title: Beyond the spore: the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans

city: Gainesville

first: Michael

last: Norris

state: FL

address: 2055 Mowry Rd

institute: University of Florida

summary: In preliminary experiments, the absence of anthrose in our genetic Sterne knockout was found to decrease pagA expression in BHI broth containing glucose (Fig 5A and B). This contrasted with the large spike in pagA expression when the Sterne antC mutant is grown in protein rich HIB media which does not contain sugars. When exogenous anthrose was added during growth in BHI broth, expression from PpagA increased in both WT (purple line in Fig 5A) and antC Sterne (purple line in Fig 5B). Many bacteria respond to levels of metabolic intermediates and modulate gene expression accordingly. We hypothesized intracellular or extracellular anthrose levels could impact the vegetative cells through modification of gene expression during vegetative growth. Wildtype B. anthracis Sterne was grown in the presence and absence of exogenously added pure anthrose to avoid any possibility of confounding data in a deletion mutant. Bacteria were harvested at two timepoints post-addition of anthrose, 30 min and 2 h, and compared to diluent only treated cultures (Fig 5C). After 30 min treatment, there were 6 genes significantly upregulated more than two-fold while 17 genes were downregulated (Fig 5D). These genes were mainly involved in generating metabolic intermediates such as pyruvate and trehalose. The most upregulated gene was a putative membrane protein (log2FC=10.98) followed by a gene encoding a GerPF homologue at a log2FC of 10.98. Mutation of GerPF family proteins have been linked to a super-dormant spore phenotype[10]. The gene experiencing the highest downregulation was a putative lipoprotein (log2FC = -20.02). No genes located on pXO1 were detected at 30 min. A subset of differentially transcribed genes from the 30 min timepoint are listed in Fig 5F. After 2 h of anthrose treatment, 52 genes experienced significant up regulation, 18 of which were hypothetical proteins (Fig 5E). Forty-five genes experienced significant down regulation across replicates, 13 of which were hypothetical proteins.

overall_design: B. anthracis Sterne strain 34F2 was grown overnight in BHI broth at 37C and standardized to an OD600 of 0.5 and divided into 6 tubes: triplicate for pure anthrose (Sigma) as treatment at a final concentration of 10 ug/ml, and triplicate for a mock of water added. Samples were collected in triplicate at 30 min and triplicate at 120 min after introduction of either liquid. Samples at each timepoint were immediately processed through the Zymo Direct-zol RNA Miniprep Plus (Zymo Resrearch; Irvine, CA, USA) kit including the optional bead beating steps as well as the on column DNAse treatment. Resulting RNA was quantified on a NanoDrop 2000 (Thermo Fisher Scientific; Waltham, MA, USA) and saved at –80°C. To remove contaminating rRNAs ~1.6ug of each sample was treated with Terminator™ 5′-Phosphate-Dependent Exonuclease (Lucigen; Middleton, WI, USA) and cleaned up using the Ambion MEGAclear Transcription Clean-Up Kit (Thermo Fisher Scientific; Waltham, MA, USA) while removing tRNAs and sRNAs.


title: Liver Circadian RNA-Seq from WT and Bmal1 muscle-specific KO (mKO) mice

status: Public on Apr 05 2023

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

country: USA

institute: University of California, Irvine

type: Expression profiling by high throughput sequencing

summary: Transcriptomic analysis to reveal the impact of muscle-specific Bmal1 knockout on daily cycles of gene expression in the liver

overall_design: To study how the muscle clock affects liver circadian function, livers were harvested at 4 hour intervals over circadian time beginning at ZT0 (lights on) from WT and Bmal1 muscle-specific KO mice (n=3 per timepoint), then subjected to RNA-Sequencing analysis. WT and mKO mice were fed ad libitum on a normal chow diet (Mucedola, Settimo Milanese, Italy), and corresponding muscle tissue samples were published in Dyar et al., Mol Metab. 2014 Feb; 3(1): 29–41 (GSE43071).

first: Kenneth

last: Dyar

first: Jacob

last: Smith

first: Carolina

last: Greco


title: Short-term effects of human versus bovine sialylated milk oligosaccharide microinjection on zebrafish larvae survival, locomotor behavior and gene expression

status: Public on Apr 04 2023

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Milk oligosaccharides are a complex class of carbohydrates that act as bioactive factors in numerous defensive and physiological functions, including brain development. Early nutrition can modulate nervous system development and can lead to epigenetic imprinting. We attempted to increase the sialylated oligosaccharide content of zebrafish yolk reserves, with the aim of evaluating any short-term effects of the treatment on mortality, locomotor behavior, and gene expression. Wild-type embryos were microinjected with saline solution or solutions containing sialylated milk oligosaccharides extracted from human and bovine milk. The results suggest that burst activity and larval survival rates were unaffected by the treatments. Locomotion parameters were found to be similar during the light phase between control and treated larvae; in the dark, however, milk oligosaccharide-treated larvae showed increased test plate exploration. Thigmotaxis results did not reveal significant differences in either the light or the dark conditions. RNA-seq analysis indicated that both treatments exert an antioxidant effect in developing fish. Moreover, sialylated human milk oligosaccharides seemed to increase the expression of genes related to cell cycle control and chromosomal replication, while bovine-derived oligosaccharides caused an increase in the expression of genes involved in synaptogenesis and neuronal signaling. These data shed some light on this poorly explored research field, showing that both human and bovine oligosaccharides support brain proliferation and maturation.

overall_design: Wild-type AB strain larvae were divided in 3 groups: non-microinjected embryos as a reference (control group), embryos microinjected with human sialylated milk oligosaccharides (SHMO group) and embryos microinjected with bovine sialylated milk oligosaccharides (SBMO group). For each group 3 replicates were included.

first: Rosario

last: Licitra

first: Valentina

last: Naef

first: Maria

last: Marchese

first: Devid

last: Damiani

first: Asahi

last: Ogi

first: Stefano

last: Doccini

first: Baldassare

last: Fronte

first: Jingyu

last: Yan

first: Filippo

middle: M

last: Santorelli


title: Effect of Sclerostin Inactivation in a Mouse Model of Severe Dominant Osteogenesis Imperfecta

city: Montreal

first: Ghalib

last: Bardai

state: Quebec

address: 1003 Boulevard Decarie

department: Clinical Laboratories

country: Canada

institute: Shriners Hospital for Children

summary: Osteogenesis imperfecta (OI) is a rare bone disease that is associated with fractures and low bone mass. Sclerostin inhibition is being evaluated as a potential approach to increase bone mass in OI. We had previously found that in Col1a1Jrt/+ mice, a model of severe OI, treatment with an anti-sclerostin antibody had a minor effect on the skeletal phenotype. In the present study, we assessed the effect of genetic sclerostin inactivation in the Col1a1Jrt/+ mouse. We crossed Col1a1Jrt/+ mice with Sost knockout mice to generate Sost-deficient Col1a1Jrt/+ mice and assessed differences between Col1a1Jrt/+ mice with homozygous Sost deficiency and Col1a1Jrt/+ mice with heterozygous Sost deficiency. We found that Col1a1Jrt/+ mice with homozygous Sost deficiency had higher body mass, femur length, trabecular bone volume, cortical thickness and periosteal diameter as well as increased biomechanical parameters of bone strength. Differences between genotypes were larger at the age of 14 weeks than at 8 weeks of age. Transcriptome analysis of RNA extracted from the tibial diaphysis revealed only 5 differentially regulated genes. Thus, genetic inactivation of Sost increased bone mass and strength in the Col1a1Jrt/+ mouse. It appears from these observations that the degree of Sost suppression that is required for eliciting a beneficial response can vary with the genetic cause of OI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data form tibia of Sclerostin-deficient OI mice and the  controls, such as OI and WT mice.

first: Juliana

last: Marulanda

first: Josephine

middle: T

last: Tauer

first: Iris

last: Boraschi-Diaz

first: Frank

last: Rauch


title: Matrix Gla Protein acts as a driver of stemness and tumor initiation in ovarian cancer

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpopulation of neoplastic cells, termed ovarian cancer stem cells (OCSC), that are endowed with self-renewing and tumor-initiating properties. This implies that interfering with OCSC function should offer novel therapeutic perspectives to defeat OC progression. To this aim, a better understanding of the molecular and functional makeup of OCSC in clinically relevant model systems is essential. We have profiled the transcriptome of OCSC vs. their bulk cell counterpart from a panel of patient-derived OC cell cultures. This revealed that Matrix Gla Protein (MGP), classically known as a calcification-preventing factor in cartilage and blood vessels, is markedly enriched in OCSC. Functional assays showed that MGP confers several stemness-associated traits to OC cells, including a transcriptional reprogramming. Patient-derived organotypic cultures pointed to the peritoneal microenvironment as a major inducer of MGP expression in OC cells. Furthermore, MGP was found to be necessary and sufficient for tumor initiation in OC mouse models, by shortening tumor latency and increasing dramatically the frequency of tumor-initiating cells. Mechanistically, MGP-driven OC stemness was mediated by the stimulation of Hedgehog signaling, in particular through the induction of the Hedgehog effector GLI1, thus highlighting a novel MGP/Hedgehog pathway axis in OCSC. Finally, MGP expression was found to correlate with poor prognosis in OC patients, and was increased in tumor tissue after chemotherapy, supporting the clinical relevance of our findings. Thus, MGP is a novel driver in OCSC pathophysiology, with a major role in stemness and in tumor initiation.

overall_design: A total of 4 samples were processed including biological replicates.

first: Ugo

last: Cavallaro


title: Nervous system reduction in branched-chain amino acid metabolism disrupts hippocampal neurogenesis and memory

status: Public on Apr 06 2023

city: Durham

first: Khadar

last: Abdi

state: NC

address: 300 North Duke St.

department: DMPI

institute: Duke University

summary: To study the role of branched-chain amino acid metabolism in neural stem cells we generated two primary neural stem cell culture lines in which on was deleted for the Ppm1k gene using floxed cells and adenovirus delviered cre-recombinase.

overall_design: Neural stem cell cultures were generated from control (wild-type/wild-type) and ppm1k flox/flox mice in triplicate and pooled to make control and ppm1l flox/flox lines. Ppm1k was knocked out of the flox/flox line using adenovirus delivered cre-recombinase. After 68 hours primary cell cultures were isolated and submited for 10X genomic sequencing.

