title: Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice

city: Austin

first: Tanya

middle: T.

last: Paull

state: TX

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

summary: The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate the sites of MRN-dependent processing by isolating and sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated with highest efficiency when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show much greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that Mre11 and DNA-PK both bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for phospho-DNA-PKcs(S2056), GLASS-ChIP DNA sequencing for phospho-DNA-PKcs(S2056), and Mre11 ChIPseq

first: Rajashree

last: Deshpande

first: Alberto

last: Marin-Gonzalez

first: Taekjip

last: Ha

first: Hannah

last: Barnes

first: Phillip

last: Woolley


title: STING mediates hepatocyte pyroptosis in liver fibrosis via epigenetic activating NLRP3 inflammasome

status: Public on Sep 18 2023

city: chengdu

first: yang

last: xiao

address: NO. 1, 4th Keyuan Road

country: China

institute: Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University

type: Expression profiling by high throughput sequencing

summary: Background and Aims: The activation of stimulator of interferon genes (STING) and NOD-like receptors protein 3 (NLRP3) inflammasomes-mediated pyroptosis signaling pathways represent two distinct central mechanisms in liver disease. However, the interconnection between these two pathways and the epigenetic regulation of the STING-NLRP3 axis in hepatocyte pyroptosis during liver fibrosis remain unknown and is the focus of this study.  Approach and Results: Liver fibrosis was induced in Sting knockout, Gasdermin D (Gsdmd) knockout mice, and in mice with hepatocyte-specific Nlrp3 deletion. RNA-sequencing, metabolomics, epigenetic compound screening system, and chromatin immunoprecipitation were utilized. STING and NLRP3 inflammasome signaling pathways were activated in cirrhotic livers but were suppressed by Sting knockout. Sting knockout also ameliorated hepatic pyroptosis, inflammation, and fibrosis in the murine cirrhotic model. In vitro, STING induced pyroptosis in primary murine hepatocytes via activating the NLRP3 inflammasome. H3K4-specific histone methyltransferase WD repeat-containing protein 5 (WDR5) and DOT1-like histone H3K79 methyltransferase (DOT1L) were identified to regulate NLRP3 expression in STING-overexpressed AML12 hepatocytes. WDR5/DOT1L-mediated histone methylation enhanced interferon regulatory transcription factor 3 (IRF3) binding to the Nlrp3 promoter and promoted STING-induced Nlrp3 transcription in hepatocytes. The RNA-sequencing and metabolomics analysis in murine livers and primary hepatocytes showed that metabolic reprogramming might participate in NLRP3-mediated hepatocyte pyroptosis and liver fibrosis. Moreover, hepatocyte-specific Nlrp3 deletion and downstream Gsdmd knockout attenuated hepatic pyroptosis, inflammation, and fibrosis in murine cirrhotic models.  Conclusions: This study describes a novel epigenetic mechanism by which the STING-WDR5/DOT1L/IRF3-NLRP3 signaling pathway enhances hepatocyte pyroptosis and hepatic inflammation in liver fibrosis.

overall_design: 1.The primary murine hepatocytes were stimulated with LPS (1 µg/mL) for 6 hours and nigericin (10 µM) for 30 minutes. The NLRP3 inhibitor MCC950 (10 µM) were added 2 hours before stimulation  2. One liver fibrosis model was induced by intraperitoneal injection of thioacetamide (TAA) in mice with hepatocyte-specific Nlrp3 deletion and wild type for 8 weeks. Control mice received the same volume of normal saline (NS). Another model was induced by intraperitoneal injection of carbon tetrachloride (CCl4) in mice with Sting knock out and wild for 8weeks. Control mice received the same volume of olive oil.

first: Yang

last: Xiao

last: Tai

first: Bei

last: Li

first: Jinhang

last: Gao

first: Chengwei

last: Tang


title: Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [RNA-seq]

status: Public on Sep 19 2023

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

summary: A major hurdle to the application of precision oncology in pancreatic cancer is the lack of molecular stratification approaches and targeted therapy for defined molecular subtypes. In this work, we sought to gain further insight and identify molecular and epigenetic signatures of the basal-like A pancreatic ductal adenocarcinoma (PDAC) subgroup that can be applied to clinical samples for both patient stratification and for choice of therapy. We generated and integrated global gene expression and epigenome mapping data from patient-derived xenograft (PDX) models to identify subtype-specific enhancer regions that were validated in patient-derived samples. In addition, complementary nascent transcription and chromatin topology (HiChIP) analysis revealed a basal-like A subtype-specific transcribed enhancer program (B-STEP) in PDAC characterized by enhancer RNA (eRNA) production that is associated with higher chromatin interactions and subtype-specific gene activation. Importantly, we successfully confirmed the validity of eRNA detection as a possible histological approach for PDAC patient stratification by performing RNA in situ hybridization analyses for subtype-specific eRNAs on pathological tissue samples. Thus, the finding in this study provides proof-of-concept that subtype-specific epigenetic changes relevant for PDAC progression can be detected at a single cell level in complex, heterogeneous, primary tumor material.

overall_design: mRNA-Seq was performed in a cohort of pancreatic ductal adenocarcinoma (PDAC)  patient-derived xenografts (PDX)  to determine the represenation of PDAC subtypes associated gene signatures. Moreover, to investigate the function of ∆NP63 in regulating the PDAC-subytpe specific gene expression, mRNA-Seq in L3.6pl cells was performed following P63 knockdown. mRNA-Seq with JQ1 treatment in L3.6pl cells was additionally utilized to analyze the effect of BET protein inhibition on ∆NP63- regulated transcriptional program.

first: Zeyna

middle: b

last: Najafova

first: Steven

middle: A

last: Johnsen


title: Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [HiChIP]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K27ac HiChIP was performed in L3.6pl cells to specifically identify P63 bound active enhancer promoter interactions

first: Zeynab


title: Identifying main functional pathways associated with cognitive resilience to Alzheimer ´s Disease

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

summary: Understanding the mechanisms involved in cognitive resilience in Alzheimer’s disease (AD) represents a promising strategy to identify novel treatments for dementia in AD. Previous findings from our group revealed that the study of aged-Tg2576 cognitive resilient individuals is a suitable tool for this purpose. Here, by performing a transcriptomic analysis of the prefrontal cortex of demented and resilient Tg2576 mice, we have been able to hypothesize that pathways involved in inflammation, amyloid degradation, memory function and neurotransmission may be playing a role on cognitive resilience in AD. Intriguingly, the results obtained in this study are suggestive of a reduction of the influx of peripheral immune cells into the brain on cognitive resilient subjects. Indeed, Cd4 mRNA expression is significantly reduced on Tg2576 mice with cognitive resilience and interestingly, we have found a negative correlation between CD4 mRNA levels in the periphery and the score in the Mini-Mental State Exam of AD patients. All of this, highlights the importance of understanding the role of the immune system on the development of neurodegenerative diseases and points out to the infiltration of CD4+ cells in the brain as a key player of cognitive dysfunction in AD.

overall_design: Comparison of transcripts in the frontal cortex between good learner (GL) or resilient and poor learner (PL) or memory impaired trasngenic Alzheimer´s disease (AD) mice

first: Mar

last: Cuadrado-Tejedor

last: García-Osta


title: In vitro differentiation of M1, M2, and TAM-like macrophages from healthy donor PBMC

city: Waltham

first: Ming

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

country: USA

institute: Immunitas Therapeutics

summary: To  understand the immunological role of different macrophage populations in the tumor, we generated transcriptional profiles of macrophages differentiated from PBMC-derived monocytes in vitro under three conditions to compare with: M1-like macrophages were developed in vitro through polarization of human monocytes by IFNg and TLR4 stimulation. This population is considered to have anti-tumor activities; releasing proinflammatory cytokines, performing phagocytosis, and possessing antigen cross presentation abilities. Second, M2-like macrophages were developed in vitro through intensive IL4 stimulation of monocytes. M2 macrophages are known to promote many pro-tumorigenic processes such as angiogenesis, immune suppression, hypoxia induction, tumor cell proliferation,  metastasis. Lastly, we deployed a third population that represents a better in vitro model for tumor associated macrophages (TAM), developed under conditions better resembling the TME.Monoctyes derived from two individual patient donors were cultured separately under four (4) different conditions in vitro, for a total of eight (8) samples to be processed for bulk RNA sequencing.

