title: Effect of endurance training on expression signatures of mouse type I and type IIb myofibers

city: Beijing

first: Minghong

last: Leng

address: No.38, Xueyuan Road, Beijing, China

institute: Health Science Center

summary: Skeletal muscle myofibers, categorized into slow-twitch (type I) and fast-twitch (type II) fibers based on myosin heavy chain (MHC) isoforms, exhibit varying fatigue resistance and metabolic reliance. Type I myofibers are fatigue-resistant with high mitochondrial density and oxidative metabolism, while Type II myofibers fatigue quickly due to glycolytic metabolism and fewer mitochondria. Endurance training induces remodeling of myofiber and mitochondrial, increasing slow-twitch myofibers and enhancing mitochondrial oxidative capacity, improving muscle fitness. In our study, conducted using single-cell techniques, we delved deeply into the transcriptomic differences between type I and type IIb myofibers. In response to endurance training, type I myofibers exhibited heightened signals in essential adaptive responses, such as fatty acid oxidation, mitochondrial biogenesis, and protein synthesis, compared to type IIb myofibers. By analyzing untrained myofibers, we identified specific signaling pathways that explain the differences in their responses to endurance training. These findings provide nuanced insights into the molecular mechanisms governing endurance adaptations in fast and slow-twitch muscles, offering valuable guidance for tailored exercise routines and potential therapeutic interventions.

overall_design: Switching Mechanism At the 5' end of RNA Template-Sequencing (SMART-seq) of type I and type IIb myofibers isolated from soleus and extensor digitorum longus of endurance trained and untrained mice

first: Ming

last: Zheng


title: Tumour PSGL-1 suppresses macrophage phagocytosis via impeding LFA-1 activation

status: Public on Dec 31 2024

city: guangzhou

first: wang

middle: l

last: x

state: guangdong

address: zhongshan

department: immunity

country: China

institute: sysu

type: Expression profiling by high throughput sequencing

summary: To investigate the immune suppression of PSGL-1 on hematological tumour cells, we established PSGL-1 KO EL4 cell line with CRISPR-Cas9 technique, which is used to construct subcutaneous model of hematoma on mice. After inoculation, CD45 positive immune cells were sorted from resected tomour tissue and prepared for RNA-seq in two groups: vector EL4 tissue and PSGL-1 KO EL4 tissue. We then analyzed gene expression profiling using sequencing data to look for differences occurred inside TME.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for immune cells, derived from different subcutaneous tumour tissues.

first: Cheng

last: Zhong

first: Lixiang

last: Wang

first: Yujia

last: Liu

first: Chunliu

last: Huang

first: Jing

last: Liao

first: Zijin

last: Xia

first: Xinyu

first: Yiyi

last: Li

first: Xiumei

first: Chengzhou

last: Mao

first: Yongyi

last: Feng

first: Congzhou

last: Luo

first: Wenhao

last: Mai

first: Hongrui

last: Song

first: Yue

last: Sheng

first: Yingyi

last: He

first: Xiaolei

last: Wei

first: Hui

last: Zhang

first: Wei

last: Yi

first: Hong

last: Yuan

first: Jun

last: Chen


title: SET-9 and SET-26 impact transgenerational epigenetic inheritance and germline mortality through their PHD finger and SET domains [small RNA-seq]

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

country: USA

institute: Rutgers University

type: Non-coding RNA profiling by high throughput sequencing

summary: Transgenerational epigenetic inheritance (TEI), the transmission of epigenetic states between generations, has been observed in complex organisms ranging from plants to nematode worms, insects and mammals. One form of TEI that has been robustly studied is the inheritance of gene silencing. In Caenorhabditis elegans transgenerational gene silencing can be partitioned into three phases: the initiation of silencing, establishment of a heritable silencing signal within the parent individuals, and maintenance of this silencing signal within subsequent generations. Silencing involves nuclear and cytoplasmic components, and most genes involved in the process are linked to small RNA processing pathways. To date, two predicted histone methyltransferases have been implicated in the establishment of TEI, set-25 and set-32. Here, we demonstrate that the closely related paralogues set-9 and set-26 function in establishment and maintenance of TEI. We also identify a third related gene that lacks any predicted ordered domains; we name this gene intrinsically disordered protein-1 (idp-1). Strikingly, idp-1 also plays a role in establishment of TEI. SET-9 and SET-26 each contain a PHD finger and a SET domain. We show that the SET domains of SET-9 and SET-26 likely have no histone lysine methyltransferase activity, but that the PHD fingers bind trimethylated histone 3 lysine 4 (H3K4me3) in the absence of adjacent histone marks. We demonstrate that despite modelling data that suggests that set-9 and set-26 lack histone lysine methyltransferase activity, the function of both genes in TEI requires their PHD finger and SET domains. Our data confirm that the SET domain is functional and identifies three new chromatin factors required for epigenetic inheritance.

overall_design: small RNA-seq libaries were prepared from gonads dissected from adult hermaphrodite C. elegans strains that carry set-9, set-26, and set-9;set-26 mutations, as well as the wild type (N2) strain.

middle: G

first: Julie

middle: N

last: Ni

first: Alyson

last: Ash


title: Identification and Characterization of Human Retinal Stem-Like Cells with Regenerative Potential [bulk RNA-seq]

city: Wenzhou

first: Chenghao

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

summary: Human retinal stem cells (hRSCs) hold great promise in regenerative medicine due to their ability to directly differentiate into retinal cells. However, the characteristics and roles of hRSCs remain ambiguous. Here, we employed single-cell multi-omics profiles of human ciliary marginal zone (CMZ) of fetal retinas and human retinal organoids (hROs). We discovered a unique cell population of human retinal stem-like cells (hRSLCs) that specifically resides in the retinal tip and non-pigmented CMZ and possess a new regenerative lineage into neural retinal cells. Analysis of single cell and spatial transcriptomes show that the hRSLCs of hRO exhibit consistent characterization of cellular and molecular functions with fetal retinas. Functionally, several transcription factors were identified involved in the regulation of stemness from single cell RNA-seq and ATAC-seq data, and deficiency of gene MECOME in hRSLCs leds to impaired homeostasis and diminished retinal regeneration. Furthermore, transplantation of hRO-derived hRSLCs into retinal degeneration mice exhibit the high potential for retinal repair and improved visual function. Our work combines single cell multi-omics and organoid technologies to identify and comprehensively characterize a promising hRSLCs population in both human fetal retinas and organoid, opening up new avenues for potential therapy in retinal regeneration.

overall_design: Bulk RNA-seq for retinal organoids samples: Day 20 (three samples); Day 80 (three samples).

last: Liu


title: SET-9 and SET-26 impact transgenerational epigenetic inheritance and germline mortality through their PHD finger and SET domains

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

overall_design: Refer to individual Series


title: Identification and Characterization of Human Retinal Stem-Like Cells with Regenerative Potential

last: Li


title: Effect of Ginsdenoside Rb2 to brown adipose tissue

city: La Jolla

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Ginsenoside Rb2 is one of components in Panax ginseng, which has been traditionally used to treat metabolic diseases. In this study, we investigated the function of Rb2 in BAT by intraperitoneally injecting the Rb2 into mouse. To examine the systematic changes by Rb2 in BAT, we performed RNA sequencing, and analyzed DEG and pathways. Our analysis identified 727 genes significantly altered by Rb2 treatment. These genes were linked with BAT activation pathway such as adrenergic signaling, cAMP signaling, PKA signaling and lipolysis. Interestingly, adrb1 and adrb2 were upregulated by Rb2 treatment, while adrb3 was not, suggesting that Rb2 modulates BAT activation via specific adrenergic receptors. To confirm these findings, we conducted molecular experiment and found that Rb2 activates lipolysis via ß adrenergic receptor – cAMP – PKA signaling. Specifically, Rb2 enhanced the phosphorylation of HSL and PLIN, which are well known target of PKA. Our study provides a better understanding of the molecular mechanisms underlying the effects of Rb2 on BAT and may have implications for the development of novel therapeutics for metabolic disorders

overall_design:
To investigate the function of Rb2 in brown adipose tissue, we intraperitoneally injected the PBS or Rb2 into male wild-type C57Bl6/J mice for two weeks.
We harvested brown adipose tissues from injected mice and extracted RNA from three mice per each condition.
We performed RNA-seq and analyzed differentially expressed genes and related pathways between PBS and Rb2

first: Ye

middle: J

first: Sanghun

last: Lee

first: Junho

last: Kim

first: Su

middle: M

last: Jung

middle: S


title: FH enhances the therapeutic effect of PD-1 inhibitors on colorectal cancer by inhibiting the expression of PCSK9.

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed FH knockdown in colorectal cancer cells along with RNA sequencing. The expression profiling showed PCSK9 as a potential FH target and the conclusions were also verified in clinical samples.

overall_design: RNA sequencing in SW620 cell lines with si-Control or si-FH

first: H

first: L

last: Qin


title: Transcriptomic analysis of Col plants and wrky48 mutants subjected to high light, heat stress and their combination

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Plants growing in the field are subjected to high light intensities that are often accompanied by high temperatures. In this work, we analyzed transcriptomic responses of wild type Col plants and mutants defective in the transcription factor WRKY48 to understand why wrky48 mutants are more tolerant to the combination of high temperatures and high light stress. Our results indicate that jasmonic acid accumulation induced by the combination of high light and heat stress could repress WRKY48 expression, enabling the expression of acclimation genes to this stress combination.

overall_design: Arabidopsis thaliana wild-type Col-0 (var Columbia-0) and homozygous knockout mutants (Col-0 background) wrky48-1 (Salk_066438C) were grown in peat pellets (Jiffy-7; http://www.jiffygroup.com/) at 23°C under long-day growth conditions (12-h light from 7 AM to 7 PM; 50 μmol m−2 s−1/12-h dark from 7 PM to 7 AM). Individual high light stress (HL) and heat stress (HS), and combined HL and HS (HL+HS) were applied in parallel using 30-day-old Arabidopsis plants (wild-type Col-0 and wrky48-1). HL was applied by exposing plants to 900 µmol m−2 s−1 at 23 °C for 8 h. HS was applied by subjecting plants to 40 °C, 50 µmol m−2 s−1, for 8 h. HL+HS was performed by simultaneously subjecting plants to 900 µmol m−2 s−1 of light stress and 40°C for 8 h. Control (CT) plants were maintained at 50 µmol m−2 s−1 and 23°C throughout the entire experiment. All experiments were conducted during the light cycle, from 9 A.M. to 5 P.M., and were repeated at least three times with 45 plants per stress treatment and biological repeat. True leaves pooled from at least 20 different plants subjected to each of the control and stress treatments were used for each biological repeat for RNAseq analysis, and three biological repeats were performed. Total RNA was isolated using RNeasy plant mini kit (Qiagen) according to the manufacturer's instructions. RNA libraries for sequencing were prepared using standard Illumina protocols and RNA sequencing was performed using NovaSeq 6000 by Novogene co. Ltd (Cambridge, UK).

