title: Transcriptional analysis reveals the progression of PCOS to ovarian cancer in medaka fish ancestrally exposed to BPA

city: Columbia

first: Ramji

last: Bhandari

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

summary: As a heterogeneous reproductive disorder with unclear etiopathogenesis, polycystic ovary syndrome (PCOS) can be caused by genetic, diet, and environmental factors. Bisphenol A (BPA), a global environmental contaminant, can induce PCOS and NAFLD due to direct exposure; however, whether these phenotypes persist in future unexposed generations is not currently understood. We observed genes abnormally expressed in the ovary of BPA lineage, similar to human PCOS patients. IPA analyses revealed activation of the cancerous pathway, arginine-proline metabolism, insulin signaling, AMPK, and HOTAIR regulatory pathways, as well as upstream regulators esr1 and tgf β.

overall_design: RNA seq of the ovary of three biological replicates from BPA lineage and control lineage of Medaka fish

first: Sourav

last: Chakraborty

first: Santosh

last: Anand


title: Normal and ineffective erythropoiesis scRNA seq

status: Public on Sep 06 2023

city: Seattle

first: Christopher

last: Lausted

state: WA

address: 401 Terry Ave N

country: USA

institute: ISB

type: Expression profiling by high throughput sequencing

summary: Ineffective erythropoiesis, the death of maturing erythroid cells, is a common cause of anemia. To better understand why this occurs, we studied the fates and adaptations of single erythroid marrow cells from individuals with Diamond Blackfan anemia (DBA), del(5q) myelodysplastic syndrome (del(5q) MDS), and normal controls, and defined an unhealthy (vs. healthy) differentiation trajectory, using velocity pseudotime and cell surface protein assessment. The pseudotime trajectories diverge immediately after the cells upregulate transferrin receptor (CD71), import iron, and initiate heme synthesis, although cell death occurs much later. Cells destined to die highly express heme-responsive genes, including ribosomal protein and globin genes. In contrast, surviving cells downregulate heme synthesis, while upregulating DNA damage response, hypoxia, and HIF1 pathways. Surprisingly, 24±12% of cells from controls follow the unhealthy trajectory, implying that heme also regulates cell fate decisions during normal red cell production. Del(5q) MDS (unlike DBA) results from somatic mutations, so many normal (unmutated) erythroid cells persist. By independently tracking their trajectory, we gained insight into why they cannot expand to prevent anemia. In addition, we show that intron retention is especially prominent during red cell differentiation. The additional information provided by messages with retained introns also allowed us to align data from multiple independent experiments and thus accurately query the transcriptomic changes that occur as single erythroid cells mature.

overall_design: We compared the transcriptomes of erythroid cells from Diamond-Blackfan Anemia, Myelodysplastic Syndrome, and normal donors.  Cryo-preserved bone marrow mononuclear cells were thawed and cultured for six days.  Single-cell analysis was performed at Day 0 (uncultured) and at Day 3 and 6 (cultured).

first: Raymond

last: Doty

first: Adam

last: Munday

first: Zhantao

last: Yang

first: Xiaowei

last: Yan

first: Changting

last: Meng

first: Qiang

last: Tian

first: Janis

last: Abkowitz


title: Impact of miR-203-3p overexpression on human primary keratinocytes

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: To identify putative novel specific targets of miR-203-3p, we overexpressed this miRNAs in primary keratinocytes using a synthetic mimic (pre-miR-203a-3p) or a synthetic “negative” control mimic (pre-miR-ctrl). RNA samples were harvested 30 hours post-transfection and 3 independent experiments were carried out.

overall_design: 3 independent experiments performed in a one color design, corresponding to 2 conditions (pre-miR-ctrl and pre-miR-203a-3p) for a total of 6 samples.

first: C

last: Marionnet

first: R

last: Rezzonico

first: B

last: Mari

first: K

first: P

last: Barbry


title: Single-cell transcriptomic profile of CD45+ and CD45- cells from dermis and hypodermis of C57BL/6 mice

city: Bethesda

first: Keisuke

last: Nagao

state: MD

address: 10 Center Dr, Bldg 10, 12N240B

institute: National Institutes of Health

summary: In order to explore and compare the transcriptomic profile of leucocytes and stromal cells present in the dermis and hypodermis of C57BL/6 mice, isolated cells from each of these skin layers were subjected to single-cell RNA-sequencing analysis.

overall_design: Back skins from 3 adult C57BL/6 female mice were harvested and the dermal and hypodermal layers isolated by mechanical force and enzymatic treatments. Cells were liberated from each skin layers after enzymatic digestion of the tissues. Leukocytes (CD45+) and stromal cells (CD45-) cells were isolated  by fluorescence-activated cell sorting (FACS) and their transcriptome assessed by single-cell RNA-sequencing using the 10X genomics plateform.

first: Benjamin

last: Voisin

first: Thomas

last: Doebel

first: Michael

middle: C

last: Kelly

first: Ying

last: Hu

first: Chunhua


title: Dermal and hypodermal macrophages and dendritic cells

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic profile of dermal and hypodermal CCR2+ macrophages, CCR2- macrophages and dendritic cells from C57BL/6 mice

summary: In order to explore and compare the transcriptomic profile of CCR2+ macrophages, CCR2- macrophages and dendritic cells present in the dermis and hypodermis of C57BL/6 mice, isolated cells were subjected to RNA-sequencing analysis.

overall_design: Back skins from C57BL/6 female mice were harvested and the dermal and hypodermal layers isolated by mechanical force and enzymatic treatments. Cells were liberated from each skin layers after enzymatic digestion of the tissues. Macrophages (CD45+ CD11b+ EpCAM–Ly6C-lo CD11c-lo/mid CD64+) expressing or not CCR2 as well as dendritic cells (CD45+ CD11b+ EpCAM–Ly6C-lo CD11c-lo/mid CD64- MHC-II+) were isolated by fluorescence-activated cell sorting (FACS) and their transcriptome assessed by RNA-sequencing.


title: Identification of potential abnormal methylation modified genes in coronary artery ectasia

city: Shijiazhuang

first: Xiao

last: Bing

address: No.215, Heping West Road, Shijiazhuang, Hebei, China

country: China

institute: The Second Hospital of Hebei Medical University

summary:
Coronary artery ectasia (CAE) is a rare but easily recognized abnormality of coronary artery anatomy and morphology. Up to now, the pathogenesis of CAE remains unclear.
Firstly, the peripheral venous blood samples of patients with CAE were obtained for the RNA sequencing to identify differentially expressed genes (DEGs), followed by functional analysis. Secondly, DNA methylation profile in CAE was downloaded from the dataset of GSE87016 to identify differentially methylated genes (DMGs). Lastly, after taking interaction genes between DEGs and DMGs, abnormal methylation modified genes were identified.

overall_design: The aim of this study was to find abnormal methylation modified genes in CAE, which may provide a certain research basis for the pathogenesis of CAE.

first: Xiuchun

first: Yijun

last: Zong

first: Zhentian

last: Zhang

first: Yan

last: Zhao

first: Xueying

last: Gao

first: Jie

first: Qian

last: Hou

first: Renyi

last: Li

first: Bing

last: Xiao


title: Inflammation alters young and old CD8 T cells

city: San Antonio

first: Anna

last: Allue Guardia

state: Texas

address: 8715 Military Dr W

institute: Texas Biomedical Research Institute

summary: Inflammation plays a significant role in lung infection caused by Mycobacterium tuberculosis (M.tb), and both adaptive and innate lymphocytes can affect infection control. How inflammation affects infection is understood in a broad sense, including inflammaging (chronic inflammation) seen in the elderly, but the explicit role that inflammation can play in regulation of lymphocyte function is not known. To fill this knowledge gap, we used an acute lipopolysaccharide (LPS) treatment in young mice and studied lymphocyte responses compared to old mice, focusing on CD8 T cell subsets. LPS treatment decreased the total numbers of T cells in the lungs of LPS mice, while also increasing the number of activated T cells. We demonstrate that lung CD8 T cells from LPS mice became capable of an antigen independent innate-like IFN-gamma secretion, dependent on IL-12p70 stimulation, paralleling innate-like IFN-gamma secretion of lung CD8 T cells from old mice. Overall, this study provides information on how acute inflammation can affect lymphocytes, particularly CD8 T cells, which could potentially affect immune control of various disease states.

overall_design: RNA-seq analysis was performed on CD8 T cells isolated from the lungs of LPS treated, young, and old mice (4 replicates/group).

first: Tucker

middle: J

last: Piergallini

first: Julia

middle: M

last: Scordo

last: Allué-Guardia

first: Paula

middle: A

last: Pino

first: Hao

first: Hong

last: Cai

first: Yufeng

last: Wang

first: Larry

middle: S

last: Schlesinger

first: Jordi

middle: B

last: Torrelles

first: Joanne

last: Turner


title: Pleural CD14+ monocytes/macrophages of healthy adolescents showa high expression of metallothionein family genes

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

country: Germany

institute: Hannover Medical School

overall_design: We employed a technique to isolate pleural monocytes/macrophages from healthy young adults who underwent a correction of pectus excavatum. High quality CD14+ monocytes/macrophages (plMo/Mφ) were used for RNA-sequencing (RNA-seq) in comparison with human monocyte-derived macrophages (MDM) natural (MDM-0) or IL-4-polarized(MDM-IL4).

first: Nagoud

last: Schukfeh

first: Bin

last: Liu

first: David

last: DeLuca

first: Srinu

last: Tumpara

first: Christoph

last: Nikolin

first: Benno

last: Ure

first: Joachim

middle: F

last: Kuebler

first: Tobias

last: Welte

first: Dorothee

last: Viemann

first: Sabina

last: Janciauskiene Wallmark

first: Gertrud

last: Vieten


title: Transcriptome analysis of CARNMT1 knockout cells

city: Hirakata

first: Rei

last: Yoshimoto

state: Osaka

address: 45-1 Nagaotoge-cho

department: Faculty of Agriculture

country: Japan

institute: Setsunan University

summary: Examination of transcriptome of CARNMT1 knockout cells by Ribosomal RNA depleted RNA-Seq

first: Tadahiro

last: Shimazu


title: DNA methylation of human FFPE meningioma samples

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

institute: UCSF

type: Methylation profiling by genome tiling array

summary:
DNA methylation profiling of human FFPE meningioma samples
These samples were processed as part of a study developing and validating a targeted gene expression biomarker of meningioma outcomes and benefit from radiotherapy.