first: Bernstein

last: Matthew N

first: Scott

last: Dillon

first: Huggins

last: Matthew A

first: Tabrizi

last: Siamak

first: Hession

last: Cynthia C

first: Nieuwenhuis

last: Tim

first: Duan

last: Meixue

first: Nandivada

last: Vandana

first: Gerritsen

last: Jacqueline

first: Malu

last: Shruti

first: Tang

last: Ming


title: Microscopic and transcriptomic characterization of Listeria monocytogenes aggregation and biofilm formation on stainless steel surfaces in the presence of cantaloupe juice extract

city: College Park

first: Jie

last: Zheng

state: MD

address: 5001 Campus Drive

institute: FDA

summary: Listeria monocytogenes (Lm) cells can attach to both cantaloupe surface and food contact surfaces and promote biofilm growth. This study was to understand the impact of cantaloupe juice on the physiology and transcriptome of Lm planktonic cells and biofilm cells grown on stainless steel coupons using confocal laser scanning microscopy (CLSM), Cryo-Scanning Electron Microscopy (Cryo-SEM) and RNA Seq technology. Lm showed a strong autoaggregation phenotype when grown in cantaloupe juice at room temperature. It is interesting to note that Lm formed significantly more biofilms on stainless steel (SS) coupons when grown in cantaloupe juice than in TSB. SEM images revealed a different attachment profile of Lm on SS coupons. In TSB, Lm cells were mainly found in scratches/groves of the metal surface, whereas, in cantaloupe juice they attached to the smooth surface as well. Interestingly, Lm planktonic and biofilm cells in cantaloupe juice showed an elongated cell shape which might be a stress-induced phenotype in cantaloupe juice. Cantaloupe juice induced a distinct transcriptional profile of biofilm and planktonic cells of Lm from TSB. Functional annotation indicated that the significantly differentially expressed genes (DEGs, Padj < 0.05, log2foldchange ≥ 1) from the comparison mainly participated in metabolism, signaling and stress response. Notably, certain pathways downregulated for planktonic cells were significantly upregulated for biofilm cells in cantaloupe juice compared to TSB, including ABC transporters, two-component system, quorum sensing, chemotaxis, and flagellar assembly.  These data highlighted the interaction of Lm with food matrix (i.e., cantaloupe) and the role of food matrix on Lm survival and adaptation. These results provided the basis for future functional characterization of genes with potential roles in biofilm formation and persistence of Lm in cantaloupe juice, as well as for development of mitigation practices for Lm biofilms on produce and food contact surfaces.

overall_design:
We investigated the effect of food matrix (i.e., cantaloupe juice) vs. lab medium on Lm physiology by microscopic analysis (CLSM & SEM) and on Lm gene expression by RNA-Seq.
Lm planktonic cells were collected after 48h static growth at RT in 1X cantaloupe juice or TSB and Lm biofilm cells were collected from stainless steel coupons after 3 days static growth in 0.5X media, all samples were from 3 independent experiments.

first: Marina

last: Redding

first: Joseph

last: Mowery

first: Ganyu

last: Gu

first: Samantha

last: Bolten

first: Yaguang

last: Luo

first: Xiangwu

last: Nou


title: Sustained and intermittent hypoxia combined with TNF additively promote pro-thrombotic gene and protein changes in primary endothelial cells.

status: Public on Sep 17 2023

city: TROMSOE

first: Casper

middle: Jan Elis

last: Wahlund

address: Hansine Hansens veg 18

department: Clinical Medicine

country: Norway

institute: UiT - The Arctic university of Norway

summary: Venous thromboembolism (VTE) is a common and deadly disease with unclear pathophysiological initiation. Hypoxia and inflammation are believed to contribute to promoting thrombosis, but how and if these potential triggers interact is unclear. We have stimulated primary endothelial cells with sustained and intermittent hypoxia, in the presence or absence of TNF. Effects to the cells were analyzed with RNA sequencing and flow cytometry after 24H and 48H stimulations. RNA sequencing confirmed strong pro-inflammatory effects of TNF, and indicated that hypoxia alone had modest effects, but when combined with TNF there were clear additive effects on the number of differentially expressed genes, as well as modest increases of pro-inflammatory GO terms assessed by GSEA. On protein level, flow cytometry confirmed additive effects of combingin hypoxia and TNF for several adhesion molecules including E-selectin and ICAM-1, as well as on associated molecules including tissue factor. Unsupervised clustering of the flow cytometric data also revealed the expansion of a subset of endothelial cells with strongly pro-thrombotic phenotype. Taken together, our data suggests that hypoxia combines with inflammatory cues in the in vivo situation to promote pro-thrombotic responses by endothelial cells in the venous valve pocket.

overall_design:
To assess the impact on the transcriptome of hypoxia (sustained and intermittent) alone and combined with TNF, endothelial cells were stimulated for 48 hours in normoxia, sustained hypoxia or intermittent hypoxia in the absence or presence of TNF. RNA seq was performed on RNA isolated from the stimulated endothelial cells from three experiments.

**RAW data will be deposited in the Norwegian federated European Genome Archive (EGA)**

middle: J

first: Safak

last: Caglayan

first: Paulo

last: Czarnewski

first: John-Bjarne

last: Hansen

first: Omri

last: Snir


title: TIM4 enables large peritoneal macrophages to cross-present tumor antigens at early stages of tumorigenesis

city: Trieste

first: Sonal

last: Joshi

state: Trieste

address: Localita Padriciano, 99

department: Cellular Immunology

country: Italy

institute: International Center for Genetic Engineering and Biotechnology

summary: Cross-presentation of ingested tumor antigens by cells of the myeloid lineage is critical to shape anti-tumoral immune responses. However, the identity of cross-presenting macrophages, the cellular mechanism and the impact on anti-cancer CD8 T cell responses along tumor progression needs to be clarified. Here we examined the capacity of TIM4+ large peritoneal macrophages (LPM) to capture and cross-present antigens of incipient peritoneal metastasis in a model of ovarian cancer. We show that TIM4+ LPM, the most abundant myeloid population in the cavity, avidly engulf cancer cells and cross-present tumor-associated antigens, specifically at tumor inception. The phosphatidylserine (PS) receptor TIM4 promotes maximal uptake and triggers inflammatory and metabolic gene programs coupled to cytoskeletal remodeling and upregulation transcriptional signatures related to antigen processing. At the cellular levels, TIM4 is recruited with F-actin at the phagocytic cup and translocates in nascent phagosomes, controlling the kinetic of phagosomal acidification and cargo degradation. TIM4 deletion abrogates cross-presentation of tumor-associated antigens and blunts expansion of effector CD8 T cells at tumor inception. In addition, targeting tumor antigens to LPM by PS liposomes can trigger CD8 T cell activation. Together these results suggest that TIM4 enables LPMs to scan the antigenic content of incoming tumor cells to promote immune surveillance by CD8 T cells and, at defined temporal windows, may be exploited for therapeutic purposes.