first: Vaibhav

last: Jain


title: Anionic pulmonary surfactant lipid treatment inhibits rhinovirus A infection of the human airway epithelium

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

summary: Rhinoviruses (RVs) are major instigators of acute exacerbations of asthma, COPD and other respiratory diseases. RVs are categorized into three species (RV-A, RV-B, and RV-C), which comprise more than 160 serotypes, making it difficult to develop an effective vaccine. Currently no effective treatment for RV infection is available. Pulmonary surfactant is an extracellular complex of lipids and proteins that plays a central role in regulating innate immunity in the lung. The minor pulmonary surfactant lipids, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and phosphatidylinositol (PI), are potent regulators of inflammatory processes, and exert antiviral activity against respiratory syncytial virus (RSV) and influenza A viruses (IAV). In the current study, we examined the potencies of POPG and PI against rhinovirus A16 (RV-A16) in primary human airway epithelial cells (AECs) differentiated at an air-liquid interface (ALI). After AECs were infected with RV-A16, PI reduced viral RNA copy number by 80% and downregulated (55-65%) expression of antiviral genes (MDA5, IRF7 and IFN-lambda). In contrast, POPG only slightly decreased MDA5 (24%) and IRF7 (11%) gene expression but did not inhibit IFN-lambda gene expression or RV-A16 replication in AECs. However, both POPG and PI inhibited (50-80%) IL6 and CXCL11 gene expression and protein secretion. PI treatment dramatically attenuated global gene expression changes induced by RV-A16 infection in AECs. Cell type enrichment analysis of viral regulated genes opposed by PI treatment revealed that PI inhibited viral induction of goblet cell metaplasia and virus-induced downregulation of ciliated, club, and ionocyte cell types. Notably, PI treament altered the ability of RV-A16 to regulate expression of some phosphatidylinositol 4-kinase (PI4K), acyl-CoA binding domain containing (ACBD) and low density lipoprotein receptor (LDLR) genes that play critical roles in the formation and functioning of replication organelles (ROs) required for RV replication in host cells. These data suggest PI can be used as a potent, non-toxic antiviral agent for RV infection prophylaxis and treatment.

overall_design: To examine anti-viral effects of the phospholipids, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and phosphatidylinositol (PI) against the RV-A16 virus or the control lipid palmitoyl-oleoyl-phosphatidylcholine (POPC), we generated three replicate ALI samples from each of three tracheal donors (T22, T51, T56) treated in each of the following ways: (1) mock (i.e., Control), (2) lipid only (PI, POPG, or PC), (3) RV-A16 infection alone at 4hr or 48hr (RV-A16_4hr, RV-A16_48h, respectively), or (4) lipid pretreatment followed by RV-A16 infection (RV-A16+PI, RVA-16+POPG, RV-A16+PC).

first: Mari

last: Numata

first: Satria

middle: P

last: Sajuthi

first: Yury

middle: A

last: Bochkov

first: Jessica

last: Loeffler

first: Jamie

middle: L

last: Everman

first: Eszter

middle: K

last: Vladar

first: Riley

last: Cooney

first: R

last: Reinhardt

first: Andrew

middle: H

last: Liu

first: Max

last: Seibold

first: Dennis

middle: R

last: Voelker


title: Canagliflozin impairs T-cell effector function via metabolic suppression in autoimmunity.

city: Swansea

first: Benjamin

middle: James

last: Jenkins

address: Singleton Park

country: United Kingdom

institute: Swansea University

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

overall_design: Refer to individual Series


title: miR-142-3p Regulates Cortical Oligodendrocyte Gene Co-expression Networks Associated with Tauopathy

city: Los Angeles

first: Brent

last: Fogel

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

summary: Oligodendrocytes exist in a heterogenous state and are implicated in multiple neuropsychiatric diseases including dementia. Cortical oligodendrocytes are a glial population uniquely positioned to play a key role in neurodegeneration by synchronizing circuit connectivity but molecular pathways specific to this role are lacking. We utilized oligodendrocyte-specific translating ribosome affinity purification and RNA-seq (TRAP-seq) to transcriptionally profile adult mature oligodendrocytes from different regions of the central nervous system. Weighted gene co-expression network analysis (WGCNA) reveals distinct region-specific gene networks. Two of these mature myelinating oligodendrocyte gene networks uniquely define cortical oligodendrocytes and differentially regulate cortical myelination (M8) and synaptic signaling (M4). These two cortical oligodendrocyte gene networks are enriched for genes associated with dementia including MAPT and include multiple gene targets of the regulatory microRNA, miR-142-3p. Using a combination of TRAP-qPCR, miR-142-3p overexpression in vitro, and miR-142-null mice, we show that miR-142-3p negatively regulates cortical myelination. In rTg4510 tau-overexpressing mice, cortical myelination is compromised, and tau-mediated neurodegeneration is associated with gene co-expression networks that recapitulate both the M8 and M4 cortical oligodendrocyte gene networks identified from normal cortex. We further demonstrate overlapping gene networks in mature oligodendrocytes present in normal cortex, rTg4510 and miR-142-null mice, and existing datasets from human tauopathies to provide evidence for a critical role of miR-142-3p-regulated cortical myelination and oligodendrocyte-mediated synaptic signaling in neurodegeneration.

overall_design: Mutliple WGCNA of RNA-seq datasets

first: Jason

middle: D

last: Hinman

first: Kathie

middle: J

last: Ngo


title: Canagliflozin impairs T-cell effector function via metabolic suppression in autoimmunity [Metabolic Pathways]

summary: Augmented T-cell function leading to host damage in autoimmunity is supported by metabolic dysregulation. Targeting immunometabolism for the treatment of autoimmunity by repurposing clinically approved metabolic modulators, such as those used to treat people with type 2 diabetes (T2D), is therefore an attractive avenue. Canagliflozin, a class of the newest type of T2D drug – sodium glucose co-transporter 2 (SGLT2) inhibitors – has known off-target effects including mitochondrial glutamate dehydrogenase (GDH) and complex I inhibition. To date, the effects of SGLT2 inhibitors on human T-cell function are extremely limited. Here, we analysed 748 genes using the Nanostring nCounter® Metabolic Pathways Panel and discovered 38 genes that were differentially regulated between canagliflozin-treated (cana, C; n = 6) and DMSO vehicle control (V; n = 6) T-cells. Of these genes, 24 were downregulated, whilst 14 were upregulated. Notably, 17 of the 24 genes that were downregulated following canagliflozin treatment were associated with the cell cycle, whilst SMAD3 was the only cell cycle-associated gene upregulated by canagliflozin. These analyses allowed a greater understanding of the global changes in T-cell metabolism that occur in response to treatment with SGLT2 inhibitors.

overall_design: Two treatment conditions - DMSO vehicle control and canagliflozin-treated

first: Julianna

last: Blagih

first: Fernando

last: Ponce-Garcia

first: Mary

last: Canavan

first: Nancy

last: Gudgeon

first: Simon

last: Eastham

first: David

last: Hill

first: Megan

last: Hanlon

first: Eric

last: Ma

first: Emma

last: Bishop

first: April

last: Rees

first: James

middle: G

last: Cronin

first: Elizabeth

middle: C

last: Jury

first: Sarah

last: Dimeloe

first: Douglas

last: Veale

first: Catherine

last: Thornton

first: Karen

last: Vousden

last: Finlay

first: Ursula

last: Fearon

first: Gareth

middle: W

last: Jones

first: Linda

middle: V

last: Sinclair

middle: E

last: Vincent

first: Nicholas


title: Melatonin ameliorates simulated-microgravity-induced mitochondrial dysfunction and lipid metabolism dysregulation in hepatocytes

city: Shenzhen

first: yue

last: xiong

address: Xueyuan Avenue 1068

country: China

institute: SIAT

summary: The liver is an essential multifunctional organ, which constantly communicates with nearly all tissues. It has raised the concern that microgravity exposure can lead to liver dysfunction and metabolic syndromes. However, systematic studies, molecular mechanisms, and intervention measures of the adverse effects of microgravity on hepatocytes are limited. In this study, we utilized the Random Positioning Machine culture system to investigate the adverse effects on hepatocytes under simulated microgravity (SMG). Our results showed that SMG impaired hepatocyte viability, causing cell cycle arrest and apoptosis. Compared to normal gravity (NG), it also triggered lipid accumulation, elevated triglyceride (TG) and ROS levels, and impaired mitochondria function in hepatocytes. Furthermore, RNA-seq results showed that SMG upregulated genes implicated in lipid metabolisms, including PPARγ, PLIN2, CD36, FABPs, etc.. Importantly, all these defects can be suppressed by melatonin, a potent antioxidant secreted by the pineal gland, suggesting its potential use as a novel strategy of therapeutic intervention.

overall_design: We uesed melatonin to ameliorate simulated-microgravity-induced hepatic defects

first: Yue

last: Xiong

first: Chiyuan


title: Genome-wide maps of p-STAT3 in PD-L1 silenced uveal melanoma cells and control cells

city: Shanghai

first: Jie

last: Yu

address: No. 639, Zhizaoju road, Huangpu district

department: Department of Ophthalmology

institute: Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed CUT&Tag with anti-p-STAT3 antibodies in PD-L1 silenced uveal melanoma cells and control cells

overall_design: Examination of regulatory role of PD-L1 in uveal melanoma cells.

first: Peiwei

last: Chai


title: Transcriptional and chromatin accessibility profiling of neural stem cells differentiating into astrocytes reveal dynamic signatures under homeostatic and inflammatory conditions [RNA-Seq]

city: New Delhi

first: Kartikeya

last: Singh

address: Outer Ring road

country: India

summary:
Astrocytes arise from multipotent neural stem cells (NSCs) and represent the most abundant cell type of the central nervous system (CNS) playing key roles in the developing and adult brain. Since the differentiation of NSCs towards a gliogenic fate is a precisely timed and regulated process, its perturbation gives rise to dysfunctional astrocytic phenotypes. Inflammation, which often underlies neurological disorders, including neurodevelopmental disorders and brain tumors, disrupts the accurate developmental process of NSCs. However, the specific consequences of an inflammatory environment on the epigenetic and transcriptional programs underlying NSCs differentiation into astrocytes is unexplored yet. Here, we address this gap by profiling glial precursors from neural tissue derived from early embryonic stages along their astrocytic differentiation trajectory in the presence or absence of tumor necrosis factor-alpha (TNF), a master pro-inflammatory cytokine. By using a combination of RNA- and ATAC-sequencing approaches, together with footprint and integrated gene regulatory network analyses, we here identify key differences during the differentiation of NSCs into astrocytes under physiological and inflammatory settings. Notably, in agreement with its role to turn cells resistant to inflammatory challenges, we detect Nrf2 as a master transcription factor supporting the astrocytic differentiation under TNF exposure. Further, under these conditions, we unravel additional transcriptional regulatory hubs, including Stat3, Smad3, Cebpb and Nfkb2, highlighting the interplay between signaling pathways underlying physiological astrocytic developmental processes and those involved in inflammatory responses.
Overall, our study reports key transcriptional and epigenetic changes leading to the identification of molecular regulators of the astrocytic differentiation. Furthermore, our analyses provide a valuable resource for understanding inflammation-induced astrocytic phenotypes that might contribute to the development and progression of CNS disorders with an inflammatory component.