overall_design: 230 FFPE meningioma samples

middle: R

last: Raleigh


title: Health outcomes in SARS survivors 18 years after infection: A longitudinal cohort study

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

summary: We aimed to characterize the long-term health outcomes of survivors of severe acute respiratory syndrome (SARS) and determine their recovery status and possible immunological basis. Although health outcomes continued to improve, SARS survivors still suffered from physical fatigue, osteoporosis, and necrosis of the femoral head 18 years after discharge, possibly related to plasma metabolic disorders and immunological alterations.

overall_design: Plasma samples were collected for single-cell transcriptomic analyses.

first: Qian

last: Wu

first: Hongjie

first: Haibai

last: Sun

first: Zhiheng

last: Xing

first: Li

first: Huaiyong


title: CD11c+ autoimmune-associated B cells have an increased phagocytosis activity and T cell activation which is regulated by metabolic intervention in lupus mice

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Specific metabolic program is required for generation of immune cells and their proper function. Since the description of age-associated or autoimmune-associated B cells (ABCs), there has been a growing interest in the role of these cells in autoimmunity. ABCs have many distinct functional properties, including antigen presentation to T cells and autoantibody production in lupus mouse models. Metabolic properties which support these functions are unknown in ABCs. In this study, we showed that ABCs are metabolically hyperactivated than follicular (FO) B cells. There was an increased glycolysis and oxidative phosphorylation (OXPHOS) in ABCs. In line with this observation, ABCs express key costimulatory molecules for T cell activation with distinct group of cytokines. T cell proliferation and activation were induced by both FO B and ABCs in antigen-dependent manner. However, ABCs induce stronger T cell receptor signaling from naïve CD4+ T cells, leading to differentiation of follicular helper T (Tfh) cells. ABCs actively internalize OVA protein and increased autophagy formation. Treatment of ABCs with metformin suppressed antigen presentation by decreasing antigen uptake, leading to a defective generation of Tfh cells. Taken together, these findings reveal distinct metabolic activity in ABCs and define fundamental connection between metabolism and function within ABCs.

overall_design: Differential gene expression profiling analysis of RNA-seq data for age associated B cells vs follicular B cells in 8 month old Sle 1/2/3 triple congenic mice

first: Ivan

last: De Oleo

first: Vera

last: Kim

first: Yemil

last: Atisha-Fregoso

first: Kyungwoo

last: Lee

first: Betty

last: Diamond

first: Sun


city: Nanjing

first: rui

last: duan

address: No.68 changle road

institute: Nanjing First Hospital

summary: Stroke is a kind of cerebrovascular disease with high mortality. TMAO has been shown to aggravate stroke outcomes, but its mechanism remains unclear. Mice were treated with TMAO in normal saline by oral gavage for 14 consecutive days. Then, mice were made into MCAO models. Neurological score, infarct volume, neuronal damage and markers associated with inflammation were assessed. Since microglia played a crucial role in stroke, microglia of MCAO mice were isolated for high-throughput sequencing to identify the most differentially expressed gene following TMAO treatment. Afterward, the downstream pathways of TMAO were investigated using primary microglia. Our results demonstrated that TMAO promoted the release of inflammatory cytokines in the brain of MCAO mice and promoted the activation of OGD/R microglial inflammasome, thereby exacerbating stroke outcomes. FTO/IGF2BP2 inhibited NLRP3 inflammasome activation in OGD/R microglia by downregulating the m6A level of NLRP3, TMAO can inhibit the expression of FTO and IGF2BP2, thus promoting the activation of NLRP3 inflammasome in OGD/R microglia. In conclusion, these results demonstrated that TMAO promotes NLRP3 inflammasome activation of microglia aggravating neurological injury in stroke through FTO/IGF2BP2.

overall_design: Microglial mRNA profiles of 6 months old   C57BL/6J mice  were treated with TAMO

first: Pengxin

last: Ge

first: Huijie

last: Duan

first: Chunrong

last: Tao

first: Sensen

last: Niu


title: Lmx1a is a master regulator of the cortical hem.

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Development of the nervous system depends on signaling centers – specialized cellular populations that produce secreted molecules to regulate neurogenesis in the neighboring neuroepithelium. Some signaling centers also generate key types of neurons. The formation of a signaling center involves its induction, the maintenance of expression of its secreted molecules, and cell differentiation and migration events. How these distinct processes are coordinated during signaling center development remains unknown. Here we show that Lmx1a acts as a master regulator to orchestrate the formation and function of the cortical hem (CH), a critical signaling center that controls hippocampus development. Lmx1a co-regulates CH induction, its Wnt signaling, and the differentiation and migration of CH-derived Cajal-Retzius neurons. Combining RNAseq, genetic, and rescue experiments, we identified major downstream genes that mediate distinct Lmx1a-dependent processes. Our work revealed that signaling centers in the mammalian brain employ master regulatory genes and established a framework for analyzing signaling center development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and Lmx1a-/- (dreherJ) cortical hem (CH). CH cells were isolated by laser capture microdissection from five wild type and five Lmx1a-/- embryos at embryonic day 13.5 and used for RNAseq analysis.

first: Igor

middle: Y

last: Iskusnykh

first: Victor

middle: V

last: Chizhikov

first: Yiran

first: Laure

last: Bihannic


title: Transcriptomic profiling of SGLT2 inhibitor-treated hypertensive rats

city: ChongQing

first: Jianlin

last: Du

address: No.1, medical college road, ChongQing, China

institute: ChongQing Medical University

summary: Background: Sodium-glucose co-transporter-2 inhibitor (SGLT2i) compounds are antihyperglycemic medications that may improve cardiovascular disease (CVD) and chronic kidney disease prognosis in patients with diabetes mellitus.   Methods: We conducted a detailed RNA-sequencing-based exploration of transcriptomic changes in response to empaglifozin in eight different tissuesfrom a rat model of spontaneous hypertension. Corresponding computational analyses were performed to analyze these data.  Results: We discovered that empaglifozin exerts potent transcriptomic effects upon various tissues. Empaglifozin therapy may exert effects upon the kidney by impacting aldosterone-regulated sodium resorption, lyosome. The functional enrichment of DEGs indicated empaglifozin may regulate blood pressure, blood glucose, lipid homeostasis and nervous system in SHR. Consistent with our RNA-Seq findings, following 1-month empaglifozin administration, immunofluorescence staining revealed enhanced renal expression of caveolin-1.  Conclusions: These findings offer value as a foundation guiding further exploration regarding the effects associated with SGLT2i therapy in the context of hypertension.

overall_design: spontaneous hypertension rat (male, aged 8 weeks, 220-260g) were treated with empaglifozin by gavage at the dose of 10 mg/kg/d (n=3) or saline vehicle control(n=3) daily for a period of 30 days. Then RNA-sequencing-based exploration of transcriptomic changes in response to empaglifozin in eight different tissues (i.e., atrial, aortic, ventricular, white adipose, brown adipose, renal, lung, and brain) were performed.

first: Xin

last: Yuan

first: Fangyan

last: Tan

first: Jing

last: Wang


title: Transcriptome analysis by RNA sequencing of the cortical brain in a mouse model of early life pain

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary: Preterm children are frequently exposed to various painful stimuli in the early days of life. Early-life-pain (ELP) may affect cortical development and reduce the fitness and resilience in during youth and adult life. We developed an optogenetic Cre/loxP mouse model of "early-life-pain" (ELP) using mice with transgenic expression of an improved channelrhodopsin-2 (ChR2)/Td-Tomato fusion protein under control of the advillin promoter, that drives expression of ChR2/td-Tomato specifically in primary somatosensory neurons of the dorsal root ganglia (Avil-ChR2 mice). Floxed ChR2/td-Tomato littermates (ChR2-flfl) were used as controls. Mice were exposed to blue light in a chamber once daily from postnatal day P1-P5. Cortical gene expression was analyzed at P7 via RNA-sequencing in eight biological replicates per group. Cortices were rapidly excised and snap froze in liquid nitrogen. Total RNA was extracted from with Qiagen RNeays spin columns and quantified on a Nanodrop. Sequencing libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit, and sequencing was performed on an Illumina NGS platform. The alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Sequence reads were normalized with EdgeR and analyzed in ArrayStar 17 (Lasergene). Differential gene expression was assessed with general linear models and adjusted according to Benjamini Hochberg.

overall_design: RNA from the mouse cortex was analyzed by RNA sequencing of 8 biological replicates per group using an Illumina NextGen system (NS500213).


title: Effect of Serendipita indica-infection on the gene expression in wild-type and cbl7 knockout mutants Arabidopsis thaliana plants

status: Public on Sep 05 2023

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

country: Spain

institute: CBGP (UPM-INIA/CSIC)

summary: The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Previous studies highlighted an important role of calcium Ca2+ signaling in the establishment of the plant–fungus interaction. We here report the comparative analysis of the effect of a mock- and S. indica-infection on both wild-type Arabidopsis plants (Col-3) and cbl7 knockout mutants. Our data provide evidence for the involement of the Ca2+ sensor CBL7 in the control of potassium distribution in the plant and in adjusting plant defense responses to allow the establishment of the plant–fungus symbiosis. The impairment of CBL7 was shown to translate into increased induction of plant defense-related genes.

overall_design: To investigate differential gene expression in mock- (WOP) and S. indica-infected (WP) Arabidopsis wild-type plants (Col-3) and cbl7 knockout mutants

first: Jesús

last: Vicente-Carbajosa


title: PANDA epigenetically regulates the trade-off between panicle number and grain size in rice [ChIP-Seq]

first: Pengyue

last: Zhang

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argriculture University

summary: Next generation sequencing reveal profiles in H3K27me3 and expression levels between WT and panda mutant, anti-Flag ChIP  reveal the binding sites of  PANDA protein

overall_design: Examination of H3K27me3 and expression levels in WT and panda mutant and PANDA binding sites in WT

first: Donghai

last: Mao

first: Wenli

first: Shentong


title: RNA quantitative sequencing in bleomycin-treated p300 knockout primary ATII cells

city: Seoul

first: Soo Yeon

last: Lee

address: yonsei-ro 50-1

country: South Korea

institute: Yonsei university

summary: p300 was knockout in ATII cells of murine lung, and then treated with 4mg/kg bleomycin for 2 weeks.