first: Damián

last: Balfagón

first: Lidia

last: Pascual

first: Karen

last: Halliday

first: Aurelio

last: Gómez-Cadenas

first: María

middle: A

last: Peláez-Vico

first: Ron

last: Mittler

first: Sara

middle: I

last: Zandalinas


title: A β-1,3/1,6-glucan from Durvillaea Antarctica enhances anti-tumor effects of immune checkpoint inhibitor antibodies II

city: Yantai

first: Yuting

last: Xu

address: No. 198, Binhai East Road

institute: Bohai Rim Advanced Research Institute for Drug Discovery

summary: Immunotherapy has emerged as a frontline approach in cancer management, aiming to enhance the adaptive immune response against tumors. However, its limited efficacy across a narrow range of tumor types necessitates the exploration of novel strategies that target innate immunity. Therapeutic modulation of pattern recognition receptors (PRRs) and innate immune cells holds promise in tumor eradication. β-glucan, a pathogen-associated molecular pattern (PAMP), acts as an immunostimulator, bridging the innate and adaptive immune responses. It exhibits low toxicity and high compatibility with various antitumor strategies. Plenty of clinical trials are ongoing to evaluate β-glucan-based cancer immunotherapy and shows promising clinical benefits across multiple cancer types. A soluble β-1,3/1,6-glucan with high purity from Durvillaea Antarctica (BG136) was reported previously by our group to exhibit pan antitumor effects alone as an immune stimulator. In current study, we proved the antitumor activity of BG136 in combination with anti-PD-1 antibodies in MC38 syngeneic tumor model in vivo. Integrated transcriptomic and metabolomic analyses suggest that BG136 enhances the antitumor immunity of anti-PD-1 antibodies by reprogramming tumor microenvironment to more proinflammatory status. There are more innate and adaptive immune cell infiltration and activation, enhanced lipid metabolism, decreased ascorbate and aldarate metabolism. These findings provide mechanistic insights supporting the potent antitumor efficacy of BG136 in combination with immune checkpoint inhibitor antibodies.

overall_design: In order to assess the in vivo antitumor efficacy of BG136, a highly purified soluble β-1,3/1,6-glucan extracted from Antarctic rhododendron, in combination with anti-PD-1 antibody, we developed a mouse MC38 syngeneic tumor model. Subsequently, tumor blocks from various treatment groups, comprising vector control, anti-PD-1 antibody monotherapy, and anti-PD-1 antibody combined with BG136, were collected for gene expression profiling analysis.

first: Qiaoling

last: Song

first: Shan

first: Lijuan

last: Wu

first: Jun

last: Zhao

first: Xiaonan

last: Zhang

first: Mingming

last: Zhou

first: Xinxin

first: Xiaohan

first: Chenyang

first: Jinbo

last: Yang


title: Response and recovery in the supraoptic nucleus of a desert adapted rodent under osmotic stress

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

overall_design: Animals were randomly assigned to three experimental groups: Control (access to water ad libitum), Dehydrated (water restriction 11 days), and Rehydration (water restriction 7 days followed by access to water ad libitum 3 days). Supraoptic nucleus tissue was extracted and sequenced.

middle: T

first: Nabil

last: Amor

first: Abdulaziz

last: Alagaili

first: Michael

middle: P

last: Greenwood

first: David

last: Murphy


title: FTO-mediated RNA m6A demethylation regulates aggressive behavior and inflammation of fibroblast-like synoviocytes

city: Guangzhou

first: Yu

last: Kuang

address: No.58 Zhongshan Er Road Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China)


title: Egg white-derived peptides decreased blood pressure via the competing endogenous RNA regulatory networks in female spontaneously hypertensive rats

city: Nanjing

first: Wang

last: Liao

state: Jiangsu

address: No.87 Dingjiaqiao, Hunan Road

institute: Southeast University

summary: Despite numerous studies reporting the effects and mechanisms of antihypertensive peptides including peptides derived from egg white proteins, the role of peptides in female hypertensive animal model is unknown. On the other hand, the role of epigenetic modulation by the peptide treatment has been rarely investigated. This study sought to investigate the effect of egg white protein hydrolysate (EWH) in female spontaneously hypertensive rats (SHRs) as well as to explore the underlying mechanisms from the perspectives of transcriptome and the profiles of non-coding RNAs. Young (12-14-week-old) female SHRs were orally administered with 250 mg/kg body weight (low-dose) or 1000 mg/kg body weight (high-dose) of EWH daily for 10 weeks. Blood pressure of the rats were monitored weekly. The miRNA  in the aorta were profiled by the high-throughput RNA-seq technique. Differentially expressed (DE) RNAs in the aorta were identified for the construction of the competing endogenous RNA (ceRNA) networks and key molecules were validated by qRT-PCR. The treatment of the high-dose EWH showed a significant effect in reducing blood pressure in female SHRs. Bioinformatic analyses revealed  90 DE-miRNAs.

overall_design: The miRNA in the aorta of female spontaneously hypertensive rats were profiled by the high-throughput RNA-seq technique.

first: Evan

middle: Y

last: Yu


title: Identification and Characterization of Human Retinal Stem-Like Cells with Regenerative Potential [snRNA-seq]

first: Chenghao

last: Li

overall_design: snRNA-seq for retinal organoids sample cultured for Day 60, Day 65, Day 70, Day 80, Day 90 and Day 100

first: Hui

last: Liu


title: Assessment of the effect of nutrition level on transcriptome of mammary gland structural components (parenchyma (PAR) and fat pad (MFP)) and liver in dairy calves mammary gland in dairy calves

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: The aim of this study was to identify changes in transcriptome of parenchyma (PAR),  fat pad (MFP) and liver in dairy calves. Our earlier results showed that feeding management regulates the dynamics of organ growth in preweaned heifers. We observed that a daily dose of 5.3 kg of milk replacer inhibits mammary gland development. Therefore, this research aims at evaluation of the influence of the nutritional level in the early life period of calves on the biological processes related to the development of the mammary gland through transcriptomic alterations.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  16 parenchyma, 16 fat pad and 16 liver samples was performed using the Illumina NovaSeq platform.

first: Tomasz

last: Szmatoła

first: Artur

last: Gurgul

first: Barbara

last: Niwińska


title: Transcriptome profile of fibroblast-like synoviocytes with FTO knockdown

summary: Fibroblast-like synoviocytes (FLS) are crucial in promoting articular inﬂammation and destruction in rheumatoid arthritis (RA). As the most abundant RNA modification, the function of m6A in RA FLS is still unclear. Here, we constructed FTO-knockdown FLS to explore the mechanism of FTO in regulating the aggressive behavior  of RA FLS.

overall_design: To investigate the function of FTO in RA FLS，FTO-knockdown FLS were established by shRNA-lentivirus infection. RNA sequencing was then performed to explore the specific downstream targets of FTO.

first: Ruiru

first: Jingnan

last: Wang


title: m6A modification profiles in RA FLS with FTO knockdown

summary: Fibroblast-like synoviocytes (FLS) harbour active migration, invasion, proliferation and decreased cell-contact inhibition, and served as  a crucial component in pathogenesis of rheumatoid arthritis. However, the mechanism underlying the aggressive behavior remain unclear. In this study, we established FTO-knockdown RA FLS to investigate the molecular mechanism.

overall_design: To explore the function of m6A in regulating the aggressive behavior of RA FLS, FTO was knockdown by infected lentivirus with shRNA. meRIP-seq was performed to analyze the alteration of m6A modification and identified the potential targets.


title: A β-1,3/1,6-glucan from Durvillaea Antarctica enhances anti-tumor effects of immune checkpoint inhibitor antibodies

first: Yuting

last: Xu

overall_design: In order to assess the in vivo antitumor efficacy of BG136, a highly purified soluble β-1,3/1,6-glucan extracted from Antarctic rhododendron, in combination with anti-PD-1 antibody, we developed a mouse MC38 syngeneic tumor model. Subsequently, tumor blocks from various treatment groups, comprising vector control and BG136 alone, were collected for gene expression profiling analysis.

first: Qiaoling

last: Song

first: Shan

first: Lijuan

last: Wu

first: Jun

last: Zhao

first: Xiaonan

last: Zhang

first: Mingming

last: Zhou

first: Xinxin

first: Xiaohan

first: Chenyang

first: Jinbo


title: Identification and validation of lipid metabolism gene FASN-associated miRNA in Wilms tumor

city: Jinan

first: Xiaoqing

state: Shandong

address: 324 Jingwu Street, Jinan, Shandong 250021, P.R. China

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: miRNA has been a research hotspot in recent years, and its scope of action is very wide, involving the regulation of cell proliferation, differentiation, apoptosis, and other biological behaviors. This study intends to explore the role of miRNA in the lipid metabolism and development of Wilms tumor (WT) by detecting and analyzing the differences in the expression profiles of miRNAs between the tumor and adjacent normal tissue. Gene detection was performed in tumor tissues and adjacent narmal tissues of 3 cases of WT to screen differentially expressed miRNAs (DEMs). According to our previous research, FASN, which participates in the lipid metabolism pathway, may be a target of WT. The starBase database was used to predict FASN-targeted miRNAs. The above two groups of miRNAs were intersected to obtain FASN-targeted DEMs, and then GO Ontology (GO) functional enrichment analysis of FASN-targeted DEMs was performed. Finally, the FASN-targeted DEMs were compared and further verified by qRT‒PCR. Through gene sequencing and differential analysis, 316 DEMs were obtained, including 150 upregulated and 166 downregulated miRNAs. The top ten DEMs were all downregulated. Fourteen miRNAs targeted by the lipid metabolism-related gene FASN were predicted by starBase. After intersection with the DEMs, three miRNAs were finally obtained, namely, miR-107, miR-27a-3p, and miR-335-5p. GO enrichment analysis was mainly concentrated in the Parkin-FBXW7-Cul1 ubiquitin ligase complex and response to prostaglandin E. Further experimental verification showed that miR-27a-3p was significantly correlated with WT (P=0.0018). Imbalanced expression of miRNAs may be involved in the occurrence and development of WT through lipid metabolism. The expression of miR-27a-3p is related to the malignant degree of WT, and it may become the target of diagnosis, prognosis, and treatment of WT in the later stage.

overall_design: Analyze the differential expression of miRNA in the tumors and adjacent tissues of three patients with wilms tumor.

