: Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages [polyA-enriched RNA-seq]


title: Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages [ChIP-seq]


title: RNA-sequencing of LNCaP prostate cancer cells with and without treatment of enzalutamide

city: Berlin

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

institute: Bayer AG

summary: LNCaP prostate cancer cells were stimulated with the synthetic androgen R1881. RNA-sequencing was performed to identify changes induced by enzalutamide treatment on the transcriptome level.

overall_design: Prostate androgen-sensitive cell lines LNCaP were grown for two days in starvation medium prior to treatment with synthetic androgen R1881 at a concentration of 1 nM or R1881 with enzalutamide at a concentration of 2 µM. The cells were harvested 22 h post-induction for RNA isolation and sequencing.

first: Bernard

last: Haendler

first: Ekaterina

last: Nevedomskaya


title: Molecular mechanisms in Murine Syngeneic Leukemia Stem Cells

city: Be'er Sheva

first: Omri

last: Koren

address: David Ben Gurion Blvd 1

department: The Shraga Segal dept. of Microbiology, Immunology, and Genetics

country: Israel

institute: Ben-Gurion University of the Negev

summary: Cancer treatments usually gain good response, but some tumors relapse frequently. Acute My-eloid Leukemia (AML) is notorious for its robust relapse. This is attributed to the Leukemic Stem Cells (LSCs). We use a murine syngeneic leukemia model, ML23, in search for possible identifi-cation and study of LSCs in syngeneic settings. Hereby, we present prospective isolation of a de-fined LSC sub-population, encompassing the potency to passage disease from mouse to mouse. We further provide molecular insights of whole transcriptome analysis. Importantly, the ML23 LSC sub-population is expressing therapeutic targeted genes and provides a model for research in immune-competent animals.

overall_design: ML23 leukemia line was generated as previously reported [Keinan et al; Cell Death & Disease (2021) 12: 193]. essentially, transgenic rtTA mice (Jax strein 6965) cells transformed using lentiviruses over expressing oncogenic factors. ML23 cells were passaged in C57BL/6 mice.   Seq description:  We used the NEXTflex Rapid Directional RNA-Seq Kit (catalog # NOVA-5138-01) for li-brary construction; we then used the Qubit DS DNA chip for quality assurance of the samples. The samples were then sent to the G-INCPM facility for RNA-sequencing. Cells were frozen in SMARTer buffer (100 cells per sample, in 10.5 µL) and stored at -80° C. Li-brary preparation and sequencing were carried out at the INCPM facility (Rehovot, Israel), yielding 5-15 million single-reads of 61 bases per sample. Data were analyzed using Partek (http://www.partek.com) online services, briefly: alignment carried out with STAR v2.5.3a (reference index: mm10 - Ensembl Transcripts release 92), quantification with the in-house Partek algorithm (Quantify to annotation model (Partek E/M)) followed by nor-malization and differential expression analysis DEseq2 v3.5. Annotated GO gene lists were obtained from MGI (http://www.informatics.jax.org/function.shtml).

first: Roi

last: Gazit

first: Michael

last: Chamo


title: Effects of (−)-Epigallocatechin-3-O-gallate (EGCG) on miRNAs’ expression in extracellular vesicles (EVs) derived from human umbilical vein endothelial cells (HUVECs)

city: Fukuoka

first: Yuki

last: Marugame

address: 744 Motooka, Nishi-ku

institute: Kyushu university

summary: EGCG, one of the major catechins in green tea, exerts an antifibrotic property, although its mechanism remains unclear. Recently, it has been reported that microRNA (miRNA) transported by extracellular vesicles (EVs) from vascular endothelial cells (VECs) are involved in PF. In this study, we assessed the effects of EGCG on miRNAs’ expression in EVs derived from HUVECs.

overall_design: In this study, we measured miRNA expression in EVs derived from HUVECs treated with or without EGCG (n = 3, respectively).

