title: Modelling inflammation-induced peripheral sensitization in a dish – more complex than expected?

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

summary: Peripheral sensitization of nociceptors is believed to be a key driver of chronic pain states. Here, we sought to study the effects of a modified version of inflammatory soup on the excitability of human stem-cell derived sensory neurons. For this, we used a pre-existing and a novel stem cell line, modified to stably express the calcium sensor GCamP6f.  Upon treatment with inflammatory soup, we observed no changes in neuronal transcription or functional responses upon calcium imaging, and only a very minor increase in resting membrane potential via whole cell patch clamping. Similarly small changes were observed when treating mouse primary sensory neurons with inflammatory soup. A semi-systematic re-examination of past literature further indicated that observed effects of inflammatory mediators on dissociated sensory neuron cultures are generally very small.  We conclude that modelling inflammation-induced peripheral sensitization in vitro is non-trivial and will require careful selection of mediators and/or more complex, multi-cellular setups. Especially in the latter, our novel GCamP6f induced-pluripotent stem cell line may be of value.

overall_design: To investigate changes in gene expression across maturation of day 29-30 (D30), day 50-53 (D50) and day 69-70 (D70) iPSC-derived sensory neurons. To investigate changes in gene expression of day 60 iPSC-derived sensory neurons when cultured with a modified inflammatory soup (IS) of mediators (TNF, NGF, bradykinin, serotonin, histamine, PGE2) for 24 hours. Conditions were replicated across four differentiations, from two iPSC lines (N=4).

first: Yuening

last: Li

first: Amy

last: Lock

first: Laura

last: Fedele

first: Irene

last: Zebochin

first: Alba

last: Sabate

last: Siddle

first: Silvia

last: Cainarca

first: Pascal

last: Röderer

first: Katharina

last: Montag

first: Paola

last: Tarroni

first: Oliver

last: Brüstle

first: Tanya

last: Shaw

first: Leonie

last: Taams


title: Effect of Si-711, a dual sirtuin 1 and 2 inhibitor, on gene expression in chronic myeloid leukemia K-562 cells

status: Public on Aug 02 2024

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary: The transcriptomic signature of chronic myeloid leukemia (CML) patients is characterized by heightened proliferation and mitochondrial metabolic activity. Sirtuin (SIRT)1 and SIRT2 are recognized as key regulators of metabolism homeostasis and cell proliferation/survival, and our network analyses unveiled their significant role in driving CML pathogenesis. Accordingly, we demonstrated the therapeutic potential of dual SIRT1/2 inhibition across diverse models. In particular, we investigated the effect of a dual SIRT1/2 inhibitor, which exhibits selective efficacy against imatinib-sensitive and -resistant CML cells. To get a better understanding of Si-7111’s mechanism of action, we performed RNA-seq analysis on K-562 CML cells. The transcriptomic signature induced by Si-711 revealed that SIRT1/2 inhibition disrupted the regulation of crucial transcription factors, including MYC, associated with the reprogramming of hallmark pathways associated with CML cell proliferation. This reprogramming was characterized by metabolic alterations leading to energy depletion and subsequent induction of regulated necrosis.

overall_design: K-562 cells were treated with Si-711 (SIRT1/2 inhibitor) for 0, 8, 24, and 48 h, and each point was performed in 3 independent biological replicates.

first: Michael

last: Schnekenburger

first: Anne

last: Lorant


title: Bardoxolone methyl improves nonalcoholic steatohepatitis through inhibition of macrophage recruitment

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

summary: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease caused by excess fat accumulation, closely associated with obesity and metabolic syndrome.Bardoxolone methyl (2-Cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid methyl ester, CDDO-Me) is a potent activator of nuclear factor erythroid 2-related factor 2 (Nrf2). Some clinical trials of CDDO-Me were conducted for chronic kidney diseases and pulmonary arterial hypertension, whereas the hepatoprotective effect of CDDO-Me on nonalcoholic steatohepatitis (NASH) has not yet been elucidated. The purpose of this study was to determine the hepatoprotective potential and mechanisms of CDDO-Me in a diet-induced NASH mouse model. Whole transcriptome analysis revealed that CDDO-Me markedly inhibited the expressions of chemokine ligands, Ccl3 and Ccl4, and the chemokine receptors, Ccr1 and Ccr5 that increased in NASH mice while activating Nrf2-dependent pathway. Serum protein levels of CCL3 and CCL4 upregulated in NASH mice were inhibited in a dose-dependent manner by treatment with CDDO-Me. CDDO-Me inhibited the expression levels of Ccr1 and Ccr5, and simultaneously blocked Ccl3 and Ccl4 the ligands of the receptors, respectively in RAW264.7 cell line. Taken together with the observations, CDDO-Me directly inhibits the expression of CCL3-CCR1 and CCL4-CCR5 axes in macrophages of NASH mice, which might contribute to the improvement of nonalcoholic steatohepatitis and fibrosis through the interference of monocyte-derived macrophage migration.

overall_design:
To investigate the mechanisms of hepatoprotective effect of CDDO-Me in a diet-induced NASH mouse model, CDDO-Me was orally administered to NASH mouse models for 8 weeks and the livers were collected at the end of the experiment .
We then performed gene expression profiling analysis using the data obtained from RNA-seq of the livers from vehicle or CDDO-Me treated NASH mouse models.

first: Kazuhiro

last: Onuma

first: Kenji

last: Watanabe

first: Keishiro

last: Isayama


title: Promoted Read-through and Mutation Against Pseudouridine-CMC By An Evolved Reverse Transcriptase

status: Public on Aug 08 2024

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

country: USA

institute: Boston College

summary: Pseudouridine (Y) is an abundant chemical modification that plays critical roles in cellular RNA metabolism and functions, and in RNA therapeutic applications. Transcriptome-wide mapping technologies present major advantages in discovering the functional contexts and crucial effector proteins of Y. Current mapping strategies for Ys are limited in identifying Ys at base-resolution within consecutive uridine sequence contexts where Y occurs frequently. Here we report “Mut-Y-seq” that utilities a recently evolved reverse transcriptase (“RT-1306”) coupled with the selective labeling of Y by the CMC treatment to identify Ys in mRNAs and non-coding RNAs from human cells. We showed that RT-1306 showed significantly promoted read-through and mutation signatures against the CMC-Y adduct; the mutation signatures generated by RT-1306 can discern the position of Y in consecutive uridine sequence contexts. We quantitatively characterized the Y-identification efficiencies by Mut-Y-seq under variable chemical treatment conditions by the receiver operating characteristic curve analysis and revealed the presence of potential false positive discoveries generated by side-reactions on unmodified uridines. Finally, the intersection of sites identified by orthogonal chemical treatments (i.e. CMC and bisulfite) produced a high-confidence list of Y sites in mRNAs and non-ribosomal long non-coding RNAs from HEK-293T cells. This report presents datasets for biological functional studies of endogenous Y  sites, and sheds light on the combination of the reverse transcriptase engineering and selective chemical reactions for further expanding the toolkit for studying RNA chemical modifications.

overall_design: transcriptome-wide mapping of pseudouridines in RNAs  extracted from HEK-293T cells  with CMC treatment and evolved

first: Zhiyong

last: He


title: Lung adenocarcinoma methylation analysis.

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

type: Methylation profiling by genome tiling array

summary:
Methylation analysis of lung adenocarcinoma samples.
Genomic DNA isolated directly from human lung adenocarcinoma specimens.

overall_design: Lung adenocarcinoma samples n = 196; No technical replicates.

first: Jeffrey

last: Zuccato

first: Gelareh

last: Zadeh


title: RNA-seq based transcriptome analysis of plant pathogens under salt stress condition

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

summary: Plant pathogens require lethal virulence factors, susceptible hosts, and optimal environmental conditions for disease establishment. High soil salinity, exacerbated by climate change, significantly impacts agro-biological ecosystems. However, the overall interactions between plant pathogens and salt stress are not fully characterized or understood. This study examines the effects of salt stress on representative plant pathogens: Burkholderia gladioli, Pectobacterium carotovorum subsp. carotovorum, and Ralstonia solanacearum. Using pan-genome-based comparative transcriptomics, we analyzed the comprehensive alterations within the biological systems of plant pathogens when treated with 200 mM NaCl. Our results highlight the differential responses between salt-sensitive and salt-tolerant pathogens to salt stress.

overall_design: To induce salt stress, 200 mM NaCl was applied to salt-sensitive (B. gladioli and R. solanacearum) and salt-tolerant (Pcc) pathogens. For each plant pathogen, cultures without NaCl addition were used as negative controls. After 2 hours of exposure to salt stress, we examined changes in gene expression patterns. Each sample was prepared in triplicate.

first: Hyejung

last: Jung

first: Young-Su

last: Seo


title: TERT Promoter Mutations Combined with TP53 Mutations as Potential Biomarkers for Hepatocellular Carcinoma Recurrence and Prognosis

status: Public on Aug 01 2024

city: Chengdu

first: Ling

last: Bai

state: Sichuan

address: No.37 Guoxue Alley

department: Department of Laboratory Medicine

country: China

institute: West China Hospital, Sichuan University

summary: Hepatocellular carcinoma (HCC) is the most prevalent form of liver cancer, and ranks among the most lethal malignancies globally, primarily due to its high rates of recurrence and metastasis. Despite the urgency, no reliable biomarkers currently exist for predicting tumor recurrence in HCC. Telomerase reverse transcriptase (TERT) promoter mutations (TERTpm) and cellular tumor antigen p53 mutations (TP53m) have been frequently documented in HCC, but their combined clinical significance remains undefined. In this study, we investigated the clinical implications of TERTpm, TP53m, and their co-occurrence in 50 HCC tissue samples using the next-generation sequencing (NGS) technology. We identified TERTpm (C228T) and TP53m in 16 (32%) and 24 (48%) samples, respectively. Our findings indicate that these mutations are more prevalent in male patients (100% for TERTpm, 83.33% for TP53m), in those with solitary tumors (87.5% for both), in individuals with G2-G3 hepatitis (100% / 83.3%), and in cases of moderately differentiated tumors (75.0% / 83.3%). Furthermore, patients with both TERTpm and TP53m exhibited a significantly higher risk of tumor relapse (P<0.05) and shorter progression-free survival (P<0.05). Collectively, our results suggest that presence of both TERTpm and TP53m may serve as a robust predictor of tumor recurrence and a marker of poor prognosis in HCC.

overall_design: A total of 50 HCC patients whom were reported and diagnosed as HCC for the first time at the West China Hospital of Sichuan University were randomly selected. Fresh tumor tissues (≥60 mg) were obtained by surgical resection, and paired clinicopathologic information were collected. Targeted DNA sequencing was performed on tumor tissues.

