title: CircRFWD3 promotes HNSCC metastasis by modulating miR-27a/b/PPARγ signaling

city: Chengdu

first: Ying

last: Wang

address: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan

institute: West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan

summary:
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer in the world. Its mortality rate is high, and metastasis is one of the main reasons for the poor prognosis. Therefore, it is quite urgent to elucidate the mechanism of HNSCC metastasis and to discover valuable therapeutic targets. Circular RNAs (circRNAs) have been characterized as key regulators of gene expression in numerous malignances. However, the role of circRNAs in HNSCC metastasis remains largely unknown. In this study, circRFWD3, was defined. We demonstrated a novel circRNA, circRFWD3, was significantly upregulated in HNSCC tissues and cell lines by circRNA microarray analysis and qPCR. Notably, high expression of circRFWD3 is related to highly aggressive HNSCC cell lines and lymph node metastasis in HNSCC patients. After that, Sanger sequencing, RNase R and actinomycin D assay were performed to verify the ring structure of circRFWD3. Then functional experiments found it could promote the metastasis of HNSCC cells both in vitro and in vivo. Mechanistically, dual luciferase reporter assay, FISH, RIP, RNA pull-down, RNA-seq and western blot experiments were employed, and found that circRFWD3 served as a miRNAs sponge for miR-27a/27b, leading to upregulation of PPARγ, and then activate NF-κB/MMP13 signaling. Finally, ISH and IHC were carried out to determine the expression levels and clinical significances of circRFWD3 and PPARγ in clinical cohorts of HNSCC. According to the analysis results from two independent HNSCC cohorts, upregulated expression of circRFWD3 and PPARγ were positively associated with worse survival in patients with HNSCC. Overall, our results uncover that circRFWD3 acts a critical role in promoting the aggressiveness of HNSCC cells and is a prognostic marker for the disease, indicating that circRFWD3 may act as a potential therapeutic target in HNSCC.
CircRNA microarray analysis of HNSCC

overall_design: A total of 3 pairs of tumors and adjacent non-tumor tissues  were collected from pathologically diagnosed patients with HNSCC.Nine tumor tissues were divided into groups of three, paired adjacent nontumor tissues were also divided into corresponding groups of three. Then a total of six groups tissues were deployed for circRNA microarray (Arraystar Inc.) and analyzed using Arraystar Human circRNA Array.

first: Zihao

last: Wei

first: Jiakuan

last: Peng

first: Honglin

last: Li

first: Junjie

last: Gu

first: Ning

last: Ji

first: Taiwei

first: Xikun

last: Zhou

first: Xin

last: Zeng

first: Jing

first: Qianming

last: Chen


title: Comparative transcriptomics between two potentially toxin-secreting marine annelids: Glycera alba and Hediste diversicolor

status: Public on Nov 29 2023

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

type: Expression profiling by high throughput sequencing

summary: Transcriptome profiling of whole proboscis and body wall of the marine Polychaeta Glycera alba, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2020). Transcriptome profiling of glandular and muscular regions of proboscis of the marine Polychaeta Hediste diversicolor, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2019).

sample_organism:
Hediste diversicolor
Glycera alba

platform_organism:
Hediste diversicolor
Glycera alba

overall_design: Three samples (independent replicates) were analysed (either organ for both species). Total RNA from all samples of Glycera alba (GaPR1, GaPR2, GaPR3, GaBW1, GaBW2, GaBW3) was used to build the main library. Total RNA from Replicate 2 of Hediste diversicolor (HdG2 and HdPR2) was used to build the main library.

first: Inês

last: Moutinho Cabral

first: Carolina

last: Madeira

first: Ana

middle: R

last: Grosso

middle: M


title: POU5F1 induces cellular heterogeneity in colorectal cancer

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

country: USA

institute: University of Southern California

summary: In this study, we aimed to identify CRC treatment resistance mechanisms by focusing on POU5F1-positive cells. Despite the small number of POU5F1-positive cells, single POU5F1-expressing cells produced heterogeneous cell populations in vitro and in vivo colorectal cancer organod. This study unveils a mechanism of CRC treatment resistance and highlights the potential of POU5F1-expressing cells as CTCs.

overall_design: Single-cell analysis was performed for a better understanding of this phenomenon was speculated to elucidate clinical treatment resistance, such as recurrence and relapse.

first: Shiki

last: Fujino

first: Norikatsu

last: Miyoshi


title: Distinctive Biological Properties Between Mesenchymal Stem Cells Spheroids and Clumps of Mesenchymal Stem Cells/Extracellular Matrix Complexes in 3D Culture Systems.

status: Public on Nov 28 2023

city: Hiroshima-city

first: MAI

last: YOSHINO

address: 1-2-3 Kasumi Minami-ku

country: Japan

institute: Hiroshima University

summary: mRNA sequencing of mesenchymal stem cells in 2D culture systems, mesenchymal stem cells spheroids and mesenchymal stem cells/extracellular matrix in 3D culture systems to profile gene expressions

overall_design: Total RNA was extracted from three distinct cell culture groups: (1) 2D cultures in 24-well plates seeded at 2.0×105 cells/well (n=3), (2) a set of eight MSC spheroids, each consisting of 2.5×104 cells (n=3), and (3) a single C-MSCs formed from 2.0×105 cells (n=3). RNA extraction was carried out using RNA-iso (Takara, Otsu, Japan) and the concentration of the extracted RNA was quantified spectrophotometrically at wavelengths of 260 and 280 nm. The construction and sequencing of the cDNA library were carried out by the Beijing Genomics Institute using the DNBSEQ platform. This project contains 9 samples of (3 from MSCs in 2D culture systems, 3 from MSCs spheroids and 3 from C-MSCs) RNA-seq data.

first: Mikihito

last: Kajiya

first: Toshinori

last: Ando

first: Hiroki

last: Yoshii

first: Mai

last: Yosihno


title: Intranasal SIIN-Q11 induces comparable activation of OT-1 cells in Batf3KO and WT mice

city: Chicago

first: Anita

last: Chong

state: IL

address: 5841 South Maryland Avenue

institute: The University of Chicago

summary: To investigate if CD11b+ DCs contribute to OT-1 priming, genome transcriptome analysis was performed to compare the quality of OT-1 activation in WT or Batf3KO mice.

overall_design: Comparative gene expression profiling analysis of OT-1 cells in Batf3KO and WT mice on day 6 after I.N. SIIN-Q11

first: Youhui

last: Si

first: Yihan

last: Wang


title: Transcripts related to lung cancer disease in blood samples obtained from diagnostic and pre-diagnostic cohorts

city: Tromsø

first: Ilona

last: Urbarova

address: Hansine Hansens veg 18

department: Department of Community Medicine

country: Norway

institute: UiT The Arctic University of Norway

summary: Lung cancer (LC) mortality rates are still increasing globally. As survival is linked to stage, there is a need to identify markers for earlier LC diagnosis and individualized treatment. The circulating transcriptome of LC patients represents a source of potential LC biomarkers. We used genome-wide RNA sequencing to identify LC candidate markers by comparing expression of >60,000 genes in whole blood specimens taken at LC diagnosis from cases (n=128) and controls (n=62). Further, we evaluated expression of these markers in two population-based studies with pre-diagnostic whole blood specimens taken up to eight years prior to LC diagnosis (n=163 cases, 184 matched controls). We identified 14 candidate genes in whole blood associated with LC at diagnosis. High expression of ANXA3, ARG1 and HP was strongly associated with lower survival in late-stage LC cases (adjusted p-values 0.009, 0.03, and 0.007, respectively). We observed strong association of ANXA3 and ARG1 expression with LC also in the pre-diagnostic blood specimens, and especially with late-stage LC within two years of diagnosis (odds ratios 3.47 and 5.00, respectively). Although blood neutrophils were elevated in LC cases both in the diagnostic and pre-diagnostic blood specimens, the observed associations of ANXA3, ARG1 and HP with LC were preserved also after adjusting for elevated blood neutrophils. Our results indicate that in whole blood, increased expression levels of ANXA3, ARG1 and HP are diagnostic and prognostic markers of late-stage LC.

overall_design:
mRNA expression profiles from mRNA sequencing of whole blood from lung cancer patients at diagnosis (n=128) and individuals with confirmed negative LC (n=62).

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Therese

middle: H

last: Nøst

first: Anne

last: Skogholt

first: Yi-Qian

last: Sun

first: Xiao-Mei

last: Mai

first: Bjørn

last: Grønberg

first: Torkjel

last: Sandanger

first: Pål

last: Sætrom


title: Transcriptional profiling of rainbow trout infected with   Aeromonas salmonicida

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

summary: The rainbow trout (Oncorhynchus mykiss) is one of the most important aquaculture species worlwide. In this study, transcriptional profiling of skin by oligonucleotide microarray was applied to rainbow trout individuals infected with A. salmonicida, to identified enriched genes involved in pathogen response.

overall_design: Gene expression changes in skin after infection were assessed with 44 k oligonucleotide microarray using Rainbow trout samples (n=7)

first: Roman

last: Wenne


title: Retinoic Acid Receptor β Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease

city: New York

first: Lorraine

middle: J

last: Gudas

state: NY

address: 1300 York Ave E405

department: Pharmacology

institute: Weill Cornell Medicine

summary: Background & Aims: Alcohol-associated liver disease (ALD) is associated with loss of vitamin A (retinoids), increased steatosis, and greater oxidative stress. Although a strong correlation has been observed between loss of retinoids and ALD, if retinoid loss plays a causal role in the pathophysiology of ALD is not clear. Approach & Results: Based on our prior published data indicating that a selective retinoic acid receptor beta (RARβ) agonist limits nonalcohol-related liver disease (NAFLD) pathology, we generated AlbCre;RARβ knockout (BKO) mice and fed these mice a Lieber DeCarli ethanol diet (ETOH). We also generated cultured human hepatocytes (HepG2) that lack RARβ (RARβ-KO) and treated them with ETOH.        Here we show that the livers of BKO mice develop greater steatosis, oxidative stress (assessed by 4-HNE), cell proliferation, and hypertrophy on the ETOH diet when compared to wild type (WT). Compared to ETOH-WT mice, the ETOH-BKO mice also exhibit higher hepatic transcript levels of ATF4, MYC, a subset of integrated stress response (ISR) genes (Trib3, Asns, Nqo1, and Hmox1), and the common ATF4 and MYC target, 4EBP1(EIF4EBP1). In RARβ-KO HepG2 cells, ETOH treatments (24 and 72h) resulted in more rapid and greater development of reactive oxygen species compared to parental HepG2. Notably, even without ETOH, ATF4 protein was higher in the RARβ-KO than in parental HepG2. Conclusions: Our research identifies hepatocyte RARβ as a crucial negative regulator of oxidative stress, MYC, ATF4, and proliferation in ALD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse liver tissue of females C57Bl/6 mice treated with an ethanol-based diet and a matched control diet.