first: Hirofumi

last: Tachibana

first: Mai

last: Morozumi


title: Phase 1 Study of Ulixertinib (BVD 523) in Patients with Advanced Solid Malignancies

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

summary: RNAseq from tumor samples of patients treated on clinical trial

overall_design: Pretreatment biopsies were obtained from responders and non-responders

first: Kian-Huat

last: Lim

first: Andrea

last: Wang-Gillam


title: Enteric neural crest-derived cells at the invasive wavefront are transcriptionally distinct

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

summary: Enteric nervous system (ENS) development relies on intestinal colonization by enteric neural crest-derived cells (ENCDCs). This is driven by a population of highly migratory and proliferative cells at the wavefront, but the unique molecular characteristics of the wavefront are unknown. ENCDCs from the wavefront and the trailing region proximal were isolated from 11.5 days post coitum (dpc) Wnt1-tdT mouse intestine and subjected to RNA-seq. Wavefront ENCDCs were transcriptionally distinct from trailing ENCDCs, and temporal modelling confirmed their relative immaturity. Wavefront ENCDCs exhibited altered expression of ECM and cytoskeletal genes, consistent with a migratory phenotype. Unlike postnatal enteric neural stem cells, wavefront ENCDCs possessed characteristics of cells undergoing epithelial-mesenchymal transition and lacked neuronal or glial commitment.

overall_design: Examination of mRNA profiles in enteric neural crest-derived cells at the invasive wavefront  and trailing 1-1.5mm behind the wavefront.

first: Ryo

last: Hotta

first: Richard

last: Guyer

first: Nicole

last: Picard

first: Ahmed

last: Rahman

first: Meredith

last: Omer

first: Adam

last: Soos

first: Emoke

last: Szocs

first: Jessica

last: Mueller

first: Allan

last: Goldstein

first: Nandor

last: Nagy


title: C1q-TNF-Related Protein-9 protects from diabetic cardiomyopathy by alleviating cardiac insulin resistance and inflammation

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

institute: Medical Faculty of Mannheim Heidelberg University

summary: Diabetic cardiomyopathy is a major health problem  world wide. CTRP9 is a secreted glycoprotein, which is mainly expressed in endothelial cells of the heart. In this study, we investigated the impact of CTRP9 on diabetic cardiomyopathy induced by high fat diet feeding. While the lack of CTRP9 in knock-out mice aggravated the disease, AAV9 mediated cardiac CTRP9 overexpression ameliorated diastolic cardiac dysfunction under these conditions. Mechanistically, we found that CTRP9 is required for insulin dependent cardiac glucose uptake and metabolism and that it counteracts cardiac inflammation.

overall_design: Bulk RNA sequencing from ehole heart tissue of WT and CTRP9-KO mouse after high fat diet. For overexpression approach, injection of AAV was performed. (AAV Luciferase and AAV-CTRP9)

first: Ricarda

last: Haustein

first: Felix

last: Trogisch

first: Merve

last: Keles


title: Gene expression profile at single cell level of non-myocytic cells of the heart (NCM) from TRPM4 WT and KO mice 24h or 72h after SHAM intervention or LAD ligation

city: Bern

first: Mey

last: Boukenna

address: Bühlstrasse 28

country: Switzerland

institute: IBMM University of Berne

summary: Many different cell types constitute the heterogenous group of non-cardiomyocytes (NCM) of the heart. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of NCM and especially how the absence of TRPM4 affects the inflammatory response post myocardial infarction.

overall_design: NCMs were isolated from B6.Cg-Trpm4tm1.2-PG (KO) mice or WT mice hearts either 24h after SHAM intervention or LAD ligation or 72h after LAD ligation. The live NCMs were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of Calcein-AM and DAPI signal and the NCM of 4 mice per sample/condition were pooled and analyzed using scRNAseq.

