title: SNORA42 Promote Oesophageal Squamous Cell Carcinoma Development through interacting with DHX9

status: Public on Feb 28 2023

city: Toronto

first: Yanan

last: Shan

state: ON

address: 4 Goldfinch Court, PH05

country: Canada

institute: Hebei Medical University

type: Expression profiling by high throughput sequencing

summary: Oesophageal cancer is a high malignant cancer and oesophageal squamous cell carcinoma (ESCC) is the most common subtype of oesophageal cancer. Here, we identified H/ACA box snoRNA42 (SNORA42) was upregulated in ESCC and can be applied as the diagnostic and prognostic marker. Specifically, overexpression of SNORA42 promoted ESCC proliferation, migration and invasion ability whereas knockdown of SNORA42 inhibited these phenotypes in vitro and in vivo. Using RNA pull-down assay combined with Mass Spectrometry technique, we identified protein DHX9 interacted with SNORA42. DHX9 protein expression was up-regulated in ESCC and had a positive correlation with the expression of SNORA42. Furthermore, the effects of SNORA42 overexpression on ESCC phenotypes can be reversed by knockdown of DHX9. Mechanically, SNORA42 promoted DHX9 stabilized by attenuating its ubiquitination and degradation. From KEGG analysis of next-generation sequencing, we identified the NF-kappa B pathway was one of the most regulated pathways by SNORA42. SNORA42 enhanced phosphorylation of p65 in the nucleus. Moreover, SNORA42 exerted its function through promoting DHX9 interacted with p-65, inducing transcription of NF-kappa B target genes. These findings suggest that SNORA42 promotes ESCC tumorgenesis via SNORA42/DHX9/p65 axis

overall_design: methods: Knocking down SNORA42 in KYSE30 cell and then perform next-generation sequencing to identify the mRNA level changes

first: Lianmei

last: Zhao


title: Whole blood transcriptome of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on trypanotolerance

city: MONTPELLIER

first: Sophie

last: Thévenon

address: TA A-17/G Campus International de Baillarguet

department: BIOS

country: France

institute: CIRAD

summary: Animal African trypanosomosis, caused by blood protozoan parasites transmitted mainly by tsetse flies, represents a major constraint for millions of cattle in sub-Saharan Africa. Exposed cattle include West African taurine breeds called trypanotolerant according to their ability to control parasite development and to survive and grow in enzootic areas, and indicine breeds that are trypanosusceptible to the disease. Until now the genetic basis of trypanotolerance remains unclear. Here, we improved knowledge in the biological processes involved in trypanotolerance by identifying bovine genes differentially expressed during an experimental infection by Trypanosoma congolense and their biological functions. To this end, whole blood genome-wide transcriptome profiling by RNA sequencing was performed on five West African cattle breeds, three trypanotolerant taurine breeds (N'Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou), at four dates, one before and three during infection. As expected, infection had a major impact on cattle blood transcriptome whatever the breed. The functional analysis of differentially expressed genes over time in each breed confirmed an early activation of the innate immune response, followed by an activation of the humoral response and an inhibition of T cells functions at the chronic stage of infection. More importantly, we highlighted overlooked features, as a strong disturbance in host metabolism and cell production energy that differentiate trypantolerant and trypanosusceptible breeds. N'Dama breed showed the earliest regulation of immune response, associated with a strong activation of cellular energy production, this last feature being also shared with Lagune, and to a lesser extent with Baoulé. Susceptible Zebu Fulani breed was distinguished from other breeds by the strongest modification in lipid metabolism regulation. Lastly, basal differences in gene expression reflected the structuration of cattle genetic diversity, and could have consequences on the tolerant or susceptible phenotype. Overall, it would be of value to deeper investigate interactions between immune response and cell metabolism that likely impact disease outcome.

overall_design: A total of 120 RNA-seq libraries were generated from 30 cattle from five West African cattle breeds (6 animals per breed, all males, between 1 year and 2.5 years old). The breeds were: N'Dama (NDA) from Mali, Lagune (LAG) from Benin, Baoulé (BAO) from Burkina Faso, Borgou (BOR) from Benin, and Fulani Zebu (ZFU) from Burkina Faso. These animals were experimentally infected by Trypanosoma congolense IL1180. Blood samples of the 30 animals were collected at one date before infection (0), and at three dates after infection: at 20, 30 and 40 days post-infection (DPI). RNA was extracted from the 30 cattle at these four dates and sequenced to produce 120 RNA-seq libraries. The libraries were equimolarly pooled by 12, leading to 10 multiplexes of 12 samples each. Phenotypic analysis was published in Berthier et al 2015 "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds." PLoS One 10, no. 5 (2015): e0126498. DOI: 10.1371/journal.pone.0126498. SNP genotypes using the Illumina BovineSNP50.v2 SNP are freely available in WIDDE DB, project AATTOL: http://widde.toulouse.inra.fr/widde/widde/main.do?module=cattle.

first: David

last: Berthier

first: Moana

last: Peylhard

first: Laurence

last: Flori

first: Guiguibbaza-kossigan

last: Dayo

first: Isabelle

last: Chantal

first: Guillaume

last: Martin

first: Guilhem

last: Sempéré

first: Souleymane

last: Sylla

first: Sabine

last: Nidelet

first: Emeric

last: Dubois


title: Neutrophil extracellular traps formed during chemotherapy confers  TGFβ activation in breast metastatic cancer cells

status: Public on Feb 27 2023

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: To investigate the activation of signaling pathways induced in cancer cells by NETs

overall_design: Breast 410.4 cancer cells were cultured in presence or absence of NETs formed by neutrophils

first: Alexandra

last: Mousset

first: Jean

last: Albrengues

first: Cedric

last: Gaggioli


title: AFF4 regulates cellular adipogenic differentiation via   targeting autophagy

city: Hangzhou

first: Soup

last: Chen

address: Qiutao North road

country: China

institute: Zhejiang University

summary: AFF4 was discovered as a scaffold protein of Super Elongation Complex (SEC)  and exhibites an essential function on osteogenesis, tumorigenesis and odontogenesis. However, the adipogenic biological functions of AFF4 need further explorations. Here, we demonstrate that knockdown of AFF4 inhibits adipogenesis in both human mesenchymal stem cells (hMSCs) and lineage-committed 3T3-L1 preadipocytes. Conditional knocking down of Aff4 in transgenic mouse presents a thin body phenotype and impeded adipogenesis. Mechanistically, we define autophagy signaling as a crucial downstream of AFF4 through the combination of RNA-seq and ChIP-seq analyses. Depletion of AFF4 mediates the transcription of crutial autophagy genes ATG5 and ATG16L1. Simultaneous overexpression of ATG5 and ATG16L1 rescues the lineage commitment of AFF4-deficient cells. Our data elucidate that AFF4 is indispensable for adipogenic differentiation and reveal a novel mechanism for adipogenesis at transcriptional level.

overall_design: RNA profiles of AFF4 knockdown (siRNA) hMSCs versus the control cells

first: Yaqian

first: Yuting

last: Liu

first: Weimin

last: Lin

first: Chenchen

last: Zhou


title: A role of PSK-CPK28-GS2 signalling in optimizing growth and defence in tomato

first: Shuting

last: Ding

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Horticulture

summary: Phytosulfokine (PSK) is a plant pentapeptide hormone that fulfills a wide range of functions. Although it has been frequently reported to function in the inverse regulation of growth and defence in response to (hemi)biotrophic pathogens, the mechanism involved remains largely unknown. Using tomato (Solanum lycopersicum) and Pseudomonas syringae pv. tomato (Pst) DC3000 pathogen as a system, we present compelling evidence that the tomato PSK receptor PSKR1 interacts with the calcium-dependent protein kinase CPK28, which phosphorylates the key enzyme of nitrogen assimilation glutamine synthetase GS2 at two sites (S334 and S360 sites). These post translational modifications uncouple the two PSK-induced effects on defence responses and on growth regulation, respectively. The discovery of these sites will inform breeding strategies designed to optimize the growth-defence balance. The concept that such peptide hormones can regulate plant growth and resistance in a compatible manner is attractive, not least because crop yields and fitness can be optimized simultaneously in global climate-change era.

overall_design: An RNA-seq analysis was performed to further investigate how phosphorylation at the GS2 S334 site regulates plant defences. In these studies, tomato leaves GS2 and GS2S334A  lines were sampled at 24 hpi in the absence or presence of Pst DC3000 inoculation.      We also performed an RNA-seq analysis to investigate how phosphorylation at the GS2 S360 site regulates plant growth. Leaves from the GS2S360D lines and GS2 plants were sampled.

first: Zhangjian

last: Hu

first: Jianrong

last: Lv

first: Jiao

last: Wang

first: Ping

first: Jingquan

last: Yu

first: Christine

middle: H

last: Foyer

first: Kai

last: Shi


title: Transcriptomic profiling of MLL-ENL and delta YEATS mutant

city: Ann Arbor

first: Andrew

last: Muntean

state: MI

address: 1150 W. Medical Center Dr.

department: Department of Pathology

country: USA

institute: University of Michigan

summary: To investigate the contribution of ENL YEATS domain and downstream sequences in MLL-ENL leukemogenesis program, we generated MLL-ENL and MLL-ENL ∆YEATS (ENL aa372-559) cell lines by retrovirally introducing these constructs into lineage negative hematopoietic stem and progenitor cells (HSPCs).

overall_design: We then perform gene expression profiling using dataset obtained from RNA-seq experiment of MLL-ENL and MLL-ENL ∆YEATS, with 2 technical replicates each.

first: Hsiangyu


title: Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity [CRISPR screen]

city: ShangHai

first: Tong

last: Han

address: 1239 Siping Road

institute: Tongji University

summary: The pleiotropic cytokine interferon-gamma (IFNγ) is known to be associated with cytostatic, anti-proliferation, and pro-apoptosis functions in cancer cells. However, cancer cells can become resistant to IFNγ, and the underlying mechanism is not fully understood. To investigate the potential IFNγ resistant mechanisms, we performed IFNγ sensitivity screens in more than 40 cancer cell lines and characterized the sensitive and resistant cell lines. By applying CRISPR screening and transcriptomic profiling in both IFNγ sensitive and resistant cells, we discovered that activation of double-strand break (DSB) repair genes could result in IFNγ resistance in cancer cells. In addition, suppression of single-strand break (SSB) repair genes increased the essentiality of DSB repair genes after IFNγ treatment. The relationship between the activation of DSB repair genes and IFNγ resistance was further confirmed in clinical tumor profiles from The Cancer Genome Atlas (TCGA) and immune checkpoint blockade (ICB) cohorts. Our study provides a comprehensive resource to elucidate IFNγ resistance in cancer and has the potential to inform combinational therapeutic strategies to overcome immunotherapy resistance.