overall_design: Primary ATII cells mRNA profile after p300 knockout with bleomycin treatment, in triplicate

first: Ho-Geun

last: Yoon

first: Soo

first: Soo-Yeon

last: Park


title: Genome-wide analysis of HMGA2 and H3K27me3 deposition in neocortical neural stem cells and transcriptome of Wild Type and Ring1 KO neocortical neural stem cells

city: Tokyo

first: Yukiko

last: Gotoh

state: Tokyo

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

institute: University of Tokyo

summary: We examined the dynamic changes of H3K27me3 and gene expression in neocortical neural stem cells directly isolated from various stages of embryonic brains. ChIP-seq of HMGA2 protein in the early stage of neural stem cell, and transcriptome analysis of Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/- were also performed.

overall_design: ChIP-seq : 25 sample, RNA-seq : 10 sample (a brief description of each sample is provided in the sample 'description' field).

first: Yusuke

last: Hirabayashi

last: Goto

last: Kishi


title: PANDA epigenetically regulates the trade-off between panicle number and grain size in rice


title: Genome-wide maps of chromatin state in mouse lung samples.

summary: We report the application of Chromatin immunoprecipitation sequencing technology for p300 protein in PBS- or bleomycin-treated lung of mice.

overall_design: Mice were treated PBS or 4mg/kg bleomycin intratracheally. After 2 weeks, perfused lung samples of mice were harvested for ChIP-sequencing.


title: ST6Gal1 sialyltransferase promotes acinar to ductal metaplasia and pancreatic cancer progression

city: Birmingham

first: Susan

middle: L

last: Bellis

state: ALABAMA

address: MCLM 350, 1918 University Boulevard

institute: University of Alabama at Birmingham

summary: This study describes a novel function for the ST6GAL1 sialyltransferase in promoting acinar to ductal metaplasia (ADM).  ST6GAL1 activity facilitates ADM by reprogramming acinar cells into a more progenitor-like state.

overall_design: Sequencing of RNA from organoids derived from the pancreas of genetically-engineered mouse models (GEMMs).  The GEMMs have ectopic expression of ST6GAL1 and/or KRASG12D.  Three distinct organoid lines per genotype were analyzed.

first: Nikita

last: Bhalerao

first: Asmi

last: Chakraborty

first: Michael

middle: P

last: Marciel

first: Jihye

last: Hwang

first: Colleen

last: Britain

first: Austin

middle: D

last: Silva

first: Isam

middle: E

last: Eltoum

first: Robert

last: Jones

first: Katie

last: Alexander

first: Lesley

last: Smithies

first: Phillip

last: Smith

first: David

middle: K

last: Crossman

last: Crowley

first: Boyoung

last: Shin

first: Laurie

last: Harrington

first: Zhaoqi

last: Yan

first: Maigen

last: Bethea

first: Chad

last: Hunter

first: Christopher

last: Klug

first: Donald

last: Buchsbaum


title: OTUD1 aggravates pathological cardiac hypertrophy through activation of PGAM5-ASK1 signaling pathways

city: Shanghai

first: Kai

last: Huang

address: 168 Changhai Road, Yangpu District, Shanghai, China

department: Department of Cardiovascualr Surgery

institute: Changhai Hospital

summary: Deubiquitinating enzymes have gained more and more attention in the field of pathological cardiac hypertrophy. In this study, we explored the role of a deubiquitinase, OTUD1, in the transverse aortic constriction (TAC) induced cardiac hypertrophy. We found the upregulation of OTUD1 in heart tissues of TAC mice. OTUD1 overexpression promoted cardiac hypertrophy, cardiac fibrosis and apoptosis. Conversely, OTUD1 depletion alleviated these pathological changes both in vivo and in vitro. Mechanistically, ASK1 was identified as one substrate of OTUD1 using co-immunoprecipitation followed with LC-MS/MS. Interestingly, OTUD1 didn’t deubiquitinate ASK1, but increased the phosphorylation level of ASK1 during the process of cardiac hypertrophy. We found that PGAM5, the upper stream regulator of ASK1, was stabilized by OTUD1 in a K63 ubiquitin chain dependent way, which reminded us OTUD1 increased the phosphorylation level of ASK1 by deubiquitinating PGAM5. This study identified the OTUD1-ASK1 axis as a potential therapeutic target for pathological cardiac hypertrophy.

overall_design: We performed RNA sequencing analysis on the NRCMs of three Ad-GFP+Ang II groups and three Ad-Otud1+Ang II groups.

first: Lin

last: Han


title: Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis (ChIP-Seq)

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.

overall_design: Identification of genomic regions in Mtb chromosome bound by Flag-tagged Rv0158 protein following exposure to 0.3% glucose or 0.3% propionate as sole Carbon source.

first: Somnath

last: Shee

first: Nitish

last: Malhotra

first: Aswin

last: Seshasayee


title: ScRNA-seq of Lineage-tracing Mice Identifies Smooth Muscle Cell Phenotypic Alterations in Aortic Aneurysms and Dissections

city: Houston

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

summary: ScRNA-seq analysis revealed that aortic stress induced the transition of SMCs from a primary contractile phenotype to proliferative, extracellular matrix (ECM)-producing, inflammatory, and dying phenotypes. Lineage tracing showed the complete transformation of SMCs to fibroblasts and macrophages. ScATAC-seq analysis indicated that these phenotypic alterations were controlled by chromatin remodeling marked by the reduced chromatin accessibility of contractile genes and the induced chromatin accessibility of genes involved in ECM, inflammation, and cell death. IRF3, a pro-inflammatory transcription factor activated by cytosolic DNA, was identified as a key driver for the transition of aortic SMCs from a contractile phenotype to an inflammatory phenotype. In cultured SMCs, cytosolic DNA signaled through its sensor STING-TBK1 to activate IRF3, which bound and recruited EZH2 to contractile genes to induce repressive H3K27me3 modification and contractile gene suppression. In contrast, dsDNA-STING-IRF3 signaling induced inflammatory gene expression in SMCs. In Sting-/- mice, the aortic stress–induced transition of SMCs into an inflammatory phenotype was prevented, and SMC populations were preserved. Finally, profound SMC phenotypic alterations in diverse directions were detected in human ATAAD tissues.

overall_design: To understand aortic SMC dynamics during AAD development, we performed the single-cell transcriptomic analysis of aortic tissues collected from Myh11-CreERT2+ mT/mG lineage-tracing mice that were infused with Saline or angiotensin II (AngII; 1000 ng/kg/min) for 7 days. SMCs became green in color upon Cre induction, whereas non-SMCs remained red in color. For mice infused with AngII, aortas were separated as intramural hematoma/dissection (IMH/D) and non-IMH/D according to the condition of aorta. For each group, single-cell suspensions from the ascending thoracic aorta of 3 mice were pooled. SMCs (GFP+ cells) and non-SMCs (RFP+ cells) from the ascending aorta of AngII-infused mice were separated by using flow cytometry and individually processed for scRNA-seq. In total, 6 samples were submitted for scRNA-seq analysis.

first: Abhijit

last: Chakraborty

first: Chen

last: Zhang

first: Scott

last: LeMaire

first: Ying

middle: H

last: Shen


title: Rawdata of mRNAs microarray from 3 fresh lung cancer tissues and 3 fresh non-tumor tissues.

city: Guangzhou

first: Neng

last: Jiang

address: 651 Dongfeng East Road, Guangzhou 510060, P. R. China

institute: Sun Yat-sen University Cancer Center

summary: We performed mRNAss microarray to analyze the differential mRNAs expression profiles according to the recommended protocols.

overall_design: In the study presented here, fresh lung cancer tissue specimens and non-tumor lung tissue specimens were collected immediately after surgical resection. MRNAs microarray was performed according to the manufacturer’s guideline.


title: PANDA epigenetically regulates the trade-off between panicle number and grain size in rice [RNA-Seq]

first: Pengyue

first: Donghai

last: Mao

first: Wenli

first: Shentong

last: Tao


title: FGF18 alleviates hepatic ischemia-reperfusion injury via the USP16-mediated KEAP1/Nrf2 signaling pathway in male mice

city: wenzhou

first: Gaozan

last: Tong

state: 浙江省

address: School of Pharmaceutical Science

institute: wenzhou medical university

summary: Hepatic ischemia-reperfusion injury (IRI) is a common complication occurs during hepatic resection and transplantation. However, the mechanisms underlying hepatic IRI have not been fully elucidated. Here, we aim to explore the role of fibroblast growth factor 18 (FGF18) in hepatic IRI. In this work, we find that Hepatic stellate cells (HSCs) secrete FGF18 and alleviates hepatocytes injury. HSCs-specific FGF18 deletion largely aggravates hepatic IRI. Mechanistically, FGF18 treatment reduces the levels of ubiquitin carboxyl-terminal hydrolase 16 (USP16), leading to increased ubiquitination levels of Kelch Like ECH Associated Protein 1 (KEAP1) and the activation of nuclear factor erythroid 2-related factor 2 (Nrf2). Furthermore, USP16 interacts and deubiquitinates KEAP1. More importantly, Nrf2 directly binds to the promoter of USP16 and forms a negative feedback loop with USP16. Collectively, our results show FGF18 alleviates hepatic IRI by USP16/KEAP1/Nrf2 signaling pathway in male mice, suggesting that FGF18 represents a promising therapeutic approach for hepatic IRI.

overall_design: to explore the role of FGF18 in hepatic ischemia reperfusion. We established hepatic stellate cells (HSC) specific fgf18 knockout mice.


title: NFIB/MLL1 complex is required for the stemness and the Dlx5-dependent osteogenic differentiation of C3H10T1/2 mesenchymal stem cells

city: Incheon

first: Jangyhun

last: Choi

state: Incheon

address: 5N521, 100 Inha-ro, Michuhol-gu

department: Department of biological sciences

institute: Inha University

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

overall_design: Refer to individual Series


title: ScRNA-seq of Sting-KO Mice Identifies Smooth Muscle Cell Phenotypic Alterations in Aortic Aneurysms and Dissections

overall_design: To understand aortic SMC dynamics during AAD development, we performed the single-cell transcriptomic analysis of aortic tissues collected from control and Sting-KO mice that were infused with Saline or angiotensin II (AngII; 2000 ng/kg/min) for 7 days. For each group, single-cell suspensions from the ascending thoracic aorta of 3 mice were pooled. In total, 3 samples were submitted for scRNA-seq analysis.