overall_design: RNA-Seq data at multiple timepoints from developing astrocytes under normal and inflammatory conditions

first: Maria

last: Angeliki S Pavlou

first: Srikanth

last: Ravichandran

first: Rashi

last: Halder

first: Nathalie

last: Nicot

first: Cindy

last: Birck

first: Luc

last: Grandbarbe

first: Antonio

last: del Sol

first: Alessandro

last: Michelucci


title: Transcriptional and chromatin accessibility profiling of neural stem cells differentiating into astrocytes reveal dynamic signatures under homeostatic and inflammatory conditions [ATAC-Seq]

overall_design: ATAC-Seq data at multiple timepoints from developing astrocytes under normal and inflammatory conditions


title: The influence of the Smac mimetic BV6 on the rhabdomyosarcoma cell line RH30

city: Frankfurt a.M.

first: Meike

last: Vogler

address: Komturstraße 3a

country: Germany

institute: Goethe-Universität Frankfurt

summary: The effect of the Smac mimetic BV6 on the transcriptional regulation in the alveolar rhabdomyosarcoma cell line RH30 was investigated by bulk RNA-sequencing. To this end, RH30 cells were treated with 5 µM BV6 for 24 h, or left untreated. Here, a regulation of several NF-κB target genes could be observed.

overall_design: Comparative gene expression analysis of bulk-RNAseq data of the rhabdomyosarcoma cell line RH30 treated with the Smac mimetic BV6 or left untreated.

first: Vinzenz

last: Särchen

first: Lisa

last: Reindl

first: Thomas

last: Bukur

first: Julia

last: Becker

first: Martin

last: Suchan

first: Evelyn

last: Ullrich


title: Effect of depletion of vhl-1 on gene expression in young adult C. elegans

city: Freiburg

first: Athina

last: Ganner

address: Hugstetterstr. 55

department: Nephrology

institute: University hospital Freiburg

summary: To investigate the function of vhl-1 on gene expression in C. elegans we compared vhl-1 loss of function mutants (CB5602) to wild type animals.

overall_design: Comparative gene expression (3 biological replicates, measured in triplicates) profiling analysis of RNA-seq data for young adult vhl-1 C. elegans mutants versus young adult wild type animals.

first: Elke

last: Neumann Haefelin


title: Acquired anoikis resistance mediates enhancer-driven subtype plasticity in pancreatic cancer [RNA-seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Genetic aberrations, including mutations or deletions in KRAS, TP53, SMAD4, and CDKN2A, are common causes of pancreatic ductal adenocarcinoma (PDA). Recent large-scale transcriptomic studies demonstrated that heterogeneous gene expressions played an essential role in determining molecular subtypes of PDA, although it remains unclear what the biological cues and consequences of distinct transcriptional programs are. Here, we describe an anoikis-induction-based experimental model that enforces the transition toward a squamous subtype of PDA cells. Characteristics of the squamous subtype, represented by aggressive behaviors, are faithfully recapitulated in vitro and in vivo, demonstrating the physiological relevance of this model. Integrated analysis of epigenome and transcriptome reveals that squamous subtype PDA cells acquire pro-angiogenic enhancer activity of which is sustained by the transcription factor TEAD2. Genetic and pharmacological inhibition of TEAD2 of these tumor cells impairs their pro-angiogenic phenotypes in vitro and cancer progression in vivo. Furthermore, we found that CD109 is a critical TEAD2 target that retains activated JAK-STAT signaling. Together, our findings implicate a TEAD2-CD109-JAK/STAT axis as a potential therapeutic vulnerability concealed in the squamous subtype-associated epigenome of pancreatic cancer cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profilings of various PDA cell lines

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Arabidopsis thaliana seedlings: Control vs Erwinia amylovora nicrobial Volatile Organic Compounds

city: Turin

first: Massimo

last: Maffei

address: Via Quarello 15/a

department: Life Sciences and Systems Biology

institute: University of Turin

summary: Arabidopsis seedling were exposed in co-culture to E. amylovora mVOC and data show that mVOCs promote plant growth and early responses

overall_design: Control vs. mVOC exposed plants

first: Chidananda

last: Nagamangala Kanchiswami


title: Acquired anoikis resistance mediates enhancer-driven subtype plasticity in pancreatic cancer [ATAC-Seq]

overall_design: ATAC-seq profilings of various PDA cell lines


title: Genome-wide maps of PD-L1 in uveal melanoma

first: Jie

last: Yu

summary: For the first time, we investigated the role of nuclear PD-L1 in tumorgenesis of ocular melanoma.

first: Peiwei

last: Chai


title: Role of the CryD photoreceptor on the F. fujikuroi transcriptome

city: Sevilla

first: Javier

last: Avalos

address: Faculty of Biology, Av. Reina Mercedes s/n

department: Genetics

country: Spain

institute: University of Seville

summary: This RNA-seq data set investigates the function of the DASH cryptochrome CryD in the fungus Fusarium fujikuroi, and are an extension of the former study on the role of the WcoA photoreceptor (GEO Series GSE159533) (Pardo-Medina J, Gutiérrez G, Limón MC, Avalos J (2021) Impact of the White Collar photoreceptor WcoA on the Fusarium fujikuroi transcriptome. Front Microbiol 11:1–17. https://doi.org/10.3389/fmicb.2020.619474)). Cryptochromes are blue/UV-A light photoreceptors related to photolyases, enzymes able to use light as an energy source to repair UV-B-induced lesions. Cryptochromes typically have a N-terminal photolyase-related domain able to bind two chromophores, flavin adenine dinucleotide (FAD) and 5,10-methenyltetrahydrofolate (MTHF) or pterin, followed by a long C-terminal domain absent in photolyases, reported to play regulatory roles related to light control of growth, development, cell signaling, and circadian rhythm in different taxonomic groups. The DASH cryptochromes are a subgroup in this family that differ from cryptochromes in the ability to repair single-stranded DNA and the lack of the long carboxy extension. The Fusarium fujikuroi genome contains a single gene for a DASH cryptochrome, called CryD. In our former work, the function of the WcoA photoreceptor was investigated through the effect of the mutation of the responsible gene on the transcriptome .  In this work, RNA samples of a cryD mutant were analyzed in parallel to those of the wild type and wcoA mutant described in GEO Series GSE159533, in dark and after one hour illumination. The results are summarized in the review "Fusarium photoreceptors", submitted for publication to Journal of Fungi (Basel, MDPI)

overall_design: To check the role of the CryD protein, we compared the transcriptomes of the wild strain and a cryD mutant incubated in the dark or illuminated for 60 min. Data were obtained from three independent biological replicates for each condition. Data of the wild type in this study were already submitted in GEO Series GSE159533

last: Medina

first: Gabriel

last: Gutiérrez

first: M

last: Limón


title: Stromal senescence following treatment with the CDK4/6 inhibitor palbociclib increases mammary cancer metastasis

city: Washington

first: Gregory

last: Gallanis

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

summary: One potential resistance mechanism to CDK4/6 inhibitors in breast cancer could be induction of cellular senescence in normal host tissues. The aim of our study was to identify CDK4/6 inhibition-induced changes to host tissues that impact metastasis. Using mouse models, we found that pre-treatment with palbociclib can increase metastatic seeding of mouse mammary cancer cells in the lungs and that this can be mitigated by eliminating senescent host cells. We describe palbociclib-induced gene expression changes in lungs that correlate with this effect and reveal altered intra-lung immune populations. Senescent endothelial cells are identifiable within lung metastases of mice pre-treated with palbociclib. Using in vitro models, we show that palbociclib treatment increases endothelial cell senescence and affects macrophage invasion and migration. These studies describe how CDK4/6 inhibition-induced cellular senescence in host tissues affects metastasis and disease progression in breast cancer, which remain key obstacles to achieving long-term survival.

overall_design: mRNA profiles of p16-INK-ATTAC mouse lungs treated with palbociclib and/or AP20187 and HUVEC cells treated with palbociclib

first: Marcel

middle: O

last: Schmidt

first: Anna

last: Riegel


city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

summary: Transcriptional profiling of populations in the clam Ruditapes decussatus determined differentiation in gene-expression along parallel temperature gradients and between races of the Atlantic Ocean and West Mediterranean sea.

overall_design: Clams of the Atlantic and West Mediterranean races were collected in two northern (cool) and two southern (warm) localities of Atlantic Ocean and Mediterranean sea. The animals were kept in running, unfiltered seawater in the Atlantic southern locality for a 15-week period, during which water temperature raised naturally to typical southern European summer values. After this period, the expression profile of each clam was obtained for a total of 34 individuals and 11,025 probes by means of an oligonucleotide microarray.

first: Carlos

last: Saavedra

last: Milan

first: Luca

last: Bargelloni


title: Hi-C ES and neocortex from Bonev et al. 2017 on mm39

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

type:
Other
Third-party reanalysis

summary: Reanalysis of some Hi-C from Bonev et al. 2017 with HiCUP v0.9.2

relation:
Reanalysis of: GSM2533818
Reanalysis of: GSM2533819
Reanalysis of: GSM2533820
Reanalysis of: GSM2533821
Reanalysis of: GSM2533835
Reanalysis of: GSM2533836
Reanalysis of: GSM2533837
Reanalysis of: GSM2533838
Reanalysis of: GSM2533839
Reanalysis of: GSM2533840
Reanalysis of: GSM2533841
Reanalysis of: GSM2533842
Reanalysis of: GSE96107

overall_design:
This is a third-party reanalysis of some datasets of GSE96107 to provide a more friendly format.
Hi-C ES from Bonev et al. (reanalysis of GSM2533818 to GSM2533821)
Hi-C ncx NPC from Bonev et al. (reanalysis of GSM2533835 to GSM2533838)
Hi-C ncx CN from Bonev et al. (reanalysis of GSM2533839 to GSM2533842)