first: Parisa

last: Aghagolzadeh

first: Sylvain

last: Pradervand

first: Corinne

last: Peter

first: Jean-Sebastien

last: Rougier

first: Sabrina

last: Guichard

first: Thierry

last: Pedrazzini

first: Hugues

last: Abriel


title: Hepatic processing of Z variant α-1-antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

summary: Homozygosity for the Z allele of α1-antitrypsin (ZAAT) predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum (ER) of hepatocytes, resulting in gain-of-function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency, suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study, global transcriptomic approach was used to identify pathways activated and operating in the ZAAT-expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2-mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER-associated degradation (ERAD) system inhibits the turnover of Srebp2-repressing elements therefore hindering the activation of Srebp2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for transgenic zebrafish liver expressing wildtype or Z-mutant human antitrypsin, and their non-transgenic siblings.

first: Brendan

last: Wilding

first: Connie

last: Fung

first: Ralf

middle: B

last: Schittenhelm

first: Robert

last: Bryson-Richardson

first: Phillip

middle: I

last: Bird


title: Anti-seed PNAs targeting multiple oncomiRs for brain tumor therapy

city: Storrs

first: Shipra

last: Malik

state: CT

address: 69 North Eagleville Road, Unit 3092

department: Pharmaceutical Sciences

institute: University of Connecticut

summary: Glioblastoma (GBM) is one of the most lethal malignancies in the United States with poor survival and high recurrence rates, suggesting the need for approaches targeting the most important molecular drivers of tumor growth. Here, we aimed to simultaneously target oncomiRs 10b and 21, which have been reported to drive the aggressive growth and invasiveness of GBM. We designed short (8-mer bases) gamma-(g)-modified peptide nucleic acids (sPNAs), which target the seed region of oncomiRs 10b and 21 with high affinity. We entrapped these anti-miR sgPNAs in nanoparticles (NPs) formed from a block copolymer of poly(lactic acid) and hyperbranched polyglycerol (PLA-HPG). The surfaces of the NPs were functionalized with aldehydes to produce bioadhesive NPs: we have previously shown that these bioadhesive NPs (BNPs) produce superior transfection efficiency, with a tropism for tumor cells. The sgPNA BNPs showed superior anti-miR efficacy in comparison to the regular full length PNA BNPs in vitro. When combined with temozolomide, sgPNABNPs administered via convection-enhanced delivery (CED) inhibited the growth of intracranial tumors and significantly improved the survival of animals (>120 days). RNA sequencing analysis revealed the downregulation of multiple genes associated with PI3-Akt, focal adhesion, and hypoxia inducible factor 1 (HIF-1) pathway to inhibit GBM progression after simultaneous inhibition of oncomiRs 10b and 21. Hence, we established that BNPs loaded with anti-seed sgPNAstargeting multiple oncomiRs is a promising approach to improve the treatment of GBM, with a potential to personalize treatment based on tumor specific oncomiRs.

overall_design: Human glioma cells (U87) were used in this study. Nucleic acid mediated kockdown of miR-21 and miR-10b was achieved. mRNA profiles in U87 cells after konckdown of miR-10b or miR-21 or miR-10b+21 was compared against the untreated U87 cells.

first: Yazhe

last: Wang

first: Hee-Won

last: Suh

first: Yong

last: Xiao

first: Yanxiang

last: Deng

first: Rong

last: Fan

first: Anita

last: Huttner

first: Ranjit

middle: S

last: Bindra

first: Vijender

last: Singh

first: W

last: Saltzman

first: Raman

last: Bahal


title: Neutral amino acid transporter SNAT2 protects renal medulla from hypertonicity-induced ferroptosis

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

summary: Hypertonicity in renal medulla is essential for urine concentration and water homeostasis. However, how renal medullary collecting duct cells (MCDs) survive and function under the harsh hypertonic stress remains incompletely understood. By using the RNA-seq technique, we identified SNAT2 (slc38a2) as a novel osmoresponsive neutral amino acid transporter in MCD cells. We found that hypertonic stress induced cell death of MCDs mainly via ferroptosis.