title: Rawdata of miRNAs microarray from 3 fresh lung cancer tissues and 3 fresh non-tumor lung tissues

summary: We performed miRNAs microarray to analyze the differential miRNAs expression profiles according to the recommended protocols.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study presented here, fresh lung cancer tissue specimens and non-tumor lung tissue specimens were collected immediately after surgical resection. MiRNAs microarray was performed according to the manufacturer’s guideline.


title: TFAP2C affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification

city: Changchun

first: Daoyu

address: Xinzhu street 1977

institute: Jilin University

summary: By knocking down TFAP2C expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development.  The RNAseq was curry out to explore the genes influenced by TFAP2C

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and TFAP2C KD porcine embryos

first: Ziyi


title: Formaldehyde regulates S-adenosylmethionine biosynthesis and one-carbon metabolism

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. Here, we show formaldehyde, a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one-carbon metabolism by inhibiting the biosynthesis of S-adenosylmethionine (SAM), the major methyl donor in cells. Formaldehyde reacts with privileged, hyperreactive cysteine sites in the proteome, including Cys120 in S-adenosylmethionine synthase isoform type-1 (MAT1A). Formaldehyde exposure inhibited MAT1A activity and decreased SAM production with MAT-isoform specificity. A genetic mouse model of chronic formaldehyde overload showed a decrease in SAM and in methylation on selected histones and genes. Epigenetic and transcriptional regulation of Mat1a and related genes function as compensatory mechanisms for formaldehyde-dependent SAM depletion, revealing a biochemical feedback cycle between formaldehyde and SAM one-carbon units.

overall_design: We performed genome-wide CpG methylation analysis in liver samples from Adh5–/– mice compared to WT controls using the Infinium Mouse Methylation BeadChip that interrogates more than 285k methylation sites per sample at single-nucleotide resolution.

first: Carlos

last: Garcia-Prieto

first: Lucas

last: Pontel


title: The transcriptome analysis of C3H10T1/2 mesenchymal stem cells its derivatives expressing shRNA against NFIB or MLL1 during osteogenic differentiation

summary: To examine the impact of the NFIB/MLL1 complex on the transcriptome of C3H10T1/2 mesenchymal stem cells (MSCs) and to identify NFIB/MLL1-dependent genes during osteogenic differentiation, we performed RNA-sequencing (RNA-seq) analysis of six different samples at two time points.

overall_design: Comparative transcriptome analysis of C3H10T1/2 MSCs and its derivatives expressing shRNA specific for NFIB (shNFIB) or MLL1 (shMLL1).

first: Hansol

last: Lee

first: Janghyun


title: Early microRNA responses in rodent liver mediated by furan exposure establish dose thresholds for later adverse outcomes

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we evaluated the utility of microRNA (miRNA) profiling in female B6C3F1 mouse liver to indicate mechanisms of liver perturbation due to short-term exposure of the known rodent liver hepatotoxicant and carcinogen, furan.  Analyses indicated a robust dose response for 34 miRNAs to furan and involvement of p53-linked pathways in furan-mediated hepatotoxicity. Overall, these results indicate mechanistic involvement of miRNA in furan carcinogenicity and provide evidence of their potential utility as accessible biomarkers of exposure and disease.

overall_design: 6–7-week-old female B6C3F1 mice were exposed by oral gavage to non-carcinogenic (0, 1 or 2 mg/kg bodyweight per day) or carcinogenic (4 or 8 mg/kg bodyweight per day) doses of furan in corn oil for 21 days.

middle: N

first: Gail

last: Nelson

first: Gleta

last: Carswell


title: Genome-wide map of NFIB/MLL1 complex binding and H3K4me3 deposition during osteogenic differentiation of C3H10T1/2 mesenchymal stem cells

summary: To explore direct targets of NFIB/MLL1 complex and to examine the role of NFIB/MLL1 complex in genome-wide deposition of histone H3-K4 tri-methylation (H3K4me3), we conducted chromatin immunoprecipitation (ChIP) followed by deep sequencing (ChIP-seq) analysis of six different samples at two time points.

overall_design: Chromatins prepared from cells expressing control shRNA (shControl), shRNA against NFIB (shNFIB), and shRNA targeting MLL1 (shMLL1) were subjected to next-generation sequencing following immunoprecipitation using antibodies against NFIB, MLL1, or H3K4me3.


title: Resolvin D1 attenuated liver injury caused by chronic ethanol and acute LPS challenge in mice

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Alcohol-associated liver disease (ALD) is a major health problem with limited effective treatment options. Alcohol-associated hepatitis (AH) is a subset of severe ALD with a high rate of mortality due to infection, severe inflammation, and ultimately multi-organ failure. There is an urgent need for novel therapeutic approaches to alleviate the human suffering associated with this condition. Resolvin D1 (RvD1) promotes the resolution of inflammation and regulates immune responses. The current study aimed to test the therapeutic efficacy and mechanisms of RvD1-mediated effects on liver injury and inflammation in an experimental animal model that mimics severe AH in humans. Our data demonstrated that mice treated with RvD1 had attenuated liver injury and inflammation caused by EtOH and LPS exposure by limiting hepatic neutrophil accumulation and decreasing hepatic levels of pro-inflammatory cytokines. In addition, RvD1 treatment attenuated hepatic pyroptosis, an inflammatory form of cell death, via downregulation of pyroptosis-related genes such as GTPase family member b10 and guanylate binding protein 2, and reducing cleavage of caspase 11 and gasdermin-D. In vitro experiments with primary mouse hepatocytes and bone marrow-derived macrophages confirmed the effectiveness of RvD1 in the attenuation of pyroptosis. In summary, our data demonstrated that RvD1 treatment provided beneficial effects against liver injury and inflammation in an experimental animal model recapitulating features of severe AH in humans. Our results suggest that RvD1 may be a novel adjunct strategy to traditional therapeutic options for AH patients.

overall_design: For the initial sequencing, a total of six conditions, with quadruplicates in each condition, were studied , including: Wild-type, pair-fed; Fat1+/-, pair-fed; Wild-type, EtOH, LPS; Fat1+/-, EtOH, LPS; Fat1+/-, EtOH, LPS + RvE1; and Fat1+/-, EtOH, LPS RvD1. An additional four conditions with triplicates in each condition were subsequently run, including Wild-type, Pair-fed, LPS; Fat1, pair-fed, LPS; Wild-type EtOH; and Fat1 EtOH.

first: Josiah

last: Hardesty

first: Jeffrey

last: Warner

first: Ying

last: Song

middle: C

first: Craig

middle: J

last: McClain

first: Dennis

first: Irina

last: Kirpich


title: Single-nucleus multiomic mapping of m6A methylome and transcriptome in native populations of cells with sn-m6A-CT [scRNA-seq, scCUT&Tag]

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

summary: N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, technologies for analyzing m6A heterogeneity across single-cells are not extensively established. Here, we report single-nucleus m6A CUT-Tag (sn-m6A-CT) for simultaneous profiling of m6A methylome and transcriptome within a single nucleus. m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells, in a highly efficient manner. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. Further, we exemplified the robust deconvolution capabilities in m6A heterogeneities with stem cells in multiple distinct pluripotency states. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and new insights into epitranscriptomic landscape in defining cell fate identity and states.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk CUT&Tag or single-nucleus CUT&Tag followed by Illumina sequencing

first: Ka

middle: W

last: Wong

first: Tsz

last: Sam

first: Jia Hao Jackie

last: Teo

first: Reshma

last: Taneja

first: Minh T. N.

last: Le

first: Qi-Jing

last: Li

first: Jacob

last: Hanna

first: Hu

first: Yuin-Han

last: Loh


title: Single-nucleus multiomic mapping of m6A methylome and transcriptome in native populations of cells with sn-m6A-CT


title: CD34+ Cell-derived Fibroblast–Macrophage Crosstalk Drives Limb Ischemia Recovery through the OSM–ANGPTL Signaling Axis

city: Beijing

first: Yuwei

address: 38 Xueyuan Road

institute: Peking University

summary: CD34+ cells improve the perfusion and function of ischemic limbs in humans and mice. However, there is no direct evidence of the differentiation potential and functional role of these cells in the ischemic muscle microenvironment. Here, we combined the single-cell RNA sequencing and genetic lineage tracing technology and then provided exact single-cell atlases of normal and ischemic limb tissues in human and mouse, consequently found that bone marrow-derived macrophages with antigen-presenting function migrated to the ischemic site, while resident macrophages underwent apoptosis. The macrophage oncostatin M (OSM) regulatory pathway was specifically turned on by ischemia. Simultaneously, bone marrow CD34+-derived pro-regenerative fibroblasts were recruited to the ischemia niche, where they received macrophage-released OSM, and promoted angiopoietin-like protein (ANGPTL)-associated angiogenesis. These findings provided novel mechanisms on the cellular events and cell–cell communications during tissue ischemia and regeneration, and provided new evidence that CD34+ cells serve as fibroblast progenitors promoting tissue regeneration.

overall_design: The muscle was obtained from four groups of hind limb ischemia model mice (Sham, HLI, tdTomato+ cells sorted from Cd34-CreERT2;R26-tdTomato mice, and tdTomato+ cells sorted from Bone marrow transplanted Cd34-CreERT2;R26-tdTomato mice) and two amputees (Ctrl and PAD), the muscle cells were discarded. Mononuclear single-cell suspensions were used to perform Single-cell RNA sequencing (scRNA-seq).

first: Xiaotong

last: Sun

first: Xiaolong

last: Ma


title: Single-nucleus multiomic mapping of m6A methylome and transcriptome in native populations of cells with sn-m6A-CT [Bulk CUT&Tag]


title: Isx-9 induces enteroendocrine cell differentiation in the intestinal organoids

first: Wei

last: Wu

address: Tsinghua Road, Medical Building

institute: Tsinghua University

summary: We investigated the cell identity and cell proportion in the intestinal organoids treated by Isoxazole-9 (Isx-9) using single-cell transcriptome analysis. Isx-9 enriches enteroendocrine cells without altering the cell identity of other lineages. To investigate the mechanism of this process, we performed RNA-seq and ATAC-seq of Isx-9 treated intestinal stem cells. Based on the gene expression pattern and differential peaks of open chromatin,  we found that Isx-9 upregulated neuroendocrine related genes, and elevated the chromatin accessibility at the promoter region of enteroendocrine related transcription factors.