overall_design: To further validate the molecular mechanisms related to IFNγ resistance, we performed CRISPR knockout (KO) screens on four IFNγ resistant cell lines (MCF7, 786O, HCT116, HUH6) and five sensitive cell lines (A549, NCIH1437, MDAMB231, PC9, CALU1).

first: Xujun

first: Sailing

first: Wubing

last: Zhang

first: Jue

first: Qiu

last: Wu

first: Ziyi

last: Li

first: Jingxin

last: Fu

first: Rongbin

last: Zheng

first: Jiamin

first: Qin

last: Tang

first: Peng

first: Chenfei


title: Molecular characterization of bat embryonic fibroblasts and induced pluripotent stem cells [RRBS]

city: New York

first: Thomas

last: Zwaka

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Genome-wide methylation state of bat fibroblasts induced pluripotent bat stem cells

overall_design: DNA was isolated from bat fibroblasts or pluirpotent stem cells in duplicate and methylation profile was determined using Reduced representation bisulfite sequencing (RRBS)

middle: P

first: Marion

last: Dejosez


title: Molecular characterization of bat embryonic fibroblasts and induced pluripotent stem cells [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide maps of H3K4me3 and H3K27me3 status in bat fibroblasts and induced pluripotent bat stem cells.

overall_design: H3K4me3 and H3K27me3 status was determined from bat embryonic fibroblasts and pluirpotent stem cells after chromatin immunoprecipitation.


title: TNF-α-Activated Adipose–Derived Stem Cells Improve the Angiogenesis of Full-Thickness Skin Grafts Through the TNF-α/NF-κB Signaling Pathway

city: Beijing

first: Shuang

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: The repair of skin and soft tissue defects has been a long-standing topic of interest in plastic surgery. Skin grafts and flaps are the most commonly used methods for such repair, but both have some disadvantages. If a high-quality skin flap transplantation outcome could be obtained through simple skin grafting, it would surely benefit a majority of patients. Transplantation of adipose-derived stem cells (ADSCs) into skin and soft tissue wounds is a promising “therapeutic angiogenesis” strategy in this context. In the present study, we used TNF-α to mobilize ADSCs for the tissue regenerative process. Then, we injected the TNF-α-activated ADSCs intradermally into the donor skin of full-thickness skin grafts (FTSGs). TNF-α may activate ADSCs through the TNF-α/NF-κB pathway and enhance the ability of ADSCs to signal the paracrine secretion of the angiogenic factor IL-8, ultimately promoting the angiogenesis of donor skin. The use of vasculature-rich donor skin for grafting presented in our study could accelerate skin graft anastomosis; shorten the nutrient deprivation time of the epidermis, hair follicles, and dermis; and thereby improve the survival of FTSGs. Overall, the findings of the present study demonstrate a possible mechanism through which TNF-α acts on ADSCs to improve their angiogenic capacity and provide a novel approach for the repair of skin and soft tissue wounds.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TNF-α-Activated Adipose–Derived Stem Cells（t-ADSCs) and ADSCs

first: Hong

last: Gao

first: Jiachao

last: Xiong

first: Minjuan

first: Lie

last: Zhu


title: Environmental-mediated vincristine drug resistance of  human precursor B-acute lymphoblastic leukemia (pre-B ALL)

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: First-line treatment for pre-B acute lymphoblastic leukemia (pre-B ALL) typically encompasses a period of so-called induction therapy in which the patient is treated for 28 days with chemotherapy to induce a remission. A bone marrow sample is subsequently taken to determine the number of remaining leukemia cells, which are called minimal residual disease (MDR). MRD is a key prognostic factor, with higher MRD levels predicting worse outcome for patients. Induction therapy usually is able to drastically reduce the number of leukemic cells but chemoresistance, as first detected by higher MRD levels, remains a major clinical problem. MRD persists not only by leukemia cell-intrinsic mechanisms such as clonal selection and genetic changes, but also through protective interactions of the leukemia cells with the surrounding supporting stroma. This mechanism of drug resistance has been named environment-mediated drug resistance (EMDR) and is a general route through which MRD cells, regardless of underlying genetics of the leukemia cells, can persist after chemotherapy. The EMDR component contributing to the persistence of MRD leukemia cells can be studied in tissue culture models by treating leukemia cells with a non-lethal drug dose in the presence of stromal cell protection. Here we analysed the transcriptome of a PDX-derived human pre-B ALL cell line co-cultured with OP9 stromal cells as they developed drug insensitivity against the chemotherapeutic drug vincristine.

overall_design: ICN13 PDX/patient-derived pre-B ALL cells were grown in co-culture with mitotically inactivated OP9 bone marrow stromal cells. Cells cultured with 2 nM vincristine or 4 nM were collected from triplicate wells for RNA isolation at day 18 and d30, respectively, along with controls cultured for the same period of time but without drug. At the time of cell harvest, total cell counts were increasing in the vincristine-treated samples and their viability (% of \Trypan-blue excluding cells/total cell number) was >70%.

first: Nora

last: Heisterkamp

first: Mingfeng

first: Lu

last: Yang


title: Molecular characterization of bat embryonic fibroblasts and induced pluripotent stem cells [ATAC-Seq]

summary: Genome-wide maps of chromatin state in induced pluripotent bat stem cells and fibroblasts

overall_design: DNA was isolated from bat fibroblasts or pluirpotent stem cells and open chromatin state was determined by ATAC-seq in duplicate per cell type.


title: Bulk RNAseq of the lung mesenchymal cells from IFNgama-gain-of-function  (Yeti+/-) and control (wildtype) adult mice

city: San Francisco

first: Tien

last: Peng

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: To test the effect of IFN-gama on mesenchymal cells. We examined the mesencyhaml transcriptome of Yeti vs. control by bulk RNAseq.

overall_design: The lung mesenchymal cells from IFNgama-gain-of-function  (Yeti+/-) and control (wildtype) adult mouse were FACSorted by negative seletion of CD45/CD31/Epcam. Dead cells were excluded by negative selection of DAPI.

first: Chaoqun

last: Wang


title: MicroRNA profiling of Basal ganglia tissue from chronically SIV infected rhesus macaques II

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: The study describes miRNA expression changes in basal ganglia (BG) of chronically SIV-infected rhesus macaques. HIV/SIV-associated neurological disorder (HAND) represents a major comorbidity affecting HIV patients on anti-retroviral therapy. Employing a systems biology approach, we report molecular changes underlying HAND and its modulation by phytocannabinoids [delta-9-tetrahydrocannabinol (9-THC)] in uninfected and SIV-infected rhesus macaques (RMs) treated with vehicle (VEH/SIV) or 9-THC (THC/SIV). VEH/SIV but not THC/SIV RMs showed significant enrichment of genes linked to anti-viral defense, interferon-beta, NFkB, RIG-1, and JAK-STAT signaling. We focused on the anti-endoplasmic reticulum (WFS1) and anti-oxidative stress (CRYM) proteins that were significantly downregulated in BG of VEH/SIV RMs. Both proteins localized to the BG neurons, and showed differential expression in the BG of THC/SIV and VEH/SIV RMs. Additionally, inflammation-associated miR-155 and miR-142-3p showed significantly higher expression in the BG of VEH/SIV RMs. In human primary HCN2 neuronal cells, miR-142-3p post-transcriptionally downregulated WFS1. These findings strongly support a role for differential miRNA expression associated with HIV/SIV induced neurological dysfunction.

overall_design: Fourteen age and weight matched adult Indian rhesus macaques were randomly divided into 3 groups. Group 1 (n=4) remained uninfected. Group 2 (VEH/SIV, n=4) animals were treated with vehicle and infected intravenously with 100TCID50 of SIVmac251. Group 3 (THC/SIV, n=6) were treated with delta-9-tetrahydrocannabinol and infected intravenously with 100TCID50 SIVmac251. Basal ganglia tissue was collected at necropsy. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. MicroRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA), which utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative miRNA expression across many genes and samples. miRNA expression data were normalized using the global normalization method. Comparisons were made between uninfected and VEH/SIV and THC/SIV and VEH/SIV rhesus macaques.

first: M


title: Augmenting vaccine efficacy against delta variant with ‘Mycobacterium-w’ mediated modulation of NK-ADCC and TLR-MYD88 pathways

city: Kolkata

first: Suparno

last: Chakrabarti

state: West Bengal

address: PGH Shah Road

department: Cellular Therapy and Immunology

country: India

institute: Manashi Chakrabarti Foundation

summary: Fifty healthcare workers (HCW) who had received Mycobacterium-w (Mw) and at least one dose of ChAdOx1 nCoV-19 vaccine subsequently (Mw+ChAdOx1 group) were monitored for symptomatic COVID-19, during a major outbreak with the delta variant of SARS-CoV-2 (April-June, 2021) in India, along with 201 HCW receiving both doses of the vaccine without Mw (ChAdOx1 group). Bulk RNA-Seq analysis was carried out on 4 subjects enrolled from each group.

overall_design: Comparative gene expression analysis between 4 subjects from Mw + ChAdOx1 and ChAdOx1 group.

first: Sarita

middle: R

last: Jaiswal

first: Ashraf

last: Saifullah

first: Jaganath

last: Arunachalam

first: Rohit

last: Lakhchaura

first: Dhanir

last: Tailor

first: Anupama

last: Mehta

first: Gitali

last: Bhagawati

first: Hemamalini

last: Aiyer

first: Subhrajit

last: Biswas

first: Bakulesh

last: Khamar

first: Sanjay

middle: V

last: Malhotra


title: Transcriptome profiling of Basal ganglia tissue from chronically SIV infected rhesus macaques

summary: The dysregulation of the microbiota-gut-brain axis (MGBA) in people living with HIV (PLWH) consequent to gastrointestinal dysfunction (dysbiosis) can lead to neuroinflammation and persistent cognitive impairment, which underscores the need for new treatments. Here, we show that delta-9-tetrahydrocannabinol (THC) reduced neuroinflammation and microbiome alterations and enhanced plasma endocannabinoid, endocannabinoid-like and indole-3-propionate levels in chronically SIV-infected rhesus macaques. Long-term low-dose THC potently blocked expression of genes associated with type I interferon responses and excitotoxicity (SLC7A11) and enhanced protein expression of WFS1 (endoplasmic reticulum stress) and CRYM (oxidative stress) in basal ganglia. Additionally, THC successfully countered miR-142-3p mediated suppression of WFS1 via a CB1R mediated mechanism in HCN2 neuronal cells. Most importantly, THC increased the relative abundance of Firmicutes and Clostridia including IPA producersing C. botulinum, C. paraputrificum, C. cadaveris and butyrate producersing C. butyricum, Faecalibacterium prauzsnitzii and Butyricicoccus pullicaecorum in the colon. This study highlights low-dose THC as a potential disease-modifying agent that can positively modulate the MGBA by concurrently reducing neuroinflammation and promoting the growth of gut microbial species that produce neuroprotective metabolites like indole-3-propionate in PLWH HIV and other neurodegenerative diseases, thus meriting clinical trials.