overall_design: To understand phagocytosis-mediated transcriptional changes in LPM in presence or absence of scavenger receptor Tim4, we performed sequencing of LPM 24 hours after challenge with ID8 expressing ZsGreen and OVA. In detail, we sorted LPM (F4/80high MHCIIlow) from naïve WT and TIM4 KO mice, and LPM ZsGreen+ (F4/80high MHCIIlow ZsGreen+)from WT ID8 and TIM4 KO ID8 mice.

first: Federica

last: Benvenuti


title: A human hereditary cardiomyopathy shares a genetic substrate with bicuspid aortic valve

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: The complex genetics underlying human cardiac disease is evidenced by its heterogenous manifestation, multigenic basis and sporadic occurrence. These features have hampered disease modelling and mechanistic understanding. Here, we show that two structural cardiac diseases, left ventricular non-compaction (LVNC) and bicuspid aortic valve (BAV), can be caused by a combined set of inherited heterozygous mutations. We used CRISPR-Cas9 gene editing to generate mice harboring two mutations in the NOTCH ligand regulator MINDBOMB1 identified in LVNC families. One Mib1 mutation causes LVNC only in heteroallelic combination with a conditional Mib1 allele, while the other leads to BAV in a NOTCH-sensitized genetic background. These data suggest that the LVNC phenotype may be influenced by genetic modifiers present in these families, while valve defects are very sensitive to NOTCH haploinsufficiency. Whole-exome sequencing revealed single-nucleotide variants in the ASXL3, APCDD1 and TMX3, CEP192 and BCL7A genes, co-segregating with the MIB1 mutations and LVNC. We generated mice harboring the orthologous variants in the corresponding Mib1 backgrounds. Triple heterozygous Mib1 Apcdd1 Asxl3 mutants show LVNC, while quadruple heterozygous Mib1 Cep192 Tmx3;Bcl7a mice show BAV and other valve-associated defects. Biochemical assays suggest interactions between CEP192, BCL7A and NOTCH. Gene profiling of murine hearts and human induced pluripotent stem cell-derived cardiomyocytes reveals defective metabolic maturation. These findings provide evidence for a common genetic substrate for LVNC and BAV involving MIB1 and genetic modifiers

overall_design: RNA was isolated at E15.5 from ventricles of Control (Mib1flox/+; Tnnt2-Cre/+) and Mib1R530X/flox; Tnnt2-Cre/+, and WT and Mib1R530X/+ Asxl3M1361V/+ Apcdd1V150I/+ embryos. Samples were distributed in three pools of four pairs of ventricles per genotype. Tissue was homogenized with a pestle mechanical homogenizer and RNA was extracted using RNEasy Mini Kit (Qiagen, 74104). RNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit and sequenced in a HiSeq2500 Illumina sequencer using a 60 bp single end elongation protocol.

first: Marcos

last: Siguero

first: Donal

last: MacGrogan

first: Jose

middle: L


title: Spinal cord of SOD1*G93A transgenic mice treated with PF-04457845 or vehicle

city: Nagoya

first: Masahisa

last: Katsuno

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology

country: Japan

institute: Nagoya University Graduate School of Medicine

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

overall_design: Refer to individual Series


title: DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity

city: shanghai

first: Guosheng

last: Hu

state: shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai

institute: fudan university


title: Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism [ATAC-seq]

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Inhibitors of bromodomain and extra-terminal proteins (iBETs), including JQ-1, have been suggested as potential therapeutics against SARS-CoV-2 infection. However, molecular mechanisms underlying JQ-1-induced antiviral activity and its susceptibility to viral antagonism remain incompletely understood. iBET treatment transiently inhibited infection by SARS-CoV-2 variants and SARS-CoV, but not MERS-CoV. Our functional assays confirmed JQ-1-mediated downregulation of angiotensin-converting enzyme 2 (ACE2) expression and multi-omics analysis uncovered induction of an antiviral NRF-2-mediated cytoprotective response as an additional antiviral component of JQ-1 treatment. Serial passaging of SARS-CoV-2 in the presence of JQ-1 resulted in predominance of ORF6-deficient variants. JQ-1 antiviral activity was transient in human bronchial airway epithelial cells (hBAECs) treated prior to infection and absent when administered therapeutically. We propose that JQ-1 exerts pleiotropic effects that collectively induce a transient antiviral state that is ultimately nullified by an established SARS-CoV-2 infection, raising questions about the clinical suitability of iBETs in the context of COVID-19.

overall_design: We performed parallel RNAseq and ATACseq on Calu-3 cells that were either naive (untreated, uninfected), treated with DMSO and uninfected, treated with DMSO and infected, treated with JQ-1 and uninfected or treated with JQ-1 and infected.

first: Baxolele

last: Mhlekude

first: Dylan

last: Postmus

last: Weiner 3rd

first: Saskia

last: Stenzel

first: Francisco

last: Zapatero-Belinchón

first: Ruth

last: Olmer

first: Jenny

last: Jansen

first: Anja

last: Richter

first: Julian

last: Heinze

first: Nicolas

last: Heinemann

first: Barbara

last: Mühlemann

first: Simon

last: Schroeder

first: Terry

middle: C

last: Jones

first: Marcel

last: Müller

first: Christian

last: Drosten

first: Andreas

last: Pich

first: Volker

last: Thiel

first: Ulrich

last: Martin

first: Daniela

last: Niemeyer

first: Gisa

last: Gerold

first: Dieter

last: Beule

first: Christine

last: Goffinet


title: Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism [RNA-Seq]

first: January

last: Weiner

first: Baxolele

last: Mhlekude

first: Dylan

last: Postmus

last: Weiner 3rd

first: Saskia

last: Stenzel

first: Francisco

last: Zapatero-Belinchón

first: Ruth

last: Olmer


title: Bone dysplasia in Hutchinson-Gilford Progeria Syndrome is associated with dysregulated differentiation and function of bone cell populations.

city: Bethesda

first: Francis

last: Collins

address: 50 South Dr

department: NHGRI

institute: NIH

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature aging disorder that affects tissues of mesenchymal origin. Most individuals with HGPS harbor a de novo c.1824C>T (p.G608G) mutation in the gene encoding lamin A (LMNA), which activates a cryptic splice donor site resulting in production of a toxic protein termed “progerin”. Clinical manifestations include growth deficiency, lipodystrophy, sclerotic dermis, cardiovascular defects and bone dysplasia. In this study we utilized the LmnaG609G knock-in (KI) mouse model of HGPS to further define mechanisms of bone loss associated with normal and premature aging disorders. Newborn skeletal staining of KI mice revealed altered rib cage shape and spinal curvature, and delayed calvarial mineralization with increased craniofacial and mandibular cartilage content. MicroCT analysis and mechanical testing of adult femurs indicated increased fragility associated with reduced cortical and trabecular bone mass, recapitulating the progressive bone deterioration that occurs in HGPS patients. We investigated underlying mechanisms of bone loss in KI mice at the cellular level in bone cell populations. Formation of wild-type and KI osteoclasts from bone marrow-derived precursors was inhibited in the presence of KI osteoblast-conditioned media in vitro, suggesting an extrinsic factor(s) responsible for the decreased number of TRAcP-positive osteoclasts observed on KI trabecular surfaces in vivo. Cultured KI osteoblasts exhibited abnormal differentiation characterized by reduced capacity to deposit and mineralize  extracellular matrix and increased lipid accumulation compared to wild-type, providing a mechanism for the reduced mineral apposition and bone formation rates observed in vivo. Furthermore, quantitative analyses of KI transcripts confirmed upregulation of adipogenic genes both in vitro and in vivo. These data demonstrate that osteoblast phenotypic plasticity, rather than dysregulated bone remodelling, contributes to abnormal bone formation in HGPS mice.

overall_design: total RNA was extracted from femoral diaphyses of 8 week-old wild-type and homozygous LmnaG609G mice for gene expression comparison.