first: Marta

last: Melis

first: Steven

middle: E

last: Trasino

first: Xiao-Han

last: Tang

first: Andrew

last: Rappa

first: Tuo

last: Zhang

first: Lihui

last: Qin


title: Transcriptional signatures in contrasting cultivars of Barley during early reproductive development of meristem

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: This study assessed developing IM tissues at double ridge stage of two contrasting cultivars, RD2715 and GP. Transcriptome data revealed a massive transcriptional reprogramming associated with meristem development accompanied by a set of uniquely expressed transcription factors, possible candidates for early and faster development of meristem. The regulation and development in GP are much slower than RD2715 at the same developmental stage, they differ in their transcriptional regulation and developmental pace. This study may further expand our understanding of inflorescence development.

overall_design: Growth and development of meristem in Barley is a result of complex regulatory networks and well-coordinated transcriptional reprogramming modulated by hormonal, photoperiod, nutrient availability and genetic makeup of cultivars. A critical double ridge stage attained by meristems during phase transitions of vegetative meristems to inflorescence meristem has a significant role in developing the number of spikelets and seeds in lateral stages of plant growth and final crop yield. The early development of meristems leads to attaining early critical stages of phenology and plant growth, completing plant ontogeny in a shorter time displays a heat escaping mechanism to avoid the effects of terminal heat stress on crop growth and yield. we compared the RNA sequencing data of developing Inflorescence meristem of contrasting cultivars RD2715 and GP targetting to find the general molecular regulation to unravel probable transcription factors with possible roles in early development and contributing to escape mechanism to terminal heat stress and having possible roles in deciding final yield.

first: Sampath

middle: K

last: Banoth


title: The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Time- and lineage-resolved transcriptional profiling uncovers gene expression programs and clonal relationships that underlie human T lineage specification

city: Vancouver

first: Peter

last: Zandstra

state: British Columbia

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: T cells develop from multi-potent hematopoietic progenitors in the thymus and provide adaptive protection against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors, and their subsequent specification to the T lineage, has been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single cell RNA sequencing revealed that cell-cycle exit, downregulation of the multipotent hematopoietic program, and upregulation of >90 lineage-associated transcription factors all occur within a highly co-ordinated and narrow developmental window. Computational gene-regulatory network inference elucidated the transcriptional logic of T lineage specification, uncovering an important role for YBX1. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and mathematical trajectory inference and discovered that mast and myeloid potential bifurcate from each other early in haematopoiesis, upstream of T lineage restriction. Collectively, our analyses provide a quantitative, time-resolved model of human T cell specification with relevance for regenerative medicine and developmental immunology.

overall_design: For time course and lineage tracing experiments, the following “Cord-blood-optimized” serum-free media was used for T cell differentiation; Iscove’s modified Dulbecco’s medium (IMDM) with GlutaMAX basal medium (Thermo Fisher Scientific, 31980030) supplemented with 20% BIT 9500 serum substitute (STEMCELL Technologies, 09500), 60 μM ascorbic acid (Sigma-Aldrich, A8960), 24 μM 2-mercaptoethanol (Sigma-Aldrich, M3148), 0.05% low-density lipoprotein (STEMCELL Technologies, 02698), stem cell factor (SCF) (23.9 ng/ml; R&D Systems, 255-SC), Flt3L (8.7 ng/ml; R&D Systems, 308-FK), IL-3 (5.3 ng/ml; R&D Systems, 203-IL), CXCL12 (9.7 ng/ml; R&D Systems, 350-NS), IL-7 (10 ng/ml; R&D Systems, 207-IL), and TNFα (4.9 ng/ml; R&D Systems, 210-TA). In parallel work that took place during the course of this study, we developed an improved “PSC-optimized” progenitor T cell differentiation media which supports more efficient survival. We therefore used this media for CRISPR perturbation experiments, and their associated controls, to maximise viable cell recovery. The improved media comprises IMDM with GlutaMAX basal media (Thermo Fisher Scientific, 31980030) with 4% B27 minus Vitamin A (Gibco, 12587010), 60 µM Ascorbic acid (Sigma-Aldrich, A8960), 24µM 2-Mercaptoethanol, SCF (12.37 ng/ml), Flt3L (8.61 ng/ml), IL-3 (0.97 ng/ml; R&D Systems, 203-IL), CXCL12 (97.39 ng/ml), IL-7 (65.25 ng/ml), and TNFα (0.07 ng/ml).  Harvested cells from the EHT culture phase were pelleted, re-suspended in T cell differentiation media at a split ratio of 1:3 (unless otherwise specified), and transferred in 100uL volume per well on to 96 well plates freshly coated with DLL4 and VCAM1 as described above . Cells were incubated at 37°C, 5% CO2. The media was topped up with an additional 100uL of media per well (bringing the total volume of media to 200uL) after 3 or 4 days of progenitor T cell differentiation. Cultures proceeded for up to a maximum of 7 days.  Timecourse dataset We performed a reverse differentiation time course such that new differentiations were initiated every 24 hours for 14 consecutive days. Thus, samples representing each developmental time point could be collected at the same time for parallel capture. For each differentiation time point, we thawed an aliquot of the same cryopreserved stock of iPS11-derived hemogenic endothelial cells produced as described above. For each timepoint, at least 5 independent wells were seeded for downstream pooling. EHT cultures and progenitor T cell differentiations were performed as described above. On the final day of the timecourse, all timepoint samples were harvested and an additional aliquot of the input population was thawed. For samples from the progenitor T cell differentiation stage, cells were harvested by pipetting, whereas for the EHT timepoints, non-adherent cells were harvested by pipetting before adherent cells were harvested using 30uL per well of 0.25%Trypsin EDTA (Thermo Fisher Scientific, 25200072). For the sample coresponding to the passage day, adherent and floating cells were sequenced separately. Each sample was pelleted by centrifugation at 300x g for 5 minutes. Replicate wells were pooled together and washed with PBS. Samples were Fc blocked (BD, 564220) and labelled with zombie-UV viability dye (BioLegend, 423108) on ice in the dark for 20 minutes. Next, each sample was labelled with 0.1 ug of a cell hashing antibody (TotalSeq-B anti-human Hashtag antibodies 1 through 8, BioLegend). Cells were labelled for 30 minutes on ice in the dark. Next, samples were washed 3 times with HF buffer and counted prior to pooling. Samples were combined in to two pools, one for the EHT time points and another for the progenitor T cell differentiation time points. To enrich for Zombie-UV-negative viable cells, the EHT time point pool was subject to Fluorescent Activated Cell Sorting (FACS) using a MoFlo Astrios (Beckman Coulter).  Lineage barcoding dataset In vitro differentiations from cryopreserved CD34+ cells were initiated as described above, with the modification that 7500 cells were seeded on to one well of 96 well plate for transduction and sampling while additional “proxy” wells were seeded at the same density for flow cytometry analysis and estimating the cell count in the experimental well. Three days after seeding, cells were transduced with 3.75uL per well of the concentrated barcoding virus. Twenty-four hours later, wells the cells were fed with an additional 100uL per well of EHT media. Five days after seeding (48 hours after transduction), the well was mixed by gentle pipetting and half of the total volume was sampled for scRNA sequencing (Chromium Single Cell 3’ Reagents kit v3.1). One week following the initiation of the differentiation culture (4 days after transduction), the remaining cells were collected and passaged 1:2 on to plates coated with DLL4 and VCAM1 in EHT media as described above. Three days later, remaining cells were harvested, counted and a sub-sample of 16,500 cells were taken for scRNA sequencing.

first: Yale

middle: S

last: Michaels

first: Matthew

middle: C

last: Major

first: Becca

last: Bonham-Carter

first: Jingqi

first: Tiam

last: Heydari

first: John

last: Edgar

first: Laura

last: Greenstreet

first: Roser

last: Vilarrasa-Blasi

first: Seungjoon

last: Kim

first: Elizabeth

middle: L

last: Castle

first: Aden

last: Forrow

first: M

middle: I

last: Ibanez-Rios

first: Carla

last: Zimmerman

first: Yvonne

last: Chung

first: Tara

last: Stach

first: Nico

last: Werschler

first: David

last: Knapp

last: Vento-Tormo

first: Geoffrey

last: Schiebinger

middle: W


title: The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models [RNA-seq]

first: Riki

last: Kawaguchi

summary: In our preliminary in-vitro studies in primary neurons, we found that changing glucose utlization using 2-deoxyglucose (2-DG, a known glycolytic inhibitor, which inhibits glucose utilization) led to a dose dependent signficant increase in Bdnf gene expression. Additionally, the dose of 2-DG that induced Bdnf gene expression also normalized learning and memory in mouse model of AD (5xFAD mouse) and improved functional recovery in mice models of ischemic and hemorrhagic strokes. With RNA Sequencing of 2-DG treated primary neuronal samples, our first goal was to identify dominant gene signatures in response to 2-deoxyglucose in order to delineate critical pathways affected by changes in glucose metabolism and our second goal was to understand if 2-deoxyglucose affect a broad gene plasticity program or only a few selective plasticity genes.

overall_design: Primary immature neurons were treated with either 1mM 2-DG or 10mM 2-DG for 6h and a parallel untreated set of primary immature neurons were used as a control. Thereafter, RNA was extracted using Nucleospin RNA kit (Macherey-Nagel) and follwing its protocol. Three independent replicates were used for the study.