overall_design: Basal ganglia tissue mRNA profiles of uninfected control (n=5) and chronically SIV-infected rhesus macaques that were treated with vehicle (n=6) or delta-9-tetrahydrocannabinol (THC) (n=6) were generated by deep sequencing using Illumina.


title: Pistia Leaf and Root transcriptome

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

summary: Bulk RNA-Seq datasets were generated for the roots and leaves of Pistia stratiotes in order to compare expression of nutrient transporters between the tissues

overall_design: Pistia leaf x 4, pistia root x 4

first: Anthony

last: Bishopp

first: Dylan

last: Jones


title: Analysis of the effect of exogenous auxin on the regulatory relationship between miRNA and its target genes in rose using high-throughput sequencing

first: Yi-Qing

last: Wang

address: Beijing University of Agriculture Street

institute: Beijing University of Agriculture

type: Non-coding RNA profiling by high throughput sequencing

summary: Rose (Rosa hybrida L.) is a major cut flowers in the world. Studying the molecular mechanism of auxin regulation in growth is of great significance for enhancing the understanding of the growth and development processes of rose and informing accurate exogenous auxin application in rose production. However, the response mechanism of rose to miRNA-mediated auxin signal transduction is unclear. In this study, rose plants were treated with IAA, and 75 known miRNAs and 168 novel miRNAs were identified by small RNA sequencing. Among them, 19 known miRNAs and 42 miRNAs were differentially expressed. Many differential miRNAs demonstrated staged responses to auxin treatment. The targeted relationship between miRNA and key transcription factors regulated by auxin in rose was analyzed, and the target genes in the ARF family and AUX/IAA family were screened. By using quantitative real-time PCR(qRT-PCR) to verify the expression patterns of the miRNA regulating the auxin signal transduction pathway and its target gene, we found that miR156a, miR160a, miR164a, miR167d, miR396b-3p, novel_miR_189, novel_miR_74, novel_miR_8, and novel_miR_207 interacted negatively with the ARF family, and miR390a-3p and novel_miR_101 interacted negatively with the AUX/IAA family. These results provide a theoretical basis for further studies on the auxin regulatory mechanisms in rose.

overall_design: we comprehensively analyzed at the transcriptome and small RNA levels by using high-throughput sequencing technology. An abundance of information at the transcriptional and miRNA regulation levels was obtained, and the genes and miRNAs related to auxin transcription regulation were screened.

first: Yiqing

first: Rong

last: Ding

first: Kezhong

last: Zhang

first: Jinteng

last: Cui


title: Bazi Bushen extents health span and mitigates epigenetic aging in nature aging mice

city: Shijiazhuang

first: Mengnan

last: Li

state: Hebei

address: No.238 Tianshan Street

institute: National Key Laboratory of Collateral Disease Research and Innovative Chinese Medicine

summary: Bazi Bushen (BZBS), a traditional Chinese medicine, has been proven effective for the treatment in age-related disease models. However, its role in health improvement during the aging process has not yet been explored. In the present study, we investigated the anti-aging effect of BZBS in nature aging mice through Frailty Index assessment, liver DNA methylome, and epigenetic age estimation. Highly differentiated DNA methylation was presented between the young and aged mice, which was mainly concentrated in the promoter region. BZBS treatment protected mice from age-associated DNA methylation changes so that rejuvenated epigenetic age. This result was consistent with the phenotypic observations, including enhanced memory and muscle endurance, less liver lesions, and lower frailty score. Aging-related database screen together with KEGG analysis suggested that methylation-targeted genes upon BZBS treatment were involved in several essential pathways including oxidation-reduction processes, genome stability, MAPK signaling, and inflammation. Up regulation of key effectors in Sirt3-Foxo1 and DNA repair signaling were confirmed. Finally, in silico analysis of the formula revealed anti-aging properties of Renshen, Shengdihuang, Yinyanghuo, and Gouqizi, as well as their potential methylation-regulatory functions. In sum, our work reports the first anti-aging effects of Traditional Chinese Medicine via epigenetic mechanism, thus providing potential life prolonging opportunities.

overall_design: RRBS-seq of livers from mice at 23 weeks and 63 weeks of age

first: Xinjing

last: Mao

first: Chao

last: Fang

first: Cong

last: Wei

first: Yunlong

last: Hou

first: Yiling

last: Wu


title: Molecular characterization of bat embryonic fibroblasts and induced pluripotent stem cells

first: Thomas

last: Zwaka

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

overall_design: Refer to individual Series


title: Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity

first: Tong

last: Han


title: Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity [RNA-seq]

overall_design: To investigate the IFNγ resistant mechanisms, we applied IFNγ stimulation (10ng/ml) to five IFNγ sensitive cell lines (A549, NCIH1437, MDAMB231, A375, and HCC827) and six IFNγ resistant cell lines (MCF7, HCT116, HUH6, HGC827, COLO205, and SW620) for 48 hours according to IFN-γ sensitivity screen.

first: Xujun

first: Sailing

last: Shi

first: Wubing

first: Jue

first: Qiu

first: Ziyi

first: Jingxin

last: Fu

first: Rongbin

last: Zheng

first: Jiamin

first: Qin

last: Tang

first: Peng

first: Chenfei


title: Cannabinoid modulation of gene and microRNA expression in brain (basal ganglia) during chronic HIV/SIV infection

first: Mahesh

last: Mohan

platform_organism:
Macaca mulatta
Homo sapiens


title: Identification of differentially expressed mRNAs after activation of  LX-2 cells

city: Kunming

first: hai

last: liu

address: yuhua road

institute: Kunming Medical University

summary: In this study, high-throughput RNA sequencing technology combined with bioinformatics analysis was used to compare the differentially expressed mRNA of TGF-β1-treated LX-2 cells with that of the control group in hopes of gaining a deeper understanding of the biological function and signaling pathway changes in the activation process of LX-2 cells, as well as to identify potential key genes regulating HSC activation.

overall_design: LX-2 cells were divided into two groups. The experimental group received 10 ng/ml TGF-β1 stimulation (n=3), while the control group received no treatment (n=3). After 24 hours, the levels of a-SMA gene and protein expression were measured by PCR and Wb, respectively, to demonstrate that the cells had been activated. Total RNA was sequenced by transcriptome to screening for differentially expressed genes (DEGs), and DEGs were bioinformatically analyzed.

first: Hai

last: Liu

first: Sihang

first: Zhong


title: Cohesin-independent STAG proteins interact with RNA and localise to R-loops to promote complex loading

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

institute: Ucl

summary: Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in cohesins localization to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin and interact with CTCF, as well as a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA and are localised to endogenous R-loops where they act to suppress R-loop formation. Our results place SA proteins on chromatin upstream of the cohesin complex and reveal a role for SA in cohesin loading at R-loops which is independent of NIPBL, the canonical cohesin loader. We propose that SA takes advantage of this structural R-loop platform to link cohesin loading and chromatin structure with diverse genome functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.

overall_design: RAD21mAC cells were treated for 4hrs with EtOH or IAA.   Two biological replicates were prepared for each condition (B1 or B2).  For ChIP-seq, chromatin was extracted and immunoprecipitation with antibodies was performed. All IPs in one biologocal replicate samples were processed together.  ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina kit and using NEBNext Multiplex Oligos.  Libraries were amplified with 6-8 cycles of PCR. Libraries were sequenced on the Illumina HiSeq2500 platform, 80bp single-end reads.  For DRIP-seq, cells were fractionated to isolate chromatin, nucleic acids were isolated and RNA:DNA hybrids were immunoprecipitated with s9.6 antibody.  DRIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina kit and using NEBNext Multiplex Oligos. Libraries were sequenced on the Illumina NovaSeq platform, 100bp paired-end reads.

first: Hadjur

last: Suzana

first: Porter

last: Hayley

first: Li

last: Yang


title: Respiratory backpressure determines normoxic distribution of terminal oxygen reduction pathways

city: Dunedin

first: Kiel

last: Hards

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Cytochrome bd (CydAB), a high-affinity oxidase that performs terminal oxygen reduction in cellular respiration, is used by various bacteria to grow in hypoxic environments, form nonreplicating persister cells, or resist antimicrobial killing. It is thought that oxygen concentration solely determines the usage of CydAB in bacteria, with the tradeoff being that CydAB-containing respiratory chains generate less ATP than those containing low-affinity proton-pumping cytochrome oxidases, as CydAB does not pump protons when generating a proton motive force (PMF). However, CydAB has roles in acid, nitrosative and oxidative stress that suggest the existence of oxygen-independent CydAB usage. Here, we show that an obligate aerobe, the soil actinomycete Mycobacterium smegmatis, uses CydAB to normoxically maintain a homeostatic balance of the PMF, involving an oxygen-independent interaction with the classical hypoxia regulator (DosR). We show that overpotentials of the PMF apply feedback inhibition on the proton-pumping, low-affinity, cytochrome c oxidase supercomplex bcc-aa3, and that CydAB can immediately escape this inhibition and promote a PMF-responsive programme.

overall_design: RNA Sequencing on Mycobacterium smegmatis wild-type or cytochrome bd deletion mutant, either treated with DMSO or treated with 50 nM TB47. Sequencing was performed across two lanes.

first: Geroge

last: Taiaroa

first: Zoe

middle: C

last: Williams

first: Gregory

middle: M

last: Cook


title: Transcriptome analysis in hepatocellular carcinoma (HCC) tissues

city: Shanghai

first: Bin

last: Sun

address: No.225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

summary: We report the application of RNA sequencing technology for high-throughput profiling  in HCC tissues. In the present study, to explore novel biomarkers of HCC, we firstly explored the expression profiles of mRNAs and miRNAs in three pairs of HCC patients (tumor tissues and non-tumorous tissues) by high-throughput RNA sequencing. A total of 1024 mRNAs were found to be significantly dysregulated (636 up-regulated and 388 down-regulated), 50 miRNAs were found to be significantly dysregulated (27 up-regulated and 23 down-regulated) in the HCC tissues compared with the non-tumorous tissues.Then validae the differentially expressed miRNAs by qRT-PCR in HCC tissues and serum. This study provides a framework for the application of miRNAs to be ideal biomarkers for HCC.

overall_design: Examination of  different expression level of mRNAs and miRNAs in HCC tissues.