DATA PROCESSING DETAILS:
Fastq were retreived from SRA with fasterq-dump version 3.0.3
They were processed with HiCUP v0.9.2 specifying DpnII, ^GATC as enzyme
Pairs were extracted with custom version of hicup2juicer. The pairs of 4 replicates were concatenated.
Pairs were split by chromosome and sorted with cooler csort version 0.9.1
Matrices were generated with cooler with bins of 5kb or 20kb and balanced with option –cis-only
All scripts are available at https://github.com/lldelisle/Hi-C_reanalysis_Bonev_2017
genome build/assembly: mm39
processed data: *csort.gz: tabulated file in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.)
processed data: *cool: cool file with balanced matrix at 5kb or 20kb

first: L


title: Norepinephrine inhibits CD8+ T cell infiltration and function, inducing anti-PD-1 mAb resistance in lung adenocarcinoma

city: Zhengzhou

last: Zhao

state: China

address: 1th Jianshe road, Zhengzhou, Henan, PR China

institute: First Affiliated Hospital of Zhengzhou University

summary:
BACKGROUND:Mental stress-induced neurotransmitters can affect the immune system in various ways, leading to tumor immune escape. Therefore, a better understanding of the potential functions of neurotransmitters in the tumor immune microenvironment is expected to promote the development of novel anti-tumor therapies, while facilitating synergistic immune therapy.
METHODS: In this study, we analyzed the plasma levels of neurotransmitters in anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb)-resistance patients and sensitive patients, to identify significantly different neurotransmitters. Subsequently, animal experiments, transcriptome analysis, metabolomic analysis, and experiments in vitro were used to reveal the specific mechanism of norepinephrine’s (NE) effect on immunotherapy.
RESULTS: The plasma NE levels were higher in anti-PD-1 mAb-resistance patients, which may be the main cause of anti-PD-1 mAb resistance. An animal model was established for verification, which further demonstrated that NE could cause anti-PD-1 mAb resistance. Then, from the perspective of the immunosuppressive microenvironment to explore the specific mechanism of NE-induced anti-PD-1 mAb resistance, we found that NE can affect the secretion of the C-X-C Motif Chemokine Ligand 9 (CXCL9) and the immunosuppressive metabolite adenosine (ADO) in tumor cells, thereby inhibiting chemotaxis and function of CD8+ T cells. Notably, the WNT7A/β-catenin signaling pathway plays a crucial role in the NE-induced decrease in the secretion of CXCL9 and disturbance of ADO metabolism.
CONCLUSION: NE can affect the secretion of CXCL9 and ADO in tumor cells, thereby inhibiting chemotaxis and the function of CD8+ T cells and inducing anti-PD-1 mAb resistance in lung adenocarcinoma (LUAD).

overall_design: To explore whether ADO affects immune cell function, we treated PBMCs with 30 uM ADO for 24 h, which were subjected to transcriptome sequencing. In order to further study the mechanism of NE-induced changes of CXCL9 and ADO secretion in tumor cells, we used transcriptome sequencing to detect gene expression levels in A549 cells after NE stimulation.

first: Qishun

last: Geng

first: Lifeng

last: Li

first: Zhibo

last: Shen

first: Yuanyuan

last: Zheng

first: Longhao

last: Wang

first: Wenhua

last: Xue

first: Mengle

last: Peng


title: Transcriptome and metabolome analyses reveal the regulatory network governing red fruitbody disease in Morchella

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

summary: True morels (Morchella spp., Morchellaceae, Ascomycota), a delicious edible mushroom, has rapidly expanded in recent years, especially in China. However, a severe disease of morels, red fruitbody disease, led to very low production of fruiting bodies. The cause reason and the mechanisms under red fruitbody are unclear. Herein, we integrated the transcriptomics and metabolomics data of M. sextelata from red fruitbody group (R) and normal group (N), which was artificial cultivation in Fujian province, China. Transcriptome data revealed the differentially expressed genes (DEGs) between R group and N group were significantly enriched in the pathways of tyrosine metabolism, riboflavin metabolism, and glycerophospholipid metabolism. Similarly, the differential accumulated metabolites (DAMs) were mainly assigned to metabolism categories, including tyrosine metabolism, biosynthesis of plant secondary metabolites, biosynthesis of amino acids, and others. Then, combined analysis of the transcriptome data and metabolome traits revealed that the most enriched pathway was tyrosine metabolism, followed by ABC transporters, alanine, aspartate and glutamate metabolism, and others. In summary, this integration of transcriptomics and metabolomics data of M. sextelata during fruitbody redness implicated several key genes, metabolites, and pathways involved in this disease. We believe that these findings will help us understand the mechanisms under fruitbody redness of M. sextelata and provide new clues for optimizing the methods for its cultivation application.


title: Matrix Gla Protein acts as a driver of stemness and tumor initiation in ovarian cancer

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

summary:
Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpopulation of neoplastic cells, termed ovarian cancer stem cells (OCSC), that are endowed with self-renewing and tumor-initiating properties. This implies that interfering with OCSC function should offer novel therapeutic perspectives to defeat OC progression. To this aim, a better understanding of the molecular and functional makeup of OCSC in clinically relevant model systems is essential.
We have profiled the transcriptome of OCSC vs. their bulk cell counterpart from a panel of patient-derived OC cell cultures. This revealed that Matrix Gla Protein (MGP), classically known as a calcification-preventing factor in cartilage and blood vessels, is markedly enriched in OCSC. Functional assays showed that MGP confers several stemness-associated traits to OC cells, including a transcriptional reprogramming. Patient-derived organotypic cultures pointed to the peritoneal microenvironment as a major inducer of MGP expression in OC cells.
Furthermore, MGP was found to be necessary and sufficient for tumor initiation in OC mouse models, by shortening tumor latency and increasing dramatically the frequency of tumor-initiating cells. Mechanistically, MGP-driven OC stemness was mediated by the stimulation of Hedgehog signaling, in particular through the induction of the Hedgehog effector GLI1, thus highlighting a novel MGP/Hedgehog pathway axis in OCSC. Finally, MGP expression was found to correlate with poor prognosis in OC patients, and was increased in tumor tissue after chemotherapy, supporting the clinical relevance of our findings.
Thus, MGP is a novel driver in OCSC pathophysiology, with a major role in stemness and in tumor initiation.

overall_design: mRNA sequencing was performed on 2 different cell lines (OVCAR3 and COV318) in 4 different treatment conditions (N=8). Samples analysed are COV318_CTR_bulk, COV318_MGP_bulk, COV318_CTR_OCSC, COV318_MGP_OCSC, OVCAR3_CTR_bulk, OVCAR3_KO_bulk, OVCAR3_CTR_OCSC, OVCAR3_KO_OCSC.

last: Nieddu

first: Fabrizio

last: Bianchi

first: Ugo

last: Cavallaro


title: Arsenite Exposure to Human Renal Progenitor Cells (HRTPT) Produces a Reversible Epithelial Mesenchymal Transition (EMT)

city: Grand Forks

first: Sandeep

last: Singhal

state: NORTH DAKOTA

address: 1301 N Columbia Rd Stop 9037

department: Pathology

institute: University of North Dakota

summary: Background  The human kidney is known to possess  renal progenitor cells (RPCs) that can assist in the repair of acute tubular injury. The RPCs are sparsely located as single cells throughout the kidney. We recently generated an immortalized human renal progenitor cell line (HRTPT) that co-expresses PROM1/CD24 and expresses features expected on a RPCs. This included the ability to form nephrospheres, differentiate on the surface of Matrigel, and to undergo adipogenic, neurogenic, and osteogenic differentiation. These cells were used in the present study to determine how the cells would respond when exposed to a nephrotoxin. Arsenite (iAS) was chosen as the nephrotoxin since the kidney is susceptible to this toxin and there is evidence for its involvement in renal disease.   Methods gene expression profiles when the cells were exposed to iAS for 3, 8, 10 passages (subcultured at 1:3 ratio) identified a shift in from the control unexposed cells. The cells exposed to iAS for 8 passages were then referred with growth media containing no iAS and within 2 passages the cells returned to an epithelial morphology with strong agreement in differential gene expression between control and cells recovered from iAS exposure.  Results  Results shows within 3 serial passages of the cells exposed to iAS there was a shift in morphology from an epithelial to a mesenchymal phenotype. EMT was suggested based on an increase in known mesenchymal markers.   Conclusion  We found RPCs can undergo EMT when exposed to a nephrotoxin and undergo MET when the agent is removed from the growth media.

overall_design: The isolation and serum-free culture conditions for the HRTPT cells has been previously described.10, 11 Confluent cultures of HRTPT cells were exposed to 4.5 µM iAS for 24 hrs and then subcultured at a 1:3 ratio in the continued presence of iAS until confluent. Following confluence, the cells were serially sub cultured again in the present of iAS until confluent. This was repeated for 10 serial passages. Additional cultures of iAS-exposed cells at passage 8 were subcultured into iAS-free growth media and continued in iAS-free media for 11 additional passages. Genome Explorations has completed a gene expression analysis of 18 samples using the Clariom™ D microarray to determine the effects of Arsenite treatment on renal proximal tubule cell gene expression.

first: Sonalika

first: Swojani

last: Shrestha

first: Donald

last: Sens


title: Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

summary: We investigated long-range interactions during preadipocyte differentiation into adipocytes using promoter Capture Hi-C.

overall_design: Promoter Capture Hi-C was produced in 2 biological replicates each for preadipocytes and differentiating preadipocytes (day 1 of differentiation).

middle: M

first: Päivi

last: Pajukanta


title: T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile

status: Public on Apr 03 2023

city: Boston

first: Bruno

last: Gegenhuber

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: RNA-sequencing of gonadal adipose tissue from Chow and HFD fed MBOAT7 Flox and ASKO mice