overall_design: Single-cell transcriptome profiles of 4 samples were generated, including WT intestinal organoids, Chgb-mCherry reporter organoids, and Chgb-mCherry reporter organoids treated by DMSO or Isx-9 for 6 days. In addition, RNA-seq and ATAC-seq of DMSO or Isx-9 treated intestinal stem cells were also performed.

first: Shangjun

last: Zhao

first: Yao

last: Su

first: Heng

first: Lei

last: Tang


title: CPSF role on APA regulation

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

summary: We found that CPSF6, a component of the CFIm, can form liquid-liquid phase separation (LLPS) and the elevated LLPS induces the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs LLPS of CPSF6 by phosphorylating its arginine/serine-like domain. Albeit higher expression of CPSF6 in cancer, the reduction of LLPS leads to shortening 3’ UTR of cell cycle related genes and then promotes cell proliferation. These results reveal that LLPS regulation of CPSF6 is a fine tuning way of APA in cancer cells and provide a new mechanism for APA regulation by regulating LLPS of 3’ end processing factors through post-translational modification.

overall_design: We knockdowned CPSF6 and CLK2 in RKO cell with shRNA and Overexpression  of CPSF6 and CPSF6 mut in HEK2293T cells, and applied a alternative polyadenylation high sequencing (IVT-SAPAS) method to detect dynamic change of 3‘UTR length.

first: Susu

last: Liu

first: Runze

last: We

first: Liutao

last: chen


title: Bulk RNA-seq of young and aged livers following influenza A virus infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Aging is known to alter the host repsonse to influenza infection. Here, we use bulk RNA sequencing (bulk RNA-seq) to identify cellular changes in the livers of young (16-week-old) and aged (80-week-old) mice following influenza infection.

overall_design: Mice were infected with influenza A/PR8/34 (~50 PFU/mouse) to establish acute infection. Infections were performed by intranasal (i.n.) administration under anesthesia as described before (Sun et al., 2009). Mice were then euthanized and the right ventricle was perfused with 10 mL cold DPBS (Corning). For bulk RNA-seq, pieces of liver were harvested after ventricular perfusion and snap frozen on dry ice. RNA was extracted using an RNAEasy Mini Kit (Qiagen). Reverse transcription was performed and the resultant cDNA was enzymatically fragmented and indexed using a Nextera XT DNA Library Preparation Kit (Illumina). Barcoded cDNA libraries were sequenced on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (75 cycles) (20024906, Illumina) with the following cycle counts: 37 (read 1), 8 (index 1), 8 (index 2), 37 (read 2). Demultiplexing was performed using bcl2fastq (v2.20, Illumina). Alignment was performed using Salmon (v1.4.0) (Patro et al., 2017) and the GRCm39 reference genome (Ensembl) with default settings. Downstream analysis was performed in R using DESeq2 (v1.28.1) (Love et al., 2014).

first: Moujtaba

last: Kasmani


title: Genome-wide maps of histone lactylation in ocular melanoma by CUT&Tag

status: Public on Sep 04 2023

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

summary: To investigate the function of histone lactylation in ocular melanoma, we analyzed histone lactylation enrichment level in ocular melanoma by CUT&Tag.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for H3K18la in 92.1 and CRMM1 cells.

first: X

first: P

last: Chai


title: Genome-wide maps of histone lactylation in ocular melanoma by CHIP-seq

summary: To investigate the function of histone lactylation in ocular melanoma, we analyzed histone lactylation enrichment level in ocular melanoma by CHIP-seq.

overall_design: Chromatin immunoprecipitation DNA-sequencing (CHIP-seq) for H3K18la in 92.1 and CRMM1 cells.


title: RNA seq of intrahepatic cholangiocarcinoma cell lines and normal bile duct epithelial cells

city: lanzhou

first: Jing

middle: Jin

last: Hu

state: 甘肃省

address: 1 West Donggang Road, The first Hospital of Lanzhou University, Lanzhou, China

institute: Lanzhou University

summary: Our data uncovered the functional heterogeneity of CAFs during ICC metastasis and set the epigenetic regulator PCGF4 as the crucial effector

overall_design: Two patient-derived primary ICC cancerous cells (ICC-X1-PCGFH and ICC-X2-PCGF4L) exhibited distinct migration capabilities in the cell scratch assays. That is, ICC-X1-PCGFH cells migrated much faster than ICC-X2-PCGF4L. RNA-Seq analyses were carried out to identify the differentially expressed genes between these two lines and also compared to a normal intrahepatic biliary epithelial cell line (HIBEpic cells)


title: Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

summary: Fungal pathogens threaten ecosystems and human health. Understanding the molecular basis of their virulence is key to develop new treatment strategies. Here, we characterize NCS2*, a point mutation identified in a clinical baker's yeast isolate. Ncs2 is essential for 2-thiolation of tRNA and the NCS2* mutation leads to increased thiolation at body temperature. NCS2* yeast exhibits enhanced fitness when grown at elevated temperatures or when exposed to oxidative stress, inhibition of nutrient signalling, and cell-wall stress. Importantly, Ncs2* alters the interaction and stability of the thiolase complex likely mediated by nucleotide binding. The absence of 2-thiolation abrogates the in vivo virulence of pathogenic baker's yeast in infected mice. Finally, hypomodification triggers changes in colony morphology and hyphae formation in the common commensal pathogen Candida albicans resulting in decreased virulence in a human cell culture model. These findings demonstrate that 2-thiolation of tRNA acts as a key mediator of fungal virulence and reveal new mechanistic insights into the function of the highly conserved tRNA-thiolase complex.

overall_design: Wild type and 2-thiolation deficient Candida albicans strains were analysed by ribosome profiling at 30 °C, 37 °C and 41 °C.

first: Fiona

last: Alings

first: Karin

last: Scharmann

first: Cristian

last: Eggers

first: Bettina

last: Böttcher

first: Mikołaj

last: Sokołowski

first: Ekaterina

last: Shvetsova

first: Joël

last: Roth

first: Leon

last: Rashiti

first: Sebastian

last: Glatt

first: Sascha

last: Brunke

middle: A

last: Leidel


title: Near Haploidization is a Genomic Hallmark of Giant Cell Glioblastoma

city: Boston

first: Adrian

last: Dubuc

state: Massachussetts

address: 75 Francis St, 5-5066 Shapiro Building

institute: Brigham and Women's Hospital

summary: Genomic characterization of rare histological subtype of glioblastoma with giant cell features.

overall_design: This study evaluated copy number imbalances and copy-neutral loss of heterozygosity across a series of 10 giant cell glioblastomas (gcGBMS). 2 samples were hybridized to [OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay.

first: Tiffany

middle: G

last: Baker

first: Jay

last: Alden

first: Adrina

middle: M

first: Cynthia

middle: T

last: Welsh

first: Iya

last: Znoyko

first: Linda

last: Cooley

first: Midhat

middle: S

last: Farooqi

first: Stuart

last: Schwartz

first: Yvonne

last: Li

first: Andrew

last: Cherniack

first: Scott

last: Lindhorst

first: Melissa

last: Gener

first: Daynna

last: Wolff

first: David

last: Meredith


title: ST6Gal1 sialyltransferase promotes pancreatic ductal adenocarcinoma by facilitating acinar to ductal metaplasia

city: Birmingham

first: Susan

middle: L

last: Bellis

address: MCLM 350, 1918 University Boulevard

institute: University of Alabama at Birmingham

summary: RNA-Seq analyses of pancreata from mice with expression of the following genes: (1) "KC" mice with KRasG12D; (2) "KSC" mice with dual expression of KRasG12D and ST6Gal1 (3) "SC" mice with expression of ST6Gal1; and (4) "WT" mice representing littermate controls lacking Cre expression.

overall_design: RNA was harvested from freshly-isolated pancreata from 20 week-old mice with PDX1-Cre driven expression of KRrasG12D (KC), ST6Gal1 (SC), or a combination of KRasG12D and ST6Gal (KSC).  "WT" littermate controls lack PDX1-Cre

last: Crossman


title: histone lactylation in ocular melanoma

city: Shanghai

first: Xiang

last: Gu

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

overall_design: Refer to individual Series


title: Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

summary: People with diabetes are more likely to develop tuberculosis (TB) and to have poor TB treatment outcomes than those without. We previously showed that blood transcriptomes in people with TB-diabetes (TB-DM) co-morbidity have excessive inflammatory and  reduced interferon responses at TB diagnosis. It is unknown whether this persists through treatment, potentially underlying adverse outcomes.   Methods  Pulmonary TB patients were recruited in South Africa, Indonesia and Romania, and classified as having TB-DM, TB with prediabetes, TB-related hyperglycaemia or uncomplicated TB, based on glycated haemoglobin (HbA1c) concentration at TB diagnosis and after 6 months of TB treatment. Gene expression in blood samples collected at diagnosis and at regular intervals throughout treatment was  measured by unbiased RNA-Seq and targeted Multiplex Ligation-dependent Probe Amplification.   Results   Gene expression was modulated by TB treatment in all groups but to different extents, such that differences remained  in people with TB-DM relative to TB-only throughout, including genes involved in innate responses, anti-microbial immunity and the inflammasome. People with prediabetes or with TB-related hyperglycaemia had gene expression more similar to people with TB-DM than TB-only throughout treatment.  The overall pattern of change was similar across clinical groups irrespective of glycaemic index, permitting models predictive of TB treatment to be developed.  Conclusions  The exacerbated transcriptome changes seen in TB-DM take longer to resolve during TB treatment, indicating that prolonged treatment or host-directed therapy may be needed to improve TB treatment outcomes. Development of transcriptome-based biomarker signatures of TB-treatment response should include people with diabetes to be useful across populations.

overall_design: Whole blood was collected from patients with TB-only, TB-DM, TB-IH throughout anti-tuberculosis therapy at four time points: Diagnosis, Week 2, Month 2 and Month 6 in three field sites; South Africa, Romania and Indonesia

first: Clare

last: Eckold

first: Cassandra

last: van Doorn

first: Hazel

last: Dockrell

first: Tom

last: Ottenhoff

first: Eleonora

last: Vianello

first: Jacqueline


title: Effect of short- and long-term Serendipita indica-infections on the gene expression in wild-type Arabidopsis thaliana plants