first: Changqing

last: Su


title: Molecular characterization of bat embryonic fibroblasts, induced pluripotent stem cells and their differentiated progeny [RNA-Seq]

first: Thomas

last: Zwaka

summary: Gene expression studies in bat fibroblasts, pluripotent stem cells, and their differentiated progeny.

overall_design: RNA-seq was performed for each cell type in triplicate.

first: Marion

last: Dejosez


title: A soybean pattern recognition receptor conferring broad-spectrum pathogen and pest resistance regulates expression of several NLR receptor proteins

city: Ames

first: Madan

middle: K

last: Bhattacharyya

state: IA

address: G303 Agronomy 716 Farm House Ln

department: Department of Agronomy

institute: Iowa State University

summary:
Understanding the molecular response of plants to innumerable pathogens and pests is crucial in managing and eradicating plant diseases.
We investigated the transcriptomic depiction of GmDR1 transgenic lines vs. their genitor Williams 82 treated with the PAMP chitin to critical gene expression changes that might lead to the defense responses manifested by the GmDR1 transgenic plants

overall_design: We conducted RNA-seq on leaves of GmDR1 transgenic lines (DR1-136 and DR1-107) and the control line Williams 82 (W82) after chitin application. The control treatment consisted of sodium phosphate buffer, the solvent for chitin in this experiment. W82 is the transgene recipient non-transgenic soybean cv Williams 82; DR1-136 is the weak transgenic soybean carrying the Promoter2-GmDR1 transgene; and DR1-107 is the strong transgenic soybean harboring the Promoter3-GmDR1 transgene

first: Micheline

middle: N

last: Ngaki

first: Subodh

last: Srivastava

first: Wang

last: Feifei


title: Transcriptome analysis of heart tissue in wild type and cTnI R193H mutation mice based on RNA-seq

city: chongqing

first: gan

last: yi

address: No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing

institute: Chongqing Children's Hospital

summary: Aim:To explore the pathogenesis of restrictive cardiomyopathy (RCM) with cTnI mutation by using RNA-Seq to detect differentially expressed genes in WT and cardiac troponin I (cTnI) mutation mouse heart. Methods: The heart of WT mice and cTnI 193H mutant mice were extracted, all mRNA of myocardial tissue was extracted, and then transcribed into cDNA. After PCR amplification, the library was constructed, and high-throughput sequencing was performed. The sequencing results were analyzed to find the differentially expressed gene, and bioinformatics method was used to analyze the biological processes among those differentially expressed genes might be involved in. Results:A total of 52 differentially expressed genes were identified including 28 highly expressed and 24 low expressed ones ,of which 42 mRNA genes  were differentially expressed (P<0.05). A total of 16 KEGG pathways were involved, and mainly participated in the immunological and metabolic processes. Conclusions:cTnI mutation may cause gene differential expression. Immune response,mitochondrial energy metabolism and myocardial cell differentiation may be involved in the progress of restrictive cardiomyopathy.The results might have offered new ideas for the research of RCM pathogenic mechanism.

overall_design: Examination of differentially expressed genes different  in heart of WT and cTnI mutant mice, three biological repeats.

first: Jing

last: Luo

first: Yi

last: Gan


title: Next Generation Sequencing Quantitative Analysis of Wild Type and Shoc2 -/- sox10-positive cells in zebrafish

city: Lexington

first: Justin

last: Levens

state: KY

address: 2365 Harrodsburg Road

institute: Markey Cancer Center

summary: To determine how Shoc2-mediated signals affect expression of genes controlling specification of neural crest cells in zebrafish development, we applied RNA-sequencing. shoc2 CRISPR/Cas9 mutants that are transgenic for sox10:dsRed – marking neural crest progenitors were utilized in these experiments. mRNAs was isolated from the FACS-purified sox10:dsRed positive cells of shoc2 CRISPR/Cas9 mutant and wild type larvae. This approach allows for a robust and targeted quantitative assessment of how Shoc2-ERK1/2 signaling affects emergence of several neural crest lineages. The differences in the transcriptome of cells purified from shoc2 crispants and control embryos were determined.

overall_design: examination of the transcriptional changes in zebrafish larvea that lost shoc2 expression

first: Eric

last: Rouchka

first: Emilia

last: Galperin

first: Rebecca

last: Norcross


title: The proteasome regulator PSME4 reduces the response to immunotherapy by abrogating tumor immunogenicity in NSCLC

status: Public on Feb 26 2023

city: Rehovot

first: Aaron

last: Javitt

state: Other/International

address: Herzl St 234,

country: Israel

institute: Weizmann Institute of Science

summary: Disruption in proteostasis is a hallmark of cancer, with aberrations in proteasome-mediated degradation highly implicated in this malignancy. Proteasomes further bear critical importance in tumor immunogenicity by regulating inflammatory signaling, promoting immune cell activation and playing a crucial role in antigen processing and presentation. Indeed, response to immunotherapy in melanoma patients has been recently linked to increased expression of immunoproteasomes, a specialized form of proteasomes that are upregulated under inflammatory conditions. Yet, the percentage of patients that respond to therapy remains low, and the underlying mechanisms driving resistance remain poorly understood. Further, comprehensive analysis of the role proteasomes play in the pathophysiology of cancer and as a modulator of anti-tumor immunity is remains lacking. Here, we show that proteasome complex composition varies across cancer types and can be used to stratify patient response to immunotherapy. Specifically, we found that the proteasome regulator PSME4 is upregulated in NSCLC and associated with poor prognosis. We show that PSME4 alters proteasome activity and antigen processing attenuating the antigenic diversity and presentation. Through exacting biochemical assays, proteasome profiling of patient-derived NSCLC samples, combined with scRNA-seq, immunopeptidomics and in vivo analyses we uncovered a novel mechanism of immune evasion mediated by PSME4, which promotes an immunosuppressive tumor microenvironment and abrogates anti-tumor immunity. Collectively, our approach may be adapted to other cancer types and pathological settings and affords a novel paradigm by which proteasome composition heterogeneity should be examined and targeted in the context of precision oncology.

overall_design: RNA-seq was performed to measure changes in mRNA expression in PSME4-depleted A549 cells their control

first: Merav

last: Shmueli

first: Yifat

last: Merbl


title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma [ChIP-seq]

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: We analysed active histone marks with EBV-LMP1 inducible methylation genes by performing ChIP-seq on H3K4me3 and H3K27ac.

overall_design: Examination of active histone marks with EBV-LMP1 inducible methylation genes.

first: Satoru

last: Kondo

first: Atsushi

last: Okabe

first: Takuya

last: Nakagawa

first: Keisuke

last: Matsusaka

first: Bahityar

last: Rahmutulla

first: Hirotomo

last: Dochi

first: Harue

last: Mizokami

first: Yuki

last: Kitagawa

first: Tomoya

last: Kurokawa

first: Masato

last: Mima

first: Kazuhira

last: Endo

first: Hisashi

last: Sugimoto

first: Naohiro

last: Wakisaka

first: Kiyoshi

last: Misawa

first: Tomokazu

last: Yoshizaki

last: Kaneda


title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma

last: Fukuyo


title: Evaluation of TSTEM-like CAR-T cells

status: Public on Feb 25 2023

city: Melbourne

first: Paul

middle: J

last: Neeson

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: This study explored the difference in gene expression by conventional vs TSTEM-like CAR-T cells.  TSTEM-like CAR-T cells showed increased expression of genes associated with progenitor memory T cell differentiation and proliferation. In contrast, conventional CAR-T cells were enriched for genes associated with effector T cell differentiation and exhaustion.

overall_design: Conventional and TSTEM-like CAR-T cells were produced from three healthy donors, RNA extracted and RNAseq performed as per the methods section in Meyran D et al Science Translational Medicine 2023.

first: Deborah

last: Meyran

first: Joe

last: Zhu

first: Niko

last: Thio


title: Effect of Escherichia coli B2 on gene expression before and after citric acid-induced antibiotic tolerance

city: Changchun

first: Xue-song

last: Li

address: Xincheng Street No. 2888

institute: Jilin Agricultural University

summary: In order to explore the differentially expressed genes of E. coli B2 after citric acid induced antibiotic tolerance, we artificially induced the antibiotic tolerance of E. coli O157: H7 and verified its phenotype.

overall_design: In vitro, citric acid was added during bacterial culture to artificially induce antibiotic tolerance of E.coli B2 bacteria.


title: In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

summary: Mutations in the Gα-genes GNAQ and GNA11 are found in 85-90% of uveal melanomas (UMs). We analyzed the association between GNAQ and GNA11 mutations with disease-specific survival, gene expression profiles, and cytogenetic alterations in 219 UMs. Our analysis showed a shorter disease-specific survival of GNA11-mutated cases as compared to those carrying a GNAQ mutation (HR=1.97 [95%CI 1.12-3.46], p=0.02). GNA11 mutated UMs displayed a shorter, but not significant, median months survival of 26.97 [95% CI 25.02-37.08] versus GNAQ patients median months survival of 31.5 [95% CI 30.97-53.51]. The GNA11 mutation was also associated with: i) an increased frequency of loss of BRCA1-associated protein 1 (BAP1) expression (p=0.0005), ii) monosomy of chromosome 3 (p<0.001), iii) amplification of chr8q (p=0.038), iv) the combination of the latter two (p=0.0002), and inversely with v) chr6p gain (p=0.003). We used tandem-affinity-purification and mass spectrometry to show that the two derived G-proteins have different protein interaction partners. Specifically, the Tet Methylcytosine Dioxygenase 2(TET2), a protein that is involved in DNA demethylation, physically interacts with the GNAQ protein but not with GNA11, as confirmed by immunoprecipitation analyses. High-risk UM cases show a clearly different DNA-methylation pattern, suggesting that a different regulation of DNA methylation by the two G-proteins might convey a different risk of progression.