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Non-alcoholic fatty liver disease (NAFLD) is becoming increasingly common and is a leading cause of end stage liver diseases such as cirrhosis and hepatocellular carcinoma. The rise in NAFLD closely parallels the global epidemic of obesity and type 2 diabetes mellitus (T2DM), and there is a clear interrelationship between abnormal lipid metabolism, insulin resistance, and NAFLD progression. Several genetic loci have been identified as contributors to NAFLD progression, all of which are consistently linked to abnormal lipid metabolic processes in the liver. The common loss-of-function variant rs641738 (C>T) near the gene encoding Membrane_x0002_Bound O-Acyltransferase 7 (MBOAT7) is associated with increased susceptibility to NAFLD as well as the entire spectrum of NAFLD progression. The MBOAT7 gene encodes a lipid metabolic enzyme that is capable of esterifying polyunsaturated fatty acyl-CoAs to LPI substrates to generate phosphatidylinositol (PI) lipids. We previously showed that antisense oligonucleotide (ASO)-mediated knockdown of Mboat7 in mice promoted high fat diet-induced hepatic steatosis, hyperinsulinemia, and systemic insulin resistance (Helsley et al., 2019). Thereafter, other groups showed that hepatocyte-specific genetic deletion of Mboat7 promoted striking fatty liver and NAFLD progression but does not alter insulin sensitivity, suggesting the potential for cell autonomous roles. Here, we show that MBOAT7 function in adipocytes contributes to diet- 3 induced metabolic disturbances including hyperinsulinemia and systemic insulin resistance. The expression of Mboat7 in white adipose tissue closely correlates with diet-induced obesity across a panel of ~100 inbred strains of mice fed a high fat/high sucrose diet. Moreover, adipocyte_x0002_specific genetic deletion of Mboat7 is sufficient to promote hyperinsulinemia, systemic insulin resistance, and mild fatty liver. Unlike in the liver, where Mboat7 plays a relatively minor role in maintaining arachidonic acid (AA)-containing PI pools, Mboat7 is the major source of AA_x0002_containing PI pools in adipose tissue. Our data demonstrate that MBOAT7 is a critical regulator of adipose tissue PI homeostasis, and adipocyte MBOAT7-driven PI biosynthesis is closely linked to hyperinsulinemia and insulin resistance in mice.

overall_design: Adipose tissue mRNA profiles of MBOAT7 Flox and ASKO mice fed chow or HFD for 20 weeks

first: William

last: Massey

first: E

first: J

last: Brown


title: RNA sequencing of PD-L1 knock down in uveal melanoma cells

city: Shanghai

first: Jie

last: Yu

address: No. 639, Zhizaoju road, Huangpu district

summary: In order to study the mechanism of nuclear PD-L1 in uveal melanoma, we knocked down PD-L1 and applied RNA-seq and CUT&Tag to identify its target genes in uveal melanoma.

overall_design: Examination the target genes of  nuclear PD-L1 in uveal melanoma cells.

first: Peiwei

last: Chai


title: Acquired anoikis resistance mediates enhancer-driven subtype plasticity in pancreatic cancer [ChIP-Seq]

first: Jae Seok

last: Roe

overall_design: ChIP-seq profilings of various PDA cell lines

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Characterization of mixed origins MGC 803 cell line

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

summary: Investigation of the mixed origins of the MGC 803 cell line reveals it is a nasopharyngeal HeLa hybrid cell line

overall_design: mixed origins of the MGC 803 cell line

first: Meime


title: Mechanism of CyPA in regulating the occurrence and development of atherosclerosis

city: Urumqi

first: Yang

middle: wen

last: wen

address: Liyushan South Road

department: The Second Department of General Internal Medicine

institute: the First Affiliated Hospital of Xinjiang Medical University

summary: Background: We investigated the effect of PPIA overexpression on downstream gene expression at the cellular level.  Methods: The PPIA gene was overexpressed in human umbilical vein endothelial cells. Then, transcriptome sequencing was performed. The differentially expressed genes and genes with alternative splicing were screened. GO and KEGG analyses were performed. Nine differentially expressed genes and 7 genes with alternative splicing were validated by real-time quantitative PCR.  Results: After PPIA overexpression, 328 genes were differentially expressed, including 157 up-regulated genes and 171 down-regulated genes. GO enrichment analysis of up-regulated genes found that the enriched GO terms included extracellular region, protein binding and metal ion binding, etc. For down-regulated genes, the enriched GO terms included neuron projection, protein binding, endoplasmic reticulum unfolded protein response, etc. KEGG showed that the up-regulated genes were mainly enriched in gastric acid secretion, AMPK signaling pathway, etc; and, the down-regulated genes were enriched in transcriptional misregulation in cancer, TNF signaling pathway, etc. Real-time quantitative PCR analysis of ATF4 (activating transcription factor 4), PPP1R15A (protein phosphatase 1, regulatory (inhibitor) subunit 15A protein phosphate 1, regulatory (inhibitor) subunit 15A), GADD45B (growth arrest and DNA damage inducible protein 45B), SGK1 (serum/glucocorticoid regulated kinase 1), DDIT3 (Recombinant DNA Damage Inducible Transcript 3), PMAIP1 (Phorbol-12-myristate-13-acetate-induced Protein 1), SULF1 (Sulfatase 1), GDF6 (Growth Differentiation Factor 6), and XBP1 (X-Box Binding Protein 1) obtained consistent results with the sequencing results. On the other hand, multiple genes with alternative splicing were identified and analyzed with KEGG and GO. Real-time quantitative PCR validation showed that the probability of alternative splicing in LHPP, APH1A, BRD1, and ORAI3 was increased. However, the changes of NFX1, SERGEF, and PCBP4 were inconsistent with the sequencing results.  Conclusion: The overexpression of PPIA in human umbilical vein endothelial cells causes changes in the expression of downstream genes, and induces alternative splicing in multiple genes. PPIA may be involved in the development of atherosclerosis by regulating the expression of downstream genes and causing endothelial cell dysfunction.

first: Wenwen

first: XinRong

last: Zhou

first: Qiuju

last: Li

first: Mingyue

last: Yin

first: Ning

last: Wang


title: Hepatic irradiated pigs develop radiation induced veno-occlusive liver disease with ferroptosis

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: In this study, we performed a dose escalation study of whole-liver irradiation in miniature pigs and established a novel pig model for the severe form of RILD largely resembling the clinical and histological features of the human diseases, especially VOD and hepatic necrosis. Furthermore, taking advantage of serial liver biopsy in large-sized animal, we dissected the dynamics of cellular events essential for irreversible liver dysfunction in RILD. Unexpectedly, ferroptosis was also detected in irradiated pig liver samples.

overall_design: We performed a whole-genome RNA-sequencing analysis of irradiated livers from the 20Gy, 30Gy,40Gy treated and control pigs

first: Yifan

first: Qiang

last: Zheng

first: Zhen

last: Sun

first: Ludi

last: Zhang

first: Xiujun

last: Cai


title: Epigenetic profiling of OT-I CD8+ T cells after T cell activation

city: La Jolla

first: Jennifer

last: Hope

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: T cells undergo epigenetic changes upon T cell activation. We used the Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) to analyze epigenetic changes in T cells that were sufficient for or lacked PSGL-1 (gene: Selplg) two hours after T cell activation.

overall_design: Naive PSGL-1+/+ or PSGL-1-/- OT-I CD8+ T cells were isolated using magnetic bead separation and activated using immobilized anti-CD3 antibody for 2 hours.

first: Linda

last: Bradley


title: Transcriptome of Triticum aestivum genotypes associated with resistance against the Wheat dwarf virus

city: České Budějovice

first: Abdoallah

last: Sharaf

address: Branišovská 31

country: Czech Republic

institute: Biology Centre ASCR, v.v.i.

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus.
Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Nuc

last: Przemyslaw

first: Jan

last: Ripl

first: Glenda

last: Alquicer

first: Emad

last: Ibrahim

first: Xifeng

first: Midatharahally

middle: N

last: Maruthi

first: Jiban

last: Kumar


title: Non-phosphorylatable cyclin D1 mutant potentiates endometrial hyperplasia and drives carcinoma with Pten loss

first: Ernest

last: Chan

summary: Cyclin D1 is a regulatory subunit of cyclin-Dependent Kinases 4 and 6 (CDK4/6) and regulates progression from G1 to S phase of the cell cycle. Dysregulated cyclin D1-CDK4/6 contributes to tumor development. Enforced expression of non-phosphorylatable cyclin D1T286A mutant, frequently observed in human cancers, drives tumorigenesis. However, physiological functions of cyclin D1T286A is unclear. We have generated a conditional knock-in mouse model where cyclin D1T286A is expressed under the control of its endogenous promoter, permitting us to study the precise functions of cyclin D1T286A in tumorigenesis. The expression of cyclin D1T286A from its endogenous promoter induces inflammation-mediated lymphocyte disorder and mesenteric tumor formation. Uterine-specific expression of cyclin D1T286A accelerates Pten loss driven endometrial hyperplasia to promote uterine cancer.

overall_design: Examiniation of gene expression profiles. Total RNA was extracted for RNA seq from mouse embryonic fibroblasts. Treatmets are as follows

first: Akihiro

last: Yoshida

first: J

middle: A

last: Deihl

first: E


title: Transcriptome sequencing facilitates reveal molecular mechanisms between GSK2 and WRKY53

city: Harbin

first: Enyang

last: mei

address: haping street num 138

institute: Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences

summary:
Purpose:  Revealed molecular mechanisms between GSK2 and WRKY53 at the transcriptome level
Results: We identified 38,338 transcripts in the leaf of ZH11 and GSK2-RNAi and GSK2-RNAi-oswrky53 with DESeq2. RNA-seq data confirmed GSK2 and WRKY53 co-regulated 2570 gene.

overall_design: Leaf mRNA profiles of  rice booting  stage wild type (ZH11) and GSK2-RNAi and GSK2-RNAi_oswrky53  were generated by deep sequencing,  using Illumina HiSeq 2000 .

last: Mei

first: Xiaojie

last: Tian

first: Qingyun

last: BU


title: Anoikis resistance drives transcriptional plasticity in pancreatic cancer

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University


title: T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile [single-cell RNA-seq]

first: Bruno

last: Gegenhuber

summary: Stromal fibroblasts reside in inflammatory tissues that are characterized by either immune suppression or activation. Whether and how fibroblasts adapt to these contrasting microenvironments remains unknown. Cancer-associated fibroblasts (CAFs) mediate immune quiescence by producing the chemokine CXCL12, which coats cancer cells to suppress T cell infiltration. We examined whether CAFs can also adopt an immune-promoting chemokine profile. Single-cell RNA-sequencing of CAFs from mouse pancreatic adenocarcinomas identified a sub-population of CAFs with decreased expression of CXCL12 and increased expression of the T cell-attracting chemokine, CXCL9 in association with T cell infiltration. TNFa and IFNg containing conditioned media from activated CD8+ T cells converted stromal fibroblasts from a CXCL12+/CXCL9- immune suppressive phenotype into a CXCL12-/CXCL9+ immune-activating phenotype. Recombinant IFNg and TNFa acted synergistically to induce CXCL9 expression, whereas TNFa alone suppressed CXCL12 expression. This coordinated chemokine switch leads to increased T cell infiltration in an in vitro chemotaxis assay. Our study demonstrates that CAFs have a phenotypic plasticity that allows their adaptation to contrasting immune tissue microenvironments.