first: Wayne

last: Cabral

first: Chris

last: Stephan

first: Masahiko

last: Terajima

first: Abhirami

last: Thaivalappil

first: Owen

last: Blanchard

first: Urraca

last: Tavarez

first: Narisu

last: Narisu

first: Tingfen

last: Yan

first: Stephen

middle: M

last: Wincovitch

first: Yuki

last: Taga

first: Mitsuo

last: Yamauchi

first: Kenneth

last: Kozloff

first: Michael

middle: R

last: Erdos

middle: S


title: RNA-Seq result of Bulk spinal cord of SOD1*G93A transgenic mice treated with PF-04457845 or vehicle

first: Masahisa

last: Katsuno

summary: SOD1*G93A transgenic mice were treated with PF-04457845 (a FAAH inhibitor)or vehicle . PF-04457845 extended survival of SOD1*G93A transgenic mice and resucued loss of motor neurons.

overall_design: SOD1*G93A transgenic mice were treated with PD-04457845(1mg/kg/day) or vehicle by chow from age of week 8 until endpoint

first: Daisuke

last: Ito

first: Madoka

last: Iida

first: Yohei

last: Iguchi


title: The androgen receptor does not directly regulate the transcription of DNA damage response genes.

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: The clinical success of combined androgen deprivation therapy (ADT) and radiation therapy (RT) in prostate cancer (PCa) created interest in understanding the mechanistic links between androgen receptor (AR) signaling and the DNA damage response (DDR). Convergent data have led to a model where AR both regulates, and is regulated by, the DDR. Integral to this model is that the AR regulates the transcription of DDR genes both at steady state and in response to ionizing radiation (IR). In this study, we sought to determine which immediate transcriptional changes are induced by IR in an AR-dependent manner. Using PRO-seq to quantify changes in nascent RNA transcription in response to IR, the AR antagonist enzalutamide, or the combination of the two, we find that enzalutamide treatment significantly decreased expression of canonical AR target genes but had no effect on DDR gene sets in PCa cells. Surprisingly, we also found that the AR is not a primary regulator of DDR genes either in response to IR or at steady state in asynchronously growing PCa cells. Our data indicate that the clinical benefit of ADT and RT is not due to the direct regulation of DDR gene transcription by AR.

overall_design: LNCaP cells were treated with Enzalutamide and/or 6 Gray ionizing radiation and collected for PRO-seq

first: Daniel

last: Gioeli


title: Single cell RNA-Seq result of  spinal cord of SOD1*G93A transgenic mice treated with PF-04457845 or vehicle

overall_design: SOD1*G93A transgenic mice were treated with PD-04457845(1mg/kg/day) or vehicle by chow from age of week 8 until endpoint. The spinal cords at the age of 16 weeks were analyzed.

first: Tomohiro

last: Akashi

first: Kunihiko

last: Hinohara


title: Identification of GLYMA.13G153200 binding sites in soybean early maturation stage embryos.

status: Public on Sep 16 2023

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.13G153200 in early maturation stage embryos using ChIP-seq.

overall_design: Identification of GLYMA.13G153200 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina NovaSeq 6000 platform.

first: Julie

last: Pelletier

first: Leonardo

last: Jo

first: Rie

last: Uzawa

first: Min

last: Chen

first: Robert

middle: B

last: Golberg


title: Non-coding small RNA expression analysis of rat pancreatic acinar cells(AR42J) treated with sodium taurocholate

city: Beijing

first: Bo

last: Gao

address: No.11 Xizhenmen South Street

department: General Surgery

institute: Peking University People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute pancreatitis (AP) is a common digestive disorder with high morbidity and mortality. At present, the pathogenic mechanisms of AP remain unclear. Pancreatic acinar intracellular trypsinogen activation is considered to be an important cause of AP and is an important event in the early stages of AP. The activation of trypsinogen is a key factor for the pancreas to maintain normal function and that the abnormal activation of trypsinogen in pancreatic acinar cells is an initiating factor for the occurrence of AP. In the past decade, microRNA-related research results suggest that small non-coding RNAs play an important role in AP. Recently, endogenous transfer RNA-derived small RNA (tsRNA), a newly identified non-coding small RNA, is reported to be associated with multiple diseases. tsRNAs can be broadly classified into two main groups: tiRNAs (tRNA halves) and tRFs (tRNA-derived fragments). tiRNAs are produced by specific cleavage in the anticodon loop under various stress conditions (29-50 nucleotides). tRFs are separated to 4 subtypes by their sites of origin in pre-tRNA or mature tRNA, and generally shorter than tiRNAs (16-28 nucleotides). Similar to the function of microRNA, tsRNA can inhibit their functions by binding to target genes. However, the role of tsRNA in regulating AP pathogenesis has not been investigated. In this experiment, sodium taurocholate was used to treat the rat pancreatic acinar cell (AR42J) to establish the AP-related intracellular activation of trypsinogen model. Then we used RNA sequencing to identify the differentially expressed non-coding small RNAs including microRNA and tsRNA in the cell model.

overall_design: Non-coding small RNA profiles from AR42J cell line treated with 200 μM sodium taurocholate for 30min and their untreated controls were sequenced in an Illumina NextSeq.

first: Dongbo

last: Xue


title: Neuronal MML-1/MXL-2 regulates autophagic and peroxidase activity via glutamate transporter to prolong lifespan

city: Suita

first: Tatsuya

last: Shioda

state: Osaka

address: Yamadaoka 1-1

institute: Osaka University

summary: Accumulating evidence has demonstrated the presence of inter-tissue communication regulating systemic aging, but the underlying molecular network has not been fully explored. We and others previously showed that two basic helix-loop-helix transcription factors, MML-1 and HLH-30, are required for lifespan extension in several longevity paradigms, including germline-less Caenorhabditis elegans. However, it is unknown what tissues these factors target to promote longevity. Here, using tissue-specific knockdown experiments, we found that MML-1 and its heterodimer partners MXL-2 and HLH-30 act primarily in neurons to extend longevity in germline-less animals. Neuronal functions of MML-1/MXL-2 and HLH-30 are also essential to prevent aging in non-neuronal tissues, including muscle and the intestine. Interestingly, however, both the temporal requirement and the downstream function of MML-1 in neurons were distinct from those of HLH-30. MML-1 was active early, while HLH-30 functioned later in life to sustain longevity in germline-less animals. Moreover, neuronal RNA interference (RNAi)-based transcriptome analysis revealed that the glutamate transporter GLT-5 is a novel downstream target of MML-1 but not HLH-30. Furthermore, the MML-1–GTL-5 axis in neurons is critical to prevent an age-dependent collapse of proteostasis and increased oxidative stress through autophagy and peroxidase MLT-7, respectively, in long-lived animals. Collectively, our study revealed that systemic aging is regulated by a novel molecular network involving neuronal MML-1 function in both neural and peripheral tissues.

overall_design: Neuronal knockdown of mml-1 or mxl-2 in germline-less glp-1 nematodes

first: Shuhei

last: Nakamura

first: Tamotsu

last: Yoshimori


title: Identification of GLYMA.04G093300 and GLYMA.06G314400 binding sites in soybean cotyledon stage embryos.