overall_design: mIMCD3 cells were cultured in either isotonic (300mOsm) or hypertonic (600mOsm) condition for 6 hours and mRNA was then extracted for RNA-Seq analysis. There are four biological replicates of cells under isotonic and hypertonic conditions respectively.

first: Youfei

last: Guan

first: Xiaoyan

last: Zhang


title: CD47-dependent regulation of immune checkpoint gene ex-pression and MYCN mRNA splicing in murine CD8 and human Jurkat T cells

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Elevated expression of CD47 in some cancers is associated with poor survival, related to its function as an innate immune checkpoint when expressed on tumors cells. In contrast, elevated CD47 ex-pression in cutaneous melanomas is associated with improved survival. Previous studies impli-cated protective functions of CD47 expressed by immune cells in the melanoma tumor microen-vironment. RNA sequencing analysis of responses induced by CD3 and CD28 engagement on wild type and CD47-deficient Jurkat T lymphoblast cells identified additional regulators of T cell func-tion that were also CD47-dependent in mouse CD8 T cells. MYCN mRNA expression was up-regulated in CD47-deficient cells but down-regulated in CD47-deficient cells following activa-tion. CD47 also regulated alternative splicing that produces two N-MYC isoforms. The CD47 ligand thrombospondin-1 inhibited expression of these MYCN mRNA isoforms as well as induction of the oncogenic decoy MYCN opposite strand (MYCNOS) noncoding RNA during T cell activation. Analysis of mRNA expression data for melanomas in The Cancer Genome Atlas identified signif-icant coexpression of MYCN with CD47 and known regulators of CD8 T cell function. Throm-bospondin-1 inhibited the induction of TIGIT, CD40LG and MCL1 mRNAs following T cell acti-vation in vitro. Increased mRNA expression of these T cell transcripts and of MYCN in melanomas was associated with improved overall survival.

overall_design: WT and CD47- Jurkat T cells were cultured routinely as described earlier(PMID: 21343308).  CD3 Monoclonal Antibody (OKT3), eBioscience™ and anti-CD28 (CD28 Monoclonal Antibody (CD28.2), Functional Grade, eBioscience™ were purchased from ThermoFisher Life Technologies Corporation. For T cell activation assay, 10 cm plates (BD, Biosciences) were coated with 2mg/ml anti-CD3 and 4 μg/ml of anti-CD28 in PBS at 4°C overnight.  Approximately 5x106 cells in 5 ml were plated for 1 h, 3 h and 6 h for each treatment using HITES medium, and 1 μg/ml of TSP1 was added either alone or in combination with anti-CD3 and anti-CD28. Cell pellets from each treatment were washed with PBS, and total RNA was extracted using TriPURE. The concentration of RNA and RNA quality was measured via Nanodrop.

first: Kaur

last: Sukhbir

first: Meyer

last: Thomas J.

first: Cam

last: Maggie

first: David

last: Roberts

first: Finney

last: Richard


title: TET2 regulates genes expressed in the differentiated corneal epithelium through 5hmC modification

first: Natasha

last: Frank

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: We performed RNA-seq to identify the genes regulated by TET2 using human cultured corneal epithelial cells. Also, we performed RNA-seq to identify the genes expressed in MUC16-positive differentiated corneal epithelial cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Yuzuru

last: Sasamoto

first: Siyuan

last: Wu

first: Jiang

last: Yusheng

middle: Y


title: Epigenetic regulation during salinity stress response in chickpea (WGBS)

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

summary: Bisulphite sequencing of salinity sensitive and salinity tolerant chickpea genotypes during salinity stress response using Illumina platform has been performed. At least 195 million reads in bisulphite sequencing were generated in each sample. Methylated cytosines in each sample were identified for their genomic location and sequence context.