overall_design: Single-cell RNA-seq of mouse orthotopic tumors derived from Krt19-edited, Tgm2-edited, and non-targeting control pancreatic cancer cells

first: Ran

last: Yan

first: Philip

last: Moresco

first: Douglas

last: Fearon


title: T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile [bulk RNA-seq]

overall_design: Bulk RNA-seq from mouse PSCs treated with or without TNFa/IFNg for 6 hr


title: Single cell gene expression profiling of slow cycling and actively dividing mouse glioblastoma (GBM) cells isolated based on H2B-GFP label retention.

city: London

first: Gordon

last: Beattie

address: Gower Street

institute: UCL

summary: A slow cycling, dormant cell state is thought to contribute to the therapeutic resistance of GBM tumour cells, yet not much is known about the biology of this slow-cycling cell population in GBM. By using somatic mouse model of GBM, combined with the inducible H2B-GFP label retention system, we isolated dormant tumour cells from their in vivo niches, and characterised them by single cell RNA sequencing.

overall_design: Mouse GBM cells isolated by Fluorescence activated cell sorting (FACS) according to the presence or absence of H2B-GFP signal and analyzed by single cell RNA Sequencing

first: Parrinello

last: Simona

first: Pöysti

last: Anni

first: Beattie

last: Gordon

first: Marguerat

last: Samuel


title: Transcriptome analysis in buds of citrus trees of different Huanglongbing severity levels

city: Lake Alfred

first: Faisal

last: Shahzad

address: 700 Experiment Station Road, CREC

department: Horticultural Sciences

institute: University of Florida

summary: Devastating citrus disease Huanglongbing (HLB) is without existing cures. Herein, we present results demonstrating the possible  mechanisms (hypoxia stress) behind HLB-triggered shoot dieback by comparing the transcriptomes, hormone profiles, and key  enzyme activities in buds of severely and mildly symptomatic ‘Hamlin’ sweet orange (Citrus sinensis). Within six months (October –  May) in field conditions, severe trees had 23% bud dieback, greater than mild trees (11%), with a concomitant reduction in canopy  density. In February, differentially expressed genes (DEGs) associated with responses to osmotic stress, low oxygen levels, and cell  death were upregulated, with those for photosynthesis and cell cycle downregulated in severe versus mild trees. For severe  trees, not only were the key markers for hypoxia, including anaerobic fermentation, reactive oxygen species (ROS) production,  and lipid oxidation, transcriptionally upregulated, but also alcohol dehydrogenase activity was significantly greater compared to  mild trees, indicating a link between bud dieback and hypoxia. Tricarboxylic acid cycle revival, given the upregulation of  glutamate dehydrogenase and alanine aminotransferase DEGs, suggests that ROS may also be generated during hypoxiareoxygenation.  Greater (hormonal) ratios of abscisic acid to cytokinins and jasmonates and upregulated DEGs encoding NADPH  oxidases in severe versus mild trees indicate additional ROS production under limited oxygen availability due to stomata closure.  Altogether, our results provided evidence that as HLB progresses, excessive ROS produced in response to hypoxia and during  hypoxia-reoxygenation likely intensify the oxidative stress in buds leading to cell death, contributing to marked bud and shoot  dieback and decline of the severely symptomatic sweet orange trees.

overall_design: Samples (bud tissue) of severely and mildly symptomatic ‘Hamlin’ sweet orange in November and February; each sample was analyzed in four biological replicates.

first: Shahzad

last: Faisal

first: Lisa

last: Tang

first: Tripti

last: Vashisth


title: Aberrant cell state plasticity mediated by developmental reprogramming precedes cancer initiation  [CUT&RUN]

city: BOSTON

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INSTITUTE

summary: Cell state (phenotypic) plasticity is a carefully regulated feature of adult epithelial cells that enables adaptive responses to injury, inflammation, and other forms of stress.Aberrant expansion of the normally restricted capability for cell state plasticity to escape terminal differentiation is a critical aspect of neoplasia. The nongenetic factors and specific programs that mediate aberrant cell state plasticity and impaired differentiationrequire deeper characterization to understand this elusive aspect ofcancer pathogenesis. Using genetically engineered andcarcinogen-induced murine models of intestinal neoplasia, wedemonstrate that impaired differentiation is a conserved eventpreceding cancer development. Single cell RNA-sequencing (scRNA-seq)of neoplastic intestinal lesions from both mouse models and a patientwith familial adenomatous polyposis revealed that cancer initiates byadopting an aberrant transcriptional state characterized bynonoverlapping expression of a regenerative pathway, marked by Ly6a(Sca-1), and a fetal intestinal program, positive for Tacstd2 (Trop2).Genetic inactivation of Sox9 prevented adenoma formation in ApcKOmice, obstructed emergence of aberrant regenerative and fetalintestinal programs, and restored multi-lineage differentiation byscRNA-seq. Expanded chromatin accessibility at regeneration and fetalgenes upon Apc inactivation was reduced by concomitant Sox9suppression. These studies indicate that aberrant cell stateplasticity mediated by unabated regenerative activity anddevelopmental reprogramming precedes cancer development.

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN)  for SOX9 in Adenoma and Normal organoids derived from a patient with Familial Adenomatous Polyposis syndrome.

first: Pratyusha

last: Bala

first: Daulet

last: Aitymbayev

first: Zhixin

last: Li

first: Jonathan

last: Rennhack


title: Obesity defined molecular endotypes in the synovium of patients with osteoarthritis provides a rationale for therapeutic targeting of fibroblast subsets

city: Birmingham

first: Susanne

last: Wijesinghe

address: Mindelsohn Way

department: Institute of Inflammation and Ageing

institute: University of Birmingham

summary: This study aimed to establish molecular endotypes in osteoarthritis soft joint tissue driven by obesity in both load-bearing and non-load bearing joints. Transcriptomic analysis found the inflammatory landscape of OA synovial fibroblasts (SF) are independently impacted by obesity, joint loading, and anatomical site with significant heterogeneity between obese and normal weight patients. These findings demonstrate the significance of obesity in changing the inflammatory landscape of synovial fibroblasts in both load bearing and non-load bearing joints. The molecular endotypes identified may provide a route for the stratification of patients in clinical trials, providing a rational for the therapeutic targeting of specific SF subsets in specific patient populations with arthritic conditions.

overall_design: Hand, hip, knee, and foot joint synovial tissue were collected peri-operatively from osteoarthritis patients (n=24) classified as obese (BMI > 30) or normal weight (BMI 18.5-24.9). Each joint sample collected was from an independent patient undergoing arthroscopy at a single anatomical joint. Total RNA was extracted using Qiagen's RNeasy Mini Kit, following manufacturer's instructions for on column DNase treatment. Library preparation and RNA-sequencing was performed by Genomics Facility at University of Birmingham using Lexogen QuantSeq 3’ kit and sequenced on Illumina's NextSeq 500. The sequence reads quality checks were carried out using fastQC, following which the bbduk from BBMap (version 38.87) software was used to trim Illumina adapters and polyA tails. Reads were mapped to hg38 reference human genome using Star Aligner. The R package DESeq2 was used to normalise raw read counts and perform statistical comparisons using VST transformations.

first: Amel

last: Badoume

first: Dominika

last: Nanus

first: Archana

last: Sharma-Oates

first: Hussein

last: Farah

first: Michelangelo

last: Certo

first: Fawzeyah

last: Alnajjar

first: Edward

middle: T

last: Davis

first: Claudio

last: Mauro

first: Mark

last: Lindsay

first: Simon

last: Jones


title: Cell cycle mRNA half-life profiling.

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in synchronized cells collected from different stages of the cell cycle including swarmer cells, stalk cells (45 min post synchrony), and predivisional cells (90 min post synchrony).  For each cell population, transcription was disrupted by the antibiotic rifampicin, and RNA samples were collected at different time points to measure the mRNA half-lives.

overall_design: mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in synchronized cells collected from different stages of the cell cycle including swarmer cells, stalk cells (45 min post synchrony), and predivisional cells (90 min post synchrony).  For each cell population, transcription was disrupted by the antibiotic rifampicin, RNA samples were collected. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Total RNA samples were collected just prior to rifampicin addition, and after 1, 3, or 9 minutes incubation with 100ug/mL rifampicin. Each total RNA sample was depleted of rRNA using the ribozero kit (Illumina) for gram negative bacteria, and subjected to total RNA-seq libraries as in (Ingolia et al. Science 2009). tRNA was left in each sample as an internal control for stable RNA.


title: Low protease activity in B cell follicles promotes retention of intact antigens after immunization

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main St

institute: Broad Institute of MIT and Harvard

summary: The structural integrity of vaccine antigens is critical to the generation of protective antibody responses, but the impact of protease activity on vaccination in vivo is poorly understood. We characterized protease activity in lymph nodes and found that antigens were rapidly degraded in the subcapsular sinus, paracortex, and interfollicular regions, whereas low protease activity and antigen degradation rates were detected in the vicinity of follicular dendritic cells (FDCs). Correlated with these findings, immunization regimens designed to target antigen to FDCs led to germinal centers dominantly targeting intact antigen, whereas traditional immunizations led to much weaker responses that equally targeted the intact immunogen and antigen breakdown products. Thus, spatially compartmentalized antigen proteolysis affects humoral immunity and can be exploited.

overall_design: Dissociated cells from lymph nodes of mice that were either untreated or 6 hours after vaccination with 200 mg of ovalbumin peptide and 20 mg CpG 1826 adjuvant.