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.04G093300 and GLYMA.06G314400 in cotyledon stage embryos using ChIP-seq.

overall_design: Identification of GLYMA.04G093300 and and GLYMA.06G314400 binding sites in soybean embryos at the cotyledon stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 7 samples were sequenced using the Illumina NovaSeq 6000 platform.


title: Effect of thermoneutral housing conditions on the hepatotoxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in male C57BL/6 mice

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

summary: Typical rodent toxicology experiments are performed at human thermoneutral temperatures (thermostandard;  TS = 20 – 24° C). Reports have indicated that investigation of metabolic endpoints at mouse thermoneutral temperatures (TNM =  28 – 30° C) improves translation to humans when they are not chronically cold-stressed. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been shown to dose-dependently induce metabolic disease in mice at  including liver steatosis, steatohepatitis, and periportal fibrosis. To test whether dose-dependent hepatotoxicity caused by TCDD is altered by housing temperature we gavaged male C57BL/6 mice every 4 days for 28 days with TCDD (0.03 – 30 µg/kg) or sesame oil vehicle at TS and TNM. Mice held at TNM exhibited less marked relative liver weight gain and histopathology with milder steatosis, immune cell infiltration, hepatocellular hypertrophy, and an absence of biliary hyperplasia compared to mice held at Ts. Mice housed in both temperature conditions had a similar dose-dependent decrease in total cholesterol, but mice at TS had more elevated serum ALT and decreased glucose and triglycerides at 30 µg/kg TCDD. Mice at TNM had fewer differentially expressed genes (DEGs) than TS, although most of the DEGs at TNM were shared with the DEGs at TS. Benchmark Dose (BMD) analysis performed on the DEGs revealed largely similar trends, however, the most induced DEGs, which constituted some of the AhR-battery genes (e.g. Cyp1a1), exhibited lower BMDs at TNM.  Moreover, at 30 µg/kg TCDD both sets of mice had increased pro-inflammatory cytokines. The only cytokine which was clearly different between the two sets of mice irrespective of dose was VEGF-A. Overall, mice held at TNM showed reduced severity at equivalent doses to mice held at TS.

overall_design: Beginning on post-natal day (PND) 30, male C57BL/6 mice were repeatedly gavaged at 28° C every 4 days for 28 days with some dose of 2,3,7,8-tetrachlorodibenzo-p-dioxin (0.03 - 30 µg/kg TCDD) or sesame oil vehicle (n = 5 per dose) and sacrificed on PND 58 with CO2. Gavaging and tissue collection always occurred between ZT0 and ZT3. Tissues were flash frozen in liquid nitrogen and stored at -80°C. For total RNA extraction using trizol, 100 mg was used per liver sample. Only samples which passed Nanodrop and RIN quality control were used. 150 bp paired-end RNA reads were sequenced using a NovoSeq 6000.

first: Warren

last: Sink

first: Rance

last: Nault


title: LncRNA MSAR stabilizes c-Myc to promote pancreatic cancer malignancy

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: We identify a collection of candidate lncRNAs interacted with c-Myc in pancreatic cancer and show for the first time that an lncRNA among them, which is named as c-Myc-stabilizing and activating RNA (MSAR), promotes pancreatic cancer proliferation and metastasis through c-Myc. MSAR enhances the interaction of c-Myc and SNIP1. These findings shed light on the pro-tumorigenic role of MSAR and might provide a novel therapeutic strategy for indirect targeting c-Myc in PDAC.

overall_design:
We identified lncRNAs interacted with c-Myc protein in PANC-1 cell lines using RNA immunoprecipitation sequencing (RIP-Seq) experiment. To explore the molecular mechanism underlying the effects of MSAR on PDAC cell phenotypes, we performed RNA-seq analysis in MSAR-silenced and their control PANC-1 cells. We further performed cross-linking and immunoprecipitation sequencing (CLIP-seq) of SNIP1 to explore the mechanism underlying the interaction of SNIP1 and MSAR.
Comparative gene expression profiling analysis of RNA-seq data in MSAR-overexpression and their control PANC-1 cells.

first: Jian

last: Zheng

first: Guandi

last: Wu


title: Genome-wide Identification  of Fusarium graminearum-Responsive lncRNAs in Triticum aestivum

city: Nanjing

first: Xiaoxin

last: Duan

address: No.1 Weigang, Xuanwu District

institute: Nanjing Agricultural University

summary: We identified the long non-coding RNAs (lncRNAs) in Triticum aestivum infected with Fusarium graminearum by high-throughput RNA sequencing. More than 393 million clean reads were obtained from Illumina Hiseq 4000 system and 126,391 transcripts was identified as high-confidence lncRNAs in T. aestivum against F. graminearum by an integrated approach. Already well over 4,130 of the total 4,276 differentially expressed lncRNAs were specifically expressed at 12 h post-inoculation (hpi), but only 89 of these were specifically expressed at 24 hpi, indicating that the initial stage was the crucial stage for lncRNA-mediated gene regulation of wheat defense against F. graminearum. Target analysis showed the lncRNAs participated in various biological stress processes.

overall_design: RNA profiles of wheat post-inoculated with Fusarium graminearum 12h and 24h

first: Xiush

last: Song


title: The Glucocorticoid Receptor couples endocrine signalling to synaptic activity dependent gene transcription via a metabotropic glutamate receptor-regulated pathway in zebrafish - BisPCR2 data

city: Sheffield

first: Dheemanth

last: Subramanya

address: Firth Court, Western Bank

department: Department of Biomedical Science

country: United Kingdom

institute: University of Sheffield

type: Methylation profiling by high throughput sequencing

summary: The Glucocorticoid Receptor (GR) co-ordinates metabolic and behavioural responses to stressors. We hypothesised that GR influences behaviour by modulating epigenetic and transcriptional processes in the brain. Using the zebrafish as a model organism, the brain methylomes of wild-type and grs357 mutant adults were analysed and GR-sensitive, differentially methylated regions (GR-DMRs) were identified. DMRs linked to genes with biologically salient functions were selected for confirmatory deep sequencing analysis in wild-type and GR mutant 5dpf larval heads, using the BisPCR2 technique (Bernstein et al., 2015). Our results demonstrate that the genes fkbp5 and aplp1 exemplify two distinct modes of GR-regulated, glucocorticoid-responsive DNA methylation in the brain.

overall_design: 96 larval head BisPCR2 samples (24 GRWT, 24 GRWT-BM, 24 GRmut,  24 GRmut-BM)


title: Expression of Human Lung Biopsies Before and at 6 hours of EVLP

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary:
Ex vivo lung perfusion restores normothermia, ventilation and circulation to donor lungs, typically after a period of cold ischemia. This allows donor lungs to be evaluated prior to transplantation. We used microarrays to study the biological response of human lungs to Ex Vivo Lung Perfusion.
These are a subset of samples previously described in the paper: Yeung, Jonathan C., et al. Towards donor lung recovery—gene expression changes during ex vivo lung perfusion of human lungs. American Journal of Transplantation 18.6 (2018): 1518-1526.

overall_design: Samples were collected at the end of cold ischemia (CIT). Lungs were then placed on the EVLP circuit and a second sample was collected at 6 hours of EVLP.

first: Aaron

last: Wong

first: Jonathan

last: Yeung

first: Gary

middle: D

last: Bader

first: Claudia

last: Dos Santos

first: Xiaohui

last: Bai

first: Yubo

last: Wang

first: Shaf

last: Keshavjee

first: Mingyao

last: Liu


title: RNA-seq analysis identifies differentially expressed genes regulated by acidification exposure on HNEpC cells

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

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

summary: In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of  Human Nasal Epithelial Cells (HNEpC) (C-12620, PromoCell, Heidelberg, Germany) after exposure to acidification for 6 hours.

overall_design: Comparison of mRNA expression profiles between acidification (PH6.0) exposed HNEpC cells  and control cells incubated under normal PH conditions (PH7.4).

first: Weitian

last: Zhang


title: Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism

first: January

last: Weiner


title: Gene expression at the transcriptional level of the white-rot fungus Lenzites gibbosa during wood degradation.