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

address: Campus de Montegancedo, Autovia M-40 (km 38)

institute: CBGP (UPM-INIA/CSIC)

summary: The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Co-cultivation of Arabidopsis thaliana seedlings with the fungus triggers a substantial induction of the growth of the root system. However, the molecular mechanisms by which the fungus promotes plant growth over an extended period of time is still unclear. We here report the comparative analysis of the effect of a mock- and S. indica-infection on wild-type Arabidopsis plants (Col-0) after 2 and 10 days of co-cultivation. Our data provide evidence for the induction of a number of genes that are consistingly induced during the plant–fungus interaction.

overall_design: To investigate differential gene expression in mock- and S. indica-infected Arabidopsis wild-type plants (Col-0) during early stages (2 days) and later stages (10 days) of co-cultivation.

first: Jesús

last: Vicente-Carbajosa


title: Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells

first: Markus

last: Schröder

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

institute: ETH Zürich

summary: Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA degradation pathway that targets for degradation faulty mRNAs with premature termination codons as well as many physiological mRNAs encoding full-length proteins. Consequently, NMD functions in both, quality control and post-transcriptional regulation of gene expression, and it has been implicated in the modulation of cancer progression. To investigate the role of NMD in cancer, we knocked out SMG7 in the HT1080 human fibrosarcoma cell line. SMG7 is involved in deadenylation-coupled exonucleolytic mRNA decay, one of the two main degradation pathways in mammalian NMD. Genome-wide proteomic and transcriptomic analyses confirmed that NMD is severely compromised in these SMG7-knockout HT1080 cells. We compared the oncogenic properties between the parental, the SMG7-knockout, and a rescue cell line in which we re-introduced both isoforms of SMG7. In parallel, we tested the effect of a drug inhibiting the NMD factor SMG1 on the HT1080 cells to distinguish NMD-dependent effects from putative NMD-independent functions of SMG7. Using cell-based assays as well as a mouse xenograft tumor model, we show that the oncogenic properties of the parental HT1080 cells are severely compromised when NMD is inhibited. Molecular pathway analysis revealed a strong reduction of the matrix metalloprotease 9 (MMP9) gene expression in NMD-suppressed cells. Since MMP9 expression promotes cancer cell migration and invasion, metastasis and angiogenesis, its downregulation in NMD-suppressed cells explains, at least partially, their reduced tumorigenicity. Collectively, our findings emphasize the therapeutic potential of NMD inhibition for the treatment of certain types of cancer.

overall_design: Comparative gene expression analysis of RNAseq data from subcutaneous tumors formed by HT1080, SMG7KO and RESCUE cells, in NSG mice.

first: Sofia

last: Nasif

first: Martino

last: Colombo

first: Anne-Christine

last: Uldry

first: Simone

last: de Brot

first: Oliver

last: Mühlemann


title: DNA mimic foldamers affect chromatin composition and disturbs cell cycle progression

city: Planegg-Martinsried

first: Axel

last: Imhof

address: Großhadernerstr. 9

institute: BioMedical center

summary: The use of synthetic chemicals to selectively interfere with chromatin and the chromatin-bound proteome represents a great opportunity for pharmacological intervention. Recently, synthetic foldamers that mimic the charge surface of double-stranded DNA have been shown to interfere with selected protein-DNA interactions. However, to better understand their pharmacological potential and to improve their specificity and selectivity, the effect of these molecules on complex chromatin needs to be investigated. We therefore systematically studied the influence of the DNA mimic foldamers on the chromatin-bound proteome using an in vitro chromatin assembly extract. Our studies show that the foldamer efficiently interferes with the chromatin-association of the origin recognition complex in vitro and in vivo, which leads to a disturbance of cell cycle in cells treated with foldamer. This effect is mediated by a strong direct interaction between the foldamers and the origin recognition complex and results in a failure of the complex to organise chromatin around replication origins. Foldamers that mimic double-stranded nucleic acids thus emerge as a powerful tool with designable features to alter chromatin assembly and selectively interfere with biological mechanisms.

overall_design: MNase-seq samples of in vitro reconstituted SGD (salt-gradient dialysis) chromatin incubated together with purified ORC (Origin Recognition Complex), INO80 (INOsitol requiring 80) and different amounts of a synthetic foldamer (Ziach et al., 2018; Corvaglia et al., 2019; Corvaglia et al., 2023).

first: Vera

last: Kleene

first: Valentina

last: Corvaglia

first: Erika

last: Chacin

first: Ignasi

last: Forne

first: David

middle: B

last: Konrad

first: Pardis

last: Khosravani

first: Céline

last: Douat

first: Christoph

middle: F

last: Kurat

first: Ivan

last: Huc


title: Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression [Nanostring]

city: Urbana

first: Erik

last: Nelson

address: 523 Burrill, 407 South Goodwin Ave

institute: University of Illinois at Urbana-Champaign

summary: Due to the limited efficacy of Immune checkpoint blockade (ICB) in mammary solid tumors alternative strategies are required. We demonstrated that cholesterol homeostasis plays a significant role in myeloid immune function and breast cancer progression. In this study, we focus on NR0B2. We conducted both in vitro and in vivo studies along with developing a small molecule agonist. NR0B2 functions within myeloid immune cells as a regulator of the NLRP3 inflammasome, which further facilitates T cell differentiation away from immune-suppressive regulatory T cells (Treg). Furthermore, this signaling pathway was demonstrated to attenuate breast tumor growth and metastasis in mouse models.

overall_design: To understand if NR0B2 plays a role in breast cancer metastasis, we grafted 4T1 cells to Balb/c mice and started treating mice with placebo (DMSO) or NR0B2 agonist (DSHN). Dendritic cells (CD11B+;CD11C+) were isolated from lungs. RNA was isolated. Gene expression profiling analysis was then performed on data obtained from Nanostring. Differentially expressed gene profiles between groups were generate

first: Yu

last: Wang

middle: R


title: A Cryptic Basic Groove formed by Ubiquitin and Histone H3 Mediates the Selective Recognition of H2AK119Ub Nucleosomes by Synovial Sarcoma X Breakpoint 1 Protein

first: Kezhang

last: He

address: Shuangqing Road

summary: The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the chromatin-remodeling BAF complex from the promoters or enhancers to the H2AK119Ub-marked polycomb-repressed chromatin regions. Relocation of the BAF complex was achieved through selective recognition of the H2AK119Ub nucleosomes by the synovial sarcoma X breakpoint 1 protein SSX1, which neither has a ubiquitin (Ub)-binding domain nor binds to free Ub. To elucidate the mechanism by which SSX1 selectively recognizes H2AK119Ub nucleosomes, here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at a resolution of 3.1 Å. The structure reveals that the SSX1 N-terminal basic region (residues W164, R167, L168, R169) is anchored to the H2A/H2B acidic patch, while the aromatic amino acid (residue Y177) in the middle of SSX1 interacts with the hydrophobic pocket formed by the H2A α2 and α3 helixes. Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 (residues R49, R52, K56) and the Ub motif (residues R42, R72, R74) on the H2AK119 site. Our results describe a novel mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to polycomb regions by SS18-SSX1 in synovial sarcoma.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for H2AK119Ub, SS18, SS18-SSX1 and its mutants in HEK293T cells.

first: Zebin

last: Tong

first: Huasong

last: Ai

first: Ziyu

last: Xu


title: Differential gene expression analysis of colonic epithelial cells from wildtype and PRMT5 heterozygote mice

city: San Diego

first: Wendy

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: PRMT5 is a type II arginine methyltransferase enzyme that is abundantly expressed in intestinal epithelial cells (IECs) of the colon. Here, we compared the transcriptome of the colonic epithelium from wildtype and PRMT5 heterozygote mice under steady state. We found that PRMT5-regulated genes are involved in anti-microbial responses and immune signaling.

overall_design: Colons from two pairs of 8wk old WT and PRMT5 Het cohoused littermates were incubated in 5 mM EDTA containing HBSS for 20 minutes at 37 degree to enrich for IECs (80-90%). Results of colonic epithelia from PRMT5 Het mice were compared to those from gender-matched WT littermates.

first: Juan

last: Hernandez


title: Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression [PyMT_RNA-Seq]

summary: Due to the limited efficacy of Immune checkpoint blockade (ICB) in mammary solid tumors alternative strategies are required. We demonstrated that cholesterol homeostasis plays a significant role in myeloid immune function and breast cancer progression. In this study, we focus on NR0B2. We conducted both in vitro and in vivo studies along with developing a small molecule agonist. NR0B2 functions within myeloid immune cells as a regulator of the NLRP3 inflammasome, which further facilitates T cell differentiation away from immune-suppressive regulatory T cells (Treg). Furthermore, this signaling pathway was demonstrated to attenuate breast tumor growth and metastasis in mouse models

overall_design: The MMTV-PyMT mouse model was crossed with NR0B2+/+ or NR0B2-/- to generate NR0B2+/+ PyMT+ and NR0B2-/- PyMT+ colonies. Tumors were collected and processed for dissociation followed by RNA isolation. Bulk RNA-seq was performed. Differentially expressed genes were determined between tumors from NR0B2+/+ PyMT+ and NR0B2-/- PyMT+

first: Sayyed

last: Shahoei


title: Transcriptome profiling analysis after down-regulation of MALAT1 in NSCLC cell lines

city: Cheongju-si

first: Wanyeon

last: Kim

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

institute: Korea National University of Education

summary: MALAT1 is a lncRNA known to contribute to the development of non-small cell lung cancer (NSCLC). We performed transcriptome sequencing analysis to investigate genes interacting with MALAT1 in NSCLC.

overall_design: An experimental group treated with si-MALAT1 and a non-treated control group were constructed in NSCLC cell lines (H460, H1299, A549). Transcriptome analysis was performed on six samples.