first: Amit

last: Kumar

first: Saravanan

last: Karuppagounder

first: Yingxin

last: Chen

first: Carlo

last: Corona

first: Yuyan

last: Cheng

first: Mustafa

last: Balkaya

first: Botir

middle: T

last: Sagdullaev

first: Zhexing

last: Wen

first: Charles

last: Stuart

first: Giovanni

last: Coppola

first: Sunghee

last: Cho

first: Guo-Li

last: Ming

first: Daniel

last: Geschwind

first: Rajiv

last: Ratan


title: The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models [ChIP-seq]

summary: Intermittent fasting (IF) has broad beneficial effects on brain pathophysiology. Here, we sought to identify the target required for beneficial effects of IF using its pharmacological mimic, 2-deoxyglucose (2-DG), which could also eliminate limitations of human IF application due to dosage and schedule issues. 2-DG transcriptionally induced plasticity gene, Bdnf in vitro and in vivo. A 2-DG dose that induced Bdnf transcription in vivo also normalized hippocampal long-term potentiation and memory in an AD mouse model (5xFAD) and significantly improved functional recovery in stroke models. 2-DG enhanced Bdnf transcription by decreasing N-linked glycosylation that induced ER stress and the activity of newly translated ATF4 at +3kb intronic enhancer region of Bdnf gene. These data highlight the critical role of N-linked glycosylation in glucose sensing and suggest that 2-DG can improve outcomes without inducing ketosis via an adaptive ER stress pathway culminating in the transcription of CNS-associated resilience genes including Bdnf. n our preliminary in-vitro studies in primary neurons, we found that changing glucose utlization using 2-deoxyglucose (2-DG, a known glycolytic inhibitor, which inhibits glucose utilization) led to a dose dependent signficant increase in Bdnf gene expression. Additionally, the dose of 2-DG that induced Bdnf gene expression also normalized learning and memory in mouse model of AD (5xFAD mouse) and improved functional recovery in mice models of ischemic and hemorrhagic strokes. With RNA Sequencing of 2-DG treated primary neuronal samples, our first goal was to identify dominant gene signatures in response to 2-deoxyglucose in order to delineate critical pathways affected by changes in glucose metabolism and our second goal was to understand if 2-deoxyglucose affect a broad gene plasticity program or only a few selective plasticity genes.

overall_design: ChIP-Seq study was conducted using ATF4 antibody (Sigma-Millipore: catalog number ABE387) in primary neurons that were either untreated (Control) or treated with 10mM 2-DG for 6h. Three independent replicates were used for the study.


title: MDA5 guards against infection by surveying cellular RNA homeostasis

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research


title: Interspecific single-cell transcriptomic analysis reveals differences in signaling pathways governing gonadal primordial germ cells between chicken and zebra finch (Taeniopygia guttata) [chicken scRNA-seq]

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: Primordial germ cells (PGCs), major cell resource used in the production of germline chimeras in birds, have been used in conservation of avian genetic resources and production of transgenic animals. Numerous bird species have been put on the brink of extinction due to habitat loss and degradation caused by environmental destruction and climate change, but research on PGCs is limited to specific poultry, such as chickens. Although it has recently been expanding to various bird species, it is still difficult to utilize PGCs due to biological differences and difficulties in in vitro long-term culture. Here, we constructed a single-cell landscape of chicken gonadal PGCs with established long-term culture systems of PGCs and compared them with those of the vocal learning wild bird, the zebra finches. Our results identified the interspecific differences in signaling pathways in gonadal PGCs and somatic cells, respectively. In particular, the NODAL and insulin signaling pathways were more active in zebra finch than in chickens, whereas the FGF downstream signaling pathway known to be important for the proliferation of chicken PGCs, was more active in chickens. These differences may contribute to optimizing the in vitro culture conditions of zebra finch PGCs. This study is the first cross-species single-cell transcriptomic analysis targeting birds, and laid an essential groundwork to contribute to the restoration of endangered birds and the production of transgenic birds by securing sufficient PGCs from various bird species in the future.

overall_design: Gonadal cells profiling of male and female chickens at single cell level

first: JaeYong

last: Han

first: Minseok

last: Seo

first: KyungMin

last: Jung


title: Activity of EP300/CBP bromodomain inhibitor CCS1477 across diverse hematologic malignancies (ATAC-Seq)

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

summary: E1A binding protein (p300) and CREB binding protein (CBP) are two homologous histone acetyl transferases that co-activate key oncogenes such as MYC and IRF4, which are relevant transcription factors in a number of haematological malignancies. In this work, we studied the effects of CCS1477 (also known as Inobrodib), a first in class orally available inhibitor of the p300/CBP bromodomains. We found that this compound causes cell cycle arrest in a panel of different hematologic cell lines and primary samples, together with a concomitant induction of myeloid differentiation in most of the AML samples. Mechanistically, we discovered that 6 hours exposure to CCS1477 triggers a rapid and selective loss of EP300 from MYB-bound enhancers in THP1 AML cells. Interestingly, after 48 hours treatment EP300 redistributes to alternate sites to induce up regulation of differentiation genes. Displacement of EP300 from MYB-bound enhancers is significantly associated with the rapid collapse in the expression of nearby genes, most of which correspond to key myeloid identity transcription factors such as MYC, MYB, CEBPA, GFI1, SPI1 and IRF8. In most of these down-regulated genes after CCS1477 treatment, the RNA-Pol II is stalled along the gene body thus failing in completing the transcriptional elongation. In OPM2 myeloma cells, CCS1477 releases EP300 from FGFR3, the target of the common (4;14) translocation, with loss of EP300 from enhancer sites bound by IRF4. We also showed that in leukaemia patients this drug causes a substantial increase in blood neutrophil count and up-regulation of MYB-regulated differentiation genes in the population of blast cells, while in myeloma patients it conferred a sustained reduction in urinary free light chains. Overall, our study describes the molecular activity of a novel epigenetic drug in different haematological malignancy settings, with promising effects in vivo both as single agent and in combination with standard of care agents such as azacitidine and venetoclax.


title: Activity of EP300/CBP bromodomain inhibitor CCS1477 across diverse hematologic malignancies (RNA-Seq)

overall_design: RNA-seq analysis after treatment with EP300/CBP bromodomain CCS1477 and DMSO as control


title: Activity of EP300/CBP bromodomain inhibitor CCS1477 across diverse hematologic malignancies


title: Expression profiling and function analysis identified new microRNAs regulating cumulus expansion and apoptosis in cumulus cells

city: TaiAn

first: min

last: zhang

state: ShanDong

address: 61 Daizong Street

department: College of Animal Science and Technology

country: China

institute: ShanDongAgricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA- and miRNA-sequencing and bioinformatics using CCs from these cultured COCs/OOXs identified candidate apoptosis- and/or CE-regulating miRNAs. Transfection of COCs/OOXs with miRNA mimic or inhibitor validated that miR-212-5p and 149-5p promoted CE by facilitating Has2 expression; miR-31-5p and 27a-3p promoted CE by increasing both Has2 and Ptx3 expression; and miR-351-5p and 503-5p inhibited CE by suppressing Ptx3 expression. Furthermore, miR-212-5p, 149-5p and Nov798 inhibited CC apoptosis, involving both Bcl2/Bax and Fas signaling. Analysis using in vivo matured COCs further verified the above apoptosis- and/or CE-regulating miRNAs except for miR-149-5p. In conclusion, this study identified and validated new CE- and apoptosis-regulating miRNAs in CCs, which can be used as biomarkers to select competent oocytes/embryos and for elucidating how the oocyte-derived factors regulate CE and CC apoptosis.

overall_design: we established that mouse cumulus-oocyte complexes (COCs) cultured in expansion-supporting medium supported full CE while suffering mild apoptosis, whereas mouse oocytectomized COCs (OOXs) cultured in apoptosis-triggering medium underwent severe apoptosis while supporting no CE.

first: Jing-He

last: Tan

first: Shuai

last: Gong

first: Xiao

first: Min

last: Zhang


title: LncRNA ITGB8-AS1 functions as a ceRNA to promote colorectal cancer growth and migration through integrin-mediated focal adhesion signaling

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: ITGB8-AS1 functions as a ceRNA to regulate cell proliferation and tumor growth of colorectal cancer (CRC) via regulating focal adhesion signaling. Targeting ITGB8-AS1 is effective in suppressing CRC cell growth and tumor growth. Elevated plasma levels of ITGB8-AS1 was detected in advanced-stage CRC. Thus, ITGB8-AS1 could serve as a potential therapeutic target and circulating biomarker in CRC.

overall_design: RNA-seq was performed to identify target genes of ITGB8-AS1 in colorectal cancer cell HCT116.

first: Wen

last: Liu

first: Jian-Cheng

first: Xiao-Ting

last: Lin

first: Xue

last: Chen


title: Activity of EP300/CBP bromodomain inhibitor CCS1477 across diverse hematologic malignancies (scRNA-Seq)

overall_design: Single-cell RNA profiling from an leukaemia patient sample pre and post-treatment with CCS1477 at two timepoints.


city: La Jolla

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: TWEAK Upregulates atopic dermatitis related genes in human kearatinocytes

overall_design: Bulk RNA seq. analysis from human epidermal keratinocytes stimulated with 100 ng/ml of hTWEK, hIL-13 & hIL-22 for 24 hrs.

first: Rinkesh

last: Gupta

first: Kai

last: Fung


title: The nerve roots avulsion induced time-specific expression patterns of lncRNA and mRNA occurred before the motoneurons loss of the injured spinal segments

city: Guangzhou

first: Guangyin

last: Yu

address: No. 74 Zhongshan Road 2, Guangzhou 510080, P.R. China

institute: Zhongshan School of Medicine, Sun Yat-sen University

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

summary: In this study, we study the expression pattern of the lncRNAs in rat’s spinal cord of at 3 days and 14 days after the unilateral BPRA. By comparing the expression patterns of mRNAs and lncRNAs, ipsilateral vs contralateral, on the 3rd and the 14th day, in the same spinal segments using microarray analysis. We identified 55 lncRNAs, which were significantly altered at the 3rd day after BPRA. Two weeks after BPRA, 70 lncRNAs which were significantly altered. Among these DE lncRNAs, 17 were consistently over-regulated at 3- and 14- days after injury while 5 lncRNAs were consistently down-regulated. At 3-days after injury, 399 mRNAs were signiﬁcantly differentially expressed while two weeks after BPRA, 445 were downregulated. Among these mRNAs, 198 were consistently over-regulated, and 15 mRNAs were consistently under-regulated.

overall_design: The brachial plexus root avulsion model (C5-T1) were builted, then we study the expression pattern of the lncRNAs in rat’s spinal cord of at 3 days and 14 days after the brachial plexus root avulsion.