first: Xiao

first: Guoqiang

last: Du

first: Wei


title: Elucidating the molecular pathology of DEPDC5 mutation induced mTOR-hyperactivation associated with epilepsy and autism spectrum disorder

city: Frankfurt am Main

first: Afsheen

last: Kumar

address: Theodor-Stern-Kai 7

country: Germany

institute: University Hospital Frankfurt am Main

summary: To observe the effects of DEPDC5-KO on the transcriptome, 3‟-mRNA analysis was performed

overall_design:
RNA was extracted from three biological replicates of D62-NTC, DEPDC5-2.1, and DEPDC5-2.2 with or without rapamycin progenitors and after 1 month of neuronal differentiation.
Comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1).

first: Mattson

last: Jones

first: Andreas

last: Geburtig-Chiocchetti


title: Tissue factor binds to and inhibits interferon-α receptor-1 signaling

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Tissue factor (TF), which is a member of the cytokine receptor family, promotes coagulation and coagulation-dependent inflammation. TF also exerts protective effects through unknown mechanisms. Here, we showed that TF binds to interferon-α receptor 1 (IFNAR1) and antagonizes its signaling, preventing spontaneous sterile inflammation and maintaining immune homeostasis. Structural modeling and direct binding studies revealed binding of the TF C-terminal fibronectin III domain to IFNAR1, which restricted the expression of interferon-stimulated genes (ISGs). Podocyte-specific loss of TF in mice (TFΔPOD) resulted in sterile renal inflammation, which was characterized by JAK/STAT signaling, proinflammatory cytokine expression, disrupted immune homeostasis, and glomerulopathy. Inhibiting IFNAR1 signaling or the loss of IFNAR1 expression in podocytes attenuated or prevented these effects in TFΔPOD mice, respectively. Intriguingly, in the heteromer, TF and IFNAR1 are both inactive, while dissociation of the TF-IFNAR1 heteromer promotes TF activity and IFNAR1 signaling. These data suggest that the TF-IFNAR1 heteromer is a new molecular switch that controls thrombo-inflammation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The aim of this study was to examine the impact of podocyte TF loss on kidney immune homeostasis. Initially, primary mouse podocytes carrying TFLoxP and TFΔPOD genotypes were cultured and differentiated for 14 days in vitro, followed by comprehensive analysis of their whole cell transcriptome. Subsequently, to delve into the repercussions of podocyte TF loss on kidney immune homeostasis, we conducted a screening of whole kidney RNA extracted from TFLoxP and TFΔPOD mice. Lastly, the regulatory role of human podocyte TF in IFNAR1 signaling was confirmed by simultaneously disrupting TF and IFNAR1 in immortalized human podocytes. This multifaceted approach sheds light on the intricate interplay between podocyte TF, immune responses, and kidney homeostasis.

first: Jayakumar

last: Manoharan

first: Berend

last: Isermann


title: CD9- Fibro-Adipose Progenitor Cells in Skeletal Muscle are associated with differences in intramuscular fat deposition content in different pig breeds

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

summary: Intramuscular fat (IMF) deposition not only holds implications for human health but also greatly impacts the taste and flavor of meat. In this study, Single-cell RNA sequencing was employed to analyze intramuscular vascular stem cells (IVSC) obtained from Guangdong small-ear spotted pig (GDSS) and Yorkshire differing in IMF content.

first: Xian

last: Tong

first: Yaosheng

last: Chen


title: Single-cell RNA-Sequencing data of peri-gastrulation embryoids

city: Ann Arbor

first: Shiyu

last: Sun

state: Michigan

address: G.G. Brown Building, 2350 Hayward St

department: Mechanical Engineering

institute: University of Michigan

summary: We analyzed scRNA-seq data in human pluripotent stem cells derived peri-gastrulation trilaminar embryonic disc (PTED) human embryo models with trilaminar embryonic disc-, amnion- and yolk sac-like structures.

overall_design: scRNA-seq was performed on dissociated cells from PTED embryoids at three timepoints (day 2, day 5, day 8) and endoderm differentiation promoted PTED embryoids on day 3 and day14.

first: Jianping

last: Fu


title: The mRNA Profiles of podocytes exposed to high glucose and AGEs

city: nanchang

first: jiao

last: wang

state: jiangxi

address: 17 Yongwai Street

department: Endocrinology and metabolism

institute: The First Affiliated Hospital of Nanchang University

summary: Podocyte dysfunction is considered as the main contributor to the development and progression of diabetic kidney disease(DKD).High glucose(HG)or advanced glycation end products (AGEs) can lead to podocyte dysfunction.To explore the the molecular mechanism of podocyte dysfunction, we screened the mRNA expression profiles of podocytes treated with HG(50mmol/L)and AGEs(400µg/mL) through transcriptomics.

overall_design: To investigate the differentially expressed genes in podocytes among control group, high glucose group, and AGEs group

first: Jiao

last: Wang

first: Honghong

last: Liu

first: Guanru

last: Yue

first: Jixiong

last: Xu


title: Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma

city: Rehovot

first: Ofir

last: Griess

address: Hetzel

country: Israel

institute: Weizmann Institute of Science

summary: Diffuse large B cell lymphomas and follicular lymphomas show recurrent mutations in epigenetic regulators; among these are loss-of-function mutations in KMT2D and gain-of-function mutations in EZH2. To systematically explore the effects of these mutations, alone or in combination, on the epigenetic landscape, we applied a single cell approach, based on Cytometry by Time of Flight (CyTOF), to probe a wide array of histone modifications. We show that mutant-EZH2 elicits extensive effects on the epigenome of lymphomas, beyond alterations to H3K27 methylations, and is dominant over KMT2D mutations. Utilizing the single-cell data, we present computational methods to measure epigenetic heterogeneity. We identify an unexpected characteristic of mutant-EZH2, but not KMT2D, in increasing heterogeneity, shedding light on a novel oncogenic mechanism mediated by this mutation. Finally, we present analysis to reveal potential cross talk between various modifications in the epigenetic network, validated by functional perturbations. Our work highlights novel roles for mutant-EZH2 in lymphomagenesis and establishes new concepts for measuring epigenetic heterogeneity and intra-chromatin connectivity in cancer cells

overall_design: MARS-seq (RNA) sequencing of cells lines - WT and CRISPR mutants. WT DLBCL cell line is OCI-Ly7 and over its background we generated mutants in either kmt2d, EZH2 GOF or a double mutant. We included three replicates of RNA from each cell line; 2m of cells were lysed and extracted for RNA with Nucleospin RNA kit, examined in tapestation and sequenced with Illumina NextSeq500

first: Noa

last: Furth

first: Nofar

last: Harpaz

first: Nicoletta

last: Di Bernardo

first: Tomer

last: Salame

first: Ioannis

last: Karagiannidis

first: Yusuke

last: Isshiki

first: Ari

last: Melnick

first: Wendy

last: Beguelin

first: Guy

last: Ron

first: Efrat

last: Shema


title: Histone methyltransferase Setd2 mitigates T cell-mediated autoimmunity by targeting Lpcat4-mediated phospholipid remodeling [IV]

city: shanghai

first: Yali

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: Purpose: RNA-seq analysis of gene expression in Th0 cells from wild-type and Setd2-CD4 cre mice. The goals of this study are to compared the gene expression between wildtype and Setd2-CD4 cre mice Th0 cells by RNA-seq analysise.

overall_design: Naive CD4+ t cells stimulate with αCD3/CD28 for two days to obtain Th0 cells and then subjected to RNA seq.

first: Xuetao

last: Cao


title: CircRNAs differentially expressed in brain metastases and primary lung cancer tissues of three pairs of non-small cell lung cancer patients with brain metastases

first: Yang

last: Daolu

address: 101 Longmian Road

institute: Nanjing Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We searched for three NSCLC patients with brain metastases in the First Affiliated Hospital of Nanjing Medical University. After obtaining informed consent, the lung cancer brain metastasis surgical specimens and lung carcinoma in situ puncture specimens were collected from the three patients. The histopathological characteristics were examined using hematoxylin and eosin (H&E) staining. We searched for three pairs of differentially expressed RNAs in brain metastasis tissues and lung carcinoma in situ tissues by ceRNA microarray.

overall_design: In the First Affiliated Hospital of Nanjing Medical University, we searched three patients with brain metastasis of non-small cell lung cancer, and obtained the primary lung cancer tissue and brain metastasis cancer tissue samples respectively. Differentially expressed RNAs in brain metastatic cancer tissue and lung primary cancer tissue of three patients were detected by high-throughput sequencing.

first: Daolu

last: Yang

first: Zhaoxia

last: Wang


title: Post-transcriptional characterization of the vertebrate aging brain sheds light on the origin of protein-transcript decoupling

city: Jena

first: Domenico

last: Di Fraia

address: Beutenbergstraße 11

institute: Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)

summary: Aging is associated with impaired proteostasis and reduced correlation between protein and mRNA levels. The mechanisms underlying such age-dependent alterations remain unclear. Here, we used the short-lived killifish Nothobranchius furzeri to define how aging affects the transcriptome, translatome and proteome of the vertebrate brain. Integrating these analyses with protein subcellular localization, solubility, and posttranslational modifications data we uncover that basic proteins, including ribosomal and RNA-binding proteins, progressively decrease with age. In contrast, abundant and long-lived proteins, including components of the mitochondrial respiratory chain, increase or remain stable despite a decrease in their mRNA levels. Chronic proteasome inhibition can induce some aging signatures in vivo, but it does not recapitulate the age-related protein-transcript decoupling. Instead, we find increased ribosome pausing in the aging brain reprograms the translation landscape accounting for age-dependent proteome alterations independent of transcription. These changes in protein biogenesis likely reduce availability of key protein complexes in older brains.

overall_design: Comparative analysis of transcriptome (RNA-seq)  of Nothobranchius furzeri brain after in-vivo proteasome inhibition

first: Antonio

last: Marino

first: Erika

last: Kelmer Sacramento

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

last: Ori


title: Transcriptional profiles of Tead1/4 Knockout and Unedited CT26 Cells

city: Kunming

first: Jiahong

last: Duan

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences

institute: Yunnan University

summary: The Hippo kinase cascade converges on the transcriptional effectors YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif), which regulate gene expression programs by interacting with the transcriptional enhanced associate domain (TEAD) family of transcription factors (TFs). As a key pathway in organ growth, tissue homeostasis, and regeneration, the YAP/TAZ-TEAD complex controls the transcription of genes crucial for replication, S-phase entry, and mitosis. To further elucidate the transcriptional regulatory network, we monitored the target genes of TEAD1 and TEAD4 using CUT&Tag and transcriptome sequencing.

overall_design: The samples in this study included normal CT26 unedited group and Tead1/4 knockout group. Each group contained four samples.