overall_design: Eight different uveal melanoma cell lines MEL285, MEL290, OMM1, UPMM1, UPMM2, UPMM3, UPMD1, and UPMD2 (wild type or specifically mutated for GNAQ or GNA11 as indicated in the main text) were selected as cellular model for the α- protein signaling analysis. Cell were analyzed in triplicate

first: Francesca

last: Piaggio

first: Michela

last: Croce

first: Francesco

last: Reggiani

first: Paola

last: Monti

first: Cinzia

last: Bernardi

first: Marianna

last: Ambrosio

first: Barbara

last: Banelli

first: Mehmet

last: Dogrusöz

first: Ralf

last: Jockers

first: Domenico

last: Bordo

first: Roberto

last: Puzone

first: Silvia

last: Viaggi

last: Coviello

middle: B

last: Lanza

first: Martina

last: Bartolucci

first: Andrea

last: Petretto

first: Carlo

last: Mosci

first: Rosaria

last: Gangemi

first: Pieter

middle: A

last: van der Velden

first: Martine

last: Jager

first: Ulrich

last: Pfeffer


title: Effect of upf1 knockout on gene expression of Neurospora crassa with H2O2 treatment or not

city: Beijing

first: Yuanhao

last: Meng

address: China Agricultural University (West Campus), No. 2, Yuanmingyuan West Road

institute: China Agricultural University

summary:
In order to explore the stress-resistance related genes that may be regulated by upf1 in Neurospora crassa,
we conducted RNA-seq experiments with upf1 knockout/WT strains treated with or without 20mM H2O2, and obtained gene expression data.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and upf1 strain with H2O2 treatment or not

first: Shuangjie

last: Shen

first: Chengcheng

last: Zhang

first: Guofei

last: Cui

first: Ying

last: Wang

first: Xiao

last: Liu

first: Qun

last: He


title: Physiological and morphological status of cells dictates RNA biosignature of their exosomes

city: Manhattan

first: Meena

last: Kumari

state: KS

address: 231 Coles Hall

institute: Kansas State University

summary: P19 cells, a pluripotent embryonal cell line derived from mouse teratocarcinoma, can be stimulated with retinoic acid to induce neural differentiation forming P19 neurons (McBurney et al., 1982). P19 cells (undifferentiated cells abbreviated as UD-P19 cells) and P19 neurons were cultured in a defined medium lacking fetal bovine serum and conditioned medium was collected. Exosomes were purified from conditioned medium by ultracentrifugation method. Exosomes were characterized using a number of techniques according to the guidelines of ISEV. RNA was purified from exosomes using miRCURY™ RNA isolation kit (Exiqon, Inc.; now Qiagen) according to the instructions of the Supplier. Exosomal RNA concentration was measured using NanoDrop™ 8000 spectrophotometer. The approximate size of exosomal RNAs was analyzed on BioAnalyzer and by 5' end labeling and their separation on denaturing gel. Differential expression of RNAs in exosomes from P19 cells and P19 neurons was determined by RNA-Seq method. Double stranded barcoded cDNA libraries were generated and sequenced on Illumina NextSeq 500 platform. Three biological replicates were used from P19 cells. P19 neurons exosomes were from P19 neurons at 8, 10, 12 days of differentiation. RNA-Seq data was analyzed using bioinformatics pipeline.

overall_design: Six biological replicates were analyzed by RNA-Seq method. Three samples were from undifferentiated P19 cells and three samples were from P19 neurons.

first: Antje

last: Anji

first: Srinivas

last: Mummidi


title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma [RNA-seq]

first: Masaki

last: Fukuyo

summary: To identify the significant EBV-LMP1 inducible methylation genes in nasopharyngeal cancer, two cell lines (NP69T, NP69T-LMP1) were subjected to RNA-seq analysis.

overall_design: RNA analysis with EBV-LMP1 inducible methylation genes.

first: Satoru

last: Kondo

first: Atsushi

last: Okabe

first: Takuya

last: Nakagawa

first: Keisuke

last: Matsusaka

first: Bahityar

last: Rahmutulla

first: Hirotomo

last: Dochi

first: Harue

last: Mizokami

first: Yuki

last: Kitagawa

first: Tomoya

last: Kurokawa

first: Masato

last: Mima

first: Kazuhira

last: Endo

first: Hisashi

last: Sugimoto

first: Naohiro

last: Wakisaka

first: Kiyoshi

last: Misawa

first: Tomokazu

last: Yoshizaki

last: Kaneda


title: Ginsenoside Rg3 Reduces the Toxicity of Graphene Oxide Used for pH-Responsive Delivery of Doxorubicin to Liver and Breast Cancer Cells

city: Goteborg

first: Shadi

last: Rahimi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: RNA sequencing experiments revealed that the killing effect of the GO-Rg3-DOX nanoplatform proceeds primarily by downregulation of anti-apoptotic and angiogenesis related genes

overall_design: Cells were seeded onto 6-well plates at a density of 400,000 cells per well and cultured for 24 h before treatment with GO, GO-Rg3-GO-Rg3-DOX, and DOX for 6 h. Medium only was used as the negative control. Three replicates were included from each treatment. After treatment the cells were washed with PBS buffer 3 times.


title: sRNA137 regulation in Sphingomonas melonis TY

status: Public on Feb 24 2023

city: Hangzhou

first: Xiaoyu

last: Wang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

summary: Transcriptome of the wild type (WT) of S. melonis TY and snc137 deleted cells carrying either a plasmid overexpressing SNC137 (Δsnc137 comp.), or an empty control vector (Δsnc137)

overall_design: The wild type (WT) of S. melonis TY and snc137 deleted cells carrying either a plasmid overexpressing SNC137 (Δsnc137 comp.), or an empty control vector (Δsnc137) were grown in Luria-Bertani (LB) culture to an OD600 of 0.6.

first: Lvjing

first: Haixia

first: Zhenmei

last: Lu


title: A-to-I editing is a major contributor to viral and cellular transcriptome diversity in primary effusion lymphoma

city: Nashville

first: John

last: Karijolich

state: TN

address: 1161 21st Ave S MCN B3301 Room / Suite A-4301, MCN B3301 Room / Suite A-4302

department: Pathology Microbiology and Immunology

institute: Vanderbilt University Medical Center

summary: RNA editing is a major contributor to transcriptome diversity with far reaching biological consequences. Adenosine to Inosine (A-to-I) RNA editing is the most common type of RNA editing in animals and is carried out by a family of proteins called adenosine deaminases acting on RNAs (ADARs). Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of several human malignancies including primary effusion lymphoma (PEL). The extent of RNA editing within the KSHV transcriptome in PEL is unclear as is its contribution to regulating the KSHV lifecycle. Herein, we leverage a combination of biochemical and genomic approaches to determine the RNA editing landscape in host- and KSHV transcriptomes during reactivation in PEL. Analysis of host editomes indicates the editing efficiency is increased in reactivation and by analyzing BCBL1 and BC-3 editomes, we discover conserved as well as cell type specific editing events. In addition, we de novo predict and validate viral editing sites within KSHV pre-miR-K12-4. Editing at the stem region regulates miRNA biogenesis while editing within the seed region of mature miR-K12-3p regulates miRNA target specificity and viral transmission. Together, these results expand the transcriptome of PEL cells and describe a role for A-to-I editing KSHV miRNA biogenesis and target specificity.

overall_design: We collected latent and lytic BCBL1 and BC-3 cells 48 h post-dox induction and prepared rRNA-depleted RNA-sequencing libraries generating approximately 100 million reads per biological replicate.

first: Suba

last: Rajendren

first: Xiang

last: Ye

first: Antiana

last: Richardson

first: William

last: Dunker


title: Early adipogenesis is regulated through the newly identified FHL2-NFAT5 signaling complex

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam University Medical Center

summary: To investigate the effect of FHL2 overexpression in the regulation of adipogenic differentiation, we established a stable cell line overexpressing FHL2-GFP and CTRL-GFP by lentiviral transduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3T3-L1 cells overexpressing either FHL2-GFP or CTRL-GFP at day 0 and day 2 of adipocyte differentiation.

first: Maria

last: Clemente-Olivo

first: Miguel

last: Hernandez-Quiles

first: Aldo

last: Jongejan

first: Eric

last: Kalkhoven


title: Effects of zinc deficiency on the regeneration of olfactory epithelium in mice

city: Miyagi

first: Hiroyuki

last: Ikushima

address: 1-1 Seiryotyou Aobaku Sendai

institute: Tohoku Univercity

summary: To investigate the Effect of Zinc Deficiency on Olfactory Epithelial Regeneration after Injury by Methimazole

overall_design: Comparative gene expression profiling analysis of RNA-seq data for olfactory mucosa of zinc-deficient and control mice (ZnD, Control).

first: Jun

last: Suzuki

first: Tomotaka

last: Henmi

first: Nobuo

last: Ota

first: Yukio

last: Katori


title: An obesogenic feedforward loop involving ACBP/DBI, GABAA receptors and PPARγ

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: Total liver RNA extracts from adult male mice (3 months old, Gabrg2tm1Wul/J +/+ or Gabrg2tm1Wul/J F77I/F77I) subjected to Regular-chow or High-fat diet (regime duration: 4weeks) were analyzed to describe the effect of Gabrg2tm1Wul/J genetic background to obesity-induced transcriptomic alterations.

overall_design: Regular Chow Diet, Gabrg2tm1Wul/J +/+ (n=3), Regular Chow Diet, Gabrg2tm1Wul/J F77I/F77I (n=5), High-fat Chow Diet, Gabrg2tm1Wul/J +/+ (n=9), High-fat Chow Diet, Gabrg2tm1Wul/J F77I/F77I (n=6).

first: Gerasimos

last: Anagnostopoulos

first: Vincent

last: Carbonnier


title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma [methylation data]

first: Masaki

last: Fukuyo

summary: The comprehensive DNA methylation analysis with nasopharyngeal carcinoma cases with normal nasopharyngeal epithelial tissues, and nasopharyngeal epithelial cell lines. Infinium HumanMethylation850 BeadChip was used to obtain DNA methylation profiles across 850,000 CpG sites. Samples included 2 nasopharyngeal carcinoma cases, 3 normal nasopharyngeal epithelial tissues, and NP69T and NP69T-LMP1 cell lines.

overall_design: Bisulphite converted DNA from the 7 samples were hybridised to the Infinium HumanMethylation850 BeadChip.

first: Satoru

last: Kondo

first: Atsushi

last: Okabe

first: Takuya

last: Nakagawa

first: Keisuke

last: Matsusaka

first: Bahityar

last: Rahmutulla

first: Hirotomo

last: Dochi

first: Harue

last: Mizokami

first: Yuki

last: Kitagawa

first: Tomoya

last: Kurokawa

first: Masato

last: Mima

first: Kazuhira

last: Endo

first: Hisashi

last: Sugimoto

first: Naohiro

last: Wakisaka

first: Kiyoshi

last: Misawa

first: Tomokazu

last: Yoshizaki

last: Kaneda


title: Expansion of quiescent hematopoietic stem cells in mice

city: Tianjin

first: Yao

last: Ma

address: Nanjing Street

institute: Chinese Academy of Medical Sciences

summary: Hematopoietic stem cells (HSCs) are maintained in the quiescent state for protection from exhaustion by a number of self-renewal divisions. To understand the in vivo kinetics of quiescent HSCs, we analyzed the cell cycle of CD201+150+48-Lin-Kit+Sca-1+ cells after transplantation and during development and aging using fluorescent ubiquitination-based cell cycle indicator (Fucci) mice to distinguish HSCs at the G0, G1, and S/G2/M phases. The quiescent HSC population, representing a functional HSC pool, rapidly expanded by three weeks after transplantation and by three weeks of age in development and gradually accumulated in bone marrow with aging. Single-cell RNA-sequencing with flow cytometric index sorting suggested that high CD201 and Sca-1 expression levels and a low level of mitochondrial activity were associated with quiescent HSCs. A novel set of candidate quiescent genes in HSCs was also provided. This study implied that controlling quiescent HSCs is important for the in vivo expansion and maintenance of functional HSCs.