first: Jin

last: Li

first: Zhaodan

last: Xin

first: Jiajia

last: Song

first: Hao

last: Chen

first: Xingbo

first: Juan


title: Brown Adipose Tissue undergoes pathological perturbations and shapes C2C12 myoblast homeostasis in the SOD1-G93A mouse model of Amyotrophic Lateral Sclerosis.

status: Public on Aug 05 2024

city: Rome

first: Marco

last: Rosina

state: Rome

address: Viale Regina Elena 299

department: Neuroscience

country: Italy

institute: Italian National Institute of Health

summary: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by the selective loss of motor neurons. While the contribution of peripheral organs remains incompletely understood, recent evidence suggests that brown adipose tissue (BAT) and its secreted extracellular vesicles (EVs) could play a role in diseased context as ALS. In this study, we employed a multi-omics approach, including RNA sequencing and proteomics, to investigate the alterations in BAT and its EVs in the SOD1-G93A mouse model of ALS. Our results revealed significant changes in the proteomic and transcriptomic profiles of BAT from SOD1-G93A mice, highlighting ALS-related features such as mitochondrial dysfunction and impaired differentiation capacity. Specifically, primary brown adipocytes (PBAs) from SOD1-G93A mice exhibited differentiation impairment, respiratory defects, and alterations in mitochondrial dynamics. Furthermore, the BAT-derived EVs from SOD1-G93A mice displayed distinct changes in size distribution and cargo content, which negatively impacted the differentiation and homeostasis of C2C12 murine myoblasts, as well as induced atrophy in C2C12-derived myotubes. These findings suggest that BAT undergoes pathological perturbations in ALS, contributing to skeletal muscle degeneration through the secretion of dysfunctional EVs. This study provides novel insights into the role of BAT in ALS pathogenesis and highlights potential therapeutic targets for mitigating muscle wasting in ALS patients.

overall_design: Total mRNA was extracted from brown adipose tissue of wild type and SOD1-G93A mice at symptomatic stage (120 days old) and processed for RNA-Seq

first: Silvia

last: Scaricamazza

first: Flaminia

last: Riggio

first: Gianmarco

last: Fenili

first: Flavia

last: Giannessi

first: Alessandro

last: Matteocci

first: Valentina

last: Nesci

first: Illari

last: Salvatori

first: Daniela

middle: F

last: Angelini

first: Katia

last: Aquilano

first: Valerio

last: Chiurchiù

first: Daniele

last: Lettieri Barbato

first: Nicola

last: Biagio Mercuri

first: Cristiana

last: Valle

first: Alberto

last: Ferri


title: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protist

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Cleavage and polyadenylation are the final steps of eukaryotic mRNA 3' end formation. The most critical element in humans and other model organisms is the poly(A) signal, an AAUAAA hexamer. We recently discovered that the deeply branching eukaryote – Giardia lamblia uses a different but well-defined poly(A) signal, AGURAA. To better characterize when this evolutionary shift in the poly(A) signal occurred, we performed direct RNA  sequencing of four protists within the Metamonada supergroup and two outgroup protists. Both outgroup protists and the non-Giardia Metamonada species use the AAUAAA poly(A) signal, indicating it is the ancestral signal. In contrast, all Giardia species use the WGURAA  poly(A) signal, indicating it is a derived feature within Giardia or Fornicata. The change in this ubiquitous regulatory element raises questions about the sequence features that specify genuine poly(A) sites and how to avoid premature cleavage in the coding sequence. Therefore, we used a sequence classifier, a gapped k-mer support vector machine, that could discriminate between WGURAA sites in 3'UTRs and those in the  CDS (F1 = 0.97). We found that Giardia lamblia uses nucleotides directly flanking the poly(A) signal for its recognition, with downstream nucleotides being the most important. Another member of the Giardia genus, Giardia muris, uses a different strategy: almost complete depletion of WGURAA hexamers in coding sequences. Ones that remain in the coding sequence can be recognized as poly(A) signals and undergo premature cleavage. These results identify unique features of the Giardia pathogens that could be targeted for drugs and highlight the diversity and evolution of mRNA 3' end formation in eukaryotes.

sample_organism:
Trichomonas vaginalis
Giardia duodenalis
Giardia muris
Entamoeba histolytica
Naegleria gruberi
Tritrichomonas foetus

overall_design: Total RNA was extracted from 6 protists species and subjected to ONT direct RNA sequencing.

first: Marcin

middle: P

last: Sajek

first: Danielle

middle: Y

last: Bilodeau

first: Michael

middle: A

last: Beer

first: Emma

last: Horton

first: Yukiko

last: Miyamoto

first: Katrina

middle: B

last: Velle

first: Lars

last: Eckmann

first: Lillian

last: Fritz-Laylin

first: Olivia

middle: S

last: Rissland


title: NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

city: Hefei

first: Yong

last: Jin

address: No.96, JinZhai Road Baohe District, Hefei, Anhui, 230026, P.R.China.

institute: University of Science and Technology of China

summary: Metabolic abnormalities associated with liver disease have a significant impact on the risk and prognosis of cholecystitis.  However, the underlying mechanism is complicated and remains to be elucidated.  In particular, the effect of metabolic abnormalities on the progression of cholecystitis through the regulation of immune cell function is poorly understood.  In this study, we investigated this issue using Wilson’s disease (WD) as a model.  Wilson’s disease is a genetic disorder characterized by impaired mitochondrial function and abnormal copper metabolism.  Our retrospective clinical study of over 600 patients with WD found that they have a significantly higher incidence of cholecystitis and a poorer prognosis.  The immune cell landscape in the hepatic mesenchymal stromal microenvironment using single-cell RNA sequencing showed that the tissue immune microenvironment is altered in patients with WD, mainly a major change in the constitution and function of the innate immune system, including enhanced antigen presentation process, activation of immune response, and activation of lymphocytes.  Exhaustion of natural killer (NK) cells is the fundamental factor, supported by an increase in the expression of the inhibitory receptors NKG2A and TIGIT and a decrease in the expression of cytotoxic molecules.  Clinical tissue and blood samples verified increased NKG2A+ and TIGIT+ NK cells and decreased IFNγ+ NK cells in WD.  Further bioinformatic analysis has confirmed a positive correlation between NK cell exhaustion and poor prognosis in cholecystitis and other inflammatory diseases.  The study demonstrated abnormal function of liver mesenchymal immune cells triggered by specific metabolic dysfunction in WD, with a focus on the correlation between NK cell exhaustion and poor healing of cholecystitis.  Our findings highlight the immune cell dysfunction due to hepatocytes metabolic changes, and provide new insights into improvement of inflammatory diseases by assessing immune cell function.

overall_design: The hepatic mesenchymal cells from three patients with Wilson's disease and three liver hemangioma patients were analyzed using the 10X Genomics platform for scRNA-seq.

first: Qiyu

last: Feng

first: Qingsheng

last: Yu

first: Hongyang

last: Wang


title: PAX8 interacts with the SWI/SNF complex at enhancers to drive proliferation in ovarian cancer

status: Public on Aug 04 2024

city: South San Francisco

first: Karen

last: Gascoigne

state: California

address: 1 DNA way

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Activation of lineage-specific gene expression programs is mediated by the sequence-specific recruitment of transcriptional coactivators to chromatin. This occurs via interaction with lineage specific DNA binding transcription factors. The lineage factor PAX8 drives essential gene expression in ovarian cancer cells and is required for tumor proliferation. However, the molecular details surrounding co-factor recruitment and specific activation of transcription by PAX8 remain unknow. Here, we identify an important functional interaction between PAX8 and the Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex. We show that PAX8 can recruit SWI/SNF complexes to DNA, where they function to open chromatin and facilitate expression of PAX8 target genes. Genetic deletion of PAX8 results in loss of SWI/SNF from PAX8 bound enhancers, loss of expression of associated target genes, and reduced proliferation. These results can be phenocopied by pharmacological inhibition of SWI/SNF ATPase activity. These data indicate that PAX8 mediates the expression of an essential ovarian cancer proliferative program in part by the recruitment of chromatin remodelers.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PAX8, SMARCA4 and H3K27Ac with or without dox inducible CRISPR mediated knock out of PAX8 in IGROV1 cells.

first: Kostianna

last: Sereti

first: Anna

last: Russo

first: Ryan

last: Raisner


title: Robust snRNA-seq protocol revealing mouse white adipose tissue remodeling during obesity

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary:
Using our robust snRNA-seq protocol effectively enhancing nucleus integrity and RNA quality,
we comprehensivly characterize the dynamics of cell populations within mouse epididymal and inguinal adipose tissues during obesity.

overall_design: Comparative gene expression profiling analysis of snRNA-seq data for epididymal and inguinal white adipose tissues from lean and obese mice.

first: Hyun

middle: C

last: Roh

first: Avishek

last: Paul


title: Intestinal epithelial cell NCoR deficiency ameliorates obesity and metabolic syndrome

city: Beijing

first: Shaocong

last: Hou

address: 1st Nanwei Street

department: State Key Laboratory of Bioactive Substance and Function of Natural Medicines

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Obesity has emerged as a common disease worldwide. Risks of developing other metabolic diseases, such as Type 2 diabetes are also higher in obese population. However, current treatment options are limited. Here we discovered a new approach for mitigating obesity and metabolic disorders by targeting intestinal nuclear receptor corepressor (NCoR). In mice with diet-induced obesity, NCoR deficiency in intestinal epithelial cells (IECs) improved obesity, insulin resistance, and glucose intolerance, corrected atherogenic dyslipidemia, and reduced hepatic steatosis. These effects were mediated through regulation of energy expenditure, energy harvest, and gut hormone secretion. Mechanistically, NCoR deficiency in IECs stimulated peroxisome proliferator-activated receptor α (PPARα) signaling pathway-mediated succinate production and thermogenesis. Intestinal cholesterol excretion was induced by derepression of intestinal liver X receptor (LXR), and triglyceride and fatty acid absorption in the upper intestine was reduced by disrupted bile acid synthesis and altered bile acid composition. In the distal intestine, increased fatty acid uptake stimulated glucagon-like peptide-1 (GLP-1) secretion and improved glycemic control.

overall_design: To investigate the role of nuclear receptor corepressor (NCoR) in intestinal epithelial cells (IECs), wild type (WT) and IEC NCoR knock out (IKO) mice were fed with high fat diet for 15 weeks. After sacrifice, mucosa of ileum from WT and IKO mice was scraped and subjected to RNA sequencing. Each group includes 7 biological replicates.