first: Yicheng

last: Ma

first: Chenggang

last: Zou


title: Single cell transcriptomic analysis of acute and early ART-treated HIV-1-infected CD4+T cells from a reservoir-marking humanized mouse model

city: New York City

first: Benjamin

state: New York

address: 1468 Madison Avenue

department: Infectious Disease

institute: Icahn School of Medicine at Mount Sinai

summary: Human immunodeficiency virus (HIV-1) infects and depletes CD4+ T helper cells and can persist within these cells in a latent state during treatment with effective antiretroviral therapy (ART).  A latent viral reservoir represents a major barrier to a cure for HIV-1 infection.  A longstanding obstacle to understanding the reservoir has been the inability to identify and characterize latent cells without activating them and disrupting their resting state.  To address this challenge, we have developed an HIV-1-induced lineage tracing (HILT) humanized mouse model that irreversibly marks HIV-infected cells.  The system employs a genetically encoded Cre-lox switch transduced into hematopoietic stem cells which are transplanted into immunodeficient mice.  Infection of CD4+ T cells in HILT mice with a Cre-expressing HIV clone irreversibly marks infected cells by switching dsRedExpress2 to EGFP expression, a phenotype that is maintained in cell harboring proviruses that are transcriptionally silent during ART.  Single cell RNA sequencing (scRNAseq) of infected T cells in the presence or absence of ART reveals HIV infection in diverse CD4+ T cell transcriptional lineages indicating that infected cells with active or suppressed transcription exist in many different T cell lineages.  We examined genetic pathways that are more frequently altered in infected cells when compared with uninfected bystander cells.   A comparison of pathways that are regulated in opposite directions in acute versus early ART-treated (persistent) infection identified EIF2α-, sirtuin-, and ILK-signaling pathways which contain known transcriptional regulators of HIV transcription.  Lastly, we find that resveratrol, a drug that impact sirtuin pathways can influence latency establishment in an acute infection setting.

overall_design: Utilizing the HIV-induced-lineage-tracing (HILT) system within humanized mice. Humanized mouse model was based on NOD-NSG Il2rgNULL (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ, NSG). 0-3 days old neonates of NSG mice were non-lethally irradiated (100 cGy) and injected intra-hepatically with 1 x 105 human cord blood-derived CD34+ cells (Stemcell Technologies, Cat# 70008) that had been transduced with pHR_SIN CS(RG)W. Mice were injected with NLCreI (RHPA) virus intravenously into the retro-orbital sinus. At 12 days post infection, some infected mice were placed under ART treatment to study latent population. Spleens were harvested and processed. The remaining cells were stained with antibodies described in engraftment panel and sorted using Fluorescence activated cell sorting (FACS). Cells were sorted to enrich for GFP+ infected cells. In mouse A1 GFP+ and dsRed+ cells were pooled and processed together as a mixed population. In acutely infected mice A2/A3, GFP+ HIV infected cells were pooled with unmarked cells, dsRed+ sample processing. Within T1 and T2, GFP+ latently infected cells were sorted into carrier wild type mouse B cells and processed. In T3 GFP+ and dsRed+ cells were pooled and processed together as a mixed population. Within, U1 and U2, Unmarked and dsRed+ bystander cells were sorted separately and sequenced separately. Processing was done using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 (CG000204 Rev D). For sequencing, batched libraries were run on an Illumina NovaSeq S4 flowcell (2 x 100 nt paired-end read length) with a target of 50,000-100,000 reads per cell.

first: Namita

last: Satija

first: Foramben

last: Patel

first: Donald

middle: V

last: Doanman

first: Gerrit

last: Schmidt

middle: K


title: Histone methyltransferase Setd2 mitigates T cell-mediated autoimmunity by targeting Lpcat4-mediated phospholipid remodeling [I]

first: Yali

last: Chen

summary: Purpose: RNA-seq analysis of gene expression in Th17 cells from wild-type and Setd2-CD4 cre mice. The goals of this study are to compared the gene expression between wildtype and Setd2-CD4 cre mice Th17 cells by RNA-seq analysise.

overall_design: Th17 cells were collected at 3 days under Th17 differentiation conditions, and then subjected to RNA seq.

first: Xuetao

last: Cao


title: Histone methyltransferase Setd2 mitigates T cell-mediated autoimmunity by targeting Lpcat4-mediated phospholipid remodeling [III]

summary: Purpose: RNA-seq analysis of gene expression patterns in Naïve t, Th0, Treg and Th17 cells of wild-type mice. The goals of this study are to compared the gene expression between Naïve T and other types Th cells by RNA-seq analysise.

overall_design: Naïve T cells were CD4+ T cells directly selected from the spleen. Th0 cells were stimulated with αCD3/CD28 for three days. Th17 cells were collected at 3 days under Th17 differentiation conditions, Treg cells were collected at 3 days under Treg differentiation conditions,and then subjected to RNA seq.


title: Histone methyltransferase Setd2 mitigates T cell-mediated autoimmunity by targeting Lpcat4-mediated phospholipid remodeling [II]

summary: Purpose: RNA-seq analysis of gene expression in Treg cells from wild-type and Setd2-CD4 cre mice. The goals of this study are to compared the gene expression between wildtype and Setd2-CD4 cre mice Treg cells by RNA-seq analysise.

overall_design: Treg cells were collected at 3 days under Treg differentiation conditions, and then subjected to RNA seq.


title: Altered lncRNA involoved in the development  of lupuis nephritis

city: Changsha

first: Yang

last: Jia

address: renmin road No.139

institute: the second xiangya hospital of central south university

summary: As a newly discovered type of long non-coding RNAs (lncRNAs), we aimed to assess the expression profiles of lncRNAs in children with lupus nephritis (LN) by microarray analysis. 6 venous blood samples were obtained from LN patients and controls for this study. Sequencing of small RNAs was performed to evaluate the expression profiles of lncRNAs and mRNAs in these two groups.  We identified 502 altered lncRNAs and 291 mRNAs in LN patients compared to healthy controls. A coding-non-coding gene co-expression (CNC) network profile based on eight validated altered lncRNAs as well as 258 interacted mRNAs. Following by Gene Ontology analysis, the target genes of the lncRNAs were most enriched in neutrophil degranulation, secretory granule, and catalytic activity. In addition, Kyoto Encyclopedia of Genes and Genomes pathway analysis reported that the target genes were most enriched in NOD-like receptor signaling pathway and Th1/Th2/Th17 significant pathway. The present study showed that lncRNAs were significantly altered in children with LN compared to healthy controls and may play a critical role in the development and pathogenesis of LN.

overall_design: To assess the expression profiles of  lncRNAs and mRNAs in children with lupus nephritis (LN), we use PBMC from LN children

first: Xiaochuan

last: Wu


title: RNA Immunoprecipitation and Sequencing of Isolated RNAs (RIP-SIR) Identifies Endogenous miRNA-Target Interactions

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: MicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression in species ranging from plants to mammals. Unraveling the complex networks of miRNA-mediated regulation of gene expression requires the ability to identify the mRNA targets of individual miRNAs in native cellular contexts. Here we describe RIP-SIR, an unbiased genome-wide method for identifying interactions between endogenous miRNAs and their targets in almost any tissue or cell type.

overall_design: Experimental methods for identifying the targets of individual miRNAs typically require expression of exogenous, tagged miRNAs which may perturb native stoichiometry, are limited to the study of cultured cells and cannot be used to monitor miRNA-mediated regulation during processes such as differentiation or disease progression. Additional methods such as Argonaute High-Throughput Sequencing of RNAs isolated by CrossLinking and ImmunoPrecipitation (Ago HITS-CLIP) and CrossLinking And Sequencing of Hybrids (CLASH), cannot match individual miRNAs to their targets or rely upon very low efficiency intramolecular ligation, respectively 9,10. To overcome the limitations of current methods for miRNA target identification, we developed RNA ImmunoPrecipitation and Sequencing of Isolated RNAs (RIP-SIR) and demonstrate that RIP-SIR identifys which miRNAs are bound to individual transcripts in lung tissues from both healthy mice and those bearing late-stage pulmonary adenocarcinomas.

first: Julie

last: Wells

first: Anuj

last: Srivastava

first: Richard

last: Maser

first: Rupesh

last: Kesharwani

first: Vishal

last: Kumar Sarsani

first: Sandra

middle: L

last: Daigle

first: Ryan

last: Lynch

first: Heidi

last: Munger

first: Rosalinda

last: Doty

first: Ruth

last: Saxl

first: Carol

last: Bult


title: Effect of methionine restriction on gene expression of non-KMT2A-rearranged NALM-6 and KMT2A-rearranged SEM BCP-ALL cell lines

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Current intensive chemotherapy regimens have improved overall survival in pediatric acute lymphoblastic leukemia but fail to cure some high-risk patient subgroups. While exploring amino acid depletion strategies, we observed that KMT2A-rearranged (KMT2A-r) leukemia, an aggressive subset with a dismal prognosis, is particularly vulnerable to perturbations of the methionine cycle. We demonstrated that this methionine dependency is primarily driven by an increased need for S-adenosylmethionine to maintain the hypermethylated state of KMT2A-r leukemias. Important pro-survival KMT2A-r target genes are repressed under methionine restriction, which, combined with other downstream metabolic changes, results in rapid cell death. FIDAS-5, an orally active methionine adenosyltransferase 2A (MAT2A) inhibitor, successfully impaired leukemia progression in patient-derived xenograft models, and a high-throughput drug screen revealed a strong synergy between MAT2A inhibition and histone deacetylase inhibitors. Our results identified the methionine cycle as a targetable vulnerability in KMT2A-r leukemia, which may increase the efficacy of epigenetic targeting agents.

overall_design: To investigate the effect of methionine restriction on KMT2A-r versus non-KMT2A-r leukemias, we performed gene expression profiling analysis using triplicate samples of RNA-seq data of non-KMT2a-r BCP-ALL cell line NALM-6 and KMT2A-r cell line SEM after 24-hours complete methionine restriction.

first: Trisha

last: Tee

first: Laurens

last: van der Meer

last: van Leeuwen


title: Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and HFD-induced adipose hypertrophy.