first: Ang

last: Cui

first: David

last: Lieb


title: Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing

city: Hangzhou

first: Ling

last: Chen

address: 12 Lingyin Road

institute: Zhejiang Hospital

summary:
The aim of this study was to identify key immune-related genes in ALF by constructing an ALF mouse model for transcriptome sequencing.
We performed RNA-seq in ALF mice and healthy control mice

overall_design: Gene expression profiling analysis of RNA-seq data from ALF mice and normal control mice

first: Li

last: Yuan

first: Jingle

last: Yang

first: Yizhi

last: Pan

first: Hong

last: Wang


title: Retapamullin and Chloramphenicol treated mRNA half-life profiling.

summary: mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in cells that were inhibited in translation initiation (retapamullin) or elongation (chloramphenicol) by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures.

overall_design: WT NA10000 cells were treated with Chloramphenicol or Retapamullin, then globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Total RNA samples were collected just prior to rifampicin addition, and after 1, 2, 4, 8, or 15 minutes incubation with 100ug/mL rifampicin. Each total RNA sample was depleted of rRNA using the ribozero kit (Illumina) for gram negative bacteria, and subjected to total RNA-seq libraries as in (Ingolia et al. Science 2009). tRNA was left in each sample as an internal control for stable RNA.


title: Gene expression profile at single cell level of OT-I CD8+ T cells from B16-OVA melanoma tumors

first: Jennifer

last: Hope

summary: Tumor infiltrating T cells are a diverse and heterogeneous population. We used single cell RNA sequencing (scRNA-seq) to analyze gene expression changes in tumor-specific T cells that were sufficient for or lacked PSGL-1 (gene: Selplg).

overall_design: In vitro activated congenically marked PSGL-1+/+ or PSGL-1-/- OT-I CD8+ T cells were adoptively transferred into separate C57BL/6 host mice bearing B16-OVA tumors. 6 days after transfer, donor OT-I cells were isolated by fluorescence-activated cell sorting (FACS) based on donor marker (CD90.1 or CD45.1) expression and analyzed using scRNA-seq (10X genomics). Biological replicates were pooled prior to sorting to generate one sample per condition.

first: Hope

last: Jennifer L

first: Bradley

last: Linda M


title: mRNA expression quantitative Analysis of BaF3-T315I cell lines treated with I13 compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are to evaluate the mRNA expressions of genes in BaF3-T315I cell lines treated with I13

overall_design: There are 6 samples for BaF3-T315I cell line (control and I13-treated)

first: C

last: Gao

first: L


title: Differential RNA expression in kidney of mice with septic AKI induced by lipopolysaccharide

first: Yang

last: Chong

state: Heilongjiang

address: 23, YouZheng Street, Nangang District

department: Critical Care Medicine

institute: The First Affiliated Hospital of Harbin Medical University

summary: Since septic AKI is a common type of AKI in ICU, we need to understand the differences in renal RNA expression in septic kidney injury. Therefore, we used lipopolysaccharide intraperitoneal injection to construct a mouse model of septic renal injury, and verified that the model was successful, then RNA sequencing was performed. To know the difference of RNA expression through the comparison of kidney sequencing between the normal group and the septic AKI group.

overall_design: We selected  6-8 weeks wild type C57BL/6 mice , 3 mice in the normal control group, and 3 mice with septic kidney injury by intraperitoneal injection of LPS. 24 hours after LPS modeling, the blood and kidney tissue of the two groups of mice were tested for blood creatinine and urea nitrogen levels to determine the presence of renal injury, and then the renal RNA-seq of the two groups was performed.

first: Chong

first: Wang

last: Yiqi


title: Impact of a gain of function mutation in Fgfr3 gene on mandibular bone repair in a mouse model of hypochondroplasia, Fgfr3N534K/+

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

country: France

institute: Institut Imagine

summary: TO BE UPDATED.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Two FFPE slides with 8  samples each were prepared using calluses of mutant and control mice at 14-day post mandibular fracture. 32 regions of interest (ROIs) were manually placed in newly formed bone and cartilage callus areas.

first: Anne

last: Morice

first: Laurence

last: Legeai-Mallet


title: The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Extra-chromosomal selfish DNA elements can evade the risk of being lost at every generation by behaving as chromosome appendages, thereby ensuring high fidelity segregation and stable persistence in host cell populations. The yeast 2-micron plasmid and episomes of the mammalian gammaherpes and papilloma viruses that tether to chromosomes and segregate by hitchhiking on them exemplify this strategy. We document for the first time the utilization of a SWI/SNF type chromatin remodeling complex as a conduit for chromosome association by a selfish element. One principal mechanism for chromosome tethering by the 2-micron plasmid is the bridging interaction of the plasmid partitioning proteins (Rep1 and Rep2) with the yeast RSC2 complex and the plasmid partitioning locus STB. We substantiate this model by multiple lines of evidence derived from genomics, cell biology and in vivo and in vitro interaction analyses. We describe a Rep-STB bypass system in which a plasmid non-covalently associated with the RSC complex mimics segregation by chromosome hitchhiking. Given the ubiquitous prevalence of SWI/SNF family chromatin remodeling complexes among eukaryotes, it is likely that the 2-micron plasmid paradigm or analogous ones will be encountered among other eukaryotic selfish elements.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing for the partitioning proteins Rep1, Rep2 and controls in wild-type (wt) and rsc2 mutant strains of yeast Saccharomyces cerevisiae

first: Chien-Hui

last: Ma

first: Deepanshu

last: Kumar

first: Santanu

middle: K

last: Ghosh

first: Vishwanath

middle: R

first: Makkuni

last: Jayaram


title: Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation [scRNA-seq]

first: Nilay

last: Sethi

summary: Cell state plasticity is carefully regulated in adult epithelia, enabling adaptive responses to stressors. The nongenetic factors that control aberrant expansion of the normally restricted capability for cell state plasticity to escape terminal differentiation in neoplasia require deeper characterization. Using genetically-engineered and carcinogen-induced murine models of intestinal neoplasia, we demonstrate that impaired differentiation is a conserved event preceding cancer development. Single cell RNA-sequencing (scRNA-seq) of intestinal neoplasia from both mouse models and a patient with hereditary polyposis revealed that cancer initiates by adopting an aberrant transcriptional state characterized by regenerative activity, marked by Ly6a (Sca-1), and reactivation of fetal intestinal genes, including Tacstd2 (Trop2). Genetic inactivation of Sox9 prevented adenoma formation, obstructed emergence of regenerative and fetal programs, and restored multi-lineage differentiation by scRNA-seq.  Expanded chromatin accessibility at regeneration and fetal genes upon Apc inactivation was reduced by concomitant Sox9 suppression. These studies indicate that aberrant cell state plasticity mediated by unabated regenerative activity and developmental reprogramming precedes cancer development.

overall_design: scRNA-seq of mouse models of CRC as well as FAP patients associated with study

first: Pratyusha

last: Bala

first: Jonathan

last: Rennhack


title: Tofacitinib reduces skin inflammation in a patient with severe autosomal recessive congenital ichthyosis

city: Tainan

first: Yu-Chen

last: Lin

address: 138 Sheng-Li Rd

country: Taiwan

institute: National Cheng Kung University

summary: To investigate the skin transcriptome changes of patients with ARCI under tofacitinib treatment.

overall_design: Comparative gene expression profiling analysis of skin RNA-seq data for a patient with ARCI pre- and post-tofacitinib and for two healthy controls.

first: Yu


title: Malignant Peripheral Nerve Sheath Tumors are Comprised of Two Epigenetic Subgroups with Distinct Molecular Landscapes, Outcomes and Therapeutic Targets: Bulk RNA Seq Samples

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary: We focused on studying the methylation signature of the spectrum of PNSTs to develop a methylome-based classification of these common tumors. We studied the genome-wide DNA methylation patterns using the Illumina MethylationEPIC array and classified the samples into 5 subgroups. Gene Expression comparing the subgroups were performed using bulk RNA Seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different methylation subgroups of PNSTs.

first: Suganth

last: Suppiah

first: Gelareh

last: Zadeh


title: Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation [ATAC-seq]

overall_design: ATAC-seq

first: Daulet

last: Aitymbayev

first: Zhixin

last: Li


title: Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice [Transcriptome Dataset]

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary:
Episodes of chronic stress can result in psychic disorders like post-traumatic stress disorder, but also promote the development of metabolic syndrome and type 2 diabetes. We hypothesize that muscle, as main regulator of whole-body energy expenditure, is a central target of acute and adaptive molecular effects of stress in this context. Here, we investigate the immediate effect of a stress period on energy metabolism in Musculus gastrocnemius in our established C57BL/6 chronic variable stress (Cvs) mouse model.
Cvs decreased lean body mass despite increased energy intake, reduced circadian energy expenditure (EE), and substrate utilization. Cvs altered the proteome of metabolic components but not of the oxidative phosphorylation system (OXPHOS), or other mitochondrial structural components. Functionally, Cvs impaired the electron transport chain (ETC) capacity of complex I and complex II, and reduces respiratory capacity of the ETC from complex I to ATP synthase. Complex I-OXPHOS correlated to diurnal EE and complex II-maximal uncoupled respiration correlated to diurnal and reduced nocturnal EE. Bioenergetics assessment revealed higher optimal thermodynamic efficiencies (ƞ-opt) of mitochondria via complex II after Cvs. Interestingly, transcriptome and methylome were unaffected by Cvs, thus excluding major contributions to supposed metabolic adaptation processes.
In summary, the preclinical Cvs model shows that metabolic pressure by Cvs is initially compensated by adaptation of mitochondria function associated with high thermodynamic efficiency and decreased EE to manage the energy balance. This counter-regulation of mitochondrial complex II may be the driving force to longitudinal metabolic changes of muscle physiological adaptation as the basis of stress memory.

overall_design: C57/Bl6 male mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012), or left untreated (Ctrl). Transcriptome analyses (MTA array, Affymetrix) was performed in Ctrl and Cvs gastrocmnemius muscle biopsies of each condition. Mice were phenotyped for body composition, serum analyses, methylome,  mitochondrial proteome and mitochondrial function and thermodymamic efficency immediately after stress to determine CVS dependant molecular alterations im metabolic regulation.

first: Aleksandra

last: Nikolic

first: Pia

last: Fahlbusch

first: Joerg

last: Kotzka


title: Hyperlipidemia elicits an atypical, Th1 like CD4+ T cell response: a key role for VLDL