city: Harbin

first: Yu Jie

last: Chi

state: Heilongjiang

address: Hexing road, No.26; Xiangfang district

department: School of Forestry

institute: Northeast Forestry University

summary:
To determine the wood degradation mechanism and its key genes of Lenzites gibbosa, we sequenced 15 transcriptomes of mycelial samples under woody environments at 3, 5, 7, and 11 d (D3, D5, D7, and D11) and non-woody environments (CK).
All the transcripts were annotated as much as possible in eight databases to determine their function. The key genes and biological processes, relating to wood degradation, were predicted and screened. A total of 2069 differentially expressed genes (DEGs) were obtained in ten differential groups.
Comparing wood with non-wood treatment conditions, the key genes were those participating in oxidation-reduction process, they were oxidoreductases and peroxidases genes, and their regulators genes; these genes mainly focused on the three biological processes of carbohydrate metabolism, lignin catabolism, and secondary metabolites biosynthesis, transport and catabolism. The mostly enriched subcategories in molecular function were oxidoreductase activity, peroxidase activity, and heme binding in GO annotation. One cellulose and hemicellulose degradation pathway and seven pathways related to lignin-derived aromatic compounds degradation or late lignin degradation were found.
In conclusion, during the process of L. gibbosa growing on wood, gene expression at the transcriptional level indicated that lignin catabolism and hyphal growth were promoted, but the metabolism of carbon and carbohydrates including cellulose in lignocellulose in overall trend was inhibited to some extent. The results have important reference value for the study of degradation mechanism of wood white rot.

overall_design: The tested strain was cultured under wood sawdust treatment (3d, 5d, 7d, and 11d) and non-woody control (0d) on LNAS liquid medium. Total RNAs were extracted from different mycelia and transcriptome sequencing was performed, the transcriptome libraries and gene expression profile related to the lignocellulose degradation of the white rot fungus were obtained, which provides a basis for the degradation mechanism of wood white rot.

first: Y

first: J


title: DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (ChIP-seq II)

first: Guosheng

last: Hu

summary: DDB1 is typically recognized as a component of the Cullin4 (CUL4)-RING E3 ubiquitin ligase complex. Here, we show that DDB1 functions independently of CUL4 to promote adipogenesis and diet-induced obesity. In contrast to depletion of CUL4A or CUL4B that stimulates adipogenesis, lack of DDB1 dramatically suppresses the process. Re-introduction of a DDB1 mutant that lacks the binding ability to CUL4A or CUL4B fully restores adipogenesis in DDB1-deficient preadipocytes. Furthermore, while inducibly knocking out Cul4a or Cul4b in mice aggravates diet-induced obesity, Ddb1+/- mice are lean on high-fat diet. Mechanistically, by binding the bromodomain-containing histone reader BRWD3, DDB1 is recruited to acetylated histones in the proximal promoters of immediate-early response genes, where it facilitates the release of paused RNA polymerase II (Pol II) and activates the transcription of these genes. Our findings have thus uncovered a mechanism of activating the transcriptional cascade in adipogenesis by DDB1-mediated release of paused Pol II.

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying DDB1 in gene transcription regulation.

first: Tong-Jin

last: Zhao

first: Xu

first: Hao-Yan

first: Guo-Sheng

first: Huiling

last: Guo

first: Min

first: Ying

last: Chen

first: Wen

first: Peng

last: Li


title: DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (RNA-Seq)


title: Real-time quantitative PCR analysis of rat's brain miRNAs

status: Public on Sep 15 2023

city: Moscow

first: Diana

last: Salikhova

address: Miklukho-Maklaya, 8

department: Institute of molecular and cellular medecine

country: Russia

institute: RUDN University

summary: We investigated the therapeutic effect of the extracellular vesicles secreted by glial progenitor cells (GPC-EV) derived from human induced pluripotent stem cell in a traumatic brain injury model. The injury was modeled using the dosed concussion to the open brain method. The male Wistar rats were performed traumatic brain injury (TBI), and after 24 hours animals were randomly divided into two groups: group 1  — rats with intranasal administration of PBS (control), and group 2  — rats with similar administration of extracellular visicles (EV) derived from glial progenitor cells. miRNA PCR analysis of brain tissues ( cortex, striatum, hippocampus) were performed on postoperative day 7 to investigate miRNA associated with apoptosis, and inflammation.

overall_design: qPCR miRNA expression profiling.  The brain tissue was collected at 7 day post-TBI, as indicated in the summary.


title: Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8

first: Jing

last: He

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: School of Medicine

institute: Tsinghua University

summary: We report the presence of many long non-coding RNAs (lncRNAs) which were specifically expressed in the germ cells during human gonadal development by single-cell profiling, and the functional characterization of one divergent lncRNA, LNC1845. Functional dissection using in vitro differentiation of human pluripotent stem cells to germ cells revealed the regulatory role of LNC1845 on a transcription factor essential for ovarian follicle development, LHX8. Molecular characterization elucidated that LNC1845 upregulated LHX8 expression by modulating the levels of histone modifications, H3K4me3 and H3K27Ac. Our study provides a comprehensive analysis of lncRNAs in developing human germ cells and a concrete example of lncRNA acting as a cis regulator during female germ cell development.

overall_design: We checked the differences between ESCs, WT PGCLCs and LNC1845KO PGCLCs, LHX8 OE H9 cells by RNA-seq, and examined 2 different histone modifications, H3K4me3 and H3K27Ac, in PGCLCs from WT H9, LNC1845 KO and OE cell lines, and performed FOXP3 ChIP-Seq in FOXP3 OE 293FT cells.


title: Comparison of mRNA expression in white adipose tissue from LLC tumor-bearing mice and controls

first: Chenyang

last: Jin

address: 180 Fenglin Road

department: Department of General Surgery

institute: Zhongshan Hospital of Fudan University

summary: Cancer-associated cachexia (CAC) is a wasting syndrome caused by malignant tumors. Fat loss plays a significant role in the pathophysiology of cancer-associated cachexia. The mechanism of fat loss in CAC includes enhancement of lipolysis, inhibition of lipogenesis and browning of white adipose tissue. In order to discover potentially functional genes in white adipose tissue of CAC,  we used transcriptome sequencing technology to find research-valuable genes in white adipose tissue (WAT) of CAC rodent model. C57/bl6 mice with LLC tumors were used as the in vivo model for CAC, while normal mice subcutaneously injected with phosphate buffer solution were used as the control group. Overall, our data revealed genes that were differentially expressed in the white adipose tissue of LLC tumor-bearing mice, providing a molecular framework for the investigation into CAC fat loss.

overall_design: We harvested epididymal white adipose tissue(eWAT) from 3 LLC tumor-bearing mice labeled as samples TE1 to TE3. In addition, eWAT was collected from 3 control mice labeled as samples E1 to E3.

first: Qingyang

last: Meng

first: Xiangyu

last: Sui


title: A genetically defined mPFC-thalamic circuit underlies pain chronicity

city: Kunming

first: Chao

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: Chronic pain is a major health care problem with great social and economic consequences. Although the medial prefrontal cortex (mPFC) and the thalamus have been implicated in regulating pain, whether and how these regions may involve in pain chronification process have remained largely unknown. Here, we show that Foxp2+ neurons in mPFC, which are corticothalamic (CT) neurons representing the major mPFC output to thalamus, are deactivated in chronic inflammatory pain. Interestingly, prolonged, but not short-term, inactivation of the Foxp2+ neurons in mPFC increases the sensitivity to noxious stimulations. Conversely, chemogenetic activation of this neuronal cluster induces robust antinociceptive effects in both naïve mice and mice with chronic inflammatory pain. Furthermore, we found that the mPFC Foxp2+ neurons project to several thalamic relay nuclei and that activation of the mPFC to the parataenial nucleus of thalamus (PTN) circuit relieves pain. Finally, RNA-seq of the mPFC Foxp2+ neurons revealed that many genes related to neuronal activity are dysregulated in mice with chronic inflammatory pain. Collectively, our studies revealed that Foxp2+ neurons in mPFC that project to thalamus play a critical role in somatosensory processing and pain chronification.