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young Dr.

department: Pathology & Laboratory Medicine

institute: University of California, Los Angeles

summary:
To analyze the contribution of dietary PUFAs and adipocyte LPCAT3 expression in modulating the transcriptome of murine inguinal white adipose tissue during adipocyte hypertrophy.
We performed bulk RNA sequencing with a two-factor experimental design. WT and AdL3KO mice were fed an omega-6 enriched high-fat diet (60% Calories from fat) for 0 weeks (standard chow from weaning), 1 week, 5 weeks, or 10 weeks

overall_design: Comparative gene expression profiling analysis of iWAT from WT and AdL3KO mice on an omega-6 enriched high-fat diet (60% Calories from fat) for 0 weeks (standard chow from weaning), 1 week, 5 weeks, or 10 weeks

first: Alexander

middle: H

last: Bedard


title: Single cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation

city: Pittsburgh

first: Kathy

last: Shair

state: PA

address: 5117 Centre Avenue

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

summary: The HK1-EBV cell line is a human nasopharyngeal carcinoma cell line (RRID:CVCL_7084) infected in vitro with recombinant Epstein-Barr virus (EBV) Akata strain expressing EGFP and neoR inserted into the BXLF1 locus (PMIDs: 16611410). This cell line has been authenticated to be free of HeLa contaminants (PMIDs: 18196576; 24991015). We used bulk RNA sequencing techniques to analyze these cell lines reactivated at the air liquid interface (ALI) in a 3D cell culture model for ALI-induced EBV reactivation.

overall_design: Cells were cultured at the air-liquid interface (ALI) to induce EBV reactivation. N-terminally tagged LMP1 China 1 strain (HA Ch1) and IRES-EGFP (control) expressed from pBabe-puro vectors were stably introduced by retrovirus transduction. ALI cultures were collected on Day 0,2, and 4 post-lifting.

first: Alan

last: Bäckerholm

first: Shweta

last: Kitchloo


title: Single Cell RNA Sequencing of Primary Nasopharyngeal Organotypic Rafts infected with Epstein-Barr virus (EBV)

summary: The EBV infects nasopharyngeal cells. Infection program can be lytic or latent. Latent EBV infection is associated with the development of nasopharyngeal carcinoma. This study aims to elucidate the preneoplastic mechanisms of EBV in nasopharyngeal cells via singel cell RNA sequencing.

overall_design: Nasopharyngeal primary cells were cultured in a 3D cell culture model (organotypic rafts). Rafts were subjected to EBV infection (4 days post-rafting) by co-culture with anti-hIgG reactivated Akata21 Burkitt lymphoma cells infected with EBV according to PMID: 35434197. Rafts were collected, cells were filtered, viable single cells were counted, and subjected to single cell RNA library construction and sequencing.


title: Genes regulated by BRD3 in LPS-primed THP1 monocytes

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

summary: To screen the genes and pathways regulated by BRD3 in the THP1 monocytes induced by LPS, THP1 monocytes were transfected by BRD3shRNA and then treated by LPS for 3 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP1 monocytes and BRD3 shRNA with or without LPS treatment..

first: Daolin

last: Tang


title: Transcriptional responses to SAMD9 overexpression in A549 cells

city: St. Louis

first: Gaopeng

last: Hou

state: MO

address: McDonnell Pediatric Research Building, Rm 9220

department: molecular microbiology

institute: Washinton University inSt. Louis

summary: The goal of this study is to use RNA-sequencing to profile the transcriptional changes in A549 cells with SAMD9 overexpression by plasmid transfection. Specifically, we were interested in determining the interferons and chemokines induced by SAMD9 overexpression. We observed that each of the type III interferons and several pro-inflammatory cytokines such as CCL5 and CXCL10 were among the top induced genes following SAMD9 overexpression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for empty vector and SAMD9-Myc-DDK transfected A549 cells

first: G

first: S

last: Ding


title: Expression data from pairwise non-tumor and tumor  liver of -MYC and C-MYC/REG3A transgenic mice

city: VILLEJUIF

first: Nicolas

middle: Benoni

last: Moniaux

address: 12 Avenue Paul Vaillant Couturier

country: France

institute: INSERM

summary: Antimicrobial proteins of the REG3 family represent, like a wide variety of C-type lectins to which they belong, the first line of protection against infections and transformed cells. Their expression is inducible, particularly in response to inflammation, making their role in cancer biology less clear and controversial, as an immune-inflammation background may pre-exist or co-exist. We show that REG3A presents a suppressive role of REG3A in hepatocellular carcinoma (HCC) in a mouse models of HCC driven by c-MYC. By comparing the transcriptional profiles of liver tumors from MYC-REG3A-TG mice with those from MYC-TG mice, we found that MYC-REG3A tumors belonged to the S3 and G5 molecular subclasses of the human HCC classification proposed by Hoshida et al. and Boyault et al., respectively, subclasses that concentrate well-differentiated and CTNNB1-mutated HCCs. Tumors from MYC-TG mice exhibited features of S1 and G2/G3 subclasses. Results of the GSEA analysis indicate marked differential gene expression profiles. MYC-REG3A tumors and adjacent liver are enriched in metabolic pathways including bile acid, xenobiotic, and fatty acid metabolism, oxidative phosphorylation, and activation of Wnt/β-catenin signaling, whereas transcriptional reprogramming of MYC-TG mouse livers resulted in activation of cell cycle-, inflammation-, and glycolysis-related pathways as expected.

overall_design: Pairwise non-tumor and tumor liver tissues from 4 C-MYC and 4 C-MYC/REG3A transgenice mice were analysed

first: Jamila

last: Faivre


title: Bulk-RNA Sequencing of Nasopharyngeal Carcinoma Cell Lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation


title: Bulk-RNA and single-cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation

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

overall_design: Refer to individual Series


title: MOF-mediated PRDX1 acetylation regulates LPS-induced macrophage activation.

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Macrophages respond to environmental cues in a plastic manner and play a crucial role in host defense, inﬂammation, and tissue homeostasis. Macrophage activation undergoes metabolic and transcriptomic reprogramming to adapt and tailor an appropriate response, regulating inﬂammation. Reactive oxygen species (ROS) have been shown to play a pivotal role in macrophage activation. Nevertheless, the detailed molecular mechanism of how initial redox signals direct macrophage activation is not fully elucidated. Here, we uncover an unconventional role for histone acetyltransferase MOF (also known as KAT8) in regulating LPS-induced macrophage activation via modulating the acetylation of peroxiredoxin 1 (PRDX1), an H2O2 scavenger. We demonstrate that PRDX1 is a novel substrate of MOF and identify the major MOF-mediated acetylation site at lysine 197. K197 acetylation of PRDX1 (K197ac PRDX1) is dynamic and reversely regulated by HDAC6 or SIRT2. We observe that this acetylation is readily diminished in the immediate response to LPS. We demonstrate that K197ac PRDX1 fine-tunes its peroxidase activity, leading to the modulation of intracellular ROS levels in early response to LPS stimulation. Moreover, K197ac PRDX1 specifically regulates ERK1/2 phosphorylation, thereby modulating glycolytic metabolism in inflammatory macrophages. Consequently, K197ac PRDX1 tunes the expression and production of the proinflammatory cytokine, IL-6. Taken together, our findings describe a novel signaling module, MOF-PRDX1-ERK, which regulates LPS-induced macrophage activation at the metabolic and transcriptional levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT (shCTRL) and MOF depletion (shMOF Knockdown) in mouse bone-marrow derived macrophage.

first: Hui-Ru

last: Chen


title: monocyte reprogramming by oxLDL

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We have performed analyses of murine primary bone marrow derived monocytes challenged with either PBS or oxLDL.  oxLDL selectively enhances growth and adhesion potential of monocytes. Purified bone marrow monocytes were treated with PBS or 20 microgram/ml oxLDL for a five day period, and cells were harvested for scRNAseq analyses.

overall_design: WT murine monocytes were treated with either PBS, 10 microg/ml oxLDL for a five day period

first: Shuo

last: Geng

first: Ziyue

last: Yi


title: RNA-Seq analysis HDAC9 knockdown effect on vascular smooth muscle cells

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

summary: Vascular smooth muscle cells (VSMCs) phenotype switch has been thought to be critical to the development of thoracic aneurysm/dissection. To investigate the function HDAC9 in the regulation of VSMCs phenotype switch, we used siRNA knockdown of HDAC9 in human aortic smooth muscle cells (HASMC)we established Human aortic smooth muscle cells (HASMCs).

overall_design: HASMCs were transfected with  siHDAC9 or control (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Zhiqiao

last: Dang

first: Wenqian

last: Yu


title: Schisandrin C Regulates Obesity through CD36, CYP7A1 and CYP7B1 in High Fat Diet induced Obese Mice

city: Goyang

first: Hee-sung

last: Chae

state: Gyeonggi-do

address: Dongguk-ro 32

department: Department of pharmacy

country: South Korea

institute: Dongguk university

summary: Using the Illumina high-throughput sequencing platform, we conducted transcriptional profiling on liver tissues of C57BL/6 mice that were treated with a high-fat diet and administered Schisandrin C, simvastatin, or both. We analyzed the resulting transcript data to determine differential gene expression at the transcript level.

overall_design: We examined mRNA levels in the liver tissues of C57BL/6 mice that were treated with Schisandrin C, simvastatin, or a combination of Schisandrin C and simvastatin, and fed a high-fat diet.

first: Hee-Sung

first: Dong-Yeop

last: Kim

first: Byoung

last: You

first: Pisey

last: Pel

first: Young-Mi

first: Gyeoung-Jin

last: Kang

first: Chang

last: Lee

first: Young

last: Choi

first: Young-Won

last: Chin


title: Transcriptional regulation of microglia priming by IRF7, IRF9 and SMAD3 in accelerated aging mice [ATAC-seq]

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

institute: University Medical Center Groningen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Microglia are the tissue resident macrophages of the central nervous system (CNS). Dysregulation of inflammatory processes in the CNS is associated with aging, and neurodegenerative diseases, where microglia acquire a sensitized, or primed, phenotype, which is characterized by an increased inflammatory phenotype and an exaggerated reactivity to immune challenges. Transcriptomic profiling of microglia in different neurodegenerative disease and aging mouse models identified a common, primed, gene expression signature. However, the transcriptional mechanisms that mediate microglia priming still remains unclear. In DNA repair deficient (Ercc1Δ/ko) mice, microglia acquire a profound primed phenotype and by integrating RNA-seq and ATAC-seq data of Ercc1Δ/ko microglia, we identified transcription factors IRF7, IRF9 and SMAD3 as possible core regulators of microglia priming. Our data suggest that increased IRF7/IRF9 activity and decreased SMAD3 activity might be important for microglia to acquire a primed gene signature. This study provides insight in the transcriptomic regulation of primed microglia, which are implicated in aging and neurodegenerative diseases.

overall_design: ATAC sequencing analysis of FACS-isolated microglia from whole brains of Ercc1 KO and control mice at different ages (6-, 12-week-old). N =  2 per condition.

first: Inge

middle: R

last: Holtman

first: Susanne

last: Kooistra

first: Vasilis

last: Siozos

first: Evelyn

last: Wesseling

first: Erik

middle: W

last: Boddeke

first: Bart

last: Eggen


title: Transcriptional regulation of microglia priming by IRF7, IRF9 and SMAD3 in accelerated aging mice


title: Transcriptional regulation of microglia priming by IRF7, IRF9 and SMAD3 in accelerated aging mice [RNA-seq]

overall_design: Bulk RNA sequencing analysis of FACS-isolated microglia from whole brains of Ercc1 KO and control mice at different ages (6-, 12-week-old). N =  4 per condition.