first: Lihua

last: Zhou


title: Activity of EP300/CBP bromodomain inhibitor CCS1477 across diverse hematologic malignancies (ChIP-Seq)

overall_design: ChIP-seq profiling of different proteins after treatment with EP300/CBP bromodomain CCS1477 and DMSO as control


title: GPRC5A regulates keratinocyte adhesion and migration through nuclear translocation of its C-terminus region

status: Public on Nov 27 2023

city: LYON

first: Romain

last: DEBRET

address: 7 passage du Vercors

country: France

institute: CNRS

summary: G-Protein Coupled Receptor, Class C, Group 5, Member A (GPRC5A) is well-documented in lung and various epithelial cancers. However, its role in the skin remains unexplored. In this study, we investigated the function of this receptor in skin biology and our research demonstrated that its expression responds to mechanical substrate changes in human primary keratinocytes. Furthermore, we observed GPRC5A reinduction during wound healing at the leading edges in an ex vivo burn model, coinciding with the translocation of its C-terminal region into the nucleus. We identified the cleavage site of GPRC5A by N-TAILS analysis, and cathepsin G was characterized as responsible for proteolysis in cultured cells.  To gain a deeper understanding of GPRC5A's role in keratinocyte, we performed GPRC5A knockdown in N/TERT-1 cells using short-hairpin RNA. Our findings strongly suggest a close association between GPRC5A and adhesion regulation pathways, but also demonstrate that GPRC5AKD enhanced cell adhesion while reducing cell migration and differentiation. Importantly, these effects were reversed by adding a recombinant polypeptide mimicking the C-terminal region of GPRC5A.  Overall, our study reveals an unexpected role of GPRC5A in regulating keratinocyte behavior, implicating its C-terminal region translocation into the nucleus. These results open up interesting strategic pathways for wound healing.

overall_design: In order to identify novel mechanosensitive elements from epidermal cells, primary human keratinocytes were isolated from 3 different individuals and subjected to cell culture on substrates of different stiffness prior to total RNA extraction. We compared the transcriptomic profiles of cells grown for 72 h on glass coverslips (glass) or on 4kPa hydrogels (soft), or after transplanting the cells from hydrogel to plastic support for 24 h (soft.glass).

last: Debret

first: Choua

last: Ya


title: Genomic profiling of spermatogonial stem cells differentiation into putative female stem cells

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: In this study, we showed that the SSCs isolated and cultured can transdifferentiate into putative female germ cells (PFGCs) in vitro. To demonstrate difference of SSCs and PFGCs, microarray analysis was carried out.

overall_design: Total RNA was isolated from cells, including spermatogonial stem cells (SSCs), putative female germ cells (PFGCs), and oocytes, and gene expression profile was detected by microarray.

first: Huacheng

last: Luo


title: Sustained PGC-1α2 or PGC-1α3 expression induces astrocyte dysfunction and degeneration.

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α) transcriptional coactivators are key regulators of energy metabolism-related genes and are expressed in energy-demanding tissues. There are several PGC-1α variants with different biological functions in different tissues. The brain is one of the tissues where the role of PGC-1α isoforms remains less explored. Here, we used a toxin-based mouse model of Parkinson's disease (PD) and observed that the expression levels of variants PGC-1α2 and PGC-1α3 in the nigrostriatal pathway increases at the onset of dopaminergic cell degeneration. This increase occurs concomitant with an increase in glial fibrillary acidic protein levels. Since PGC-1α coactivators regulate cellular adaptive responses, we hypothesized that they could be involved in the modulation of astrogliosis induced by MPTP. Therefore, we analysed the transcriptome of astrocytes transduced with expression vectors encoding PGC-1α1 to 1α4 by massively parallel sequencing (RNA-seq) and identified the main cellular pathways controlled by these isoforms. Interestingly, in reactive astrocytes the inflammatory and antioxidant responses, adhesion, migration, and viability were altered by PGC-1α2 and PGC-1α3, showing that sustained expression of these isoforms induces astrocyte dysfunction and degeneration. This work highlights PGC-1α isoforms as modulators of astrocyte reactivity and potential therapeutic targets for the treatment of PD and other neurodegenerative disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from primary mouse astrocytes infected with adenovirus endoding either PGC-1α isoforms or GFP as a control. Experiment contains three replicates for each condition

first: Maria

last: Nunes

first: Andreia

middle: N

last: Carvalho

first: Carlota

last: Sá-Lemos

first: Margarida

last: Colaço

first: Viviana

last: Ciraci

first: Susana

middle: G

last: Santos

first: Mariana

last: Ribeiro

last: Castanheira

first: Paulo

last: Jannig

last: Gama

last: Castro-Caldas

first: Cecilia

middle: P

last: Rodrigues

first: Elsa

first: Jorge

last: Ruas


title: Photothrombotic Cerebral Stroke as a Model of Post-Stroke Seizures/Epilepsy in aged mice

city: Sanuki

first: Rie

last: Komori

department: Kagawa School of Pharmaceutical Sciences

institute: Tokushima Bunri University

summary: Stroke is a prevalent disorder representing the third leading cause of death and major cause of disability. Post-stroke epilepsy (PSE) has been recognized as a common clinical issue after stroke, accounting for 30-40% of the causes of epilepsy among older adults.  In this study, we determined GABAA receptor-mediated seizure susceptibility after PT cerebral stroke in aged mice. Young adult mice around 10 weeks of age are widely used in stroke experiments. However, as most strokes are diagnosed in the elderly and PSE has been recognized as a common clinical incidence after stroke, we utilized photothrombosis (PT) model of cerebral ischemia and examined seizure susceptibility and brain injury using combined behavioral (video) and EEG monitoring and histological (MRI) assessments. To investigate GABAA receptor-mediated convulsive/non-convulsive seizures, lower-doses of pentylenetetrazol (PTZ) was injected. PTZ susceptibility in aging mice increased compared to young adults. One month after PT stroke, aged PT stroke mice exhibited severe convulsive seizures (late-onset). These findings exhibited the increase of GABAA receptor-mediated seizures susceptibility in PT stroke aging mice, but not in young adults.

overall_design: Photothrombosis (PT) model of cerebral ischemia was created by irradiating with LED light (wavelength; 565 nm, output; 200 mW) in a circle region with a diameter of 3.5 mm in the left parietal lobe region for 30 minutes after administration of rose bengal (35 mg/kg, i.p.) to C57BL/6N male mice (8-10 and 65-85 weeks old). One week after the PT stroke, MRI images were taken to observe the state of cerebral infarction, and chronic EEG screw electrodes were placed in the frontal lobe/parietal lobe. To investigate GABAA receptor-related convulsive/non-convlsive seizures after PT stroke, low-doses (20~30 mg/kg, i.p.) pentylenetetrazol (PTZ), GABAA receptor antagonist, was injected, and video-EEG monitoring was performed to detect seizures. One month after PT, mice were treated with anti-seizure medication, levetiracetam (LEV, free drinking, 5 mg/mL) for 2 weeks, and were withdrawal for 1 week after administration with LEV.

first: Kouichi

last: Itoh

first: Yasuhiro

last: Ishihara


title: Levetiracetam normalized E/I imbalance in the hippocampus after cortical stroke in aged mice

summary: Stroke is a prevalent disorder representing the third leading cause of death and major cause of disability. Post-stroke epilepsy (PSE) has been recognized as a common clinical issue after stroke, accounting for 30-40% of the causes of epilepsy among older adults. In this study, we determined GABAA receptor-mediated seizure susceptibility after PT cerebral stroke in aged mice. Young adult mice around 10 weeks of age are widely used in stroke experiments. However, as most strokes are diagnosed in the elderly and PSE has been recognized as a common clinical incidence after stroke, we utilized photothrombosis (PT) model of cerebral ischemia and examined seizure susceptibility. To investigate in vitro drug-induced seizure susceptibility (E/I imbalance) of GABAA receptor antagonist, gabazine (GZ), voltage-sensitive dye (VSD) imaging techniques were used in hippocampal brain slices. One month after PT stroke, in vivo aged PT stroke mice exhibited severe convulsive seizures (late-onset). in vitro GZ-induced E/I imbalance in hippocampus of aging mice increased compared to young adults. In addition, Anti-seizure medication (levetiracetam) normalized in vitro GZ-induced E/I imbalance in hippocampus of aging mice. These findings exhibited that GABAA receptor-mediated seizures susceptibility (E/I imbalance) in hippocampus after cortical PT stroke in aging mice, but not in young adults.

overall_design: Photothrombosis (PT) model of cerebral ischemia was created by irradiating with LED light (wavelength; 565 nm, output; 200 mW) in a circle region with a diameter of 3.5 mm in the left parietal lobe region for 30 minutes after administration of rose bengal (35 mg/kg, i.p.) to C57BL/6N male mice (8-10 and 65-85 weeks old). One month after PT, mice were treated with anti-seizure medication, levetiracetam (LEV, free drinking, 5 mg/mL) for 2 weeks, and were withdrawn for 1 week after administration with LEV. An in vitro seizure susceptibility (E/I balance) was determined by voltage-sensitive dye (VSD) imaging techniques in hippocampal brain slices. By employing this approach, we investigated the in vitro GABAA receptor antagonist, gabazine (GZ).

first: Yoko

last: Tominaga

first: Takashi


title: CRIP1 involves the pathogenesis of multiple myeloma via dual-regulation of proteasome and autophagy

city: Tianjin

first: Peixia

last: Tang

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Multiple myeloma (MM) is an incurable hematological malignancy of plasma cells. The maintenance of protein homeostasis is critical for the survival of MM cells. The excess paraprotein in MM cells undergoes clearance through proteasomes or lysosomes, two inter-connected yet independent pathways. While proteasome inhibitors (PIs) serve as fundamental agents significantly improving patient outcomes, heightened autophagy activity diminishes sensitivity to PI treatment.Elevated CRIP1 levels serve as a biomarker for relapsed/refractory MM and correlate with shorter overall patient survival. To further comprehend the role of CRIP1 in multiple myeloma pathogenesis, we conducted transcriptome sequencing.

overall_design: To investigate the role of CRIP1 in multiple myeloma pathogenesis, we generated multiple myeloma cells with CRIP1 knockdown by transfecting them with CRIP1-shRNA, utilizing Scramble-shRNA as a control. RNA sequencing was performed on both KMS11-CRIP1-sh and KMS11-Scr (control) cell lines, each replicated three times for biological validation.

first: Zhen

last: Yu

first: Mu

last: Hao

first: Lugui

last: Qiu


title: KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance [RNA-seq]

first: Yuan

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: Immune cells were isolated from the lungs of mice bearing KEAP1 mutant or wildtype tumors. We found that in KEAP1 mutant tumors there is a reduction in CD103 DCs and early activated T cells as well as an increase in exhausted CD8 T cells in comparison to WT controls.

overall_design: KEAP1 mutant (n=3) or wildtype (n=3) murine KP lung cancer cells were injected IV into C57BL/6 mice. Lungs were harvested and tumor were sorted by GFP reporter. RNA was extracted and processed for RNA-seq

first: Anastasia

last: Zavitsanou

first: Ray

last: Pillai

first: Aristotelis

last: Tsirigos

first: Sergei

last: Koralov

first: Thales

last: Papagiannakopoulos


title: KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance.