overall_design: scRNA-Seq were successfully performed on 48 mKO2high cells, 48 mKO2low cells, 48 mKO2neg cells and 48 mAG+ cells.

first: Sen

last: zhang

first: Lisha

last: Wang

first: Yan

last: Dong

first: Jinhong

first: Tao

last: Cheng

first: Fang

first: Hideo

last: Ema


title: A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str 1

country: Germany

institute: Hannover Medical School

summary: The clonal selection theory describes the key features of adaptive immune responses of B and T cells. For αβ T cells and B cells antigen recognition and selection principles are known at a detailed molecular level. The precise role of the antigen receptor in γδ T cells remains less well understood. To better understand the role of the γδ T cell receptor (TCR), in particular its specificity for thymic selection of γδ T cells and for γδ T cell biology in general, we generated a novel orthotopic TCRδ transgenic mouse model. We demonstrate a multi-layered functionality of γδ TCRs and diverse roles of CDR3δ-mediated selection during γδ T cell development. Whereas epithelial populations using Vγ5 or Vγ7 chains are affected to only minor extend in their biology in the presence of a single TCRδ chain, pairing with Vγ1 positively selects subpopulations of γδ T cells with distinct programs in several organs, thereby distorting the repertoire.  In conclusion, our data support dictation of developmental tropism together with adaptive-like recognition principles in a single antigen receptor.

overall_design: Murine γδ T cells were isolated from the spleen via Fluorescence-activated cell sorting (FACS) according to the presence of CD3 and γδTCR and the absence of αβTCR, B220 and CD11c, and analyzed using scRNAseq for transcriptome and V(D)J repertoire analysis.

first: Anne

last: Hahn

first: Lisa

last: Vogg

first: Stefanie

last: Brey

first: Andrea

last: Schneider

first: Simon

last: Schäfer

first: Ralph

last: Palmisano

first: Anna

last: Pavlova

first: Inga

last: Sandrock

first: Likai

last: Tan

first: Alina

middle: S

last: Fichtner

first: Immo

last: Prinz

first: Thomas

last: Winkler


title: RNA in extracellular vesicles during adolescence reveal immune, energetic and microbial imprints of early life adversity

city: Atlanta

first: Mar

last: Sanchez

state: GA

address: 954 Gatewood Road NE

institute: Emory University

summary: Comparison of bacterial species in gut microbiome and circulating extracellular vesicles

overall_design: Bacterial DNA sequencing

first: Elyse

middle: L

last: Morin


title: Effect of endothelial ADAM10 deficiency on the aorta in an atherosclerosis mouse model

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

institute: Maastricht University

summary: Mice lacking ADAM10 in endothelial cells (Tie2Cre driven) and flox-control mice were injected with an AAV8-PCSK9 virus and put on a Western-type diet for 10 weeks to induce atherosclerosis. Aorta's (Thoracoabdominal) were isolated (removal of PVAT) and processed for RNA-sequencing.

overall_design: RNAseq of mouse Aorta

first: Emiel

last: van der Vorst

first: Marjo

last: Donners


title: Transcriptome analysis of miRNA–mRNA interactions revealed regulation of multiple signaling pathways in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues under hypoxia stress [RNA-Seq]

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary: Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. Here, we first examine the hypoxia-induced damage of gill tissue by hematoxylin-eosin staining, and then constructed miRNA and mRNA libraries of GIFT gill tissue at 96h of hypoxia stress by a high-throughput sequencing technology, each library has three biological replicates. Gill lamellae of GIFT showed capillary rupture and red blood cell enlargement and overflow under hypoxia stress. Transcription sequencing results showed that the clean reads of miRNA libraries were 9,627,953-13,544,660; the clean reads of mRNA libraries were 43,817,776-53,130,102. Based on the miRNA-mRNA pairs screening principles and mRNA sequencing results, we selected and verified seven differentially expressed miRNAs and their potential target genes. The sequencing results were consistent with the qRT-PCR validation results. These selected miRNA-mRNA pairs are mainly concentrated in the signaling pathways of immune response and metabolic regulation. This study provides new insights into the mechanisms of fish adaptation under hypoxic stress.

overall_design: GIFT used in the experiment was divided into two groups: the acute experimental group and the control group, each group has four replicates. The design of hypoxia stress  were referenced by Yuan et al. Each experimental group was placed in a 500L tank with a density of 30 tails/tank, and the dissolved oxygen conditions were the same as the acclimation condition. Based on the real-time readings of the dissolved oxygen meter in the experiment, the dissolved oxygen was controlled by adjusting the rate of nitrogen and air charged into the water. The acute experimental group reduced the dissolved oxygen to (1. 02 ± 0. 10) mg · L- within 30 minutes 1. The culture conditions of the control group were the same as acclimation condition, and they were fed normally during the experiment. The acute experimental group and the control group were sampled at 96 h after hypoxia stress, and 4 fish were randomly selected from each tank. When sampling, the experimental fish was deeply anesthetized with MS-222, and the second right gill arch were dissected out on the sterilization operation platform, divided into two, and quickly placed in a 1.5 mL centrifuge tube in liquid nitrogen. Quick-freeze used by liquid nitrogen, and then transfer to -80 ℃  refrigerator for storage. In addition, two fish from each tank were randomly collected to sample the second right gill arch, rinsed with physiological saline, and fixed in 4% paraformaldehyde for the preparation of paraffin section.

first: Jie

last: He

first: Yi-Fan

last: Tao

first: Jin-Wen

last: Bao

first: Jun-Hao

last: Zhu

first: Pao

last: Xu


title: Sera of individuals chronically infected with hepatitis B virus (HBV) contain diverse RNA types produced by HBV replication or derived from integrated HBV DNA

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: This study aimed to better characterize the repertoire of serum HBV RNAs during chronic HBV infection in humans, which remains understudied. Using RT-PCR, qPCR, RNA-sequencing and immuno-precipitation, we found that (i) >50% of serum samples bore different amounts of HBV replication-derived RNAs (rd-RNAs); (ii) a few samples contained RNAs transcribed from integrated HBV DNA including 5'-HBV-human-3' RNAs (integrant-derived RNAs or id-RNAs) and 5'-human-HBV-3' transcripts as a minority of serum HBV RNAs; (iii) spliced HBV RNAs were abundant in <50% of analyzed  samples; (iv) most serum rd-RNAs were polyadenylated via conventional HBV polyadenylation signal; (v) pre-genomic RNA (pgRNA) was the major component of the pool of serum RNAs; (vi) area of HBV positions 1531-1739 had very high RNA reads coverage and thus should be used as a target for detecting serum HBV RNAs; (vii) vast majority of rd-RNAs and pgRNA were associated with HBV virions, but not with unenveloped capsids, exosomes, classic microvesicles or apoptotic vesicles and bodies; (viii) considerable rd-RNAs presence in the circulating immune complexes was found in a few samples; and (ix) serum rcDNA and rd-RNAs should be quantified simultaneously to evaluate HBV replication status and efficacy of anti-HBV therapy with nucleos(t)ide analogs.  In summary, sera contain various HBV RNA types of different origin, which are likely secreted via different mechanisms. In addition, since we previously showed that id-RNAs were abundant or predominant HBV RNAs in many of liver and hepatocellular carcinoma tissues comparing to rd-RNAs, there is likely a mechanism favoring the egress of the replication-derived RNAs.

overall_design: The serum samples collected from individuals chronically infected with HBV were analyzed for serum HBV RNA species using RNA-seq

first: Igor

last: Zaiets

first: Stephan

last: Menne

first: Steven

last: Weinman

first: Severin

middle: O

last: Gudima


title: PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)

city: West Lafayette

first: Emily

middle: C.

last: Dykhuizen

state: IN

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Using H3K14Ac and PHF10 ChIP-seq, along with CLIP-seq in Caki2 renal cancer cells, we demonstrate here that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

overall_design: Examination of H3K14Ac histone modification and PHF10 localization in Caki2 cells re-expressing V5-tagged wildtype or BD2 mutant (SKY) PBRM1 using ChIP-seq, done in 2 biological replicates

first: Alisha

last: Dhiman


title: PBRM1 bromodomains associate with RNA to facilitate chromatin association (CLIP-seq)

overall_design: Examination of RNA binding partners of wildtype and BD2 mutant (SKY) PBRM1 using CLIP-seq in Caki2 renal cancer cells. Empty Vector is the control.


title: Glucocorticoid promotes fatty acids metabolism in hypertrophic scar tissues and fibroblasts via the microRNA

city: Xi'an

first: huayu

address: No. 28 Road

institute: Fourth

summary: Hypertrophic scar (HS) is a skin lesion due to abnormal wound healing after skin injury; histologically, HS is characterized by deposition of excessive amounts of the extracellular matrix and collagen produced by wound healing-induced proliferative fibroblasts. Clinically, HS management includes surgical resection of HS, topical glucocorticoid therapy or drug injections, pressure therapy, fractional carbon dioxide laser therapy, and cryotherapy. In terms of non-surgical therapy, glucocorticoids (like Triamcinolone acetonide, a synthetic corticosteroid medication used topically to treat various skin conditions) was able to effectively inhibit HS formation safely for decades. The effects of glucocorticoids may either be due to its anti-inflammatory, anti-allergenic and immunomodulatory effects or activate fatty acids metabolism by promotion of lipid accumulation in fibroblasts. However, it is no clear why and how glucocorticoids-upregulated fatty acid metabolisms benefit in HS treatment and prevention.And it remains to be defined how altered microRNAs regulated-fatty acid metabolism involved in pathological scars.

overall_design: These patients were diagnosed by routine pathological examination and were given local injections of glucocorticoid triamcinolone acetonide mixed with lidocaine in for more than 3 months. Patients who had received lidocaine treatment were enrolled as controls. Patients received surgical treatment to resect the HS tissues.

first: Huayu

last: Li


title: PBRM1 bromodomains associate with RNA to facilitate chromatin association

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

overall_design: Refer to individual Series


title: Effect of platycodon D on gene expression in AZ-521 cell line

status: Public on Feb 23 2023

first: Guangzhao

last: Pan

address: Dongfang street

department: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

summary: We used the data obtained from three independent repeats of RNA-seq of AZ521 cell line for gene expression profile analysis.