middle: J


title: Zfp362 potentiates inflammatory T cell responses independent of Th17 cell differentiation

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

institute: HCI - Helmholtz Centre for Infection Research

summary: Th17 cells play an important role for mucosal barrier integrity and pathogen clearance, but also have been implicated in inflammatory and autoimmune disorders. Recently, we had described the DNA methylation profile of Th17 cells, and identified Zinc finger protein (Zfp)362 among the genes being uniquely demethylated in Th17 cells (Yang et al., DOI: 10.1093/nar/gkv014 ). Here, we prepared nuclei from CD4+ T cells deficient in Zfp362 (CD4creZfp362flox/flox mice) or CD4+ T cells capable to express Zfp362 (Zfp362flox/flox mice), subjected them to single-nucleus RNA-sequencing (snRNA-seq) and analyzed the influence of Zfp362 on the transcriptome.

overall_design: Cells from colon and small intestine were prepared from the tissue of seven Zfp362flox/flox mice or CD4creZfp362flox/flox mice  and CD8a-CD11c-CD45R-F4/80-CD4+CD44+CD62L- effector T cells isolated by Fluorescence-activated cell sorting (FACS). Nuclei from sorted cells were subjected to a droplet-based library preparation technique (10x Genomics). The resulting libraries were sequenced on a Novaseq 6000 (Illumina).

last: Herppich

first: Lisa

last: Hoenicke

first: Fabian

last: Kern

first: Andreas

last: Keller

first: Stefan

last: Floess

first: Jochen

last: Huehn


title: Effect of gallic acid on gene expression during sepsis-induced liver injury in mice

city: Hangzhou

first: Xiao

last: Yan

address: No.2318 Yuhangtang Road

institute: Hangzhou Normal University

summary: Our study helps to understand the molecular pathogenesis of gallic acid-mediated effects on sepsis-related injury in C57BL/6 mice and identifiy genes and pathways that may be potential therapeutic targets for gallic acid treatment.

overall_design: Hepatic mRNA profiles in gallic acid or vehicle-treated C57BL/6J mice after cecal ligation and puncture (CLP)


title: Overexpression of RNA deaminase ADAR2 in Th17 cells

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: ADAR2 is induced upon T cell activation and its immunological function is not known. Here, we performed RNA-seq on control and Th17 cells overexpressing wildtype or catalytic dead ADAR2 to identify A-to-I edited transcripts that are targets of ADAR2.

overall_design: Cultured cells from two independent wildtype mice were used. Results of ADAR2 overexpressed (ADAR2_WT) or enzymatic dead (ADAR2_E396A) Th17 cells were compared to Th17 cells from the same donor transduced with the MSCV empty vector.

first: Shengyun

last: Ma

first: Yajing

last: Hao

middle: M


title: Piezoeletric Cold Atmospheric Plasma Induces Cancer Cell Death and Disrupts Cancer Cell Survival in Hepatocellular Carcinoma through Multi-pathway Regulation

city: Beijing

first: xinyu

last: mang

address: Dongdan Three

institute: Peking Union Medical College,

summary:
To explore whether Piezo-CAP induced apoptosis and autophagy through inhibiting multiple cancer survival pathways together of human hepatocellular carcinoma cells in vitro and in vivo.
RNA-sequence (RNA-seq), Western blot and quantitative real-time PCR (qRT-PCR) were utilized to investigate the mechanism of Piezo-CAP treatment HCC cells.

overall_design: RNA sequencing (RNA-seq) was performed to detect the mRNA expression profiles of Piezo-CAP treated liver hepatocellular carcinoma (LIHC) cells using the HiSeq3000 System (Illumina, USA).

first: Yanhong

last: Wang

first: Xinyu

last: Mang

first: Danni

last: Li

first: Yiliang

last: Chen

first: Zhenyu

last: Cai

first: Fei

last: Tan


title: Knockdown of RNA deaminase ADAR2 in Th17 cells

summary: ADAR2 is induced upon T cell activation and its immunological function is not known. Here, we performed RNA-seq on Cas9+ control and Th17 cells expressing the PSIN empty vector control or guide RNAs against the ATG start codon or ADAR2 to identify ADAR2 dependent A-to-I edited transcripts.

overall_design: Cultured cells from two independent wildtype mice were used. Results of ADAR2 knockdown (sgAdarb1) Th17 cells were compared to Th17 cells from the same donor transduced with the PSIN empty vector.


title: Effect of Dectin-1 and Fcgr2b on IVIg mediated reprogramming of monocytes

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

summary:
To investigate the role of Dectin-1 and FcgRIIb on monocytes as signaling hubs for IVIg
Immunoglobulin G (IgG) antibodies are major drivers of inflammation during infectious and autoimmune diseases. In pooled serum IgG (IVIg), however, antibodies have a potent immunomodulatory and anti-inflammatory activity, but how this is mediated is unclear. We studied IgG-dependent initiation of resolution of inflammation in cytokine- and autoantibody-driven models of rheumatoid arthritis and found IVIg sialylation inhibited joint inflammation while inhibition of osteoclastogenesis was sialic acid-independent. Instead, IVIg-dependent inhibition of osteoclastogenesis was abrogated in mice lacking receptors Dectin-1 or FcgRIIb. Atomistic molecular dynamics simulations and super-resolution microscopy revealed that Dectin-1 promoted FcgRIIb membrane conformations that allowed productive IgG binding and enhanced interactions with mouse and human IgG subclasses. IVIg reprogrammed monocytes via FcgRIIb-dependent signaling that required Dectin-1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for in vivo IVIg primed monocytes sorted from splenocytes of C57BL/6, Dectin-1 -/- and FcgRIIb-/- mice, isolated via Cell sorting; 3 independent mice per group

first: Michaela

last: Seeling

first: Falk

last: Nimmerjahn

first: Meik

last: Kunz


title: Poly-Adenylation Lengthening of Short RNAs for Simultaneous Short and Long Nanopore Sequencing (PALS-NS)

city: Albuquerque

first: Christos

last: Argyropoulos

state: New Mexico

address: 1 University of New Mexico MSC 04-2785

department: Internal Medicine

institute: University of New Mexico

summary: Sequencing of long coding RNAs informs about the abundance and the novelty in the transcriptome, while sequencing of short coding RNAs (e.g., microRNAs) or long non-coding RNAs informs about the epigenetic regulation of the transcriptome. Currently, each of these goals is addressed by separate sequencing experiments given the different physical characteristics of RNA species from biological samples. Sequencing of both short and long RNAs from the same experimental run has not been reported for long-read Nanopore sequencing to date and only recently has been achieved for short-read (Illumina) methods. We propose a library preparation method capable of simultaneously profiling short and long RNA reads in the same library on the Nanopore platform and provide the relevant bioinformatics workflows to support the goals of RNA quantification. Using a variety of synthetic samples we demonstrate that the proposed method can simultaneously detect short and long RNAs in a manner that is linear over 5 orders of magnitude for RNA abundance and three orders of magnitude for RNA length. In biological samples the proposed method is capable of profiling a wider variety of short and long non-coding RNAs when compared against the existing Smart-seq protocols for Illumina and Nanopore sequencing.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Two by Two factorial design testing single tube polyadenylation reactions to extend the scope of long-read (Nanopore) sequencing to short (e.g. microRNA) and long (coding and non-coding) experiments

first: Morgan

last: MacKenzie

first: Susan

last: Tigert

first: Debbie

last: Lovato

first: Kamyar

last: Zahedi

first: Sharon

last: Barone

first: Marybeth

last: Brooks

first: Manoocher

last: Soleimani

first: Hamza

last: Mir


title: Dynamics of γδ TCR repertoire during the de-differentiation and treatment course of thyroid cancer [human scRNA]

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Although the de-differentiation process of thyroid cancer has been studied, it remains unclear how T cell antigen receptor (TCR) dynamically changes during the cancer progression and treatment. Here we characterized the γδ TCR repertoire along the de-differentiation of thyroid cancers cross-sectionally and investigated the longitudinal changes of TCR components over time in thyroid cancer patients receiving different treatment. We found that better differentiated status was significantly related to greater diversity and lower clonality. Expanded TCRs show enhanced convergent recombination and improved antigen-driven anti-tumor immune responses. The longitudinal study suggested that post-radiotherapeutic immunotherapy led to favorable clinical outcome, which was attributed to the appearance and expansion of neo clonotypes and was validated by scRNA-seq data and murine model experiment. These findings provided a novel understanding in the progression of thyroid cancer and highlighted the role of γδ T cells in anti-tumor immunity.

overall_design:
We dissociated the pre- and post-treatment tumor tissue on ATC patient and applied single-cell RNA-sequencing (scRNA-seq).
***Raw data for human samples have been submitted to China's Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa/) with BioProject Accession: PRJCA014738***

first: Han

last: Luo

first: Qing

last: Hao


title: LINC00261 Suppresses Epithelial-Mesenchymal Transition and Metastatic Potential of Colorectal Cancer by Down-regulating the MeCP2-ZEB1 Feedback Loop

city: Guangzhou

first: Yuyi

last: Huang

address: Changgang Street

institute: The Second Affiliated Hospital of Guangzhou Medical University

summary: Accumulating evidence suggests that epithelial-mesenchymal transition (EMT) contributes to metastasis, a major cause of death in patients with colorectal cancer (CRC). MeCP2 (methyl CpG binding protein 2), a key modulator for initiating gene transcription, plays a pivotal role in EMT, but its upstream signaling pathways are poorly understood. We collected 137 colorectal cancer patients’ samples, including tumor tissues (n=137), adjacent normal tissues (n=137) and liver metastases (n=11). Three pairs of colorectal cancer cell lines were sequenced to identify high abundance of lincRNAs in primary tumor tissues. Two independent experiments (electrophoretic mobility shift assay and RNA immunoprecipitation assay) were used to characterize the interaction between LINC00261 and MeCP2. Subsequently, the effects of LINC00261 on phosphorylation of MeCP2 and promotion of the MeCP2-ZEB1 feedback were examined. Consequently long intergenic non-protein coding RNA 261 (LINC00261) was down-regulated in highly metastatic CRC cells and liver metastases from patients with CRC. Down-regulating LINC00261 promoted the expression of EMT markers and increased the invasive and migratory properties of multiple CRC cell lines. Furthermore, knocking down LINC00261 increased colon-derived liver metastasis in an orthotopic CRC model and promoted distant metastatic colonization in a lung metastasis model. Mechanistic studies revealed that LINC00261 interacted with MeCP2 and stabilized it in the nucleus by inhibiting Ser80 phosphorylation Interestingly, ZEB1 could re-modulate MeCP2 expression by binding to the MeCP2 promoter, and they formed a positive feedback loop consequently. In contrast, the lower LINC00261 expression in CRC samples correlated with reduced E-cadherin and membrane β-catenin levels, and was associated with shorter overall survival. Taken together, LINC00261 suppresses EMT and CRC cells’ metastatic potential by negatively regulating the MeCP2-ZEB1 feedback loop; LINC00261’s loss in metastatic tissues may be a potential prognostic marker of aggressive disease.