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

overall_design: Refer to individual Series


title: Transcriptional Response of Phosphomimetic (T380D) and Phosphoablative (T380A) NarS mutants in Mycobacterium tuberculosis H37Rv

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

summary: To test the consequence of NarS T380 phosphorylation on downstream signaling, we explored transcriptional changes associated with either phosphorylation state.

overall_design: Bacteria were induced with anhydrotetracycline for the over expression of the mutant and then all the bacteria were harvested at stationary phase.  RNA was isolated and gene expresion quantified by sequencing.

first: Andrew

last: Frando

first: Vishant

last: Boradia


title: KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance [scRNA-seq]

overall_design: KEAP1 mutant (n=1) or wildtype (n=1)  murine KP lung cancer cells were injected IV into C57BL/6 mice. Lungs were harvested and extravascular CD45 cells were sorted for scRNA-seq. Samples were stained with hashtag antibodies. Libraries were generated for gene expression, hashtags, and TCR sequencing and were then sequenced.


title: Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation [bisulfite-seq]

city: Cold Spring Harbor

first: Jonathan

last: Cahn

address: 1 Bungtown Rd

institute: CSHL

type: Methylation profiling by high throughput sequencing

summary: Epigenetic inheritance refers to the faithful replication of DNA and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferase during S phase, unless they are remodeled by Decrease in DNA methylation 1 (DDM1Lsh/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1. Inddm1mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a di-sulphide bond in the helicase domain is essential for activity in vivo and in vitro. Differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1. DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome and contributes to epigenetic inheritance.

overall_design: Bisulfite sequencing was performed on wild-type, ddm1, hira and ddm1hira mutants in two series of biological replicates (groupA), as well as on wild-type, ddm1, atrx and ddm1 atrx mutants in two series of biological replicates (groupB)

first: Seung

last: Lee

first: Robert

middle: A

last: Martienssen


title: Suclg2 maintains the tolerogenic function of regulatory dendritic cells by suppressing Lactb succinylation

city: shanghai

first: xiaomin

last: zhang

address: 800 Xiang Yin Road

institute: National Key Laboratory of  Medical Immunology & Institute of Immunology, Naval Military Medical University

summary: Purpose: mRNAs sequencing of the gene expression differences in maDC and diffDC, the goals of this study are to investigate the biological effect of the metabolic enzyme succinate-CoA ligase subunit beta Suclg2 in regulating regulatory DC differentiation and function.

overall_design: Bone marrow cells from  C57/BL6 mice were cultured with GM-CSF and IL-4 for 6 days and stimulated with LPS for 24 hours to generate bone-marrow derived DC (BMDC). CD11c+ BMDC were isolated by anti-mouse CD11c magbeads to generate maDC. maDC were then cocultured with spleen stroma cells for 9 days to generate diffDC. maDC and diffDC were subjected to RNA seq.

first: Xiaomin

last: Zhang

first: Xuetao

last: Cao


title: Expression data from Hap1 parental control and Baz2B-KO cell lines

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

summary:
Baz2B protein was shown to form a chromatin remodelig complex mit Snf2H or Snf2L catalytic subunits. It is known that chromatin remodeling proteins regulate diffferent DNA-templated processes, therefore we wanted to know whether Baz2B plays a role in transcription regulation.
We used microarrays to detail the global expression of transcripts in Hap1 parental cell line and compare them to Baz2B-KO. We found up- and down-regulated trasncripts that could be associated with the decreased cellular proliferation in Baz2B-KO cell line

overall_design: Baz2B-KO (n=2) against parental Hap1 cells (ctrl, n=2)

first: Dominika

last: Spitzer

first: Laura

last: Manelyte


title: Urinary Extracellular Vesicle Whole-Transcriptome Analysis in Diabetic Nephropathy

city: Zheng Zhou

first: Zihao

last: Zhao

state: Henan

address: Jianshe Road 1

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

summary: Enrolled 24 participants, including twelve renal biopsy-proven T2DN and twelve T2DM, and isolated uEV s by ultracentrifugation to perform adequate parallel microarrays for mRNAs, lncRNAs and circRNAs and sequencing for miRNAs.One hundred mL of first-morning urine was collected.All urine samples were retained and immediately transferred to the laboratory and centrifuged at 2500 x g at 4°C for 15 min using a horizontal rotor (Dynamica V14R Pro, UK) and at 17,000 x g at 4°C for 40 min using a fixed angle rotor (FA15C rotor, Dynamica, UK). Supernatants were filtered using 0.22µm PES filters (Jet Bio-Filtration, Guangzhou, China) and transferred to new centrifuge tubes and stored at -80 degrees. After overnight melting through a 4 degree, ultracentrifuged at 200,000 xg at 4°C for 2h in a fixed angle P45AT rotor (k factor= 130, CP100NX, Hitachi, Tokyo, Japan) and repeat again after resuspending the pellet in PBS. Supernatants were discarded and the pellets were washed in PBS to obtain the uEVs.

overall_design: 12 T2DN vs. 12 T2DM urinary extracellular vesicle samples

first: Jiayu

last: Duan


title: Gene expression profile at single cell level of adrenal glands from the Tmem127 wild type (WT) and knocked out (KO) mice

city: San Antonio

first: QIANJIN

last: GUO

email: guoq1@uthscsa.edu, dahia@uthscsa.edu

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

summary: Tmem127 is a tumor suppressor gene that has been linked to inherited susceptibility to pheochromocytomas. We used single nuclei RNA sequencing (snRNA-seq) to explore the cellular role of Tmem127.

overall_design: Nuclei from 6 pairs frozen adrenal glands were extracted and isolated by Fluorescence-activated cell sorting (FACS) according to the DPI signal and analyzed using snRNAseq.

first: Qianjin

last: Guo

first: Patricia

last: Dahia


title: Suclg2 maintains the tolerogenic function of regulatory dendritic cells by suppressing Lactb succinylation [si-nc/si-Suclg2]

summary: Purpose: mRNAs sequencing of the gene expression differences in diffDC transfected with si-nc or si-Suclg2, the goals of this study are to investigate the biological effect of the metabolic enzyme succinate-CoA ligase subunit beta Suclg2 in regulating regulatory DC differentiation and function.

overall_design: Bone marrow cells from  C57/BL6 mice were cultured with GM-CSF and IL-4 for 6 days and stimulated with LPS for 24 hours to generate bone-marrow derived DC (BMDC). CD11c+ BMDC were isolated by anti-mouse CD11c magbeads to generate maDC. maDC were then cocultured with spleen stroma cells for 9 days to generate diffDC. And then diffDCs were transfected with si-Suclg2 or si-nc. diffDCs transfected with si-Suclg2 or si-nc were subjected to RNA seq.


title: High throughput RNA sequencing of Cd34+ve HSPC upon Leucine alteration

city: Mohali

first: Lolitika

last: Mandal

state: Punjab

address: Sector 81, SAS Nagar

department: Biological Sciences

institute: Indian Institute of Science Education and Research Mohali

summary: We are analyzing the transcriptomic landscape in Primary Cd34+ve HSPCs following a pulsed leucine deprivation as well as excess supplementation of Leucine

overall_design: Control set of HSPCs were cultured in media containing 0.8 mM of Leucine as our control. Experiment1 was HSPCs cultured for 6 hrs in a media containing no leucine in it (0mM). Experiment 2 is HSPCs cultured for 6 hrs in a media containing excess leucine (2mM)

first: Sushmit

last: Ghosh

first: Sreemoyee

last: Chakraborti


title: Prolonged sleep deprivation induces cytokine storm-like syndrome in mammals

city: Beijing

first: Erquan

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

summary: Sleep is deeply involved in neuroimmune regulation, while the mechanism is yet to be elucidated. Experimental manipulation of sleep duration provides a reliable measure for evaluating how sleep regulates innate immunity. Here we report a modified sleep deprivation paradigm (SD) that can constantly awaken the mice with more than 95% efficiency, and investigate the effects of prolonged sleep deprivation on mice's immune systems.


title: Prolonged sleep deprivation induces cytokine storm-like syndrome in mammals [RNA-Seq]

overall_design: Blood leukocytes were isolated from the mice under control (Con), sleep deprivation(SD), or a previously reported sleep restriction method (SASD) condition after different time points to investigate the transcriptome alteration

first: Keteng

last: Lin

first: Di

last: Sang


title: Prolonged sleep deprivation induces cytokine storm-like syndrome in mammals [scRNA-Seq]

overall_design: Blood leukocytes were isolated from the mice under control (Con), sleep deprivation(SD), or a previously reported sleep restriction method (SASD) condition after different time points and investigate the transcriptome alteration on single-cell level


title: SENP2 suppresses browning of white adipose tissues by de-conjugating SUMO from C/EBPβ

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

institute: Kangwon National University

summary: The adipose tissue is a key site regulating energy metabolism. One of the contributing factors behind this is browning of white adipose tissue (WAT), however, knowledge of the intracellular determinants of browning process remains incomplete. By generating adipocyte-specific Senp2 knockout (Senp2-aKO) mice, here we showed that SENP2 negatively regulates browning by de-conjugating SUMO from C/EBPβ. Senp2-aKO mice were resistant to diet-induced obesity and insulin resistance due to increased energy expenditure and heat production. Senp2 knockout promoted beige adipocyte accumulation in inguinal WAT by upregulation of thermogenic gene expression. In addition, SENP2 knockdown promoted thermogenic adipocyte differentiation of precursor cells isolated from inguinal and epididymal WATs. Mechanistically, sumoylated C/EBPβ, a target of SENP2, suppressed expression of HOXC10, a browning inhibitor, by recruiting a transcriptional repressor DAXX. These findings indicate that a SENP2-C/EBPβ-HOXC10 axis operates for the control of beige adipogenesis in inguinal WAT.

overall_design: The transcriptomic profiles of iWAT obtained from control or Senp2-aKO mouse

first: Ji-Seon

last: Lee

first: Daehee

last: Hwang

first: Sung-Soo

last: Chung

first: Kyong-Soo

last: Park


overall_design: The transcriptomic profiles of SVF-derived adipocytes of WATs (eWAT and iWAT) of control or Senp2-aKO mice with and without C/EBPβ knockdown.