first: Boseong

first: Jungwook

last: Roh

first: Mijung

last: Im

first: Wonyi

last: Jang


title: Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression [BMDM_RNA-Seq]

overall_design: NR0B2 is known to play an inhibitory role to LXR, one of the major regulators of cholesterol homeostasis, and we had previously demonstrated that NR0B2 functions in myeloid immune cells. Here, murine bone marrow derived macrophages were treated with placebo (DMSO), the NR0B2 agonist DSHN (50µM), the LXR agonist GW3965 (1µM) or a combination of GW3965 and DSHN, for 24h. RNA was isolated. Bulk RNA-seq was performed. Differentially expressed gene profiles between groups were generated


title: Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression


title: Species-specific metabolic reprogramming in human and mouse microglia during inflammatory pathway induction

city: Groningen

first: Alejandro

last: Marmolejo

state: Groningen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University of Groningen

summary: Metabolic reprogramming is considered a hallmark of murine macrophages and microglia  response to inflammatory stimuli. Alterations in metabolic pathways include oxidative  phosphorylation, glycolysis, the pentose phosphate pathway, and fatty acid oxidation. Mouse  immune cells can switch their metabolism from mitochondrial oxidative phosphorylation  (OXPHOS) to glycolysis in response to inflammatory conditions. The potential targeting of  these metabolic pathways led to an exponential surge of interest in reprogramming  metabolic pathways. However, most of these experimental findings have been acquired in  murine immune cells. Limited information on metabolic reprogramming in human immune  cells, including innate brain immune cells, is available. Studies of human microglia have  been hindered by the limited availability of human brain microglia availability. In this study,  we investigated transcriptomic and metabolic profiles in mouse and iPSC-derived human  microglia challenged with TLR4 agonist LPS. We analyzed and compared the transcriptome  profiles, phagocytosis, and metabolism of microglia from mouse and human by various  methods, including RNA-seq, Incucyte imaging, xCELLigence real-time impedance  measurements, extracellular acidification rate and oxygen consumption rate (OCR). We  observed a metabolic shift and an overall increased glycolytic gene signature upon LPS  treatment in both species. However, the dysregulation of oxidative metabolism was  discrepant among species: mouse microglia exhibited a decrease in mitochondrial  respiration after long-term LPS treatment, while human microglia did show a decrease after  short-term LPS treatment. This study highlights the species-specific pathways involved in  immunometabolism, linking the glycolytic metabolic switch without a necessary attenuation  of respiration to classical inflammatory phenotypes in human microglia, and providing an  informative report for future translational studies in mouse models and humans.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of mouse primary microglia, mouse acutely isolated microglia, and human iPSC-derived microglia-like cells.

first: Marmolejo-Garza

last: Alejandro

first: Sabogal-Guáqueta

last: Angélica

first: Dolga

last: Amalia


title: Epigenetic downregulation of hsa-miR-193b-3p increases Cyclin D1 expression level and cell proliferation in human meningiomas

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

summary: Meningiomas are common intracranial tumors in adults. Abnormal miRNA expression plays a role in their pathogenesis. Change in miRNA expression level can be caused by impaired epigenetic regulation of miRNA-encoding genes. We found genomic region covering MIR193B gene as DNA hypermethylated in meningiomas based on analysis of genome-wide methylation (HM450k Illumina arrays). Hypermethylation of MIR193B was as also confirmed by bisulfite pyrosequencing. Both hsa-miR-193b-3p and hsa-miR-193b-5p are downregulated in meningiomas as found with qRT-PCR. Lower expression of hsa-miR-193b-3p and higher MIR193b methylation was observed in WHO GII/GIII as compared to GI meningiomas. 3’UTR of CCND1 mRNA was identified as target of hsa-miR-193b-3p as further validated with luciferase reporter assay in IOMM-Lee meningioma cells. IOMM-Lee cells transfected with hsa-miR-193b-3p mimic showed decreased cyclin D1 level and lower cell viability and proliferation, confirming suppressive nature of this miRNA. Cyclin D1 protein expression (immunoreactivity) was higher in atypical than in benign meningiomas, accordingly to observation of lower hsa-miR-193b-3p level in GII tumors. The commonly observed hypermethylation of MIR193B in meningiomas apparently contributes to downregulation of hsa-miR-193b-3p. Since hsa-miR-193b-3p regulates proliferation of meningioma cells through negative regulation of cyclin D1 expression, it seems to be an important tumor suppressor in meningiomas.

overall_design: Bisulphite converted DNA from 27 samples were hybridised to the HumanMethylation 450 K Infinium Methylation BeadChip (Illumina)

first: Paulina

last: Kober

first: Beata

last: Mossakowska

middle: P

first: Mateusz

last: Bujko


title: Single-cell RNA sequencing reveals a distinct profile of bone immune microenvironment and decreased osteoclast differentiation in Type 2 Diabetic Mice

city: Shenzhen

first: Lin

last: Wang

state: Guangdong

address: Liuxian

institute: Sustech Hospital

summary: The pathogenic effects of type 2 diabetes on bone are gaining attention, and a basic grasp of the cellular and molecular mechanisms underlying osteoimmunology is essential for diabetes-related bone disease. However, the influence of diabetes on osteoimmunology and bone metabolism in the BM microenvironment still remains unclear. We aimed to delineate the single-cell transcriptome of bone marrow cells from WT and type 2 diabetic mice and revealed a unique bone immune microenvironment in type 2 diabetic mice.

overall_design: Whole bone marrow cells from the femur and tibia of mice in the WT and T2D groups were collected for single-cell RNA sequencing analysis.

first: Zimei

last: Wu

first: Qiaodan

last: Hou

first: Heng

last: Chi

first: Jihong

last: Liu

first: Yixin

last: Mei

first: Tingting

last: Chen

first: Lulu

first: Xingzhu

last: Jiang

first: Jing


title: Multi-modal single cell sequencing of B cells in primary Sjögren’s Syndrome

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

summary: Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by lymphocytic infiltration in the salivary and lacrimal glands, B cell activation, SSA/SSB autoantibodies and an increased risk of B cell lymphoma. By generating sorted B cell single-cell gene expression and BCR libraries from 24 pSS patients stratified by SSA/SSB antibodies and four healthy controls, we defined 16 B cell subtypes. Interferon response genes were upregulated in pSS across all B cell subtypes, with the highest levels in pSS with both SSAB antibodies. The SSAB group showed a higher proportion of naïve B cells and lower proportion of memory B cells compared with controls. Memory B cells from SSAB patients were not class switched and expressed unmutated VDJ sequences. IGHV1-69 repertoire frequencies were higher in pSS patients than controls and 1287 clonotypes were unique for pSS. The present study describes molecular differences which may enable stratification of pSS patients at improved resolution.

overall_design:
B cells from the peripheral blood from 24 patients with primary Sjögren's syndrome (pSS), from three patient groups based on auto-antibody stratification (SSA-: pSS patients where auto-antibodies to SSA or SSB were not detected (n = 6). SSA+: pSS patients where SSA but not SSB auto-antibodies were detected (n = 8). SSAB: pSS patients where SSA and SSB auto-antibodies were detected (n = 10)), and  B cells from the peripheral blood of four healthy controls.

>>>Submitter states: Raw data are not available due to patient privacy concerns<<<

first: Paulo

last: Czarnewski

first: Alina

last: Johansson

first: Amanda

last: Raine

first: Juliana

last: Imgenberg-Kreuz

first: Jessica

last: Nordlund

first: Gunnel

last: Nordmark

first: Ann-Christine

last: Syvänen


title: Effect of high-dose glucocorticoid treatment on human brown adipose tissue activity: a randomised, double-blinded, placebo-controlled cross-over trial in healthy men

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

summary: Glucocorticoids (GCs) are widely applied anti-inflammatory drugs that are associated with adverse metabolic effects including insulin resistance and weight gain. Previous research indicated that GCs may negatively impact brown adipose tissue (BAT) in rodents and humans. Here, we demonstrate that treatment of human volunteers with high doses of GCs increases resting energy expenditure (REE) but does not reduce BAT activity. In line with the physiological results, gene expression in human BAT was not significantly altered by GCs in vivo. However, the RNA-sequencing of skeletal muscle revealed that GCs increase the expression of enzymes involved in calcium cycling as well as the respiratory chain. Collectively, these data suggest that the raise of EE after GCs exposure is mediated by skeletal muscle rather than a change in BAT activity.

overall_design: Randomized crossover trial

first: Claudia

middle: I

last: Maushart

first: Wenfei

last: Sun

first: Christian

last: Wolfrum

first: Matthias

last: Betz


title: The hippocampus on Blast-related Traumatic Brain Injury at Single-cell Resolution

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

summary: To elucidate molecular features of the cells of Hippocampus, their progeny at each differentiation stage, and surrounding cells in hippocampus under blast wave-induced changes, cells were profiled from matched hippocampus of 3 mice that had received blast injury and 3 controls.Cell type specific gene expression responding to (blast-related traumatic brain injury, bTBI) were revealed, some of which were closely associated with pathogenesis post-injury. Furthermore, the diverse cell to cell interaction networks uncovered an array of cellular processes under bTBI.  Our gene expression atlas provides extensive resources for future researches regarding bTBI induced pathogenesis, its therapeutic interventions or diagnostic tests.

overall_design: Hippocampus mRNA profiles of 8~10-week old mTBI and Sham mice were generated by  scRNA-Seq.

first: Xiameng


title: Whole genome transcriptomic analysis of T. onnuriuens NA1 wild-type and MC11 mutant strains on CO

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

summary: Previously, we reported that the TON_1525 (T55I) (designated as MC11) strain showed superior activity in CO oxidation than the wild-type strain. To understand the in vivo role of TON_1525 in this strain on CO-supplemented medium, transcriptome changes were investigated.

overall_design: The expression profiles of genes in wild-type and MC11 mutant strains under CO-supplemented conditions were measured.

first: Seong

middle: H

last: Lee

first: Hyun

first: Sung

last: Kang


title: Transcriptomic analysis of untreated log-phase  Mtb H37Rv, Mtbrv0158 Knockout strain and Mtbrv0158 complemented strain

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

institute: Indian Institute of Science

summary: We identified rv0158 gene as a major determinant of  redox homeostasis in Mtb.  Disruption of rv0158 perturbed redox balance in a carbon source-specific manner, promoted killing in response to anti-TB drugs, reduced survival in macrophages, and persistence in mice. RNA sequencing  analysis was performed to identify its regulon. The data indicated that rv0158 is required to balance the deployment of fatty acid substrates between lipid anabolism and oxidation.

overall_design: All Mtb strains were grown to early log phase (optical density =0.6) at 37 degree celsius at 180 rpm in a shaker incubator.  For H2O2 (hydrogen peroxide )- treatment, Mtb strains were grown as mentioned above and then 5 mM H2O2 was added to all the strains for 2 hours, before total RNA was isolated. Two independent experiments were done for each of the strains.