overall_design: wild type colorectal cancer cells comparing with knockdown colorectal cancer cells

first: Kang

last: Wu

first: Xiaoli

last: Wei

first: Yuewen

first: Jinduan

last: Lin

first: Zhaogang

last: Yang

first: Yifan

last: Wang

first: Shiyan

last: Dong

first: Weiye

last: Deng

first: Yan

first: Wenxuan

last: Zheng

first: Wen

last: Jiang

first: Song

first: Xuefeng

last: Li


title: β-catenin mediates endodermal commitment of human ES cells via distinct transactivation functions

city: SHATIN

first: XUN

last: MA

state: NT

address: Rm105, Area 39, CUHK

country: Hong Kong

institute: CUHK

summary: Activation of Wnt/β-catenin signaling is pivotal to the formation of definitive endoderm (DE) lineage during early embryonic development, but its regulatory mechanism was not yet fully understood. In this study, we generated new CTNNB1-/- human ES cells (hESC) through CRISPR-based insertional gene disruption approach and performed systematic rescue using various truncated or mutant β-catenin to study the Wnt/β-catenin-centered cellular mechanisms underlying DE differentiation from hESC. We used RNA-seq to examine the transcriptional information to understand the functions of β-catenin.

overall_design: Gene expression profiling analysis of RNA-seq data for CTNNB1 knockout hESC and the rescue cell clones by variant β-catenin mutants.

first: Xun

last: Ma

first: Liujiang

last: Dai

first: Bo

last: Feng


title: Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq) to Study DNA Methylation Using Low Amounts of DNA

city: Tempe

first: Vel

last: Murugan

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an epigenetic mark that has a crucial role in regulating gene expression. Aberrant DNA methylation results in severe diseases in humans, such as cancer, autoimmune disease, atherosclerosis, and cardiovascular diseases. Whole-genome bisulfite sequencing and methylated DNA immunoprecipitation are available to study DNA methylation changes, but they are typically used on a few samples at a time. Here, we developed a novel method called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), that can be used to analyze many DNA samples in parallel, requiring only small amounts of input DNA. In this method, 10 different DNA samples were fragmented, purified, barcoded, and pooled prior to immunoprecipitation. In a head-to-head comparison, we observed 99% correlation between MeDIP-Seq performed individually or combined as Mx-MeDIP-Seq. Moreover, multiplexed MeDIP led to more than 95% normalized percent recovery and a 25-fold enrichment ratio by qPCR, like the enrichment of the conventional method. This technique was successfully performed with as little as 25 ng of DNA, equivalent to 3400 to 6200 cells. Up to 10 different samples were processed simultaneously in a single run. Overall, the Mx-MeDIP-Seq method is cost-effective with faster processing to analyze DNA methylome, making this technique more suitable for high-throughput DNA methylome analysis.

overall_design: We developed method and compared traditional methylated DNA immunoprecipitation to our pooled multiplexed DNA immunoprecipitation method. We also used different concentrations of DNA and compared with same concentration of DNA to optimize the minimum amount of DNA needed for Mx-MeDIP-Seq. Detailed methods are given elsewhere in publication.

first: Inam

last: Ridha

first: Chenxi

last: Xu

first: Yining

last: Zhang

first: Yunro

last: Chung

first: Jin

middle: G

last: Park

first: Joshua

last: LaBaer


title: RNAseq-differentiated gene expression profile of people living with HTLV-1 in the Brazilian Amazon region: a pilot study

city: Belém

first: Antonio

middle: Carlos Rosário

last: Vallinoto

address: Rua Augusto Correa, 01 - Guamá

department: Instituto de Ciencias Biologicas

country: Brazil

institute: Universidade Federal do Pará (UFPA)

summary: To investigate the differential expression profile of genes and microRNA (miRNA) in peripheral blood mononuclear cells (PBMCs) from patients infected with Human T-lymphotropic Virus 1 (HTLV-1), as well as their impact on progression to Tropical Spastic Paraparesis /HTLV Associated Myelopathy (PET/HAM)

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll from 4 individuals with HAM, 3 asymptomatic individuals and 3 HTLV seronegative blood donors (control group). After RNA extraction by phycol-chloroform-isopropanol, quantification of the key proteins of the Dicer and Drosha miRNA pathway was performed by RTqPCR (SuperScript® III Platinum® SYBR® Green One-Step qRT-PCR). The β-actin cellular normalizing gene was used as an endogenous control to ensure RNA integrity of the extracted samples. The mRNA quantifications were performed by the 2-ΔΔCT method. To obtain the transcriptome, the samples were quantified (Qubit™ RNA BR Assay Kit) and their integrity evaluated with (Agilent RNA 6000 Pico Kit). Samples that had an RIN (RNA Integrity Number) greater than 7 were selected and processed for making the cDNA library according to the SureSelect Strand-Specific RNA Library Prep System guide from the Illumina platform. Sequencing was performed on the Illumina NextSeq 500 equipment. Differentially expressed genes were obtained using the EdgeR package, based on the False Discovery Rate (FDR≤ 0.05).

middle: C

first: Rommel

last: Ramos

first: Ana

last: Cruz

first: Maisa

middle: S

last: de Sousa

first: Carlos

middle: A

last: da Costa

first: Sandro

last: da Silva

last: Dantas

first: Rafaella

middle: N

last: Ferreira

first: Leonn

last: Pereira

first: Maria

last: Queiroz

first: Izaura


title: Plasma multi-omics identify early pathogenesis and biomarkers of SCD post-AMI

city: Harbin

first: Maomao

state: Heilongjiang Province

address: Baojian Road Sub district, Nangang District

institute: The Second Affiliated Hospital of Harbin Medical University

summary: Early identification and treatment of Sudden Cardiac Death (SCD) post-myocardial infarction (MI) are currently limited by unclear warning indicators and elusive pathogenesis. Here, we constructed a comprehensive multi-omics blood atlas in the acute phase of AMI from 55 pairs of SCD patients and matched survivors, confirmed immune dysregulation and metabolic disorders as the biological hubs leading to post-MI SCD. Targeted proteome quantification identified a TOP4 protein-based biomarker panel, which were validated by internal and external cohorts, and confirmed a superior early prediction power of SCD to traditional clinical risk models. Further interventions targeting complement factor D (CFD) suggested a potential therapeutic strategy for high-risk MI. Our study provided valuable knowledge about the molecular changes and pathogenesis of SCD, shed light on accurate risk stratification and potential therapeutic targets in high SCD-risk MI.

overall_design: After informed consent was obtained, fasting blood samples (5 mL) were collected within 24 hours after emergent admission using EDTA tubes.We collected  110 samples (55 SCD and their matched survivor).Total RNA from peripheral blood mononuclear cells (PBMCs) which were separated within 20 min after blood collection was isolated using TRIzol™ reagent (Invitrogen, Carlsbad, CA, USA), followed by 15 min incubation at room temperature and subsequent freezing at -80°C before total RNA extraction.


title: Dynamics of γδ TCR repertoire during the de-differentiation and treatment course of thyroid cancer [mouse scRNA]

first: Heng

overall_design: 8-week-old TBP (Tpo-Cre, Braftm1Mmcm/wz TrP53tm1Brn/tm1Brn) mice were induced by i.p. administration of 150 mg/kg tamoxifen dissolved in corn oil for two times. 40 days after induction, mice were randomized into 4 groups: the control group, radiotherapy group, immunotherapy group and combined treatment group (5 mice/group). Control group was intraperitoneally injected with Isotype antibody (5mg/kg, q.3d for 8 weeks), the radiotherapy group was received sublethal irradiated (2.5Gy, q.3d for 3 times) the immunotherapy group was intraperitoneally injected with anti-PD-1 antibody (BioXCell) (5mg/kg, q.3d for 8 weeks), and the combined treatment group received both sublethal irradiated (2.5Gy, q.3d for 3 times) and anti-PD-1 antibody (Bxcell) (5mg/kg, q.3d for 8 weeks). The mice were sacrificed after 8 weeks of treatment or euthanized due to respiratory distress caused by tumor compression or obvious body weight lost (> 20%).

first: Han

last: Luo

first: Qing

last: Hao


title: Examination of gene expression changes in wild type and nhr-131 mutants exposed to F17

city: San Francisco

first: Kaveh

last: Ashrafi

department: Physiology

institute: UCSF

summary: The relative gene expression changes in C. elegans wild type animals and nhr-131(tm1376) mutants exposed to F17 and a vehicle control (DMSO) were determined.

overall_design: Synchronized L4 C. elegans 5 independent biological replicates per condition were exposed to either DMSO (0.1%) or F17 (2.5 uM) in liquid culture for 4 hr. Total RNA was extracted from whole animals.

first: George

last: Lemieux

first: Shinja

last: Yoo

first: Lin

last: Lin

first: Mihir

last: Vohra


title: Generation of brain organoids for functional analysis

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Brain organoids were generated from human iPS cells to evaluated the neuronal function of organoids derived neurons.

overall_design: Observation study to analyse the component of human organoids and the expression levels of neuronal function-related genes.

first: Keiko

last: Imamura

first: Haruhisa

last: Inoue


title: Single cell RNA-seq of splenic Foxp3+ Treg from WT and Lta-/- mice

city: Marseille

first: Magali

last: IRLA

address: 163, avenue de Luminy - Case 906

institute: Center of Immunology Marseille Luminy (CIML)

summary: Single cell transcriptomic analyses reveal that Lta regulates the composition of splenic Foxp3+ Treg cells in C57BL/6J  mice

overall_design: Expression profiling by high throughput sequencing

last: Irla

first: Alexia

last: Borelli

first: Jeremy

last: Santamaria

first: Lionel

last: Spinelli


title: Effect of osteocytes mitochondria on chondrocytes

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary:
To investigate the regulatory role of MLO-Y4 mitochondria on chondrocytes, we isolated mitochondria from MLO-Y4 and transplanted to chondrocytes.
We then performed gene expression profiling analysis using data obtained from RNA-seq of chondrocytes from vehicle group and mitochondria transplanted group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normar chondrocytes and chondrocytes tranplanted with mitochondria.

first: Yiyang

last: Ma

first: Changqing

last: Zhang


title: Analysis of circRNA expression profiles in U937 cells after p62 knockdown

city: Shenyang

first: Xinyi

last: Long

state: State...