title: Acid ceramidase regulates innate immune memory

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Innate immune memory, also called "trained immunity," is a metabolically and epigenetically regulated functional state of myeloid cells. This phenomenon is important for host defense, but also plays a role in various immune-mediated conditions. We found that exogenously administered sphingolipids and inhibition of enzymes involved in sphingolipid metabolism modulate trained immunity. In particular, we found that acid ceramidase, an enzyme that converts ceramide to sphingosine, is a potent regulator of trained immunity. We discovered that acid ceramidase regulates the expression of genes encoding histone-modifying enzymes, resulting in profound changes in the epigenetic landscape. We confirmed our findings by identifying single-nucleotide polymorphisms in the region of ASAH1, the gene encoding acid ceramidase, that are associated with the trained immunity cytokine response. Our findings reveal a novel immunomodulatory effect of sphingolipids, provide new insight into the metabolic regulation of trained immunity, and identify acid ceramidase as a therapeutic target to modulate it.

overall_design: ChIP sequencing and RNA sequencing on trained monocytes that are treated with Rapamycin, Ceranib or HKCA

first: Nils

last: Rother

first: Raphaël

last: Duivenvoorden


title: RNA-sequencing for kidneys derived from adult Pkd1 knock-out (KO) mice treated with salsalate for two weeks

status: Public on Nov 30 2023

city: Leiden

first: Anish

last: Kanhai

address: Einthovenweg 20

department: Human Genetics

institute: Leiden University Medical Center

summary: To investigate the early and direct effects of short salsalate administration on gene expression & pathways in polycystic kidney disease. Pkd1 was knocked-out at PN18, and mice remained untreated until PN81, after which half of the experimental group received a two-week salsalate treatment. Mice were sacrificed at PN95

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iKspCre-Pkd1del mice, either wildtype (not induced), untreated PKD mice, or two-week salsalate-treated PKD mice

first: A

first: T

middle: B

last: Kuipers

first: H

last: Mei

first: D

last: Peters


title: Transcriptome analysis reveals the molecular regulatory network of dietary supplementation with succinate on muscle fiber characteristics and meat quality in Tan sheep

status: Public on Nov 26 2023

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

institute: Ningxia University

summary: To investigate the impact of adding succinate to the diet on the production performance, meat quality, muscle fiber characteristics, and transcriptome of the longissimus dorsi muscle in Tan sheep, 36 Tan sheep were selected and fed with different levels of succinate (0%, 0.5%, 1.0%, 2.0%) for a 60-day trial period. Overall, compared to the control group, the addition of succinate to the diet improved the production performance, slaughter performance, and meat quality of Tan sheep. It significantly increased dry matter intake, carcass weight, eye muscle area, and the GR value while significantly reducing the shear force and cooking loss of the longissimus dorsi muscle (p<0.05). Furthermore, the addition of succinate to the diet altered the muscle fiber characteristics of the longissimus dorsi muscle in Tan sheep, significantly increasing the fiber diameter and cross-sectional area of type I and type IIa muscle fibers (p<0.05). The addition of 1.0% succinate to the diet altered the transcriptome of the longissimus dorsi muscle in Tan sheep, with 741 differentially expressed genes identified compared to the control group. These differentially expressed genes were involved in various pathways related to lipid metabolism, energy metabolism, and muscle development, such as insulin secretion, insulin resistance, cAMP signaling pathway, PI3K-Akt signaling pathway, and FoxO signaling, among others. In summary, succinate plays a crucial role in regulating energy metabolism, protein deposition, and glucose and lipid metabolism homeostasis in Tan sheep through insulin signaling pathways and the interaction of muscle cell factors. By modulating the expression of relevant genes, succinate improves the muscle fiber characteristics of Tan sheep, thereby enhancing production performance and meat quality.

overall_design: Thirty-six 5-month-old Tan sheep with similar health statuses and weights were selected and randomly divided into four groups, with 9 sheep in each group, and reared in individual pens (4 m × 4 m). The four groups were as follows: control group (basal diet), SUC1 group (basal diet + 0.5% succinate), SUC2 group (basal diet + 1% succinate) and SUC3 group (basal diet + 2% succinate). The diets of each group were formulated according to the "Nutritional Requirements of Sheep" (Ministry of Agriculture of China, 2021) and the actual production of Tan sheep. The pretrial period was 10 days and the formal trial period was 60 days. During the experiment, all experimental sheep had free access to water and were fed twice a day (at 06:30 and 17:30).

first: Ning

last: Zhang

first: Xiaofeng

last: Xu

first: Lili


title: Antigen exposure reshapes chromatin architecture in central memory CD8+ T cells and imprints enhanced recall capacity [RNA-seq]

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

summary: Compared with naïve CD8+ T cells, antigen-experienced effector and central memory CD8 T cells show extensive CTCF redistribution and 3D genome reorgainzation, which underlie the transcriptomic diversification as well as recall capacity in response to secondary challenges.

overall_design: CreER+ WT or CTCF-floxed P14 CD8+ T cells were first transferred into B6.SJL mice followed by LCMV-Arm infection. After ≥30 days, the immune mice were treated with tamoxifen for two days, and CD62L+ P14+ central memory (Tcm) cells were sorted, and a portion was stimulated with GP33 peptide for 24 hrs. The unstimulated (resting) and stimulated Tcm cells were subjected to RNAseq analysis

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng


title: Identification of differential expressed genes after ELK4 knockdown in colorectal cancer cells

city: Shanghai

first: Zhehui

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

summary: We have demonstrated that ELK4 promted progression and tumorigenesis in colorectal cancer. In order to elucidate the transcriptional regulation mechanism of ELK4 in colorectal cancer, RNA-seq analysis was performed on ELK4 knockdown and control HCT116 cells.

overall_design: HCT116 cells with ELK4 stable knockdown were generated by three independent shRNAs.

first: Yuegui

last: Guo

first: Long

last: Cui

first: Chen-ying

last: Liu


title: Antigen exposure reshapes chromatin architecture in central memory CD8+ T cells and imprints enhanced recall capacity [ATAC-seq]

overall_design: CreER+ WT or CTCF-floxed P14 CD8+ T cells were first transferred into B6.SJL mice followed by LCMV-Arm infection. After ≥30 days, the immune mice were treated with tamoxifen for two days, and CD62L+ P14+ central memory (Tcm) cells were sorted for ATAC-seq analysis


title: Antigen exposure reshapes chromatin architecture in central memory CD8+ T cells and imprints enhanced recall capacity

overall_design: Refer to individual Series


title: BTLA+CD200+ B cells dictate the divergent immune landscape and immunotherapeutic resistance in metastatic vs. primary pancreatic cancer

city: New York

first: Joshua

middle: Caleb

last: Leinwand

address: 177 Fort Washington Ave, 7th Floor

department: Surgery

institute: Columbia University Irving Medical Center

summary: Response to cancer immunotherapy in primary versus metastatic disease has not been well-studied. We found primary pancreatic ductal adenocarcinoma (PDA) is responsive to diverse immunotherapies whereas liver metastases are resistant. We discovered divergent immune landscapes in each compartment. Compared to primary tumor, liver metastases in both mice and humans are infiltrated by highly anergic T cells and MHCII-lo IL10+ macrophages that are unable to present tumor-antigen. Moreover, a distinctive population of CD24 + CD44 – CD40 – B cells dominate liver metastases. These B cells are recruited to the metastatic milieu by Muc1 hi IL18 hi tumor cells, which are enriched >10-fold in liver metastases. Recruited B cells drive macrophage-mediated adaptive immune-tolerance via CD200 and BTLA. Depleting B cells or targeting CD200/BTLA enhanced macrophage and T-cell immunogenicity and enabled immunotherapeutic efficacy of liver metastases. Our data detail the mechanistic underpinnings for compartment-specific immunotherapy responsiveness and suggest that primary PDA models are poor surrogates for evaluating immunity in advanced disease.

overall_design: For RNA-Seq experiments, mouse pancreatic primary tumors and liver metastatic tumors were harvested 3 weeks after orthotopic implantation and processed for bulk RNA-Seq. Alternatively, for single cell RNA-seq, CD45+ leukocytes were FACS-sorted from mouse pancreatic primary tumors or liver metastatic tumors 3 weeks after orthotopic implantation, and processed for 10X droplet-based single cell RNA-seq.

first: Brian

last: Diskin


title: Antigen exposure reshapes chromatin architecture in central memory CD8+ T cells and imprints enhanced recall capacity [CUT&RUN]

overall_design: P14 CD8+ T cells were first transferred into B6.SJL mice followed by LCMV-Arm infection. On day 8 post-infection, KLRG1+IL-7Ra– P14 cells were sorted as effector CD8+ T (Teff) cells, and After ≥30 days,  CD62L+ P14 cells were sorted as central memory (Tcm) cells were sorted. The sorted cells were subjected to CTCF CUT&RUN analysis.


title: Extra-HEK293-AAV: Transcriptomics of modified HEK293 cell line for higher productivity of biologics (e.g. viral vectors, AAV)

status: Public on Nov 25 2023

city: Liege

first: Maximilien

last: Lopes

state: Liege

address: Avenue de l'hopital 11

department: Molecular Biology of Disease

country: Belgium

institute: University of Liege

summary: The human EXT1 gene has been knockdown in HEK293 cells to improve their performance in producing viral vectors such as AAV. This work compares the gene expression for the wildtype and kd_EXT1 cells, in adherent and suspension cultures.

overall_design: After 5 passages, cells were trypsinized (for adherent culture only) and collected by centrifugation. RNA was extracted using the NucleoSpin RNA extraction kit from Macherey-Nagel. RNAseq was performed with an Illumina NovaSeq X Plus. Mapping was done with the reference GRCh38 and the gene expression level analysis was calculated.

first: Jean-Claude

last: Twizere


title: ChIP-seq following AATF in BIU-87 cells

city: Shenyang

first: Shutao

last: Tan

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: With the increasing acknowledgment of the multifaceted roles of Anti-apoptotic Transcription Factor (AATF) in various cancers, our study directed its focus towards unraveling its implications in bladder cancer, particularly concerning the tumor microenvironment and immune landscape. We performed ChIP-seq to investigate the effect of AATF on chromatin status in BIU-87 cells.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for AATF in BIU-87 cells.


title: Transcriptome profile of rice genotypes ZH11 and Oseds1 by inoculation with Xanthomonas oryzae pv. oryzae

city: Nanjing

first: Yiming

last: wang

address: No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China

department: Department of Plant Pathology

institute: Nanjing Agricultural University

summary: OsEDS1 is a key regulator of SA-mediated immunity in plants. The OsEDS1 knockout mutant (Oseds1) was characterized and shown to have increased susceptibility to Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), suggesting the positive role of OsEDS1 in regulating rice disease resistance. To identify differentially regulated downstream of Oseds1, we performed transcriptome deep sequencing (RNA-seq) of wild type (ZH11) and Oseds1 inoculated with Xanthomonas oryzae pv. Oryzae (PXO99A).