first: Somnath

last: Shee

first: Reshma

last: Veetil

first: Nitish

last: Malhotra

first: Aswin

last: Narain Seshashyee


title: Metabolically activated energetic materials mediate cell anabolism for bone regeneration

status: Public on Sep 03 2023

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

summary: While cellular energy metabolism regulates tissue regeneration, it remains as a challenge with its limited understanding of activation by engineered scaffolds to regenerate tissue or organ for therapeutic purpose. This study presents a biosynthesized poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [abbreviated as P(3HB-co-4HB)] and its major degradation product, 3-hydroxybutyrate (3HB), functioning as an endogenous bioenergetic molecule to facilitate bone regeneration and promote cellular anabolism via generations of adenosine triphosphate (ATP) and citrate that enhance the progression of human bone marrow mesenchymal stem cells (hBMSCs) towards osteoblastogenesis. Our studies demonstrate that 3HB not only significantly enhances in vitro ATP generation to elevate mitochondrial membrane potential (ΔΨm) and capillary-like tube formation, but also increases the content of intermediate metabolite, namely, citrate, in tricarboxylic acid (TCA) cycle, and ultimately promotes the formation of citrate-containing apatite during osteogenesis of hBMSCs. Furthermore, 3HB administration increases the bone mass in rats with ovariectomy (OVX)-induced osteoporosis. Results also show that the P(3HB-co-4HB) scaffold significantly enhances long-term induced bone repair in a rat model with critical-sized calvarial defects, compared to the commercialized available poly-L-lactic acid (PLLA) scaffold. Collectively, these findings uncover a previously undefined role of 3HB in promoting osteogenic differentiation of hBMSCs and highlight that the P(3HB-co-4HB) scaffold functions as a metabolically activated energetic material for bone regeneration.

overall_design: Human bone marrow mesenchymal stem cells (hBMSCs) were seeded onto culture plates and allocated into three groups, namely vehicle group (control), 3HB group, and LA group. In the control group, hBMSCs were treated with OM supplemented with DPBS (10 μl) only, while in the 3HB and LA groups, hBMSCs were respectively treated with OM supplemented with 1.0 mM of 3HB or LA. After 14 days of induction, cells from different groups were harvested and total RNA was extracted using a TRIzol total RNA extraction kit (TIANGEN, China). The RNA sequencing and analysis were performed.

first: Jian

last: Li

first: Zi-Xin

last: Peng

first: Xu

last: Zhang

first: Peng


title: Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase

city: Minneapolis

first: Aaron

middle: C

last: Goldstrohm

state: MN

address: 321 Church Street S.E.

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

summary: The sequence-specific RNA-binding protein Pumilio controls development of Drosophila; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells. We also used an improved RNA co-immunoprecipitation method to identify Pumilio bound mRNAs in Drosophila embryos. Integration of these datasets with the content of Pumilio binding motifs across the transcriptome revealed novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. Additionally, we identified the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pumilio-mediated repression, and observed concordant regulation of Pumilio:CCR4-NOT target mRNAs. Computational modeling revealed that Pumilio binding site location, number, density, and context are important determinants of regulation. Moreover, the content of optimal synonymous codons exhibits a striking functional relationship to Pumilio and CCR4-NOT regulation, indicating that the inherent translation efficiency and stability of the mRNA modulates their response to these trans-acting regulatory factors. Together, the results of this work provide new insights into the Pumilio regulatory network and mechanisms, and the parameters that influence the efficacy of Pumilio-mediated regulation.

overall_design: Differential gene expression was measured by performing RNA Seq using ClickSeq library generation on polyA selected RNAs isolated from Drosophila melanogaster DL1 cells. The effect of RNAi induced knockdown of Pumilio, Not1, or Pop2 were compared to negative control samples treated with dsRNA (non-targeting control) coresponding to e. coli LacZ gene. Three biological replicates were sequenced per RNAi condition.  Additionally, the Pumilio gene was knocked out in two clonal isolates of DL1 cells and the resulting changes in RNA levels were measured relative to the parental wild type DL1 cell line by ClickSeq.

first: Rebecca

last: Haugen

first: Catherine

last: Barnier

first: Nathan

last: Elrod

first: Hua

last: Luo

first: Madeline

last: Jensen

first: Ping

last: Ji

first: Craig

last: Smibert

first: Howard

last: Lipshitz

first: Eric

last: Wagner

first: P

last: Freddolino


title: Utilizing engineered endosymbionts to modulate primary macrophage function and attenuate tumor growth by shifting the tumor microenvironment

city: Livermore

first: Cody

middle: Scott

last: Madsen

state: California

address: 4000 East Avenue Bldg 411

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Lab

summary: Modulating gene expression in macrophages can be used to improve tissue regeneration and redirect tumor microenvironments (TME) toward positive therapeutic outcomes. We have developed Bacillus subtilis as an engineered endosymbiont (EES) that resides in the host cell cytoplasm and controls the fates of macrophages. Secretion of mammalian transcription factors (TFs) from B. subtilis that expresses listeriolysin O (LLO; allowing the EES to escape destruction by the macrophage) modulated expression of surface markers, cytokines and chemokines indicating functional changes in a macrophage/monocyte cell line. The engineered B. subtilis LLO TF strains were evaluated in murine bone marrow-derived macrophages (BMDMs) by flow cytometry, chemokine/cytokine profiling, metabolic assays and RNA-Seq. Secretion of TFs by the EES shifted BMDM gene expression, production of cytokine and chemokines and metabolic patterns indicating that the TF strains could guide primary macrophage function. Therefore, the ability of the TF strains to alter the TME was characterized in vivo, in a murine 4T1 orthotopic breast cancer model to assess therapeutic effects. The TF strains altered the TME by shifting immune cell composition and attenuating tumor growth. Additionally, multiple doses of the TF strains were well tolerated by the mice. The use of B. subtilis LLO TF strains as EES showed promise as a unique therapeutic approach for cancer immunotherapy. The uses of EES could be expanded to modulate other mammalian cells over a range of biomedical applications.

overall_design: To investigate the ability of the EES to influence primary macrophage function, we delivered two strains of B. subtilis LLO secreting pairs of transcription factors to direct the macrophage function. The populations of the primary macrophages that were influenced by the transcription factor secreting strains were compared to the populations stimulated by just the B. subtilis LLO strain, typical pro- and anti-inflammatory control stimuli and controls for sugar induced transcription within the bacteria in biological triplicate at 12 and 24 hours. Bulk RNA-seq was then performed to characterize genome wide gene expression shifts after exposure to stimuli.

first: Maryam

last: Sayadi

first: Christopher

last: Contag


title: CPSF6 regulates alternative polyadenylation and proliferation of cancer cell through phase separation

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

summary:
In order to explore the impact of phase separation of CPSF6 on APA, we identified the structural domains that affect its phase separation formation and performed mutations.
In addition, we also found that the phosphorylation of CPSF6 can also affect its phase separation effect, and identified key kinases. We performed IVT-SAPAS sequencing on both cases mentioned above.

overall_design: Compare the changes in APA length between IVT-SAPAS groups

first: Susu

last: Liu

first: Runze

last: Wu

first: Liutao

last: Chen


title: Transcriptomics of rat airway epithelial cells

city: guangzhou

first: jiashuo

last: zhang

address: 135 Xingang West Road, Guangzhou

institute: Sun Yat-sen University

summary: Rat airway epithelial cells were cultured at the air-liquid interface and their total RNA was extracted for transcriptomic sequence analysis.

overall_design: total samples = 15, and n = 5

first: Jiashuo

last: Zhang

first: Peibo

last: Li

first: Weiyang

last: Fan


title: Tryptophan as a miR team organizer prevents colon cancer liver metastasis [colon]

city: Louisville

first: Fangyi

last: Xu

address: 505 S Hancock street

department: BCC cancer center

institute: University of Louisville

summary:
Tryptophan treatment play a significant role in miR expression. We have characterized the miR expression network through miR-on-chip profiling of the mouse treated with or without tryptophan.
In this dataset, we include the expression data from mouse small intestine and colon tissue treated with or without tryptophan.

overall_design: C57BL/6 mice are randomly devided into two groups. Each group of mice (n=8) were respectively fed with Trp depleted diet (TrpD, 0% tryptophan, w/w) or a paired diet (PD, 1.2% tryptophan, w/w). Mice tissue were dissected and pooled as two samples for each treatment.

first: Xu

last: Fangyi

first: Waigel

last: Sabine


title: Tryptophan as a miR team organizer prevents colon cancer liver metastasis [small intestine]


title: Assessing the effect of Flubendazole on Jurkat T cells

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

summary: Human Junket T cells grown to confluence in 100 mm plates in complete medium were incubated with 10 µM Flubendazole (FLU) or vehicle for 4 h. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. 74004) with minor modification. Samples were submitted to the UNSW Ramaciotti Centre for sequencing and gene expression analysis was carried out.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Jurket T cells with and in the absence of FLU treatment.

first: Li

last: Yue

first: Corley

last: Susan

first: Khachigian

last: Levon


title: Development and Validation of a Comprehensive Analysis of the Competing Endogenous CircRNA/miRNA/mRNA Network for Identification of Immune-Related Therapeutic Targets in Esophageal Squamous Cell Carcinoma

city: Shanghai

first: Chu-Ting

last: Yu

address: No. 168, Changhai Road

institute: Changhai Hospital

summary: Esophageal squamous cell carcinoma (ESCC) immunotherapy exhibits limited efficacy, prompting the investigation of its molecular mechanisms. Circular RNAs (circRNAs) are believed to play a significant role in the development of the tumor microenvironment (TME) in ESCC, but their role in ceRNA regulation remains indeterminate. In this study, we identified the expression of mRNA, circRNA in four tumor samples and their pair normal samples noting their paired samples by high-throughput sequencing to validate the correlation analysis.

overall_design: Eight samples (including four tumor samples and paracancerous samples) were used to detect the differential gene expression. Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.

first: Chuting

first: Bo

last: Tian

first: Yanan

last: Pang

first: Yan

last: Bian

first: Siwei

last: Zhou

first: Meijuan

last: Hao

first: Ye

last: Gao

first: Luowei

last: Wang

first: Lei

last: Xin

first: Han

last: Lin

first: Xun