first: Pingping

last: Li


title: Cardiomyocyte S1pr1 regulates cardiac regeneration via AKT/mTOR signaling pathway

first: xiuxiang

last: liu

address: 150 Jimo Rd, Pudong New District

institute: Shanghai East Hospital, Tongji University School of Medicine

summary:
Mammalian hearts had the capability to regenerate cardiomyocyte and completely recover after heart injury within a limited time window after birth. It has been shown that sphingosine 1-phospahte receptor 1 (S1pr1) was highly expressed in cardiomyocytes and played an important role in heart development and pathological cardiac remodeling. Herein, we aim to investigate the role of CM-S1pr1 for cardiac regeneration and tissue repair after heart injury.
We generated cardiomyocyte (CM)-specific S1pr1 knock-out mice and showed that CM-specific S1pr1 loss-of-function significantly severely reduced cardiomyocyte proliferation and heart regeneration in neonatal mice after both apex resection and myocardial infarction, whereas S1pr1 gain-of-function by AAV9-mediated CM-specific overexpression of S1pr1 significantly boosted cardiac regeneration and improved cardiac functions after heart injuries. We next identified that S1pr1 activated AKT/mTOR/CyclinD1 and Bcl-2 signaling pathways, and thus promoted cardiomyocyte proliferation and inhibited CM apoptosis, respectively.Of note, we applied CM-targeted gene therapy by AAV9-cTNT to specifically overexpress S1pr1 in cardiomyocytes and achieved an efficient S1pr1 overexpression in CMs in vivo. This CM-targeted strategy to overexpress S1pr1 significantly enhanced cardiac regeneration and improved cardiac functions after myocardial infarction in an adult mouse model, suggesting a potential strategy to boost adult cardiac regeneration in vivo.

overall_design: To gain insight into the molecular processes affected by CM-S1pr1 deficiency we performed gene expression analysis of heart tissues from S1pr1CMKO and WT neonates by RNA sequencing (n=2/groups).

first: Xiuxiang

last: Liu

first: Lin

last: Zhang


title: Development of Vegetative Oil Sorghum: From Lab-to-Field

status: Public on Jul 31 2024

city: Lincoln

first: Edgar

last: Cahoon

state: NE

address: 1901 Vine St

institute: University of Nebraska Lincoln

summary: Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or “vegetable oils”) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating “sweet” (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a “push-pull-protect" strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum Wrinkled1 transcription factor (“push”), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; "pull"), a modified sesame oleosin (“protect”) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount of up to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to wild-type TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.

overall_design: RNAseq was conducted to compare changes in trascriptome between WT and TAG-producing transgenic event. Field is located at Eastern Nebraska Research and Education Center (ENREC) in Mead, NE, USA (41°08'42.7"N 96°26'20.5"W). Total RNA was extracted using field-grown mature leaves at early reproductive stage in 2021. No additional treatment applied to the field or plants.

first: Kiyoul

last: Park

first: Chi


title: Effect of dexamethasone treatment on the transcriptome of injured mouse hamstring muscle

city: Brisbane

first: Kylie

last: Alexander

address: Translational Research Institute, 37 Kent St Woolloongabba

country: Australia

institute: Mater Research Institute

summary: Healthy muscle heals and repairs after injury. However, when mice are treated with dexamethasone, an agonist of glucocorticoid receptors, heterotopic ossifications (HO) develop in the injured muscle within fibrotic areas that fail to fully regenerate functional muscle. To understand the mechanisms driving heterotopic ossification in response to glucocorticoid receptor agonists, we performed RNA seqencing analysis on injured muscle. Mice underwent muscle injuries by intramuscular injection of cardiotoxin (CDTX). All mice were treated with either vehicle or dexamethasone (10mg/kg, intraperitoneal injection) daily from day 0-4. polyA+ RNA was isolated from whole muscle 4 days post injury, libraries generated and sequenced.

overall_design:
Mice underwent muscle injuries by intramuscular injection of cardiotoxin (CDTX). All mice were injected intraperitoneally daily for 4 days with either saline (group C) or 10mg/kg dexamethasone (group D). RNA was isolated from whole CDTX-injured hindlimb muscle on 4 days post injury. Just prior to tissue harvest, heterotopic ossification development quantified in CDTX-injured muscles by micro computed tomography (µCT). Only 1 mouse (mouse C4) out of 5 in saline group developed heterotopic ossification (0.67mm3) and mouse C4 therefore was excluded in further analysis. On the other hand,  all mice in dexamethasone-treated mice developed HO (2.40±5.42 mm3).  PolyA+ RNA was then purfied before library construction and sequencing.
contributor: UQ Sequencing Facility

first: Jean-Pierre

last: Levesque

first: Hsu-Wen

last: Tseng


title: Oncogenic signaling in the adult Drosophila prostate-like accessory gland leads to activation of a conserved pro-tumorigenic program, in the absence of proliferation

status: Public on Oct 01 2024

city: Ann Arbor

first: Laura

last: Buttitta

state: Michigan

address: 5218 BSB, University of Michigan

department: MCDB

institute: University Of Michigan

summary:
The Drosophila melanogaster male accessory gland (AG) is crucial for reproductive success, producing seminal fluid proteins that impact female post-mating behavior and physiology. To understand the regulatory networks governing accessory gland function, we conducted a bulk RNA sequencing (RNA-Seq) study to analyze the effects of overexpressing key regulatory genes. Specifically, we compared Gal4-induced Yki+Dp and Myc+E2F+Dp overexpression to controls not expressing these transgenes.

We found upregulated and downregulated genes in each condition compared to controls, affecting immune response, cell cycle, stress response, and reproductive functions. In both Yki constitutively active, Dp and dMyc, E2F+DP conditions, several genes known to be involved in wound healing and tumorigenic models in flies were upregulated, including JNK signaling targets Ets21C, MMP1, puckered, and Jak/STAT signaling pathway ligands upd2 and upd3. Conversely, accessory gland-specific genes, such as many Accessory Gland Proteins (Acps), and genes involved in fertility, mating behavior, and sperm competition were downregulated. There was a strong overlap between the Yki constitutively active, Dp and dMyc, E2F+Dp gene expression signatures, converging on genes commonly misregulated in proliferative tumor models in various larval tissues, including imaginal discs and brains. This study provides insights into the molecular mechanisms by which key regulatory genes influence the function and integrity of the Drosophila male accessory gland.

overall_design:
We induced adult-specific transgene expression in the accessory gland (AG) using the Gal4-UAS and Flp-FRT recombinant systems. This system includes a Gal4 gene under the control of the actin promoter, with a stop cassette flanked by FRT sites upstream of the Gal4 coding sequence. The flippase enzyme is controlled by a heat-shock promoter. The flies were exposed to 37°C for 20 min on the day of eclosion, leading to flippase expression, to remove the stop cassette, allowing Gal4 to drive transgene expression. UAS transgenes used in this study include GFP-NLS, dMyc with E2F+Dp, a wild-type Yki, a constitutively active Yki with Dp, and a P35 apoptosis inhibitor. All samples, including the control sample, had UAS-P35 and GFP-NLS expression in the background.  All samples were virgin males, kept at 25°C after transgene activation and dissected for RNA isolation 10 days of age.
Each sample contained 80-100 dissected accessory glands with the ejaculatory duct and testis removed. Samples were visually inspected for GFP expression. Glands with no or low GFP expression were excluded from downstream analysis. We performed three independent replicates per sample.
RNA was extracted from the accessory glands of adult males, followed by sequencing on the Illumina platform. The resulting data were analyzed to identify differentially expressed genes between the overexpression conditions and WT.

first: Samuel

last: Church


title: PAX8 interacts with the SWI/SNF complex at enhancers to drive proliferation in ovarian cancer [ChIP-seq]

first: Karen

last: Gascoigne

first: Kostianna

last: Sereti

first: Anna

last: Russo

first: Ryan


title: Enhanced RNAi does not provide efficient innate antiviral immunity in mice in vivo (ESCs TrapR small RNA-Seq)

status: Public on Jul 30 2024

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

type: Non-coding RNA profiling by high throughput sequencing

summary: In RNA interference (RNAi), long double-stranded RNA (dsRNA) is cleaved by Dicer endonuclease into small RNA interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates adopted sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified mouse Dicer locus to express a truncated variant (DicerΔHEL1) known to stimulate RNAi. Next, we analyzed how DicerΔHEL1/wt mice respond to four RNA viruses: Coxsackievirus B3 (CVB3) and encephalomyocarditis virus (ECMV) from Picornaviridae; tick-borne encephalitis virus (TBEV) from Flaviviridae; and lymphocytic choriomeningitis virus (LCMV) from Arenaviridae. Increased Dicer activity in DicerΔHEL1/wt mice had no antiviral effect. This result supports insignificant antiviral function of endogenous mammalian RNAi in vivo. However, we also report that sufficiently high expression of DicerΔHEL1 suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAi in vivo.

overall_design:
Bulk RNA-seq of small RNAs associated with RISC complexes (TrapR - Trans-kingdom, rapid, affordable Purification of RISCs) of mouse embryonic stem cells (mESCs) of different Dicer and Pkr genotypes, infected with LCMV in 0.01 MOI (Multiplicity of Infection), or transfected with a plasmid expressing a MosIR dsRNA hairpin:
- LCMV infection = 2x Dicer wt/wt at 0.01 MOI; 2x Dicer ΔHEL1/ΔHEL1 at 0.01 MOI; 2x Dicer S-4 at 0.01 MOI; 2x Dicer O-3 at 0.01 MOI
- MosIR transfection = 2x Dicer wt/wt; 2x Dicer ΔHEL1/ΔHEL1; 2x Dicer S-4; 2x Dicer O-3

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Marcos

middle: I

last: Roos Kulmann

first: Eliska

last: Taborska


title: Mono-allelic epigenetic regulation of bi-directional polycistronic transcription initiation by RNA Polymerase II in Trypanosoma brucei.

status: Public on Jul 29 2024

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: In vitro selection of Bloodstream form T. brucei with the trypanosome lytci factor (TLF) led to generation of parasites resistant to TLF. We not show that resistance is due to silencing Pol II transcription initiaiton at promoter for the gene array that includes the TLF receptor gene HpHbR. Reversable transcriptional silencing of the HpHbR gene array and the adjacent gene array, correlates with DNA base J modification of the shared promoter region. We demonstrate that epigenetic mechanisms exist to regulate gene expression via Pol II transcription initiation of polycitronic gene arrays in a monoallelic fashion.

overall_design: The role of PP1-1 in regulating transcription termination was investigated using RNAi ablation in T. brucei cell lines. We used 6 RNA seq libraries to determine gene expression changes following the loss of PP1-1. As a control we used 6 RNA seq libraries to determine changes following the loss of PP1-7.