overall_design: The leaves of ZH11 and Oseds1 were inoculated with Xoo, and samples were harvested at 48 hours post-inoculation. The transcriptional changes were analyzed by RNA-seq.

first: Lutong

last: Chi

first: Jinbiao

last: Ma

first: Xiaochen

last: Cen

last: Wang

first: Zhiwei

last: Ji


title: Over-expression of FLI1 in the epithelial cell line HaCaT increased expression of inflammatory markers associated with psoriasis

city: Guiyang

first: Maoting

last: Hu

state: Guizhou

address: Baiyun District, Guiyang City, Guizhou Province, China.

institute: Guizhou Medical University

summary:
Friend virus induced leukemia-1 (Fli-1) is a ETS related oncogenic transcription factor initially identified by our group as a target of retroviral insertional mutagenesis in erythroleukemia induced by Friend virus. This oncogene is also activated through translocation (EWS-FLI1) or overexpression in various human solid and liquid tumors. In addition to cancer, FLI1 is involved in the development of various illnesses including inflammatory diseases. While overexpression of Fli-1 contributes to the development of autoimmune systemic lupus erythematosus (SLE), loss of this transcription factor in fibroblasts underlines systemic sclerosis. Finally, Fli-1 is also a major regulator of immunity, hematopoiesis and stem cell maintenance and developmen.
Previously, we used RNAseq data of FLI1-depleted human leukemic cells and identified a correlation between FLI1 deficiency and reduced expression of markers of psoriasis. Accordingly, overexpression of FLI1 in the epithelial cell line HaCaT increased expression of these markers of inflammation and psoriasis.

overall_design: To investigate the tight correlation between expression of FLI1 and inflammatory genes associated with psoriasis, over-expression of FLI1 was performed in the epithelial cell line HaCaT. Gene expression profiling analysis was conducted using data obtained from RNA-seq of the two cell types. Comparative gene expression profiling analysis was then performed on the RNA-seq data for the control HaCaT cell (Migr1) and the HaCaT-FLI1 cell (MigrFLI1)

first: Yaacov

last: Ben-David

first: Xiao

last: Xiao


title: FHL2 deficiency impairs follicular development and fertility by attenuating EGF/EGFR/YAP signaling in murine ovarian granulosa cell

city: Wuhan

first: Guohua

last: Hua

state: China

address: No. 1, Shizishan Street

institute: Huazhong Agricultural University

summary: To investigate the function FHL2 in the follicle development, we established Fhl2 knockout mice by CRISPR/Cas9.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 samples of ovarian graunolosa cells

first: Chen

first: Hui

last: Sun


title: Transcriptomic landscape based on annotated clinical features reveals PLPP2 involvement in lipid raft-mediated proliferation signature of early-stage lung adenocarcinoma

first: Yibei

state: Liaoning

address: No.77 Puhe Road

institute: China Medical University

summary:
Background: Image-based screening improves the detection of early-stage lung adenocarcinoma (LUAD)but also highlights the issue of high false-positive diagnoses, which puts patients at a risk of unnecessary over-treatment. Therefore, more precise discrimination criteria are required to ensure that patients with early-stage LUAD receive appropriate treatments.
Methods: we integrated 158 early-stage LUAD cases from 2 independent cohorts, including 30 matched resected specimens with complete radiological and pathological information, and 128 retrospective pathological pair-samples with partial follow-up data. This integration allowed us to conduct a correlation analysis between clinical phenotype and transcriptome landscape. Immunohistochemistry was performed using tissue microarrays to examine the expression of phospholipid phosphatase 2 (PLPP2) and lipid-raft markers. Lipidomics analysis was used to determine the changes of lipid components in PLPP2-overexpressed cells. To assess the effects of PLPP2 on the malignant phenotypes of LUAD cells, we conducted mice tumor-bearing experiments and in vitro cellular experiments by knocking down PLPP2 and inhibiting lipid raft synthesis with MβCD, respectively.
Results: Bioinformatics analysis indicated that the co-occurrence of lipid raft formation and rapid cell proliferation might exhibit synergistic effects in driving oncogenesis from lung preneoplasia to adenocarcinoma. The enhanced activation of the cell cycle promoted the transition from non-invasive to invasive status in early-stage LUAD, which was related to an increase in lipid rafts within LUAD cells. PLPP2 participated in lipid raft formation by altering the component contents of lipid rafts, such as esters, sphingomyelin, and sphingosine. Furthermore, elevated PLPP2 levels were identified as an independent prognostic risk factor for LUAD patients. Further results from in vivo and in vitro experiments confirmed that PLPP2 could induce excessive cell proliferation by enhancing lipid raft formation in LUAD cells.
Conclusions: Our study has revealed the characteristics of gene expression profiles in early-stage LUAD patients with the different radiological and pathological subtypes, as well as deciphered transcriptomic evolution trajectory from preneoplasia to invasive LUAD. Furthermore, it suggests that PLPP2-mediated lipid raft synthesis may be a significant biological event in the initiation of early-stage LUAD, offering a potential target for more precise diagnosis and therapy in clinical settings.

overall_design: In this study, we integrated 158 early-stage LUAD cases from 2 independent cohorts, including 30 matched resect specimens with complete radiological and pathological information and 128 retrospective pathological pair-samples with part follow-up data to conduct a correlation analysis between clinical phenotype and transcriptome landscape. This integration allowed us to conduct a correlation analysis between clinical phenotype and transcriptome landscape. Our findings provided valuable insights into the trajectory of transcriptomic evolution from preneoplasia to invasive LUAD. Moreover, we had deciphered that PLPP2-mediated lipid raft synthesis might play a crucial role in driving the progression of early-stage LUAD. These results significantly contributed to our understanding of both the biological and clinical aspects of LUAD development.

first: Ziwei

last: Miao

first: Xiaoxue

last: Qin

first: Yi

last: Yang

first: Si

last: Wu

first: Qi

first: Beibei

last: Li

first: Mingyu

last: Zhang

first: Pengfei

first: Yun

last: Han

first: Bo


title: Characterization of Diabetic and Non-Diabetic Foot Ulcers Using Single-Cell RNA-Sequencing

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

summary: We examined the feasibility of single cell RNA sequencing (scRNA-seq) analysis to evaluate human chronic wound samples acquired in the clinic, subjected to prolonged cold ischemia time, and processed without FACS sorting. Wound tissue from human diabetic and non-diabetic plantar foot ulcers were evaluated using an optimized 10X Genomics scRNA-seq platform and analyzed using a modified data pipeline designed for low-yield specimens. Cell subtypes were identified informatically and their distributions and transcriptional programs were compared between diabetic and non-diabetic tissue. 139,000 diabetic and non-diabetic wound cells were delivered for 10X capture after either 90 or 180 min of cold ischemia time. cDNA library concentrations were 858.7 and 364.7 pg/µL, respectively, prior to sequencing. Among all barcoded fragments, we found that 83.5% successfully aligned to the human transcriptome and 68% met the minimum cell viability threshold. The average mitochondrial mRNA fraction was 8.5% for diabetic cells and 6.6% for non-diabetic cells, correlating with differences in cold ischemia time. A total of 384 individual cells were of sufficient quality for subsequent analyses; from this cell pool, we identified transcriptionally-distinct cell clusters whose gene expression profiles corresponded to fibroblasts, keratinocytes, neutrophils, monocytes, and endothelial cells. Fibroblast subpopulations with differing fibrotic potentials were identified, and their distributions were found to be altered in diabetic vs. non-diabetic cells.

overall_design: scRNA-seq of unsorted cells from wound debridement tissue of human diabetic and non-diabetic foot ulcers

first: Kellen

last: Chen


title: Selective inhibition of CDK9 in triple negative breast cancer

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

summary: Targeted treatment for triple-negative breast cancer (TNBC) remains an elusive clinical challenge. Cyclin-dependent kinase 9 (CDK9) is a transcriptional regulator shown to promote growth of multiple cancers, including TNBC, and represents a potential new therapeutic target. CDK9 increases RNA Polymerase II (Pol II) activity, which facilitates sustained expression of short-lived oncogenic and anti-apoptotic proteins. However, pre-clinical evaluation of CDK9 as a therapeutic target has been hampered by the poor selectivity of existing CDK9 inhibitors (CDK9i). Here, we report a novel CDK9i; D11-8, which exhibits high potency against CDK9 (Ki = 8 nM) and displays remarkable selectivity over other CDKs and human kinases. D11-8 inhibited TNBC cell line proliferation,, induced G2/M cell cycle arrest, and increased apoptosis. Mechanistically, D11-8 inhibited CDK9; reducing  Pol II phosphorylation, down-regulating expression of proto-oncogene MYC and anti-apoptotic marker MCL1, and dramatically inducing Pol II promoter-proximal pausing at MYC, G2/M checkpoint, and E2F2 target genes. D11-8 was further validated for TNBC in vivo, and inhibited TNBC cell line tumour growth without toxicity. To further elucidate the cancer cell specificity of D11-8, normal breast tissue was collected from women undergoing reduction mammoplasty surgery and treated with D11-8 ex vivo as patient-derived explants. High doses of D11-8 (2.7 µM) had no effect on the proliferative capacity of normal breast epithelial cells (Ki67 positivity), and tissues appeared histologically normal. Collectively, these data demonstrate that D11-8 effectively inhibits CDK9 in TNBC cell lines, resulting in growth inhibition without short-term toxicity.

overall_design: RNA Polymerase II (Pol II) ChIP-seq in MDA-MB-453 cells after 4 h treatment with either a vehicle or CDK9 inhibitor D11-8

first: E

last: Mustafa

first: G

first: Z

last: Kikhtyak

first: V

last: Nguyen

first: S

last: Ali

first: A

last: Pace

first: R

last: Iggo

last: Kebede

first: B

last: Noll

first: J

middle: M

last: Winter

middle: R

last: Dwyer

first: W

middle: D

last: Tilley

first: T

last: Hickey


title: Self-Assembling Hematopoietic Niche on a Chip: Bulk sequencing to investigate effect of proton radioablation

city: Philadelphia

first: Andrei

last: Georgescu

state: Pennsylvania

address: 315 Skirkanich Hall, 210 S. 33rd Street

institute: University of Pennsylvania

summary: (Radiation Experiments: bulk sequencing data) Here we present an integrative, bottom-up approach towards emulating the human bone marrow in vitro. Our method harnesses the regenerative capacity of adult stem cells to self-assemble a complex, specialized microenvironment of human hematopoietic stem cells (HSCs) in a vascularized three-dimensional microphysiological system. Through flow cytometry and single-cell transcriptomic interrogation, we show that the microengineered niche can reconstitute HSC self-renewal, multilineage hematopoiesis, and complex ligand-receptor signaling pathways of the native human marrow. The ability of our model to generate functionally mature myeloid cells also makes it possible to mimic the key physiological processes of innate immunity including neutrophil chemotaxis and intravascular mobilization. To demonstrate the advanced application of the bone marrow-on-a-chip, we present i) a specialized model of bone marrow ablation by proton beam radiotherapy and ii) a multiorgan model of innate immune response against bacterial lung infection. This work advances our ability to reconstruct, probe, and deconvolve the complexity of the bone marrow niche, and may enable new capabilities to model human hematopoiesis and immunity for biomedical and pharmaceutical applications.