overall_design: Genomic DNA was extracted from all the samples using Qiagen DNeasy kit and treated with sodium bisulphite (Zymo research) to induce cytosine to uracil conversion. Bisulphite sequencing was performed on Illumina platform to generate 90bp long reads in paired-end mode. Adapter contamination and low-quality reads were removed using NGS QC Toolkit (v2.3.3). High-quality filtered reads were mapped on Kabuli reference genome using Bismark (v0.14.3). Methylation levels in each cytosine residues and differentially methylated regions  under stress conditions and between the two different genotypes were determined using Methylkit (v1.5.3).

first: Khushboo

last: Gupta


title: Gene expression profiling during salinity stress response in chickpea (RNA-Seq)

summary: In this study, we performed transcriptomic analysis salinity stress response in salinity sensitive and tolerant genotypes of chickpea using Illumina platform. A total of 87 million reads in RNA-sequencing data were generated in all the samples. Mapping of the reads to the Kabuli genome was performed using tophat (v2.1.1). Differentially expressed genes were identified using cufflilnks-cuffdiff (2.2.1)  pipeline.

overall_design: Total RNA was extracted and cDNA libraries were prepared from salinity sensitive (ICCV2) and salinity tolerant (JG62) genotypes under salinity stress and control conditions from 17 day old seedlings. RNA-sequencing was performed on Illumina platform to generate 49 bp single-end reads. Pre-processing was performed using NGS QC Toolkit to remove adapters and low-quality reads below 20 Phred score. Filtered high-quality reads were mapped on the Kabuli chickpea genome using TopHat2 (v2.1.1). To analyze gene expression, reference-guided assembly was generated using Cufflinks (v2.2.1) and differential expression of genes was determined by Cuffdiff (v2.2.1).


title: Integrated whole-exome and transcriptome sequencing indicated dysregulation of cholesterol metabolism in eyelid sebaceous gland carcinoma

city: Tianjin

first: Yuchuan

last: Wang

address: Gansu Road

institute: Tianjin Eye hospital

type: Genome variation profiling by high throughput sequencing

summary: To identify the molecular background of eyelid sebaceous gland carcinomas (SCs), the integrated whole-exome sequencing and transcriptome sequencing for five eyelid SCs were conducted in this study.

overall_design: The genetic alterations were studied by whole-exome sequencing, and the mRNA expression was studied using Oxford Nanopore Technologies (ONT) in five paired fresh eyelid SC tissues and adjacent normal tissues.

first: Jun

last: Li

first: Peng

last: Hao

first: Xuan


title: Salinity stress response in chickpea

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

overall_design: Refer to individual Series


title: Integrated metabolomic and transcriptomic analysis reveals amino acid biosynthesis may determine differences in cold resistance of tea plants

city: HeFei

first: Yaohua

last: Cheng

address: Changjiang West Road 130

institute: Anhui  Agricultural University

summary: In order to study the differential expression of cold-tolerant variety SCZ and cold-sensitive variety YH9 during cold acclimation, we analyzed transcriptome and metabolome and found that the biosynthesis of amino acids may determine the difference of cold resistance of tea plant.

sample_organism:
Camellia sinensis
Camellia sinensis var. assamica

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCZ (NA, CA, and DA) and YH9 (NA, CA, and DA). Normal temperature controls (NA). tea plants were exposed to low temperature (10°C daytime, 4°C night) for 7 days during chilling acclimation. Subsequently, freezing acclimation was conducted by exposing tea plants to lower temperatures (4°C daytime, 0°C night) for another 7 days (CA). Lastly, the plants were exposed to normal temperature (25°C daytime, 20°C night) for 7 days for de-acclimation (DA).

first: Yeyun


title: Small RNA sequencing during salinity stress response in chickpea (small RNA-Seq)

summary: In this study, we have identified small RNA during salinity stress response in chickpea. Small RNA library was prepared and sequencing was performed using Illumina platform. A total of 79 million reads were generated. These reads were mapped to the chickpea genome using Bowtie.