last: Sabatini

first: Rudo

last: Kieft

first: Haidong

last: Yan


title: Enhanced RNAi does not provide efficient innate antiviral immunity in mice in vivo (ESCs small RNA-Seq)

overall_design:
Bulk small RNA-seq of mouse embryonic stem cells (mESCs) of different Dicer and Pkr genotypes, infected with LCMV in 0.01 or 1 MOI (Multiplicity of Infection), or transfected with a plasmid expressing a MosIR dsRNA hairpin:
- LCMV infection = 4x Dicer wt/wt at 0.01 MOI + 2x Dicer wt/wt at 1 MOI; 4x Dicer ΔHEL1/ΔHEL1 at 0.01 MOI + 2x Dicer ΔHEL1/ΔHEL1 at 1 MOI; 2x Dicer ΔHEL1/ΔHEL1, Pkr -/- at 0.01 MOI + 2x Dicer ΔHEL1/ΔHEL1, Pkr -/- at 1 MOI; 2x Dicer -/- at 0.01 MOI; 4x Dicer S-4 at 0.01 MOI; 4x Dicer O-3 at 0.01 MOI
- MosIR transfection = 2x Dicer wt/wt; 2x Dicer ΔHEL1/ΔHEL1; 2x Dicer S-4; 2x Dicer O-3


title: Enhanced RNAi does not provide efficient innate antiviral immunity in mice in vivo

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

overall_design: Refer to individual Series


title: Transcriptome data of B cells and T helper cells from patients with multiple sclerosis receiving therapeutic apheresis for the treatment of an acute relapse

status: Public on Jul 28 2024

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

summary: We analyzed the transcriptome profiles of CD19+ B cells and CD4+ T cells from the peripheral blood of patients with multiple sclerosis (MS) immediately before and after relapse therapy with apheresis. High-density Clariom D Arrays for human were used to obtain gene-level and exon-level expression profiles. This GEO entry provides the processed data from the gene-level and exon-level workflows.

overall_design:
Peripheral blood was taken from 4 MS patients before the first (T0) and after the last (T1) session of apheresis (i.e., plasma exchange or immunoadsorption) for the treatment of an acute exacerbation.
CD19+ B cells were isolated from 3 blood sample pairs, while CD4+ T helper cells were isolated from 4 blood sample pairs, resulting in a total of 14 samples. Total RNA was extracted, labeled and hybridized to Clariom D microarrays to quantify the transcript levels.

first: Dirk

last: Koczan

first: Uwe

middle: K

last: Zettl


title: Enhanced RNAi does not provide efficient innate antiviral immunity in mice in vivo (organs small RNA-Seq)

overall_design:
Bulk small RNA-seq of mouse samples, different Dicer and Pkr genotypes, 3 different organs infected with different viruses:
- brain, TBEV infection = 3x Dicer wt/wt; 3x Dicer ΔHEL1/wt; 3x Dicer wt/wt, Pkr -/-; 3x Dicer ΔHEL1/wt, Pkr -/-
- heart, EMCV infection = 2x Dicer wt/wt; 2x Dicer ΔHEL1/wt
- spleen, CVB3 infection = 2x Dicer wt/wt; 2x Dicer ΔHEL1/wt
- spleen, LCMV infection = 2x Dicer wt/wt; 1x Dicer wt/wt, Pkr -/-; 2x Dicer ΔHEL1/wt; 1x Dicer ΔHEL1/wt, Pkr -/-; 2x Dicer tg(O-HA)/tg(O-HA)


title: Antitumor efficacy of vitamin D analog in a patient-derived xenograft

status: Public on Jul 18 2024

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

summary: Determine the molecular pathways underlying the antitumor effect of vitamin D analog  on xenografts from a patient with docetaxel resistant CRPC.

overall_design: PDX-G266 mice, a model of CRPC. The tumors from mice treated with vehicle or with a combinatory regimen including a single administration of docetaxel and a daily treatment with 0.3 µg/kg/day Xe4MeCF3 (a vitamin D analog) for 14 days (termed co-treatment) were analyzed .

first: Kateryna

last: Len


title: Modulation by NPYR underlies experience-dependent, sexually dimorphic learning

status: Public on Jul 25 2024

city: Rehovot

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

department: Brain Sciences

country: Israel

institute: Weizmann Institute of Science

summary: The evolutionary paths taken by each sex within a given species sometimes diverge, resulting in behavioral differences. Given their distinct needs, the mechanism by which each sex learns from a shared experience is still an open question. Here, we reveal sexual dimorphism in learning: C. elegans males do not learn to avoid the pathogenic bacteria PA14 as efficiently and rapidly as hermaphrodites. Notably, neuronal activity following pathogen exposure was dimorphic: hermaphrodites generate robust representations while males, in line with their behavior, exhibit contrasting representations. Transcriptomic and behavioral analysis revealed that the neuropeptide receptor npr-5, an ortholog of the mammalian NPY receptor, regulates male learning by modulating neuronal activity. Furthermore, we show the dependency of the males’ decision-making on their sexual status and demonstrate the pivotal role of npr-5 as a modulator of incoming sensory cues. Taken together, we portray sex-specific plasticity in behavior toward a shared experience by modulating learning.

overall_design: To understand the whole animal transcriptomics of hermaphrodites and males towards PA14 exposure after 6 hours. We utilized bulk-optimized protocol of Marseq to derive transcriptomic datsets of 4 biological replicates of each sex after 6 hours exposure to OP50 or PA14

first: Sonu

last: Peedikayil-Kurien

first: Asaf

last: Gat

first: Meital

last: Oren-Suissa


title: Conserved long noncoding RNA TILAM promotes liver fibrosis in humans and mice.

status: Public on Jul 22 2024

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis is responsible for the development of end stage liver disease and liver failure. The activation of hepatic stellate cells (HSCs) and their transition to HSC myofibroblasts is a key step in the disease process, as these cells are the primary source of the extracellular matrix (ECM) proteins, which form the fibrotic scar. Long noncoding (lnc) RNAs can regulate the activity of HSCs, and lncRNAs that promote the fibrotic activity of HSCs may provide targets for antifibrotic therapies. Here, we identified and defined the functional mechanisms of a conserved lncRNA that plays a critical role in promoting liver fibrosis. We found that TILAM is conserved between human and mouse HSCs, and regulates expression of type 1 collagen, a major component of the ECM. To determine the role of TILAM in vivo, we annotated the mouse ortholog (Tilam), generated Tilam-deficient GFP-reporter mice, and challenged these mice in two different models of liver fibrosis. Analysis of GFP expression revealed that Tilam is induced in murine HSCs with the development of fibrosis in vivo. In both male and female mice, we also observed that loss of Tilam resulted in reduced fibrosis in the setting of injury induced by carbon tetrachloride (CCl4) and choline-deficient L-amino acid defined high fat diet (CDA-HFD). Finally, we found that TILAM interacts with PML to stabilize PML protein expression and promote the fibrotic activity of HSCs. Together, these results define an lncRNA conserved between humans and mice that is activated uniquely in HSCs to drive the development of fibrosis and could provide a therapeutic target to combat the development of end stage liver disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Primary Hepatic stellate cells with siRNA or LNA treatment

first: Cheng

last: Sun

first: Chan

last: Zhou

first: Zixiu

last: Li

first: Raa

last: Ur Rahman


title: The Tie-2 antagonist rebastinib reduces ovarian cancer growth in a syngeneic murine model

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Background: The receptor tyrosine kinase TIE2 and its ligands, angiopoietins (ANGPTs), promote angiogenesis. In addition to expression on vascular endothelial cells, TIE2 is expressed on M2-like pro-tumorigenic macrophages. Thus, the TIE2 inhibitor rebastinib was developed as a potential therapy to address multiple cancers. The objective of this study was to determine the effects of rebastinib alone and combined with chemotherapy in a syngeneic murine model of ovarian cancer.

overall_design: RNA sequencing was performed on ID8 cells and murine peritoneal macrophage cells (PMJ2R) after 6h treatment with 5 nM rebastinib, chemotherapy, or rebastinib plus chemotherapy.

first: Vijayalaxmi

last: Gupta

first: Katherine

last: Roby

first: Dineo

last: Khabele


title: Methionine Restriction Reduces Lung Cancer Progression and Increases Chemotherapy Response

status: Public on Jul 19 2024

city: LEXINGTON

first: Christine

middle: Fillmore

last: Brainson

state: KY

address: 1095 VA Drive

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: Methionine restriction sensitizes A549 cells with and without LKB1 to chemotherapy

overall_design: Cells were first treated with empty vectors (EV) or LKB1 vectors, sensitized to media with different concentrations of methionine, and then treated with carboplatin

first: Jinpeng

last: Liu

first: Kassandra

last: Naughton

first: Ryan

last: Goettl


title: Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq]

status: Public on Jul 17 2024

city: Birmingham

first: Jason

middle: Dale

last: Turner

address: Queen Elizabeth Hospital

department: Rheumatology research group

institute: University of Birmingham

summary: The key role of tertiary lymphoid structures in autoimmune and non-autoimmune conditions has been recently appreciated. While many of the molecular mechanisms involved in tertiary lymphoid structure formation have been identified, their cellular sources and temporal and spatial relationship remain unknown. Using single-cell RNA-sequencing, spatial transcriptomics and proteomics of minor salivary glands of patients with Sjogren’s disease and Sicca Syndrome, ex-vivo and in vivo functional studies, we construct a cellular and spatial map of key components involved in the formation and function of tertiary lymphoid structures. We confirm the presence of a fibroblast cell state and identify an undescribed pericyte/mural cell state with potential immunological functions. The identification of novel cellular properties associated with these structures and the molecular and functional interactions identified by this analysis provide key therapeutic cues for tertiary lymphoid structures associated conditions in autoimmunity and cancer.