overall_design: Bone marrow hematopoietic niche models cultured in vitro were irradiated with 0 Gy, 0.2 Gy, 2 Gy, and 20 Gy of proton radiation, with each group comprising 3 independent biological replicates that were multiplexed.

first: Joseph

middle: H

last: Oved

first: Samira

last: Mehta

first: Jeongyun

last: Seo

first: Michele

last: Kim

first: Eric

last: Diffenderfer

first: George

last: Worthen

first: Dan

last: Huh


title: Self-Assembling Hematopoietic Niche on a Chip: Single Cell Sequencing

summary: (Single Cell Sequencing Data) Here we present an integrative, bottom-up approach towards emulating the human bone marrow in vitro. Our method harnesses the regenerative capacity of adult stem cells to self-assemble a complex, specialized microenvironment of human hematopoietic stem cells (HSCs) in a vascularized three-dimensional microphysiological system. Through flow cytometry and single-cell transcriptomic interrogation, we show that the microengineered niche can reconstitute HSC self-renewal, multilineage hematopoiesis, and complex ligand-receptor signaling pathways of the native human marrow. The ability of our model to generate functionally mature myeloid cells also makes it possible to mimic the key physiological processes of innate immunity including neutrophil chemotaxis and intravascular mobilization. To demonstrate the advanced application of the bone marrow-on-a-chip, we present i) a specialized model of bone marrow ablation by proton beam radiotherapy and ii) a multiorgan model of innate immune response against bacterial lung infection. This work advances our ability to reconstruct, probe, and deconvolve the complexity of the bone marrow niche, and may enable new capabilities to model human hematopoiesis and immunity for biomedical and pharmaceutical applications.

overall_design: Two samples were sequenced, each of which used bone marrow hematopoietic stem cells from a different donor to establish the in vitro model of the hematopoietic niche and emergent immunity. We provide here the raw sequencing data from each donor, and the processed feature matrix that results when both samples are aggregated

middle: S


title: Age- and BAM15-related remodeling of inguinal white adipose tissue in high fat diet-fed mice

city: Baton Rouge

first: John

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: Aged (~92 weeks of age) C57BL/6J mice and young mice at 16 weeks of age were fed 60% HFD for 4 weeks containing either vehicle or 0.1% w/w BAM15. iWAT was harvested and snap frozen in liquid nitrogen. Tissue was homogenized in trizol and RNA extracted via chloroform phase separation.

overall_design: YOUNG CTRL samples are the reference/control samples.

last: King

first: M

last: Erickson

last: Dantas

last: Hall

first: Jasleen

last: Kaur

first: Sara

last: Webb

first: Richard

last: Carmouche

first: C

last: Axelrod


title: Transient restriction of intercellular communication is required for root regeneration

status: Public on Nov 24 2023

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

overall_design: 10x Genomics processes protoplasts from root tips of WT and lbd6 lbd36 lbd12 lbd15 quadruple mutants, at 16h afer root tip dissection. Experiment performed in duplicates.

first: Itay

last: Cohen


title: CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (methylation)

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Pluripotent stem cells are characterized by their differentiation potential toward endoderm, mesoderm, and ectoderm. However, it is still largely unclear how these cell-fate decisions are mediated by epigenetic mechanisms. In this study, we explored the relevance of CCCTC-binding factor (CTCF), a zinc finger-containing DNA-binding protein, which mediates long-range chromatin organization, for directed cell-fate determination. We generated human induced pluripotent stem cell (iPSC) lines with deletions in the protein-coding region in exon 3 of CTCF, resulting in overall reduced expression and shorter transcripts. These lines showed a considerable loss of CTCF binding to target sites. The CTCF deletions resulted in slower growth and modest global changes in gene expression, with down-regulation of a subset of pluripotency-associated genes and neuroectodermal genes. CTCF deletion also evoked DNA methylation changes, which were moderately associated with differential gene expression. Notably, CTCF-deletions lead to up-regulation of endo-mesodermal associated marker genes and epigenetic signatures, whereas ectodermal differentiation was defective. These results indicate that CTCF plays an important role in the maintenance of pluripotency and differentiation, especially towards ectodermal lineages.

overall_design: Bisulfite converted DNA from three samples weere hibridized to the Illumina Infinium EPIC Human Methylation Beadchip v1.0_B4

first: Deepika

last: Puri

first: Catharina

last: Maaßen

first: Mónica

last: Varona Baranda

first: Kira

last: Zeevaert

first: Lena

last: Hahnfeld

first: Annika

last: Hauser

first: Giulia

last: Fornero

first: Mohamed

last: H Elsafi Mabrouk


title: CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs

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


title: circAMN1/miR-205_R-1/SLC39A8 axis regulates ferroptosis in endometrial epithelial cells and regulates the occurrence of retained placenta in cows

city: Lanzhou

first: Chen

last: Lv

address: No.1 Yingmen Village

institute: Gansu Agricultural University

summary: In this study, we performed RNA-sequencing to characterize the expression profiles of circRNAs in caudal vein blood samples of postpartum Holstein cows whose fetal membranes were discharged normally or retained to identify retained placenta (RP)-related genes and evaluate their molecular mechanisms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for caudal vein blood samples of postpartum Holstein cows whose fetal membranes were discharged normally (NC) or retained (n=3).

first: Lv

last: Chen


title: CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (ChIP-Seq)

summary: ChIP-Seq analysis of CTCF enrichment in WT hiPSCs and hiPSCs with CTCF deletion

overall_design: Chip-Seq of CTCF enrichment in  4 samples: two iPSC WT lines (102 ,104) and two iPSC lines with a CTCF deletion (50, 55)


title: Circulating circRNA expression profiling of  Papillary thyroid cancer

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

summary: NGS was performed to detect whole human genome，including circRNA,lncRNA and mRNA.  We found many upregulated and downregulated circRNAs in PTC patients.

overall_design: Circulating circRNA profiles of five Papillary thyroid cancer patients and five healthy volunteers were generated by deep sequeHCing,using Illumina HiSeq 4000

first: Yingzhao

last: Liu

first: Huiyong

last: Peng

first: Xiangmei

last: Ding


title: CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (RNA-Seq)

overall_design: Gene expression profiling using data obtained from RNA-seq of 3 different cells lines: one iPSC WT line and two iPSC lines with a deletion in CTCF.


title: Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation (Bulk RNA-Seq)

city: Los Angeles

first: Owen

last: Witte

state: California

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

summary: Trans-differentiation from an adenocarcinoma to a small cell neuroendocrine state is associated with therapy escape in multiple cancer types. The temporal transcriptional changes of this process remain largely undefined. Here, we performed a multi-omics time course analysis of our pan-small cell neuroendocrine cancer model (termed PARCB), a forward genetic transformation using human prostate basal cells. With integrative analyses of RNA sequencing and ATAC sequencing, a shared developmental trajectory is identified among all transformed patient samples. Further mapping with single cell resolution reveals two distinct lineages defined by mutually exclusive expression of ASCL1 and ASCL2. Temporal regulation by groups of transcription factors across developmental stages reveals that cellular reprogramming precedes the induction of neuronal programs. Lastly, TFAP4 and ASCL1/2 feedback were identified as potential regulators of ASCL1 and ASCL2 expression. Our study provides temporal transcriptional patterns and uncovers pan-tissue parallels between prostate and lung cancers, and normal neuroendocrine cells.

overall_design:
To study the temporal transcriptional landscape during this trans-differentiation process, we conducted a time course study using a PARCB model by integrating multi-omics sequencing, including bulk RNA-sequencing and ATAC-sequencing on samples taken at different time point, as well as single cell RNA sequencing on serial xenograft tumors.
-------------------------------------
Authors state:
Raw data was not uploaded to GEO/not included in metadata as they are deposited in dbGaP with accession number phs003230.v1.p1

last: Chia-Chun

first: Chia-Chun


title: Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation (scRNA-Seq)


title: Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation

overall_design: Refer to individual Series


title: In vitro reconstitution of chromatin domains [ChIP-Seq]

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen

summary: A key step towards defining the structure-function relationship of the genome is to identify the molecular mechanisms that drive higher-order genome folding. To this end, we reconstituted five S. cerevisiae chromosomes in vitro and developed a high-resolution MNase-based chromosome conformation capture assay to measure their 3D organization. We show that the formation of regularly spaced and phased nucleosome arrays is sufficient to drive higher-order genome folding into domains that resemble in vivo genome organization and thereby demonstrate that neither loop extrusion nor transcription are required for domain formation. The domain boundaries correspond to nucleosome-free regions and insulation strength scales with their width. Integrated molecular dynamics simulations show that domain compaction is dependent on nucleosome linker length, with longer linkers forming more compact structures. Together, our work demonstrates that fundamental properties of chromatin fibers are important determinants of higher-order genome folding and provides a proof-of-principle for bottom-up 3D genome studies.

overall_design: We used a genome-wide in vitro reconstitution system (Oberbeckmann et al. 2021) to study how nucleosome positioning affects higher-order genome folding. To this end, we established a method to map 3D nucleosome contacts in vitro and named it in vitro Micro-C. DNA sequence of 5 chromosomes (V-IX) from S. cerevisiae was reconstituted into chromatin by salt gradient dialysis and then incubated with transcription factors only or additionally with various remodeler. Nucleosome positioning was confirmed with MNase-seq, while higher-order nucleoosme contacts were mapped with in vitro Micro-C.

first: Kimberly

last: Quililan

first: Patrick

last: Cramer

first: A

last: Oudelaar


title: In vitro reconstitution of chromatin domains (Mnase-Seq)


title: In vitro reconstitution of chromatin domains (Micro-C)