overall_design: 4 weeks after the bilateral injection of AAV expressing KASH-GFP in the mPFC of Foxp2-Cre mice, the mice were euthanized by inhalation of CO2 and the brains were rapidly removed to a matrix and mPFC was dissected with scalpals. The 3 replicates are collected for each pain and control condition.

first: Guoguang

last: Xie

first: Yi


title: DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (ChIP-Seq)

first: Guosheng

address: 2005 Songhu Road, Yangpu District, Shanghai

institute: fudan university

first: Tong-Jin

last: Wang


title: Identification of GLYMA.13G153200 binding sites in soybean mid-maturation stage embryos.

first: John

last: Harada

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.13G153200 in mid-maturation stage embryos using ChIP-seq.

overall_design: Identification of GLYMA.13G153200 binding sites in soybean embryos at the mid-maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates, using two different antibodies.  A total of 6 samples were sequenced using the Illumina NovaSeq 6000 platform.

first: Julie

last: Pelletier

first: Leonardo

last: Jo

first: Rie

last: Uzawa

first: Robert

last: Golberg


title: Single-cell RNA sequencing of coronary perivascular adipose tissue

first: mengxia

last: fu

address: xicheng road

institute: fuwai hospital

summary: Perivascular adipose tissue (PVAT) is vital for vascular homeostasis and PVAT dysfunction is associated with increased atherosclerotic plaque burden.

overall_design:
We performed single-cell RNA sequencing of the stromal vascular fraction of coronary PVAT from three groups of heart transplant recipients
>>>Submitter statement concerning raw data availability: 'Raw sequence data were provided at China Genomic Sequence Archive (GSA). The accession number will be included once the paper is accepted'<<<<

first: Mengxia

last: Fu

first: Songren

last: Shu

first: Wei

last: Feng

first: Jiangping

last: Song


title: Sequencing of osteoclast precursor cells treated with or without DKK1

first: Xin

last: Niu

address: 500 Dongchuan Road

institute: East China Normal University

summary: DKK1 recruits osteoclast precursor cells in a concentration gradient-dependent manner. In order To clarify the transcriptome changes when osteoclast precursor cells are recruited by DKK1.We compared the expression profiles of osteoclast precursor cells with or without DKK1 stimulation.

overall_design: RNA-Seq of osteoclast precursor cells treated with or without DKK1 (200 ng/ml) in 3 hours.

first: Qin

last: Qin

first: Jian

last: Luo


title: High-throughput sequencing to investigate the expression and potential role of differentially expressed microRNAs in ischemia–reperfusion myocardial cells

city: Taiyuan

first: Senjie

last: Li

address: Jiefang South Road

institute: first hospital of shanxi medical university

summary: MicroRNAs are closely associated with the pathogenesis of various diseases, but the relationship between miRNAs and myocardial ischemia–reperfusion (I/R) injury remains unclear. Therefore, we aimed to explore the role and function of miRNAs in I/R. We established hypoxia/reoxygenation (H/R) model to detect differentially expressed miRNAs using high-throughput sequencing in rat myocardial cell. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment were used to analyse the potential functions and signaling pathways of target genes. We further assessed the expression of miRNA, iron ions, reactive oxygen species, and ferroptosis markers. In the study, 113 differentially expressed miRNAs, comprising 76 and 37 up-regulated and down-regulated genes, respectively, were identified. These findings offer a novel perspective on I/R regulation, down-regulation of miRNA expression inhibits ferroptosis and alleviates myocardial damage.The specific mechanisms underlying the actions of it require further study.

overall_design: To identify differentially expressed miRNAs, we utilized high-throughput sequencing in rat myocardial cell hypoxia/reoxygenation model (H/R) model. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to determine the potential functions and signaling pathways of target genes


title: Single-cell RNA-Seq reveals novel myofibroblast charactering epithelial features in the mammary gland of dairy cows

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: Our study is the first one to investigate the heterogeneity of bovine mammary gland (MG) and to construct a bovine MG cell atlas by using scRNA-Seq. Our findings provide novel insights into lactation biology of bovine MG. We identified and validated three mature luminal epithelial cells that are involved in the different lactation processes as well as in the immune response. In addition, a novel myofibroblast showing potential differentiation into luminal epithelial cells was identified. The IGF pathway system signal may play an important role in the F13-L5 transition, and the hormone sensing luminal cell (L1), luminal progenitor cells (L2, L3) and immune-sensing luminal cell are correlated with the process.

overall_design: Single-cell RNA sequencing was applied to investigate the transcriptome of 24,472 high-quality MG cells isolated from newborn and adult cows.

first: Fengfei

last: Gu

first: Hui-Zeng


title: Rat epiblast-derived pluripotent stem cells produce functional germ cells

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

summary: In mammals, pluripotent cells transit through a continuum of distinct molecular and functional states en route to initiating lineage specification. Capturing pluripotent stem cells (PSCs) mirroring in vivo pluripotent states provides accessible in vitro models to study the pluripotency program and mechanisms underlying lineage restriction. Here, we develop optimal culture conditions to derive and propagate post-implantation epiblast-derived PSCs (EpiSCs) in rats, a valuable model for biomedical research. We show that rat EpiSCs can be reset toward the naïve pluripotent state with exogenous Klf4, albeit not with the other five candidate genes (Nanog, Klf2, Esrrb, Tfcp2l1, and Tbx3) effective in mice. Finally, we demonstrate that rat EpiSCs retain competency to produce authentic primordial germ cell-like cells that contribute to functional gametogenesis leading to the birth of viable offspring. Our findings in the rat model uncover conserved principles underpinning pluripotency and germline competency across species.

overall_design: RNA-seq of rat embryonic stem cells (ESCs), ESC-like cells (ESCLCs), epiblast stem cells (EpiSCs), epiblast-like cells (EpiLCs), and primordial germ cell like cells (PGCLCs).

first: Kenyu

last: Iwatsuki

first: Toshihiro


title: Effect of FOXA1 knockdown on gene expression in sulfasalazine-resistant OSC19SSZR cells

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary: High-throughput sequencing was performed to analyze genes regulated by the transcription factor FOXA1 in OSC19SSZR cells, a sulfasalazine-resistant oral squamous cell carcinoma cell line.

overall_design: Sulfasalazine-resistant OSC19SSZR cells were transfected with Control or FOXA1 siRNA, and total RNA was purified 48 hours later. Then, gene expression analysis was performed with RNA-sequencing.


title: Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States

city: Philadelphia

first: Jianfu

last: Zhou

state: Pennsylvania

address: 3400 Civic Center Boulevard, 12th floor

institute: University of Pennsylvania

summary: Mouse models have been widely used to understand kidney disease pathomechanisms and play an important role in drug discovery. However, these models have not been systematically analyzed and compared. We analyzed single-cell RNA sequencing data (36 samples) and bulk gene expression data (42 samples) from 18 commonly used mouse kidney disease models. We compared single-nucleus RNA sequencing data from a mouse diabetic kidney disease model with data from patients with diabetic kidney disease and healthy controls. We generated a uniformly processed mouse single-cell atlas containing information for nearly 300,000 cells, identifying all major kidney cell types and states. Our analysis revealed that changes in fractions of cell types are major drivers of differences in bulk gene expression. Although gene expression changes at the single-cell level were mostly model-specific, different disease models showed similar changes when compared at a pathway level. Tensor decomposition analysis highlighted the important changes in proximal tubule cells in disease states. Specifically, we identified important alterations in expression of metabolic and inflammation-associated pathways. The mouse diabetic kidney disease model and patients with diabetic kidney disease shared only a small number of conserved cell type-specific differentially expressed genes, but we observed pathway-level activation patterns conserved between mouse and human diabetic kidney disease samples. This study provides a comprehensive mouse kidney single-cell atlas and defines gene expression commonalities and differences in disease states in mice. The results highlight the key role of cell heterogeneity in driving changes in bulk gene expression and the limited overlap of single-cell gene expression changes between animal models and patients, but they also reveal consistent pathway-level changes.

overall_design: n=6 mouse kidney scRNA-seq samples: n=2 control, n=1 transgenic overexpression of Notch1, n=2 transgenic overexpression of PGC1a, n=1 Esrra KO

first: Amin

last: Abedini

first: Michael

last: Balzer

first: Rojesh

last: Shrestha

first: Poonam

last: Dhillon

first: Hongbo

last: Liu

first: Hailong

last: Hu

first: Katalin

last: Susztak


title: Changes in mRNA expression in lung tissue after long-term supplementation with an increased dose of cholecalciferol.