address: Shenyang

institute: China Medical university

summary: The aim of this study was to investigate the effect of p62 on circRNA and mRNA expression profiles in U-937 cells.

overall_design: In the study presented here, the Human CircRNA microarray was used for profiling circRNAs in U937 cells and p62-knockdown U937 cells.

first: Rong

last: Hu


title: Multi-omic profiling of digital papillary adenocarcinomas reveals alterations in matrix remodeling and metabolic genes

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

summary: We performed a comprehensive genomics and transcriptomics analysis of DPAC to  discover novel features that may assist in the development of more effective, targeted therapies.

overall_design: 9 cases of DPAC compared with 10 hidradenomas (a benign tumor) using a panel targeting use a nanostring panel of 770 genes to compare DPAC with hidradenomas and identify some expected changes.

last: Jour


title: Phenotype of stim2 zebrafish knockout

city: Warsaw

first: Shamba

middle: S.

last: Mondal

address: Księcia Trojdena 4

institute: International Institute of Molecular and Cell Biology

summary: Stromal interaction molecules (STIMs) are endoplasmic reticulum resident proteins that regulate Ca2+ homeostasis and signaling by store-operated calcium entry (SOCE). The different properties and functions of STIM1 and STIM2 have been described mostly based on work in vitro. Since STIM2 knockout mice do not survive till the adulthood we generated stim2a and stim2b double knockout zebrafish and characterized it. This (stim2a;stim2b)-/- fish were fertile and did not have apparent morphological phenotype. However, RNA-sequencing revealed 1424 genes differentially expressed with at least 2-fold change. One of the most upregulated gene was annexinA3a, which is a marker of activated microglia. This corresponded well to augmented Neutral Red staining observed by imaging in vivo of (stim2a;stim2b)-/- brain. The lack of Stim2 decreased survival of fish under low oxygen conditions. Behavioral tests such as visual-motor response and dark-light preferences indicated that (stim2a;stim2b)-/- larvae might have problems with vision. This is consistent with GO BP's analysis, which showed downregulation of many genes related to light perception. The Periodic acid-Schiff staining of retina sections from adult fish reveled the alteration in stratum pigmentosum suggesting involvement of Stim2-dependent process in visual perception. Together, these data reveal new functions for Stim2 in nervous system.

overall_design: Examination of differentially expressed genes in (stim2a;stim2b)-/- mutants in comparison to (stim2a;stim2b)+/+ 5 days post fertilization zebrafish larvae with RNA-sequencing (paired-end sequencing run type). Thirty larvae were pooled together and made as one RNA sample. Three samples obtained from (stim2a;stim2b)-/- and three from (stim2a;stim2b)+/+ samples were analyzed.

first: Iga

last: Wasilewska

first: Łukasz

last: Majewski

first: Dominik

last: Bielecki

first: Dobrochna

last: Adamek-Urbańska

first: Rishikesh

last: Gupta

first: Jacek

last: Kuźnicki


title: Effect of depletion of purinPurinergic P2X4 receptor on gene expression during immune-mediated acute hepatitis of mice liver tissues

city: kai feng

first: zejin

last: liu

address: ximen street

institute: henan university

summary: To investigate the broad effect of P2X4R in diverse models of acute hepatitis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ConA-treated WT or P2X4R-/- mice

first: Zejin

last: Liu

first: Yu

last: Xie

first: Wenhua

first: Junpeng

last: Wang


title: Dynamics of γδ TCR repertoire during the de-differentiation and treatment course of thyroid cancer

first: Heng

last: Xu

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

overall_design: Refer to individual Series


title: Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and dietary PUFA manipulation

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E Young Dr.

institute: University of California, Los Angeles


title: Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and dietary PUFA manipulation [snRNA-seq]

summary: To analyze the contribution of dietary PUFAs and adipocyte LPCAT3 expression in modulating the transcriptome of murine inguinal white adipose tissue

overall_design: Transcriptomes of single nuclei isolated from the inguinal white adipose tissue of WT or AdL3KO mice on a 60% high-fat diet (HFD-n6)

first: Marcus

last: Tol

first: Yuta

last: Shiminaka

first: Alexander

last: Bedard


title: Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes [anti-FUS ChIP-seq]

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

summary: This project aims to determine  the genomique distribution of the FUS protein in brain tissues of FUS∆NLS/+ (FUS) vs FUS+/+ (WT) mice, using ChIP-sequencing. Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. We show that in these mice, the hippocampus, a critical structure involved in learning and memory, paradoxically displays nuclear FUS accumulation. FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in hippocampal-dependent spatial memory task. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events.

overall_design: Nuclei were extracted from hippocampal brain of 5-month-old FUS∆NLS/+ (FUS) vs FUS+/+ (WT) mice. We performed Chip using an antibody recognizing the FUS protein. Two biological replicates from WT mice and 2 biological replicates from FUSdeltaNLS mice are used. In total we have 4 samples + 4 inputs = 8 samples were sequenced.


title: Transcriptional profiling of mature murine adipocytes of the inguinal white adipose tissue depot following LPCAT3 deletion and dietary PUFA manipulation [bulk RNA-seq]

summary:
To analyze the contribution of dietary PUFAs and adipocyte LPCAT3 expression in modulating the transcriptome of murine inguinal white adipose tissue
We performed bulk RNA sequencing with a two-factor experimental design. WT and AdL3KO mice on 3 high-fat diets (60% calories from fat) - omega-6 enriched (n6), saturated-enriched (SFA), and omega-3 enriched (n3).

overall_design: Comparative gene expression profiling analysis of iWAT from WT and AdL3KO mice on 3 high-fat diets (60% calories from fat) - omega-6 enriched (n6), saturated-enriched (SFA), and omega-3 enriched (n3).

last: Shimanaka


title: TIGIT and PD-L1 co-blockade promotes clonal expansion of multipotent, non-exhausted antitumor T cells by facilitating co-stimulation

city: South San Francisco

first: Thomas

middle: D

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

summary: Blockade of the immune checkpoints PD-1 and TIGIT has demonstrated activity in mouse tumor models and human patients with cancer.  Although these coinhibitory receptors can restrict signaling in CD8+ T cells by regulating their associated co-stimulatory receptors CD28 and CD226, the functional consequences of combining PD-1 and TIGIT blockade remain poorly characterized.  In mouse tumor models, we show that combination blockade elicited CD226-driven clonal expansion of tumor antigen-specific CD8+ T cells.  The expanded clones emerged from a population of stem-like cells in draining lymph nodes, entering the blood as a previously unidentified single-phenotype, multiclonal population.  Upon reaching the tumor, these transiting cells expanded further and differentiated into effector or exhausted T cells, with combination blockade restricting entry into the exhaustion pathway by favoring co-stimulation.  Thus, PD-1 and TIGIT inhibition helps shape the repertoire of tumor-reactive CD8+ T cells in draining lymph nodes and determines their immunological fate in the tumor to enhance therapeutic benefit.  Analysis of clinical trial samples suggests a similar mechanism may also occur in patients with cancer.

overall_design: Single-cell RNA-seq, TCR-seq, ADT-seq, and CITE-seq were performed on the tumor, blood, and draining lymph node samples from 31 mice exposed to five different treatment regimens: control anti-gp120, anti-PD-L1, anti-TIGIT, combination, and combination plus FTY720, which blocks egress of T cells from lymphoid tissue.

first: Katherine

last: Nutsch

first: Karl

last: Banta

first: Charles

last: Tran

first: Stephanie

last: Mittman

first: Ellen

last: Duong

first: Barzin

middle: Y

last: Nabet

first: Yan

last: Qu

last: Williams

first: Sören

last: Müller

first: Namrata

last: Patil

first: Eugene

last: Chiang

first: Ira

last: Mellman


title: Mutant FUS induces chromatin reorganization in the hippocampus and alters memory processes [H3K27me3 ChIP-seq]

summary: This project aims to identify  the H3K27me3 epigenomic signatures of FUS∆NLS/+ (FUS) vs FUS+/+ (WT) mice, using ChIP-sequencing performed on FACS-sorted nuclei. Cytoplasmic mislocalization of the nuclear Fused in Sarcoma (FUS) protein is associated to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS accumulation is recapitulated in the frontal cortex and spinal cord of heterozygous Fus∆NLS/+ mice. We show that in these mice, the hippocampus, a critical structure involved in learning and memory, paradoxically displays nuclear FUS accumulation. FUS binds to a set of genes characterized by the presence of an ETS/ELK-binding motifs, and involved in RNA metabolism, transcription, ribosome/mitochondria and chromatin organization. Importantly, hippocampal nuclei showed a decompaction of the neuronal chromatin at highly expressed genes and an inappropriate transcriptomic response was observed after spatial training of Fus∆NLS/+ mice. Furthermore, these mice lacked precision in hippocampal-dependent spatial memory task. These studies shows that mutated FUS affects epigenetic regulation of the chromatin landscape in hippocampal neurons, which could participate in FTD/ALS pathogenic events.

overall_design: Total hippocampus from 5 month-old FUS∆NSL/+ (FUS) and FUS+/+ (WT) mice were sorted by FACS to isolate neuronal nuclei that were then subjected to ChIP-sequencing using antibodies against the H3K27me3 histone mark. For this experiment, we have biological replicates (2 independent lots of mice).  We will compare the epigenetic profiles of this mark in WT vs FUS mice in NeuN+ FACS-sorted nuclei. We have INPUT DNA For each of the 4 conditions (2 WT and 2 FUS). Overall, this represents 8 samples.


title: A Novel Humanized Immune Stroma PDX Model for Therapeutic Studies

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

summary: Standard preclinical human tumor models lack a human tumor stroma.  However, as stroma contributes to therapeutic resistance, the lack of human stroma may make current models less stringent for testing new therapies.  To address this, we created a human in mouse model of cancer with a human tumor stroma. This humanized immune stroma patient derived xenograft (HIS-PDX) uses patient-derived tumor cells, cancer-associated mesenchymal stem cells and human endothelial cells transplanted into BLT (bone marrow, liver, thymus) humanized mice. The model contains human connective tissues, vascular and immune cell infiltrates.  RNA sequencing analysis demonstrated a 94-96% correlation with primary human tumor. Using this model, we demonstrate the impact of human tumor stroma on response to both small molecule and immune therapies. Combined our data confirm a critical role for human stoma plays an important role in therapeutic response and that this model can be an important tool for preclinical drug testing.

overall_design: After RNA quality control, mRNA was enriched, double-stranded cDNA was synthesized, ends were repaired, poly-A & adaptors were added, fragments were selected, and PCR was performed. cDNA libraries were prepared.  Library construction was performed by NOVOGENE

first: Ronald

last: Buckanovich

first: Dongli

last: Yang