overall_design: Total RNA was isolated from the control and stress samples of roots of ICCV2 and JG62 and small RNA library was prepared using TruSeq Small RNA Sample Prep Kit (Illumina Technologies) according to the manufacturer's instructions. Raw reads were obtained in FASTQ files were pre-processed to remove low-quality reads. Unique reads were mapped to the chickpea genome using Bowtie. Non-redundant set of uniquely mapped small RNA reads were retained for further processing.


title: EIF5A2 specifically regulates the transcription of aging‑related genes in neuroblastoma cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: In the present study, EIF5A2 overexpression of SH-SY5Y cell model was developed. RNA-seq and RT-qPCR experiments were then performed to explore the molecular mechanism of EIF5A2-mediated transcriptional regulation. Upon EIF5A2 overexpression, genes closely related to unfolded protein response were downregulated. Transcription factors associated with aging, such as ATF4, ATF3 and BHLHE40, were negatively correlated with EIF5A2, which was shown in the EIF5A2 overexpression human neuroblastoma cells in vitro and further verified via the published database of human glial cell tissue.

overall_design: neuroblastoma cell mRNA profiles of EIF5A2 overexpression and the control group

first: Xujun

last: Ye


title: Identification of m6A-modified YTHDF2 targets by high-throughput m6A-seq and RIP-seq in HBV-infected HepG2 cells [m6A-seq]

city: Chongqing

first: Yang

last: Yang

state: Chongqing

address: No. 1, Medical College Road

institute: Chongqing Medical University

summary: We investigated the role of O-GlcNAcylation of m6A reader YTHDF2 in HBV-related hepatocarcinogenesis and progression. We found that YTHDF2 O-GlcNAcylation was elevated upon HBV infection through upregulated HBP. OGT-mediated YTHDF2 O-GlcNAcylation at Ser263 enhanced its protein stability, and subsequently changed the gene expression profiles. Mechanistically, we identified YTHDF2 stabilized minichromosome maintenance protein 2 (MCM2) and MCM5 mRNAs in an m6A dependent manner by high-throughput profiling of m6A-seq and RIP-seq, thereby promoting HBV-related HCC tumorigenesis. Importantly, our study proposed that targeting OGT-mediated YTHDF2 O-GlcNAcylation may be a novel strategy for potential treatment of HBV-associated liver cancer.

overall_design: Identification of YTHDF2 targets by high-throughput m6A-seq.

first: Yu

last: Yan

first: Jiaxin

last: Yin


title: Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention

city: Bloomington

first: Craig

last: Pikaard

address: 915 E. Third Street

department: Department of Biology and Department of Molecular and Cellular Biochemistry

institute: Howard Hughes Medical Institute, Indiana University


title: Staged suppression of microglial autophagy facilitates remyelination by enhancing the production of linoleic acid

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

summary: Demyelinating lesions are often accompanied by the activation of autophagy biological processes, which are mostly related to microglia. But the underlying mechanism is elusive. We show that inhibition of autophagy in the early and late stages will have different effects on the remyelinating process of demyelinating lesions. In addition, the results of metabonomics as well as transcriptome and metabolic  combined analysis showed that CLA (Conjugated linoleic acid) may play an active role in the process of remyelinating.

overall_design: Microglia in primary culture treated with LPS compared with treated with LPS+Baf A1. Microglia in primary culture treated with LPS+dNC compared with treated with LPS+siAtg5. Microglia in primary culture treated with LPS compared with treated with LPS+CLA. Number of each group were 3,5,3,5,6 for LPS, LPS+Baf A1, LPS+dNC, LPS+siAtg5, LPS+CLA, separately.

first: Luoqi

last: Zhou

first: Chuan

last: Qin

first: Daishi

last: Tian