overall_design: To further explore the underlying mechanisms of the anti-gastric cancer activity of platycodon D, we performed RNA-sequencing in AZ-521 cells after treatment with 10μM platycodon D for 48h. The control groups were treated with DMSO.

first: Qianqian

first: Zhonglan

last: Wang

first: Jiang-Jiang

last: Qin


title: The NAD + Precursor Nicotinamide Riboside Rescues Mitochondrial Defects and Neuronal Loss in iPSC, iPSC derived Neural Stem Cells and cortical Organoid of Alpers’ Disease

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary:
To investigate the transcriptomic profile and molecular machnisiums using RNA sequecning analysis for the iPSC derived neural cells and brain organoids from the patient of Alpers’ Disease
We then performed gene expression profiling analysis using data obtained from RNA-seq of the iPSC derived neural cells and brain organoids from the patient of Alpers’ Disease and healthy controls

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for  neural cells and brain organoids from the patient of Alpers’ Disease and healthy controls

**RAW data not provided due to patient privacy laws**

first: Yu

last: Hong

first: Kristina

middle: X


title: Genes with specificity for expression in the round cell layer of the growth plate are enriched in genomewide association study (GWAS) of human height

city: Boston

first: Nora

middle: E

last: Renthal

state: MA

address: 3 Blackfan Circle

department: Endocrinology

institute: Boston Children's Hospital

summary: Human adult height reflects the outcome of childhood skeletal growth. Growth plate (epiphyseal) chondrocytes are key determinants of height. As epiphyseal chondrocytes mature and proliferate, they pass through three developmental stages, which are organized into three distinct layers in the growth plate: (i) resting (round), (ii) proliferative (flat), and (iii) hypertrophic. Recent genomewide association studies (GWASs) of human height identified numerous associated loci, which are enriched for genes expressed in growth plate chondrocytes. However, it remains unclear which specific genes expressed in which layers of the growth plate regulate skeletal growth and human height. To connect the genetics of height and growth plate biology, we analyzed GWAS data through the lens of gene expression in the three dissected layers of murine newborn tibial growth plate. For each gene, we derived a specificity score for each growth plate layer and regressed these scores against gene-level p values from recent height GWAS data. We found that specificity for expression in the round cell layer, which contains chondrocytes early in maturation, is significantly associated with height GWAS p values (p = 8.5 × 10−9); this association remains after conditioning on specificity for the other cell layers. The association also remains after conditioning on membership in an “Online Mendelian Inheritance in Man (OMIM) gene set” (genes known to cause monogenic skeletal growth disorders, p < 9.7 × 10−6). We replicated the association in RNA-sequencing (RNA-seq) data from maturing chondrocytes sampled at early and late time points during differentiation in vitro: we found that expression early in differentiation is significantly associated with p values from height GWASs (p = 6.1 × 10−10) and that this association remains after conditioning on expression at 10 days in culture and on the OMIM gene set (p < 0.006). These findings newly implicate genes highlighted by GWASs of height and specifically expressed in the round cell layer as being potentially important regulators of skeletal biology. © 2021 American Society for Bone and Mineral Research (ASBMR).

overall_design: WT GPLCs were grown for 1, 3, 5, or 10 days in culture. RNAseq was performed to compare these timepoints.

first: John

last: Baronas

first: Joel

last: Hirschhorn


title: Epigenetically programmed ‘stem-like’ tissue resident memory CAR T-cells exhibit robust activity against solid and liquid tumors [bulk_ATAC]

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T-cells have shown remarkable success in the therapy of hematological malignancies, but they have not yet proven nearly as effective in treating non-hematopoietic cancers. This study proposes augmentation of CAR T-cell function and accumulation in solid tumors by modifying the epigenetic landscape that governs early memory differentiation and adaptation to tissue residency. We identified that a key factor in human tissue-resident memory CAR T-cell (CAR-TRM) formation is activation in the presence of the pleotropic cytokine, TGF-β, which epigenetically enforces a core transcriptional program of both ‘stemness’ and sustained tissue residency. This strategy results in a readily actionable in vitro production method for engineering peripheral blood T-cells into large numbers of ‘stem-like’ CAR-TRM cells resistant to epigenetically-imposed exhaustion that possess enhanced ability to accumulate in situ and rapidly kill cancer cells for more effective immunotherapy.

overall_design: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. CD8+ CAR T-cells were magnetically isolated using anti-mesothelin-coated beads (ACROBiosystems) and anti-CD8 microbeads (Miltenyi Biotec), After elimination of dead cells, 100,000 CD8+ CAR T-cells were cryopreserved for ATAC-seq library preparation.

first: In-Young

first: Estela

last: Noguera-Ortega

first: Robert

last: Bartoszek

first: Sierra

last: McDonald

first: Erik

last: Williams

first: Mega

last: Davis

first: Julie

last: Jadlowsky

first: Gabriela

last: Plesa

first: Anne

last: Chew

first: Shelley

last: Berger

first: Edmond

last: Moon

last: Albelda

first: Joseph

last: Fraietta


title: Plasminogen Activator Inhibitor-1 Regulates the Cytoskeleton and Intrinsic Stiffness of Vascular Smooth Muscle Cells

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

summary: SMCs express plasminogen activator inhibitor-1 (PAI-1), which regulates SMC function and vascular remodeling. However, whether PAI-1 controls SMC cytoskeletal dynamics and stiffness is unknown, and the causal role of PAI-1 in arterial stiffening is undefined.  SMCs from human coronary arteries and aortae of wild-type vs. PAI-1-deficient mice were cultured with or without PAI-039, a specific PAI-1 inhibitor, after which cell stiffness was measured by atomic force microscopy, filamentous actin structures were assessed by confocal microscopy, and the activities cofilin, LIM domain kinase 1 (LIMK), slingshot homolog 1 (SSH), and AMP-activated protein kinase (AMPK) were measured. RNA sequencing was performed to determine the effects of PAI-039 on SMC gene expression. Effects of PAI-039 on aortic stiffness were assessed by pulse wave velocity.   PAI-039 significantly reduced intrinsic stiffness of human SMCs, which was accompanied by significant decreases in cytoplasmic actin filaments. Similar effects were observed in wild-type, but not in PAI-1-deficient SMCs. Mechanistically, PAI-039 significantly increased the activity of cofilin, an actin depolymerase, in SMCs expressing PAI-1, but not in PAI-1-deficient cells.  PAI-039 had no significant effects on LIMK or SSH activity. RNA-sequencing analysis suggested that PAI-039 up-regulates AMPK signaling in SMCs, which was confirmed by western blotting. Inhibition of AMPK prevented activation of cofilin by PAI-039. In mice, PAI-039 significantly decreased aortic stiffness without significantly altering peri-aortic fibrosis.   PAI-039 decreases intrinsic SMC stiffness by reducing cytoplasmic stress fiber content. These effects are mediated by AMPK-dependent activation of cofilin. PAI-039 also decreases aortic stiffness in vivo. These findings suggest that PAI-1 is an important regulator of the SMC cytoskeleton and that pharmacologic inhibition of PAI-1 has potential to treat cardiovascular diseases mediated by accelerated arterial stiffening.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Human coronary artery smooth muscle cells treated with an inhibitor of plasminogen activator inhibitor (PAI-1), PAI-039 vs. vehicle control. Each group had 3 replicates.

first: Hekmat

last: Khoukaz

first: Manisha

last: Vadali

first: Alex

last: Schoenherr

first: Francisco

middle: I

last: Ramirez-Perez

first: Mariana

last: Morales-Quinones

first: Zhe

last: Sun

first: Shumpei

last: Fujie

first: Christopher

last: Foote

first: Zhen

last: Lyu

first: Shuai

last: Zeng

first: Yan

last: Ji

first: Shi

middle: Y

last: Chen

first: Michael

last: Hill

first: Luis

last: Martinez-Lemus

first: William

middle: P

last: Fay


title: Epigenetically programmed ‘stem-like’ tissue resident memory CAR T-cells exhibit robust activity against solid and liquid tumors [bulk_RNA]

first: Inyoung

last: Jung

overall_design: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. CD8+ CAR T-cells were magnetically isolated using anti-mesothelin-coated beads (ACROBiosystems) and anti-CD8 microbeads (Miltenyi Biotec), followed by resuspension in 500µL of TRIzol (Invitrogen). Total RNA was prepared using RNA Clean & Concentrator™ kits (Zymo Research) following the manufacturer’s instructions. Transcriptome sequencing was performed by Novogene using the NovaSeq 6000 system (Illumina, 150bp paired end reads).

first: In-Young

first: Estela

last: Noguera-Ortega

first: Robert

last: Bartoszek

first: Sierra

last: McDonald

first: Erik

last: Williams

first: Mega

last: Davis

first: Julie

last: Jadlowsky

first: Gabriela

last: Plesa

first: Anne

last: Chew

first: Shelley

last: Berger

first: Edmond

last: Moon

first: Steven

last: Albelda

first: Joseph

last: Fraietta


title: Let-7 mediates the pro-lymphangiogenic effect of melanosomes

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

institute: Sheba Medical Center at Tel HaShomer

summary: Melanoma-derived melanosomes traffic mature let-7i to lymphatic endothelial cells, which mediate pro-lymphangiogenic phenotypic changes by the induction of type I interferon signaling. Further, transcriptome analysis upon treatments with melanosomes or let-7i reveal the enhancement of IFI6 expression in lymphatic cells.

overall_design: Evaluation of gene expression in HDLECs transfected with let-7i or a scrambled control miRNA using a microarray.

first: Shoshana

last: Greenberger

first: Carmit

last: Levy


title: Single cell transcriptome and surface protein expression analysis identify OX40+GITR+ pathogenic T helper 17 in anklyosing spondilytis [CITE-seq]

city: Daejeon

first: Song

last: Woogil

address: KAIST, Daejeon 34141, Korea

department: Graduate School of Medical science and engineering

country: South Korea

institute: KAIST

summary: We unveiled the characteristics of pTh17s, which are polyfunctional IL-17A and IFN-γ-producing memory CD4+ T cells. scRNA-seq and cytometry analysis found that the co-expression of OX40 and GITR is increased in pTh17 cells.

overall_design: We performed transcriptome and cytometric analysis to understand pTh17.

first: Kijong

last: Yi

first: Sungsin

last: Jo

first: Woogil

last: Song

first: Jeong

last: Lee

first: Eun

first: Tae-Jong

last: Kim


title: Single-Cell RNA Sequencing Analysis of Human Embryonic Stem Cell-Derived Neural Organoids