overall_design: The selected tissue samples for microdissection processing were acquired from patients recruited within the OASIS cohort at the University of Birmingham, under ethics number 10-018. Preparation of the samples for microdissection: all surfaces of the cryostat and lab bench were thoroughly cleaned with 70% Etoh and sterilised with ultraviolet (UV) light for at least 30 min. Containers used to keep store the collected samples and the filter paper used to separate slides (Membrane slides, Carl Zeiss™ 1.0 PEN NF 41590-9081-000) must also be treated with UV for 30 min and kept sterile before handling the tissue. To cut tissue for microdissection, the UV sterilised membrane slides were maintained at a cool temperature within the cryostat prior to sample cutting. The tissue was mounted on a cryostat block with as little mounting media (OCT, TissueTeK) as possible to minimise interference with laser cutter during microdissection. Sections were cut at 8 um thickness and transferred to the membrane slides.  Once the section had been mounted onto the membrane slides, the membrane slide was stored in its carrier box and in dry ice until final storage at -80oC prior to staining with Cresyl violet acetate (SIGMA). Preparation of Cresyl violet acetate is required one day prior to staining the mounted tissues. Preparation of the CresylViolet (1% solution) included dissolving the powder in 80% ethanol which had been made using sterile RNase-free water in a MSC Class II ventilator system. This solution was mixed overnight on a shaker at 4oC to ensure that the CresylViolet was completely dissolved, and the solution was then passed through a 70µm strainer before use. The slides were first dipped in RNase-free water and suspended for 2 min in 70% Etoh, also prepared in RNase-free water, to facilitate the removal of OCT on the tissue. The slides were then suspended in the CresylViolet 1% solution for 30 secs to 1 min and excess solution was tapped off. The slides were then processed for 1 min in 100% Etoh and this step was repeated three times. The PALM slides were then left to dry until the membrane was observed to be completely dry. The PALM slides were then stored at -800C in a parafilm sealed 50 ml falcon until the samples were ready for microdissection. Prior to microdissection, the PALM slides were bought to room temperature for 10 min. Microdissection was completed using the PALM Robo Software V.4.6 software using the brightfield “AxioCam CC1” setting. The objective lens used to micro dissects SG sections was 10X whilst tonsil was set at 5X. The area of interest was then identified using the ocular eye piece. Once the region had been selected the laser was aligned to the section that was to be cut. The collection tubes required for the capture of the microdissected tissue contained 20 ul of RLT buffer with B-mercaptanol, ensuring the lid was kept dry, and tube was kept on dry ice prior to use. The collection tubes were then mounted onto the Collector Set 200 CMII and set to the correct position to collect the microdissected sample as they were cut by applying the calibration procedure to collect tissue in the centre of the lid of the collection tube which were stored at -80oC prior to RNA extraction. RNA extraction from the microdissected samples was completed as per the protocols provided using the RNeasy FFPE kit (Qiagen). Library preparation and sequencing from extracted RNA was completed by Genomics Birmingham. Initial libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit. Further samples were processed using the NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina.  All libraries were sequenced using a NextSeq 500 sequencer. Adapters were trimmed with trimmomatic v0.39, reads aligned to the hg38 transcriptome with STAR v2.7.2b, and counts summed using featureCounts in Subread v2.0.1 using the University of Birmingham BlueBEAR High Performance Computing service. R v4.0.3 and DESeq2 v1.30.1 were used for downstream analysis. To minimise batch effects during differential expression analysis batch was included as a factor in the DESeq2 model and for principal component analysis and visualisations batch effects were minimised in variance stabilising transformed data using the limma v3.46.0 function removeBatchEffect.

first: Saba

last: Nayar

middle: D

last: Asam

first: Eanna

last: Fennell

first: Matthew

last: Pugh

first: Serena

last: Colfrancesco

first: Onorina

last: Berardicurti

first: Charlotte

middle: G

last: Smith

first: Joe

last: Flint

first: Ana

last: Teodosio

first: Valentina

last: Iannizzotto

first: David

middle: H

last: Gardner

first: Joel

last: Van Roon

first: Ilya

last: Korsunsky

first: Michael

last: Brenner

first: Mark

last: Coles

first: Andreas

last: Frei

first: Kara

last: Lassen

first: Fiona

middle: M

last: Powrie

first: Soumya

last: Raychaudhuri

first: Simon

last: Bowman

first: Wan-Fai

last: Ng

first: Adam

last: Croft

first: Andrew

last: Filer

first: Benjamin

last: Fisher

first: Christopher

last: Buckley

first: Francesca

last: Barone


title: Endothelial Metabolic Control of Resident Muscle Macrophage Function [bulk RNA-seq]

status: Public on Jul 26 2024

city: schwerzenbach

first: jing

last: zhang

state: Schwerzenbach

address: schorenstrasse 16

department: Department Health Sciences and Technology

country: Switzerland

institute: DHEST

summary: Endothelial cells (ECs) not only form passive blood conduits. They actively contribute to nutrient transport and establish an instructive vascular niche to maintain and restore organ homeostasis. The role of the endothelium in the maintenance of muscle glucose homeostasis is however poorly understood. Here we show that, in skeletal muscle, the endothelial glucose transporter 1 (Glut1/Slc2a1) controls glucose uptake not via affecting transendothelial glucose transport, but via vascular niche control of muscle resident macrophages. Lowering endothelial glut1 via genetic depletion (glut1EC) or upon short-term high-fat diet increased angiocrine osteopontin (OPN/SPP1) secretion, promoting resident muscle macrophage activation and proliferation which impairs muscle insulin sensitivity. Consequently, co-deleting Spp1 from the endothelium prevented macrophage accumulation, reduced muscle OPN levels, and improved insulin sensitivity in glut1EC mice. Mechanistically, glut1-dependent endothelial glucose metabolic rewiring increased OPN in a serine metabolism-dependent fashion. Our data illustrate how the glycolytic endothelium creates a niche that controls resident muscle macrophage phenotype and function and directly links resident muscle macrophages to the development of muscle insulin resistance.

overall_design: Our proposal involves investigating the impact of endothelial GLUT1 deletion on the regulation of metabolic balance in skeletal muscle. To achieve this, we obtained freshly isolated muscle endothelial cells using beads and promptly subjected them to bulk RNA sequencing. Our study included three samples from wild-type mice and four samples from mice with endothelial GLUT1 knockout.

first: Jing

last: Zhang

first: Kim

last: Sjøberg

first: Songlin

last: Gong

first: Tongtong

last: Wang

first: Fengqi

last: Li

last: Kuo

first: Stephan

last: Durot

last: Majcher

first: Raphaela

last: Ardicoglu

first: Thibaut

last: Desgeorges

first: Charlotte

last: Mann

first: Ines

last: Soro-Arnáiz

first: Gillian

last: Fitzgerald

first: Paola

last: Gilardoni

first: E

last: Abel

first: Shigeyuki

last: Kon

first: Danyvid

last: Olivares-Villagómez

first: Nicola

last: Zamboni

first: Christian

last: Wolfrum

first: Thorsten

last: Hornemann

first: Raphael

last: Morscher

first: Nathalie

last: Tisch

first: Bart

last: Ghesquière

first: Manfred

last: Kopf

first: Erik

last: Richter

first: Katrien

last: De BOCK


title: Endothelial Metabolic Control of Resident Muscle Macrophage Function [scRNA-seq]

first: jing

last: zhang

overall_design: To explore how endothelial Glut1 deletion regulates macrophages in skeletal muscle, we sort CD45+CD31- and CD31+CD45-  cells from skeletal muscle and subjected them for single cells sequencing.

first: Jing

last: Zhang

first: Kim

last: Sjøberg

first: Songlin

last: Gong

first: Tongtong

last: Wang

first: Fengqi

last: Li

first: Andrew

last: Kuo

first: Stephan

last: Durot

first: Adam

last: Majcher

first: Raphaela

last: Ardicoglu

first: Thibaut

last: Desgeorges


title: Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[scRNA-seq]

first: Jason

last: Turner

overall_design: Labial minor salivary gland samples were obtained from patients recruited in the Optimising Assessment in Sjögren’s Syndrome (OASIS) cohort which recruits new patients attending the multidisciplinary Sjögren’s clinic at the Queen Elizabeth Hospital Birmingham, UK for assessment. Sjögren’s syndrome patients had a physician diagnosis of primary Sjögren’s syndrome and fulfilled the 2016 ACR/EULAR classification criteria. Participants with non-Sjögren’s sicca syndrome had signs and/or symptoms of dryness but did not have a physician diagnosis of SS or fulfill 2016 classification criteria. Salivary gland biopsy samples were divided in two: one for the scRNAseq study and the second for histological analysis to confirm diagnosis. Histological diagnosis is reported as presence of focal lymphocytic sialadenitis (FLS, suggestive of Primary Sjögren’s Syndrome, PSS) or non-specific chronic sialadenitis (NSCS), in the case of non-Sjögren’s sicca syndrome. All OASIS participants provided written informed consent and the study was approved by the Wales Research Ethics Committee 7 (WREC 7) formerly Dyfed Powys REC; 13/WA/0392. Minor salivary gland biopsies were taken surgically from the lip and frozen in 1mL of CryoStor® CS10 (StemCell Technologies) at −80°C. For preparation of single-cell suspension, firstly the frozen tissue sample in Cryotube were quickly thawed in water bath at 37°C and washed twice in pre-warmed 5%FBS RPMI media. The salivary gland biopsies were then enzymatically digested as previously described. Dead cells were removed using the EasySepTM Dead Cell Removal (Annexin V) kit from the digested samples following manufacturer’s instructions before proceeding for the scRNA sequencing using the 10x platform. Library preparation and sequencing was completed by Oxford Genomics Centre. Cell counts in each sample were quantified using the Bio-Rad TC20. 10,000 cells per sample were used to generate libraries with the 10x Genomics v3 Single Cell 3’ kit before sequencing to a minimum depth of 50,000 reads per cell using the NovaSeq 6000.

first: Saba

last: Nayar

last: Asam

first: Eanna

last: Fennell

first: Matthew

last: Pugh

first: Serena

last: Colfrancesco

first: Onorina

last: Berardicurti

first: Charlotte

last: Smith

first: Joe

last: Flint

first: Ana

last: Teodosio

first: Valentina

last: Iannizzotto

first: David

last: Gardner

first: Joel

last: Van Roon

first: Ilya

last: Korsunsky

first: Michael

last: Brenner

first: Mark

last: Coles

first: Andreas

last: Frei

first: Kara

last: Lassen

first: Fiona

last: Powrie

first: Soumya

last: Raychaudhuri

first: Simon

last: Bowman

first: Wan-Fai

last: Ng

last: Croft

last: Filer

first: Benjamin

last: Fisher

first: Christopher

last: Buckley

first: Francesca

last: Barone


title: A pair of NUCLEAR FACTOR Y transcription factors act as  positive regulators in jasmonate signaling and disease  resistance in Arabidopsis

status: Public on Jul 15 2024

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University


summary: The plant hormone jasmonate (JA) regulates plant growth and immunity by orchestrating a genome-wide transcriptional reprogramming. In the resting stage, JASMONATE-ZIM DOMAIN (JAZ) proteins act as main repressors to regulate the expression of JA-responsive genes in the JA signaling pathway. However, the mechanisms underlying de-repression of JA-responsive genes in response to JA treatment remain elusive. Here, we report two nuclear factor Y transcription factors NF- YB2 and NF-YB3 (thereafter YB2 and YB3) play key roles in such de-repression in Arabidopsis. YB2 and YB3 function redundantly and positively regulate plant resistance against necrotrophic pathogen Botrytis cinerea ， which are specially required for transcriptional activation of a set of JA-responsive genes following inoculation. Furthermore, YB2 and YB3 modulated their expression through direct occupancy and interaction with histone demethylase Ref6 to remove repressive histone modifications. Moreover, YB2 and YB3 physically interacted with JAZ repressorsand negatively modulated their abundance, which in turn attenuated the inhibition of JAZ proteins on the transcription of JA- responsive genes, thereby activating JA response and promoting disease resistance. Overall, our study reveals the positive regulator of YB2 and YB3 in JA signaling by positively regulating transcription of JA-responsive genes and negatively modulating the abundance of JAZ proteins.

overall_design: To explore the molecular mechanism underlying the roles of YB2 and YB3 in plant resistance to B. cinerea, RNA sequencing (RNA-seq) assays were performed. Four-week-old plants with or without B. cinerea infection of WT and yb2 yb3 were collected.