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC, location AMC

summary: Hyperlipidemia and T cell driven inflammation are important drivers of atherosclerosis, the principal underlying cause of cardiovascular disease. Here, we applied an in-depth multi-omics approach to detail the effects of hyperlipidemia on T cells. In vitro, exposure of CD4+ T cells to very low-density lipoprotein (VLDL), but not to low-density lipoprotein (LDL) resulted in upregulation of Th1 associated pathways, suggesting that VLDL serves as the main lipid component driving hyperlipidemia induced T cell activation.  To further detail this response in vivo, T-cells of ldlr-/- fed a normal cholesterol or high cholesterol diet, which develop a strong increase in VLDL cholesterol and triglyceride levels, were investigated. CD4+ T cells of hyperlipidemic ldlr-/- mice exhibited an increased expression of CXC-chemokine receptor 3 (CXCR3) and produced more TNFα and interferon-γ (IFN-γ). Gene set enrichment analysis identified IFN-γ-mediated signaling as the most upregulated pathway in hyperlipidemic T cells. However, the classical Th1 associated transcription factor profile with strong upregulation of Tbet and downregulation of Gata3 was not observed. Hyperlipidemia did not affect levels of the CD4+ T-cell’s metabolites involved in glycolysis or other canonical metabolic pathways but enhanced amino acids levels. However, CD4+ T-cells of hyperlipidemic mice showed increased cellular cholesterol accumulation and an increased arachidonic acid (AA) to docosahexaenoic acid (DHA) ratio, which was associated with T cell activation and IFN-γ-mediated signaling.   In conclusion, hyperlipidemia, and especially its VLDL component induces an atypicial Th1 response in CD4+ T-cells.

overall_design: Comparison of gene expression in human CD4+ T cells exposed to LDL (n=3) or VLDL (n=3) with untreated cells (n=3)

first: Bram

last: van Os

first: Winnie

last: Vos

first: Laura

last: Bosmans

first: Claudia

last: van Tiel

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Sanne

last: Lith

first: Johannes

middle: H

last: Levels

last: Zaal

first: Celia

last: Berkers

first: Chris

last: van de Lest

first: J

middle: B

last: Helms

first: Christian

last: Weber

first: Dorothee

last: Atzler

first: Menno

middle: P

last: de Winther

first: Jeroen

last: Baardman

first: E


title: APOΕ4 lowers energy expenditure in females and impairs glucose oxidation by increasing flux through aerobic glycolysis

city: Lexington

first: Lance

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Cerebral glucose hypometabolism is consistently observed in individuals with Alzheimer’s disease (AD), as well as in young cognitively normal carriers of the Ε4 allele of Apolipoprotein E (APOE), the strongest genetic predictor of late-onset AD. While this clinical feature has been described for over two decades, the mechanism underlying these changes in cerebral glucose metabolism remains a critical knowledge gap in the field. Here, we undertook a multi-omic approach by combining single-cell RNA sequencing (scRNAseq) and stable isotope resolved metabolomics (SIRM) to define a metabolic rewiring across astrocytes, brain tissue, mice, and human subjects expressing APOE4.

overall_design: 11 to 12-month-old female E3/E3 and E4/E4 mice (pooled n = 3 per genotype) were anesthetized via 5.0% isoflurane before exsanguination and transcardial perfusion with ice-cold Dulbecco’s phosphate buffered saline.


title: Lineage-Specific Differences and Inference of Regulatory Networks Governing Human Chondrocyte Development

city: Stanford

first: Daniel

last: Richard

state: CA

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

summary: In-vitro differentiation of chondrocyte populations recapitulate in-vivo behaviours, and reveal gene regulatory networks involved in chondrocyte development

overall_design: Epigenetic and transcriptomic profiling of in-vitro and in-vivo chondrocyte populations

first: Steven

last: Pregizer

first: Divya

last: Venkatasubramanian

first: Pushpanathan

last: Muthuirulan

first: Zun

last: Liu

first: Terence

middle: D

last: Capellini

first: April

last: Craft


title: Small RNA profiles in zmp mutants

city: Riverside

first: Brandon

last: Le

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing

summary: We profiled the small RNA-ome, transcriptome, DNA methylome, and chromatin association to the study the molecular and biological functions of ZMP in Arabidopsis.

overall_design: Two to three biological replicates per genotype were obtained for this study

first: Yuan

last: Wang

first: Xuemei

last: Chen


title: Molecular and biological functions of ZMP in Arabidopsis

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Differential Effects of Estradiol on Progenitor -Smooth Muscle Cell and -Endothelial Cell Growth and Gene Response.

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

institute: FGCZ Zuerich

summary: Coronary artery disease is the leading cause of mortality in women. Abnormal growth of smooth muscle cells and endothelial damage contributes to the thickening of the blood vessels and vascular occlusion. Estradiol prevents vascular remodleing by promoting EC growth and inhibiting SMC growth. Recent studies suggest that circulating (bone marrow derived) progenitor cells also contribute to the vascular remodeling process. Whether estradiol could, in part, induce its protective actions by inhibiting P-SMC growth remains unknown. In this study, progenitor smooth muscle cells (P-SMCs) and endothelial (P-ECs)  grown from CD34+ progenitor cells (PC) magnetically separated from human cord blood derived mononuclear cells. P-SMC and P-EC cell colonies were grown and characterized for SMC and EC markers. Cultured cells were further used to assess the effects of 17β-estradiol (E2; 10nM) on their growth and gene expression. Briefly, P-SMCs or P-ECs were treated with or without 10 nM E2 for 0, 4 or 30 hours in DMEM-F12 supplemented with 2.5% FCS (steroid-free; SF). Subsequently, total RNA was extracted using RNeasy Mini Kit (QIAGEN) processed for gene analysis. Treatment of P-SMCs with E2 inhibited 2.5% SF-serum -induced growth (DNA synthesis and cell number), whereas, E2 induced cell growth in P-ECs. The growth effects of E2 in P-SMCs and P-ECs were mimicked by ER-α agonist and blocked by ER-α antagonist. The differential effects of E2 on P-SMC and P-EC growth were also reflected in ERK1/2 and Akt phosphorylation and in positive and negative regulators of cell cycle. Gene analysis revealed that P-SMCs expressed SMC alpha actin (ACTA2) where as P-ECs expressed CD34, FLT1 and vWF, confirming the differentiation of progenitor cells to SMCs and ECs. Treatment with E2 for 30 hours regulated 1791 in P-SMCs and 220 in P-ECs, with 36 that were common. Volcano analysis showed that treatment with E2 for 30 hours differentially expressed multiple genes, importantly, estradiol significantly upregulated antimitogenic pathways and downregulated  proproliferative pathways in P-SMC and P-ECs, respectively. Contrasting effects of E2 were also observed in multiple ingenuity canonical pathways that were up or downregulated in P-SMCs and P-ECs. Findings from both growth and gene expression studies provide evidence that etradiol may induce its vascular protective actions by inhibiting P-SMC activity and improving P-EC activity. Interestingly, in perpheral blood estradiol decreasd the number of c-kit+ cells and increased CD34+ cells. Since these cells evolve into SMCs and ECs respectively, our findings provide evidence that estradiol may induce its anti-occlusive actions by differentially regulating P-SMC and P-EC activity and numbers.

overall_design: Progenitor-SMCs and Progenitor-ECs grown to subconfluence were treated for 0, 4 and 30 hours with vehicle (DMSO 1µl/ml final concentration) or estradiol (10nM) in presence phenol red free DMEM/F12 medium containing 2.5% steroid free fetal calf serum. Following treatment for indicated times, the cells were washed, lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN). Concentration and purity of the samples were determined using the Agilent Bioanalyzer and the samples further processed for gene expression analysis. Both P-SMCs and P-ECs were treated in triplicates (n=3) for each treatment (with or without estradiol) and for each time point (0, 4 and 30 minutes).

first: Isabella

last: Baruscotti

first: Raghvendra

last: Dubey

first: Nikiana

last: Simigdala


title: The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells.

city: Berlin

first: Julia

last: Polansky

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin


title: Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice

first: Birgit

last: Knebel


title: Loss of G6b-B results in defective TPO signaling and blocks megakaryocyte-lineage differentiation

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: We report on a severe macrothrombocytopenia in C57BL/6 mice bearing a spontaneous intronic mutation within Mpig6b resulting in complete loss of G6b-B protein expression. In addition to the myelofibrosis described in G6b-B-deficient mice, Mpig6bmut mice displayed sex-specific differences in platelet reactivity and BM morphology including a dramatic osteosclerosis especially present in females. RNA sequencing of native BM MKs revealed markedly reduced levels of all MK-specific transcripts.

overall_design: mRNA profiles of native bone marrow derived megakaryocytes sequenced on the NextSeq-500 platform with ~30 million reads per sample in single-end mode with 75 nt read length

first: Georgi

last: Manukjan

first: Bernhard

last: Nieswandt

first: Tobias

last: Heckel

first: Sascha

last: Dietrich

first: Margarete

last: Göbel


title: Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

city: BOSTON

first: Nilay

last: Sethi

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INSTITUTE


title: The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells [ChIP-seq]

summary: Mesenchymal stromal cells (MSCs) derived from bone marrow (BM) have stronger potential for endochondral ossification compared to white adipose tissue (WAT)-MSCs, umbilical cord (UC)-MSCs, chondrocytes (CH) and skin fibroblasts (FB). We assessed active regulatory regions facilitating bone-regeneration potential.

overall_design: ChIP-seq data for H3K4me1, H3K4me3, and H3K27ac were generated from 2-3 replicates of BM-, WAT-, UC-MSC, CH and FB.

first: Sarah

last: Hochmann

first: Kristy

last: Ou

first: Rodolphe

last: Poupardin

first: Salaheddine

last: Ali

first: Sven

last: Geissler

first: Dirk

last: Strunk


title: DNA methylation profiles in zmp mutants

first: Brandon

last: Le

overall_design: Two biological replicates per genotype were obtained for this study

first: Yuan

last: Wang

first: Xuemei

last: Chen


title: Gene expression analysis after shRNA-mediated knockdown of lncRNA CRNDE in the APL cell line NB4

city: Shanghai

first: Xuefei

last: Ma

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We performed RNA sequencing to identify differentially expressed genes and associated functional pathways.

overall_design: RNA sequencing was performed in NB4 cells infected with the CRNDE shRNA (sh-CRNDE) or the non-targeting control shRNA (sh-Control). NB4 cells were harvested at day three post-infection, and total RNA was extracted.

first: Ming

last: Zhao

first: Kankan