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

institute: STEMCELL Technologies

summary: Human pluripotent stem cell-derived 3D neural organoids have been shown to recapitulate the major features and cytoarchitecture of early human brain development. We used three commercially available kits: STEMdiff™ Cerebral Organoid Kit, STEMdiff™ Dorsal Forebrain Organoid Differentiation Kit, and STEMdiff™ Ventral Forebrain Organoid Differentiation Kit. These neural organoids contain unique and diverse cell types which model the early brain and are patterned with developmental cues. Here, we sought to investigate the cellular diversity of these organoids using single-cell RNA sequencing.

overall_design: We generated dorsal forebrain, ventral forebrain, and cerebral organoids from H9 human embryonic stem cells (hESCs) that were subjected to single-cell dissociation on day 50 using an optimized dissociation protocol. We further utilized cell hashing to label multiple organoids (4 per condition) to explore intra-organoid variability within a culture.

first: Leon

middle: H

first: Eloi

last: Mercier

first: Adam

last: Añonuevo

first: Mark

last: Hills

first: Allen

middle: C

last: Eaves

first: Sharon

last: Louis

first: Erin

last: Knock


title: Neuronal activity-related transcription is blunted in immature compared to mature dentate granule cells

city: La Jolla

first: Fred

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Immature dentate granule cells (DGCs) generated in the hippocampus during adulthood are believed to play a unique role in dentate gyrus function. Although immature DGCs have hyperexcitable membrane properties in vitro, the consequences of this hyperexcitability in vivo remain unclear. In particular, the relationship between experiences that activate the dentate gyrus, such as exploration of a novel environment (NE), and downstream molecular processes that modify dentate gyrus circuitry in response to cellular activation are unknown in this cell population. We first performed quantification of immediate early gene proteins in immature (5-week-old) and mature (13-week-old) DGCs from mice exposed to a NE. Paradoxically, we observed lower immediate early gene protein expression in hyperexcitable immature DGCs. We then isolated nuclei from active and inactive immature DGCs and performed single nuclei RNA-Sequencing. Compared to mature nuclei collected from the same animal, immature DGC nuclei showed less activity-induced transcriptional change, even though they were classified as active based on expression of ARC protein. These results demonstrate that the coupling of spatial exploration, cellular activation, and transcriptional change differs between immature and mature DGCs, with blunted activity-induced changes in immature cells.

overall_design: Single-nucleus RNA-seq of mouse dentate granule neurons (PROX1+CTIP2+) collected after the mouse was exposed to a novel environment. Cells are either immature (approximately 5 weeks of age) or mature and either active (ARC protein detected at sort) or inactive (ARC protein not detected). Two time points after the novel environment exposure are included, either 1hr or 4hr.

first: Sarah

last: Parylak

first: Fan

last: Qiu

first: Sara

last: Linker


title: Transcriptomic analysis of human lens and age-related cataract

city: Shanghai

first: Yingying

last: Hong

address: No.83 Fenyang Road

department: Ophthalmology

institute: Eye and ENT hospital (Fudan university)

summary: As an ageing population trend, age-related cataracts (ARC) continue to be the primary cause of reversible severe vision impairment and blindness worldwide, with an increasing incidence. The primary disease mechanism of ARC formation is metabolic abnormalities and oxidative stress mainly caused by increasing age. Additionally, ultraviolet B exposure, systematic disease factors (diabetes and hypertension), and lifestyle factors (smoking, drinking, and malnutrition) are the risk factors for ARC formation. Although surgical removal of the onset lens and replacement of the intraocular lens is currently the only effective treatment method with a high success rate and a high-cost fee, cataracts have so far lacked effective therapeutic drugs leading to a heavy burden on the patient's family and society. Therefore, we performed transcriptomic analysis of human lens and ARC to investigate the possible pathogenesis of lens opacification in ageing people.

overall_design: Total RNA obtained from the anterior lens capsules

first: Yinghong

last: Ji


title: Single cell transcriptome and surface protein expression analysis identify OX40+GITR+ pathogenic T helper 17 in anklyosing spondilytis.

first: Song

last: Woogil


title: SRSF3-mediated Ki67 exon 7 alternative splicing regulates Head and Neck Squamous Cell Carcinoma progression via AKR1C2

city: Wuhan

first: Miaomiao

last: Liu

state: Hubei

address: 237 Luoyu Road, Hongshan District, Wuhan, China

institute: Wuhan University

summary: The roles of Ki67 exon 7 have rarely been reported.SCC-9 cells were transfected with siE7 and siNC on day 0 and day 2, total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and then used for mRNA sequencing (Wuhan Seqhealth Co., Ltd. China).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCC-9 cells treated with Ki67 exon 7 targeting siRNA and nonspecific siRNA.

first: Jihua

last: Guo

first: Rong

last: Jia


title: Mechanisms of immunoediting and immune evasion in AML1-ETO (AE) NrasG12D AML.

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer

summary: Immunoediting describes the dynamic sculpting of cancer cells to evade cancer immune control, thereby enabling the development of tumors in an immunocompetent host resulting in the outgrowth of cancer cells with reduced immunogenicity.

overall_design: Our objective was to assess the effect of immunoediting on the transcriptional landscape. To that extend, we first generated AML from oncogenes AML1-ETO and NrasG12D expressed from the retrovirus MSCV-IRES-GFP, by transducing it into lineage depleted bone marrow cells. Viable GFP+ expressing cells were transplanted into Rag2-/-γc-/- recipients and all recipients developed AML. We then extracted and transplanted GFP+ AML cells from spleen into either into C57BL/6J immunocompetent or Rag2-/-γc-/- immunodeficient secondary recipient. Finally after secondary recipients developed AML, GFP+ cells from spleens were isolated and RNA sequencing was performed.

first: Rebecca

last: Austin

first: Megan

last: Bywater

first: Steven

middle: W

last: Lane


title: Shear Stress Mediated M2 Macrophage Exosome miR-423-5p Induced Osteogenic Differentiation of BMSCs

status: Public on Feb 22 2023

city: Beijing

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: In order to find the M2 type macrophage secretion miRNA mediated by shear stress, and then regulate the bone marrow mesenchymal stem

overall_design: We extracted exosomes from the supernatant of M2 type macrophages and blank M2 type macrophages under shear stress

first: Liu

last: Wentao

first: Bai

last: Shengbin

first: Yang

last: Yi


title: Single cell transcriptome and surface protein expression analysis identify OX40+GITR+ pathogenic T helper 17 in anklyosing spondilytis [scRNA-seq]

overall_design: We performed transcriptome and cytometric analysis to understand pTh17. And in vivo suppression of ligand-receptor interactions via OX40 and GITR effectively suppressed clinical arthritis and decreased pTh17 cells in the curdlan-injected SKG mouse model.

first: Kijong

first: Sungsin

last: Jo

first: Woogil

last: Song

first: Jeong

last: Lee

first: Eun

first: Tae-Jong

last: Kim


title: Mechanisms of immunoediting and immune evasion in MLL-AF9 AML.

overall_design: Our objective was to assess the effect of immunoediting on the transcriptional landscape. To that extend, we first generated AML from oncogene MLL-AF9 expressed from the retrovirus MSCV-IRES-GFP, by transducing it into lineage depleted bone marrow cells. Viable GFP+ expressing cells were transplanted into Rag2-/-γc-/- recipients and all recipients developed AML. We then extracted and transplanted GFP+ AML cells from spleen into either into C57BL/6J immunocompetent or Rag2-/-γc-/- immunodeficient secondary recipient. Finally after secondary recipients developed AML, GFP+ cells from spleens were isolated and RNA sequencing was performed.


title: Stacking the odds: multiple sites for HSV-1 latency

city: Los Angeles

first: Shaohui

last: Wang

address: 8700 Beverly BLVD

department: Surgery

institute: Cedars Sinai Medical Center

summary: investigated the possible contribution of various cells (i.e., B cells, DCs, fibroblasts, glial cells, ILCs, macrophages, microglia, monocytes, NK cells, neurons, neutrophils, and T cells) isolated from TG of latently infected mice to HSV-1 latency

overall_design: immune cells were enriched and pooled back with original TG single cells, so that multiple type of cellls in TG can be analyzed by single cell sequencing

first: Xueying

first: Alex

last: Rajewski

first: Chintda

last: Santiskulvong

first: Homayon

last: Ghiasi


title: Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

summary: Volumetric muscle loss (VML) is an acute trauma that results in persistent inflammation, supplantation of muscle tissue with fibrotic scarring, and decreased muscle function. The cell types, nature of cellular communication, and tissue locations that drive the aberrant VML response have remained elusive. Herein, we used spatial transcriptomics on mouse and canine models of VML and observed VML engenders a unique spatial pro-fibrotic pattern driven by crosstalk between fibrotic and inflammatory macrophages and mesenchymal derived cells. The dysregulated response was conserved between murine and canine VML models, albeit with varying kinetics, and impinged on muscle stem cell mediated repair. Targeting this circuit in a murine model resulted in increased regeneration and reductions in inflammation and fibrosis. Collectively, these results enhance our understanding of the cellular crosstalk that drives aberrant regeneration and provides further insight into possible avenues for fibrotic therapy exploration.

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus

overall_design: Spatial gene expression profiling was performed on flash-frozen, OCT embedded muscle tissue from mouse and canine post VML injury. Canine tissues were collected from two animals in different wound locations for a total of three spatial samples. Four replicates were generated for each treatment in mice (vehicle and ITD1) at 7 days post injury, and two replicates were generated for 14 days post injury.

first: Jacqueline

last: Larouche

first: Emily

last: Wallace

first: Bonnie

middle: D

last: Spence

first: Scott

last: Johnson

first: Mangesh

last: Kulkarni

first: Eric

last: Buras

first: Bryan

middle: N

last: Brown

first: Stephen

middle: F

last: Badylak


title: Expression profiling following Nrf2D29H or Keap1R554Q expression in mouse embryonic fibroblasts

city: Tampa

first: Chang

last: Jiang

state: FL

address: 16309 Hyde Manor Dr.

department: Cancer Physiology

institute: H. Lee Moffitt Cancer Center and Research Institute

summary: We generated mouse embryonic fibroblasts from genetically engineered mouse models harboring conditional alleles of Nfe2l2(Nrf2)D29H and Keap1R554Q and induced expresison of these mutations using adenoviral Cre. Gene expression was profiled.

overall_design: MEFs were isolated at embryonic day 13.5-14.5. Homozygous Nrf2D29H or Keap1R554Q MEFs were infected with empty adenovirus (control) or adenoviral cre to induce expression of the mutations. Keap1 was functionally wild-type in adenoviral mock conditions, and homozygous mutant after Ad-Cre infection. Nrf2 was functionally knock-out prior to infection and in adenoviral-mock cells, and homozygous D29H after infection with adenoviral Cre. MEFs were collected 4 days after infection for RNA.

first: Gina

middle: M

last: DeNicola