first: Zeng

last: Tao


title: Transcriptome analysis of rigosertib resistant MDA-MB-453 cells, obtained from a CRISPR screen with WNK1 depletion.

status: Public on Jul 16 2024

city: Madrid

first: Guillermo

last: de Cárcer

state: Madrid

address: Arturo Duperier, 4

department: Cancer

country: Spain

institute: IIBM-CSIC

summary: In a genome-wide CRISPR-Cas9 resistance drug screen, we identified the master osmostress regulator WNK1 kinase as a modulator of the response to the mitotic drug rigosertib. Osmotic stress and WNK1 inactivation lead to an altered response not only to rigosertib but also to other microtubule-related drugs, minimizing the prototypical mitotic arrest produced by these drugs. This effect is due to an alteration in microtubule stability and polymerization dynamics, likely maintained by fluctuations in intracellular molecular crowding upon WNK1 inactivation. This promotes resistance to microtubule depolymerizing drugs, and increased sensitivity to microtubule stabilizing drugs. In summary, our data proposes WNK1 osmoregulation activity as a biomarker for microtubule-associated chemotherapy response.

overall_design: MDA-MB-453 breast cancer cells, carrying the Yusa sgRNA CRISPR library, were subjected to a RIGOSERTIB drug resistance screen. Cas9 is activated in a TET-ON inducible manner with doxycycline (DOX) for 3 days, an then cells are incubated with 100nM rigosertib during 3 days, and 4 days of drug holiday, repeating this cycle for 4 to 5 weeks. Once resistant colony cells were observed, they were allowed to grow in fresh media for 10 days more. Total RNA was extracted from three resistant colonies (Res) and two parental controls (no DOX and +DOX) to evaluate de transcriptome of the resistant cells.

first: Ana

last: Monfort-Vengut

first: Natalia

last: Sanz-Gómez


title: Transcriptomic analysis of sheep hypothalamus on sex-dependent differences in body weight of progeny born to dams supplemented with omega-3 fatty acids or methionine during late-gestation

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

institute: Ohio State Univesity

summary: Feeding dams during gestation affects the development of the offspring for their entire life. The objective of the current experiment was to evaluate the changes of the transcriptome in the hypothalamus of the offspring lambs born from dams supplemented with: i) a control diet (without lipids or methionine supplementation), ii) an omega 3 fatty acid supplementation, or iii) a methionine supplementation. The supplementation took place in the last third of gestation and the hypothalamus of male and female offspring was collected after being on a fattening diet for 54 days. Hypothalamus samples were used to extract RNA and analyzed using RNA sequencing. There was an interaction due to sex and methionine supplementation. The pathways that were modified were chromatin structure, developmental processes, and organ morphology. The modification observed on these pathways could explain the sex-by-treatment interaction differences previously observed in growth. There was no sex by omega-3 fatty acid interaction on the hypothalamus transcriptome. Therefore, the sexual dimorphism observed by methionine supplementation may be regulated by the hypothalamus.

overall_design: Ewes received i) a basal diet without omega-3 fatty acids or methionine supplementation as control (NFNM), ii) omega-3 fatty acids supplementation (PUFANM), or iii) methionine supplementation (NFM). Data were compared as NFNM vs. PUFANM, and NFNM vs. NFM. A treatment by sex interaction was also evaluated.


title: Exploration of the lipid-regulating effects of Rosa roxburghii flavonoids in hyperlipidemic mice

status: Public on Jul 12 2024

city: Guiyang

first: Jiaqi

last: Tang

state: Guizhou

address: No. 9, Beijing Road, Guiyang City, Guizhou Province

institute: GUIZHOU MEDCIAL UNIVERSITY

summary: Hyperlipidemia (HLP), an insidious threat to human health in modern society, can deteriorate and lead to various other metabolic diseases. This study focuses on transcriptomic analysis of liver samples from C57BL/6 mice, which were divided into the following groups: control group (C), hyperlipidemia model group (M), and three groups treated with flavonoids from Rosa roxburghii—quercetin at 200 mg/kg (QU), myricetin at 75 mg/kg (MY), and kaempferol at 100 mg/kg (KA). Except for the control group, all other groups were maintained on a high-fat diet for 6 weeks. To investigate the commonalities among the three flavonoid components from Rosa roxburghii, differentially expressed genes (DEGs) between each treatment group and the model group were screened to identify common expression genes.

overall_design: C (control, n=3), M (model, n=3), QU (quercetin, n=3), MY (myricetin, n=3), KA (kaempferol, n=3)


title: SOX2+ sustentacular cells are stem cells in the postnatal adrenal medulla

status: Public on Jul 13 2024

city: London

first: Cynthia

middle: Lillian

last: Andoniadou

state: -- Select State/Province --

address: Dept of Craniofacial Development, Guy's Hospital, Tower Wing, Floor 27

institute: King's College London

summary: Renewal of the catecholamine-secreting chromaffin cell population of the adrenal medulla is necessary for physiological homeostasis throughout life. Definitive evidence for the presence or absence of an adrenomedullary stem cell has been enigmatic. In this work, we show that a subpopulation of uncommitted sustentacular cells, previously thought to be support cells, are in fact adrenomedullary stem cells. These postnatal cells express the transcription factor SOX2, and give rise to chromaffin cells of both the adrenaline and noradrenaline lineages in vivo and in vitro. We present comprehensive transcriptomic data of the mouse adrenal medulla as well as of purified SOX2+ adrenomedullary stem cell populations. Through genetic tracing, we show that postnatal stem cells specialise from embryonic Schwann Cell Precursors and identify this population in the normal adult human adrenal medulla.

overall_design: 10 adrenals from 5 mixed sex P15 mice were dissected on ice, surrounding fat and excess adrenal cortex were removed manually. Medullae were placed in an enzymatic digestion mix containing 50μg/ml DNAse I (Sigma, D5025), 10mg/ml Collagenase II (Worthington, LS004177), 2.5μg/ml Fungizone (Gibco, 15290026), 0.1X Trypsin-EDTA (Sigma, 59418C) in 1X Hank’s Balanced Salt Solution (HBSS) (Gibco, 14025050) and incubated at 37°C for 15 minutes. Enzymes were inactivated by addition of 10 times volume of serum-containing Base Media: DMEM/F-12 (Gibco, 31330-038) + 5% FBS (Merk, F0804) + 50U/ml Penicillin-Streptomycin (Gibco, 15070063). The cell suspension was centrifuged at 281g for 5 minutes at room temperature, washed twice in PBS and pellets were resuspended in a solution of HBSS 2.5% FBS. An aliquot of 10,000 viable cells were used for the experiment. Library preparation and sequencing were performed by the BRC Genomics Core at KCL. Library preparation was done using the Chromium 10X Single Cell 3’ Reagent Kit v3 (10x Genomics) and a Chromium Controller (10x Genomics) following the manufacturer’s protocol. Once obtained, barcoded transcripts from single cells were sequenced with an Illumina HiSeq 2500.

first: Alice

last: Santambrogio

first: Yasmine

last: Kemkem

first: Thea

middle: L

last: Willis

first: Ilona

last: Berger

first: Maria

middle: E

last: Kastriti

first: Louis

last: Faure

first: John

last: Russell

first: Emily

last: Lodge

first: Val

last: Yianni

first: Rebecca

last: Oakey

first: Barbara

last: Altieri

first: Stefan

middle: R

last: Bornstein

first: Charlotte

last: Steenblock

first: Igor

last: Adameyko


first: Chuyu

last: Lin

overall_design: To investigate whether YB2 could directly bind to the chromatin of the indicated resistance and JA response target genes in its capacity as a transcription factor, genome-wide occupancy of YB2 were determined by ChIP-seq assays in the transgenic plants of YB2-FLAG drive with native promoter.

first: Zeng

last: Tao


title: Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [10X]

status: Public on Jul 02 2024

city: Foster City

first: Ruidong

last: Li

state: CA

address: 324 Lakeside Drive

department: Research Data Sciences

institute: Gilead Sciences, Inc.

summary: We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow via robotic implementation and established best practices to consistently achieve high cell capture efficiency and data quality. In comparison with the 10X platform, HT Smart-seq3 analysis of primary CD4+ T-cells demonstrated superior sensitivity in gene detection and similar capability to capture major cellular heterogeneity upon sufficient scaling up. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified more productive pairs of alpha and beta chains without additional primer design, enabling more comprehensive profiling of TCRs. Collectively, HT Smart-seq3 provides a cost-effective and scalable method for characterization of single-cell transcriptomes and immune repertoires.

overall_design: PPBMCs were isolated from two healthy donors and subsequently treated with either DMSO (vehicle) or PMA/Ionomycin. After a 3-hour incubation, CD4+ T-cells were sorted by FACS. 10X Genomics Chromium Next GEM Single Cell 5' Kit (v2) was used to generate GEX and VDJ libraries for each sample.

first: Hsiu-Chun

last: Chuang

first: Kai-Hui

last: Sun

first: Li


title: CD16 and CD57 Expressing Gamma Delta T Cells in Acute HIV-1 Infection are Associated with the Development of Neutralization Breadth

status: Public on Jul 03 2024

city: silver spring

first: Dohoon

last: Kim

address: 503 BLDG, Walter Reed Army institute of research

institute: Henry M Jackson Foundation

summary: New HIV vaccine approaches are focused on eliciting broadly neutralizing antibodies. We characterized early gamma-delta (γδ) T cell responses starting from pre-acquisition and during acute HIV infection (AHI) in participants previously characterized for neutralization breadth development. We found significant differences in γδ T cell surface marker expression in participants that developed neutralization breadth compared to those that did not. Activation of γδ T cells occurred within the first weeks of HIV acquisition and associated with viral load. Expression of CD16 on Vδ1 T cells and CD57 on Vδ2 T cells were found to be significantly higher in broad neutralizers during AHI, and associated with the development of neutralization breadth years later. In addition, the levels of CD16 on Vδ1 T cells was associated with early production of founder virus Env-specific IgM. Thus, γδ T cells may promote development of neutralization breadth, which has implications for HIV vaccine strategies.

overall_design: Gamma delta T cells were sorted from PBMCs from 22 participants at 4 time points: pre HIV acquisition, peak viral load (VL) (median days since first positive test for HIV-1 RNA = 18 days), set point VL (median days since first positive test for HIV-1 RNA = 42), and chronic HIV (median days since first positive test for HIV-1 RNA = 980). Sorted cells were then processed for bulk RNA sequencing.

first: Gina

last: Griffith

first: Kawthar

last: Machmach

first: Margaret

last: Costanzo

first: Matthew

last: Creegan

first: Isabella

last: Swafford

first: Gautam

last: Kundu

first: Lauren

last: Yum

first: Rasmi

last: Thomas

first: Nelson

last: Michael

first: Julie

middle: A

last: Ake

first: Leigh

last: Eller

first: Merlin

last: Robb

first: Samantha

last: Townsley

first: Shelly

last: Krebs

first: Dominic

last: Paquin-Proulx


title: Wild-type and GLO2 knockout BMDMs with infection of VSV

status: Public on Jul 01 2024

city: Shanghai

first: Qihang

last: Zhao

address: 800 xiangyin road

institute: National laboratory of medical immunology

summary: Transcriptome analysis of wild-type and GLO2 knockout BMDM infected with VSV for 12 hours .

overall_design: To analyze variation of gene expression in BMDM by konckout of GLO2, GLO2 was knockouted in BMDM of HAGHfl/fl LYZ2reERT2 mice by adding 4-OHT in medium on the process of incuding BMDM form bone marrow cells. Then, cells were infected by VSV(MOI=1) for 12 hours.

first: Pin

last: Wang

first: Zhengdong

last: Yang

first: Rong

last: Chen


title: Piezo1 induces  neutrophil extracellular traps formation directing M1 macrophage differentiation

status: Public on Jul 10 2024

city: 北京

first: Yue

address: 新街口外大街19号

institute: BNU

summary: To research the neutrophil extracellular traps in the regulation of macrophages differentiation, we performed gene expression profiling analysis using data obtained from RNA-seq of mice and control with virus infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neutrophils in bronchoalveolar lavage fluid (BALF) of infected or control mice.

first: Yuexin

first: Guangwei

last: Liu


title: Plasmid-chromosome transcriptional crosstalk in multidrug resistant clinical enterobacteria

first: Alvaro

last: San Millan

address: Darwin, 3

department: Biotecnología Microbiana

institute: Centro Nacional de Biotecnología-CSIC

summary: Conjugative plasmids are the main vehicle for the horizontal spread of antimicrobial resistance (AMR). Although AMR plasmids provide advantages to their hosts under antibiotic pressure, they can also disrupt the cell’s regulatory network, impacting the fitness of their hosts. Despite the importance of plasmid-bacteria interactions on the evolution of AMR, the effects of plasmid carriage on host physiology has remained underexplored, and most studies have focused on model bacteria and plasmids that lack clinical relevance. Here, we analyzed the transcriptional response of 11 clinical enterobacterial strains (2 Escherichia coli, 1 Citrobacter freundii and 8 Klebsiella spp.) and the laboratory-adapted E. coli MG1655 to carriage of pOXA-48, one of the most widely spread carbapenem-resistance plasmids. Our analyses revealed that pOXA-48 produces variable responses on their hosts, but commonly affects processes related to metabolism, transport, response to stimulus, cellular organization and motility. More notably, the presence of pOXA-48 caused an increase in the expression of a small chromosomal operon of unknown function in Klebsiella spp. and C. freundii, which is not present in E. coli. Phylogenetic analysis suggested that this operon has been horizontally mobilized across different Proteobacteria species. We demonstrate that a pOXA-48-encoded LysR transcriptional regulator controls the expression of the operon in Klebsiella spp. and C. freundii. In summary, our results highlight a crosstalk between pOXA-48 and the chromosome of its natural hosts.

sample_organism:
Citrobacter freundii
Escherichia coli
Klebsiella pneumoniae
Klebsiella variicola

overall_design: First, we performed differential expression (DE) analysis to analyze the transcriptional responses of clinical enterobacterial strains to carriage of the carbapenem-resistance plasmid pOXA-48. We sequenced three biological replicates per strain and condition (carrying and not carrying pOXA-48), except for strains CF13, TC_KPN10, PF_KPN10 and MG1655 that we sequenced two replicates due insufficient RNA Integrity number (RIN). Additionally, we performed a second RNA-Seq and DE analysis for strains KPN15 and CF13 carrying pOXA-48 or pOXA-48ΔlysR (three biological replicates per strain and condition) to characterize the plasmid-chromosome transcriptional crosstalk.

first: Laura

last: Toribio-Celestino

first: Ariadna

last: Fernandez-Calvet

first: Alicia

last: Calvo-Villamañan

first: Cristina

last: Herencias

first: Aida

last: Alonso-del Valle

first: Jorge

last: Sastre-Dominguez

first: Susana

last: Quesada

first: Javier

last: DelaFuente

first: Didier

last: Mazel

first: Eduardo

last: Rocha


title: Multimodal transcriptomics reveal neurogenic aging trajectories and age-related regional inflammation in the dentate gyrus

city: Philadelphia

first: Yicheng

last: Wu

state: Pennsylvania

address: 415 Curie Boulevard

department: Neuroscience

institute: University of Pennsylvania

summary: Single-cell RNA sequencing was performed on dentate gyrus of C57Bl/6 mice at ages ranging from 3 MO to 21 MO. Spatial transcriptomics was performed on whole brain sections from cage littermates

overall_design: 34732 single cells isolated from the dentate gyrus of mice for scRNA-seq. 42169 spots were profiled on the brain coronal sections.

first: Enric

last: Llorens-Bobadilla

first: Jonas

last: Frisen

first: Sebastian

last: Jessberger


title: ChIP seq of CDK6-WT and CDK6-K43M in murine BCR-ABL(p185)+ pre/pro B-cells

status: Public on Jun 30 2024

city: Vienna

first: Thorsten

last: Klampfl

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

summary: The aim of this experiment was to study the DNA interaction of a kinase-dead mutant of the cell cycle kinase CDK6 (CDK6-K43M) in a murine model of BCR-ABL driven leukemia.

overall_design: ChIP seq was performed in mouse BCR-ABL(p185)+ Cdk6-/- pre/pro B cell lines transduced with either HA-tagged wildtype (CDK6-WT), or HA-tagged mutant (CDK6-K43M) CDK6. An antibody against HA was used to pull down the CDK6 variants and associated chromatin.Two replicates per genotype were analysed.

first: Lisa

last: Scheiblecker

first: Sofie

last: Nebenführ

first: Markus

last: Zojer

first: Veronika

last: Sexl

first: Karoline

last: Kollmann


title: Characterization of intestine specific TRPM6 knockout C57BL/6J mice: effects of short-term omeprazole treatment

city: Nijmegen

first: Joost

last: Hoenderop

address: Geert Grooteplein Zuid 28-30

department: Medical Biosciences

country: Netherlands

institute: Radboudumc

summary: The transient receptor potential melastatin type 6 (TRPM6) is a divalent cation channel pivotal for gatekeeping Mg2+ balance. To study the role of TRPM6 in the intestine, we generated mice lacking intestinal TRPM6 (Vill1-TRPM6-/-). In this study, the distal colon of Vill1-TRPM6-/- mice and of the control mice (TRPM6fl/fl) was subjected to RNA sequencing.

overall_design: Total RNA from the distal colon of Vill1-TRPM6-/- and TRPM6fl/fl control mice following 1 day of low Mg2+ diet (0.02% w/w) was extracted. Furthermore, these RNA samples were subjected to RNA-sequencing.

first: Anastasia

last: Adella

first: Lisanne

last: Gommers

first: Caro

last: Bos

last: Maartens

first: Jeroen

last: de Baaij


title: Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [Bulk]

status: Public on Jun 24 2024

first: Ruidong

last: Li

overall_design: PBMCs were isolated from two healthy donors and subsequently treated with either DMSO (vehicle) or PMA/Ionomycin. Each donor/treatment has 2 replicates. After a 3-hour incubation, FACS-sorted CD4+ T-cells were collected for bulk RNA sequencing.

first: Hsiu-Chun

last: Chuang

first: Kai-Hui

last: Sun

first: Li


title: Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road, #163

department: Waksman Institute

institute: Rutgers University

summary: Smads and their transcription factor partners mediate the transcriptional responses of target cells to secreted ligands of the Transforming Growth Factor-β (TGF-β) family, including those of the conserved bone morphogenetic protein (BMP) family, yet only a small number of direct target genes have been well characterized. In C. elegans, the BMP2/4 ortholog DBL-1 regulates multiple biological functions, including body size, via a canonical receptor-Smad signaling cascade. Here, we identify functional binding sites for SMA-3/Smad and its transcriptional partner SMA-9/Schnurri based on ChIP-seq peaks (identified by modEncode) and expression differences of nearby genes identified from RNA-seq analysis of corresponding mutants. We found that SMA-3 and SMA-9 have both overlapping and unique target genes. At a genome-wide scale, SMA-3/Smad acts as a transcriptional activator, whereas SMA-9/Schnurri direct targets include both activated and repressed genes. Mutations in sma-9 partially suppress the small body size phenotype of sma-3, suggesting some level of antagonism between these factors and challenging the prevailing model for Schnurri function. A functional analysis of direct target genes revealed a novel role in body size for genes involved in one-carbon metabolism and in the endoplasmic reticulum (ER) secretory pathway, including the disulfide reductase dpy-11. Our findings indicate that Smads and SMA-9/Schnurri have previously unappreciated complex genetic and genomic regulatory interactions that in turn regulate the secretion of extracellular components like collagen into the cuticle to mediate body size regulation.

overall_design: RNA-seq was conducted at the L2 stage using N2, sma-3(wk30) and sma-9(ok1628) strains grown at 20C under 21% O2.

first: Savage-Dunn

last: Cathy

first: Rongo

last: Christopher

first: Vora

last: Mehul

first: Dietz

last: Jonathon


title: Many ETS family transcription factors can recruit mutant p53, and interaction specificity patterns correlate with ETS gene expression changes in ovarian cancer

status: Public on Jun 28 2024

city: Bloomington

first: Stephanie

last: Metcalf

address: 1001 E Third St

institute: Indiana University Bloomington

summary: The tumor suppressor transcription factor p53 is mutated in nearly 50% of all cancer cases, and this frequency increases with stage and resistance to therapy. Hotspot p53 mutations lose direct DNA binding activity while gaining oncogenic function. These structural p53 mutants can bind to new regions of the genome via interactions with other transcription factors. One example is the ETS transcription factor ETS2, which was previously reported to bind mutant p53. Yet, a comprehensive understanding of mutant p53 association with the ETS family needs to be understood. Here, we compare mutant p53 interaction across 26 ETS transcription factors. Mutant p53 bound ETS proteins better than wild-type p53. All ETS proteins tested bound to mutant p53 to some extent, yet relative binding differed. The ETS DNA binding domain provided a common interaction interface, but strong binding required a second interaction domain. Genome-wide mapping found that the ETS protein ERG could recruit mutant p53 to regulatory regions of genes necessary for morphogenesis, locomotion, and androgen response in prostate cancer cells. Lastly, ETS factors that interact strongly with mutant p53 tend to be upregulated in p53 mutant ovarian cancer. These results suggest that multiple ETS proteins can work with mutant p53 in cancer.

overall_design: Chromatin imunoprecipitation DNA-Sequencing (ChIP-Seq) for p53 (DO1, Santa Cruz) in VCaP cells that harbor the endogenous R248W p53 mutation with either shRNA for luciferase or shRNA for ERG.

first: Metcalf

last: Stephanie A.

first: Mayo

last: Lindsey D.

first: Hollenhorst

last: Peter C.


title: Gene expression and atrial fibrillation prediction

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

summary: The aim of this study was to identify a blood gene expression profile that predicts atrial fibrillation in heart failure patients

overall_design: Cardiac blood samples were obtained from the coronary sinus during CRT-D (Cardiac Resynchronization Therapy - Defibrillator) placement in heart failure patients. Patients were followed during 1 year.


title: LINC01770 mediates nasopharyngeal cancer radiation resistance and renders tumor cell vulnerable to ferroptosis [RNA-seq]

city: GuangZhou

first: xu

last: qingqing

state: GuangDong

address: 651 Dongfeng East Road, Yuexiu District

institute: State Key Laboratory of Oncology in South China

summary: Long noncoding RNAs (lncRNAs) participate in regulation of various essential biological processes including cell proliferation, differentiation, apoptosis, migration, and invasion. However, the clinical significances of lncRNAs and their functions and mechanisms in nasopharyngeal carcinoma (NPC) involved in malignant progression need to be further investigated. We find that the LINC01770-TEAD1 signal axis leads to radiotherapy resistance of NPC and causes NPC cells to be in a fragile oxidative stress equilibrium. Meanwhile radioresistant cells are more sensitive to ferroptosis inducers. LINC01770 stabilizes TEAD1 by competitive binding with microRNA 615-5p and microRNA -1293. Radiation resistant cell is in a delicate balance of lipid peroxidation and more vulnerable to ferroptosis. In conclusion, our research suggest that LINC01770 serves as an independent prognostic factor in NPC. During the malignant progression of NPC caused by high expression of LINC01770, ferroptosis can be induced to effectively kill cancer cells and reverse RT resistance of NPC cells, providing evidence for the clinical application of ferroptosis in the treatment of recurrent and refractory NPC.

overall_design: RNA-seq was performed in SUNE-1 NPC cells after LINC01770 shRNA and control shRNA transfection

first: Qing-Qing

last: Xu

first: Xin

last: Wen

first: Xuan

first: Lei

last: Chen


title: Activation of three targets by a TAL effector confers susceptibility to bacterial blight of cotton

status: Public on Jun 26 2024

city: college station

first: Brendan

last: MORMILE

state: Texas

address: 211 redmond drive

institute: University of Michigan

summary: Xanthomonas spp. employ transcription activator-like effectors (TALEs) to promote pathogenicity by activating host susceptibility (S) genes. Cotton GhSWEET10 is an S gene targeted by a TALE in an early isolate of Xanthomonas citri pv. malvacearum (Xcm), but not by recent field Xcm isolates. To understand the pathogenicity shift in Xcm and its adaptation to cotton, we assembled the whole genome and the TALE repertoire of three recent Xcm Texas field isolates. A newly evolved TALE, Tal7b, activated different GhSWEET genes, GhSWEET14a and GhSWEET14b. Simultaneous activation of GhSWEET14a and GhSWEET14b resulted in pronounced water-soaked lesions. Transcriptome profiling coupled with TALE-binding element prediction identified a pectin lyase as an additional Tal7b target, quantitatively contributing to Xcm virulence alongside GhSWEET14a/b. CRISPR-Cas9-based gene editing supported the function of GhSWEETs as S genes in cotton bacterial blight and the promise of disrupting the TALE-binding site in these genes to control the disease. Collectively, our findings elucidate the rapid evolution of TALEs in Xanthomonas field isolates and highlight the virulence mechanism wherein TALEs induce multiple S genes simultaneously to promote pathogenicity.

overall_design: To identify the genes being targeted and upregulated by virulence protein Tal7b from the plant pathogen Xanthomonas citri pv. malvacearum, we expressed Tal7b or an vector control into susceptible cotton variety FM2322.  We performed transcriptome profile analysis using data obtained from RNA-seq of 6 different cotton plants inoculated with either Tal7b or vector control     Differential gene expression profile analysis of RNA-seq data for cotton plants infected with Xanthomonas expressing Tal7b or vector control (T7b, HM)


title: Methylome comparisons between Red-Flesh and White-Flesh Mesocarps in Red-Flesh apple at 84 Days After Full Bloom (DAFB)

status: Public on Jun 18 2024

city: Beuacouzé

first: Jean-Marc

last: Celton

address: 42 ue Georges Morel

institute: IRHS

type: Methylation profiling by high throughput sequencing

summary: To functionally characterise flesh pigmentation pattern, we performed methylation analysis between RF and WF mesocarps. The transition step between fully red fruits and heterogeneously pigmented fruit were targeted during fruit development (84 Days After Full Bloom - DAFB).

overall_design: Comparative methylome analysis between white-flesh and red-flesh mesocarps in red-flesh apple

first: Pierre

last: Bouillon

first: Sandrine

last: Balzergue


title: Aberrant activation of wound healing programs within the metastatic niche facilitates lung colonization by osteosarcoma cells

status: Public on Jun 19 2024

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: Purpose: Lung metastasis is responsible for nearly all deaths caused by osteosarcoma, the most common pediatric bone tumor. How malignant bone cells coerce the lung microenvironment to support metastatic growth is unclear. This study delineates how osteosarcoma cells educate the lung microenvironment during metastatic progression.   Experimental design: Using single-cell transcriptomics (scRNA-seq), we characterized genome- and tissue-wide molecular changes induced within lung tissues by disseminated osteosarcoma cells in both immunocompetent murine models of metastasis and patient samples. We confirmed transcriptomic findings at the protein level and determined spatial relationships with multi-parameter immunofluorescence. We evaluated the ability of nintedanib to  impair metastatic colonization and prevent osteosarcoma-induced education of the lung microenvironment in both immunocompetent murine osteosarcoma and immunodeficient human xenograft models. Results: Osteosarcoma cells induced acute alveolar epithelial injury upon lung dissemination. scRNA-seq demonstrated that the surrounding lung stroma adopts a chronic, non-resolving wound-healing phenotype similar to that seen in other models of lung injury. Accordingly, metastasis-associated lung demonstrated marked fibrosis, likely due to the accumulation of pathogenic, pro-fibrotic, partially-differentiated epithelial intermediates.  Inhibitionintermediates. Inhibition of fibrotic pathways with nintedanib prevented metastatic progression in multiple murine and human xenograft models. Conclusions: Our work demonstrates that osteosarcoma cells co-opt fibrosis to promote metastatic outgrowth. When harmonized with data from adult epithelial cancers, our results support a generalized model wherein aberrant mesenchymal-epithelial interactions are critical for promoting lung metastasis. Adult epithelial carcinomas induce fibrotic pathways in normal lung fibroblasts, whereas osteosarcoma, a pediatric mesenchymal tumor, exhibits fibrotic reprogramming in response to the aberrant wound-healing behaviors of an otherwise normal lung epithelium, which are induced by tumor cell interactions.

overall_design: We utilized multiple immunocompetent murine osteosarcoma lung metastasis models coupled with single-cell RNA transcriptomics to characterize the cellular and molecular changes induced to the lung microenvironment by disseminated osteosarcoma cells. Transcriptomic findings were confirmed at the protein level with immunohistochemistry in mouse models as well as human patient samples. We tested the effect of nintedanib, an orally available tyrosine kinase inhibitor, for its ability to impair metastasis and prevent osteosarcoma education of the lung microenvironment in both immunocompetent murine osteosarcoma models and immunodeficient human xenograft models. This is the human portion of the data.

first: James

middle: B

last: Reinecke

first: Amy

last: Gross

first: Maren

last: Cam

first: Leyre

last: Garcia

first: Matthew

middle: V

first: Ruben

last: Dries

first: Berkley

last: Gryder

first: Ryan

last: Roberts


title: Optimizing in vitro spherulation cues in the fungal pathogenCoccidioides

status: Public on Jun 20 2024

city: San Francisco

first: Christina

last: Homer

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco

summary: Coccidioides spp.are part of a group ofthermallydimorphic fungal pathogens, which grow asfilamentous cells (hyphae)in the soil and transform to a different morphology upon inhalation into the host.TheCoccidioideshost form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges.Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremosttechnicalchallenges has been reliably growing spherules in culture and consistently inducing endospore release withoutthe generation ofhyphae. Here, wepresentoptimization ofin vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, usingfreshly-harvestedarthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources andwent on to define a critical role forTamolin both early spherule formation and dispersal of the outer spherule wall, which accumulatesinto a dramatic large film inTamol’sabsence. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization ofthis virulence-relevant morphology.

overall_design: We generated spores (arthroconidia) and then aged them for 0-7 weeks in PBS at 4 degrees C and characterized their transcriptome after storage in these conditions. Additionally, we generated spores (arthroconidia) by growing hyphal cells for 4 weeks at either 25 degree C, 30 degrees C, or 37 degrees C and then determined their transcriptome by RNA-seq (3 replicates from each spore stock, each spore stock was generated 2 separate times).

first: Homer

last: Christina

first: Ochoa

last: Elena

first: Voorhies

last: Mark

first: Sil

last: Anita


title: Odz4 upregulates SAN-specific genes to promote differentiation into cardiac pacemaker-like cells

status: Public on Jul 07 2024

city: Hiroshima

first: Anqi

last: Dong

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Department of Physiology and Biophysics

institute: Hiroshima University

summary: Cardiac arrhythmias stemming from abnormal sinoatrial node (SAN) function can lead to sudden death. Developing a biological pacemaker device for treating sick sinus syndrome (SSS) could offer a potential cure. Understanding SAN differentiation is crucial, yet its regulatory mechanism remains unclear. We reanalyzed published RNA-seq data and identified Odz4 as a SAN-specific candidate. In situ hybridization revealed Odz4 expression in the cardiac crescent and throughout the cardiac conduction system (CCS). To assess role of Odz4 in CCS differentiation, we utilized a Tet-Off inducible system for its intracellular domain (ICD). Odz4-ICD exogenously expressing embryonic bodies (EBs) exhibited an increased propensity to develop into pacemaker-like cells with enhanced automaticity and upregulated expression of SAN-specific genes. CellChat and GO analyses unveiled SAN-specific enrichment of ligand-receptor sets, especially Ptn-Ncl, and extracellular matrix components in the Odz4-ICD exogenously expressing group. Our findings underscore the significance of Odz4 in SAN development and offer fresh insights into biological pacemaker establishment

overall_design: EBRTcH3 cells were employed to establish the Odz4-ICD inducible cell line, and the expression was controlled by using Tet-Off system. After forming embryonic bodies for differentiation using the hanging drop method, EBs cultured with or without Tet from Day2, 2+3, 3+5, and 2+7 were dissociated for single cell sequencing.

first: Hiroki

last: Kokubo

first: Masao

last: Yoshizumi