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

summary: Maintaining an appropriate concentration of vitamin D is essential for the proper functioning of the body regardless of age. Nowadays, there are more and more indications that vitamin D supplementation at higher than standard doses may show protective and therapeutic effects. Our study identifies differences in the body's response to long-term supplementation of cholecalciferol at an increased dose. Two groups of pigs were used in the experiment. The first group received a standard dose of cholecalciferol (grower- 2000 and finisher- 1500 IU/kg feed), and the second group received an increased dose (grower- 3000 and finisher- 2500 IU/kg feed). The animals were slaughtered when they reached breeding maturity. Then the lung tissue was collected from the animals. The material was used for mRNA sequencing. The results of mRNA sequencing showed a significant change in the expression of 195 genes. Functional analysis using the KEGG database showed that increased cholecalciferol supplementation significantly activated 42 pathways. Most of the activated pathways is associated with metabolism.

overall_design: The libraries for mRNA-seq were prepared using the QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Austria). Quantitative evaluation of the prepared cDNA libraries was performed using Qubit (Thermo Scientific™, USA), while qualitative evaluation was assessed using Tapestation 2200 device (Agilent, USA). Sequencing of mRNA pooled libraries (75 bp single read) was performed using Nextseq 5500 device (Illumina, USA). The libraries were prepared for sequencing according to the Standard Normalization Method from NextSeq 500 and NextSeq 550 Sequencing Systems-Denature and Dilute Libraries Guide protocol. We used a 2nM starting library concentration and a 10% PhiX addition.

first: Maria

last: Oczkowicz

first: Tomasz

last: Szmatoła


title: Surveillance of 3’ mRNA cleavage during transcription termination requires CF IB/Hrp1

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

department: Molecular Genetics

institute: Georg-August Universität Göttingen

summary: Comparison of cytoplasmic 3' elongated transcripts in hrp1-1 and wild type.

overall_design: To invesatigate 3' elongated transcripts in the cytoplasm of the mutant strain hrp1-1 we created a cytoplasmic and total fraction of wild type and hrp1-1 cells. RNA was isolated and sequenced.

first: Jing

last: Li

first: Luisa

last: Querl

first: Ivo

last: Coban


title: HIGHLY PHAGOCYTIC LIPID-ASSOCIATED MACROPHAGES (LAMs) ARE INCREASED 2 IN COLONIC LAMINA PROPRIA IN OBESITY

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Little is known about the effects of high fat diet (HFD)-induced obesity on resident colonic lamina propria (LP) macrophages (LPMs) function and metabolism. Here, we report that obesity and diabetes resulted in increased macrophage infiltration in the colon. These macrophages exhibited the residency phenotype CX3CR1hiMHCIIhi, and were CD4-TIM4-. During HFD, resident colonic LPM exhibited a lipid metabolism gene expression signature that overlapped that used to define lipid associated macrophages (LAMs). Via single cell RNA sequencing, we identified a sub-cluster of macrophages, increased in HFD, that were responsible for the LAM signature. Compared to other macrophages in the colon, these cells were characterized by elevated glycolysis, phagocytosis and efferocytosis signatures. CX3CR1hiMHCIIhi colonic resident LPMs had fewer lipid droplets (LD) and decreased triacylglycerol (TAG) content compared to equivalent cells in lean mice, and exhibited increased phagocytic capacity, suggesting that HFD induces adaptive responses in LPMs to limit bacterial translocation.

overall_design: Obesity was induced by ad libitum feeding of C57/BL6 CX3CR1 GFP heterozygous mice for 12 weeks with irradiated high fat diet (Rodent Diet 60% kcal from fat). Control diet (chow) containing 24% protein, 47.5% 438 carbohydrate, and 4.9% fat, was given to age and sex matched animals as a control group. Lamina propria cells from 4 animals from each group were prepared for cell sorting and incubated in anti-CD16/32, stained with Live/Dead, and fluorochrome-conjugated antibody to CD45, CD11b, CD64 , MHCII.  FACS-sorted CX3CR1hi MHCIIhi LPMs using a BD FACS ARIATM III, were prepared for RNA extraction.

first: Angela

last: Castoldi

first: David

middle: E

last: Sanin


title: Host derivation of Sindbis virus influences mammalian type 1 interferon response to infection

city: Bloomington

first: Richard

last: Hardy

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: Arboviruses are defined by their ability to replicate in both mosquito vectors and mammalian hosts. There is good evidence that arboviruses “prime” their progeny for infection of the next host, such as differential glycosylation of their outer glycoproteins or packaging of host ribosomal subunits. We and others have previously shown that mosquito derived viruses more efficiently infect mammalian cells than mammalian derived viruses. These observations are coherent with arboviruses acquiring host-specific adaptations, and we hypothesized that virus derived from either the mammalian host or mosquito vector will elicit different responses when infecting the mammalian host. Here we perform an RNA-sequencing analysis of the transcriptional response of Human Embryonic Kidney 293 (HEK-293) cells to infection with either mosquito (Aedes albopictus, C7/10) or mammalian (Baby Hamster Kidney, BHK) derived Sindbis virus (SINV). We show that C7/10 derived virus infection leads to a more robust transcriptional response in HEK-293s as compared to infection with the BHK derived virus. Surprisingly, despite more efficient infection, we found an increase in interferon-β (IFN-β) and interferon stimulated gene (ISG) transcripts in response to C7/10 derived virus infection versus BHK derived virus infection. However, translation of interferon stimulated genes was lower in HEK-293s infected with C7/10 derived virus, starkly contrasting with the transcriptional response. This inhibition of ISG translation is reflective of a more rapid overall shut-off of host cell translation following infection with C7/10 derived virus. Finally, we show that C7/10 derived virus infection of HEK-293 cells leads to elevated levels of phosphorylated eukaryotic translation elongation factor-2 (eEF2), identifying a potential mechanism leading to the more rapid shut-off of host translation. We postulate that the rapid shut-off of host translation in mammalian cells infected with mosquito derived virus acts to counter the IFN-β stimulated transcriptional response.

overall_design:
To investigate factors contributing to the more rapid growth kinetics in mammalian cells of alphaviruses derived from mosquito cells we infected HEK293 (human) cells with Sindbis virus from mosquito and mammalian cells. We performed comparative gene expression analysis using RNAseq data from 8 hours post infection with viruses of mosquito (Tet C7/10) and mammalian (BHK) derivation.
We performed comparative gene expression analysis using RNAseq data from 8 hours post infection of HEK293 cells with viruses of mosquito cells (Tet C7/10) and mammalian cells (BHK), as well as Mock infected HEK293 cells.

first: John

last: Crawford

first: Aaron

last: Buechlein

first: Douglas

last: Rusch

middle: W


title: Effects of temperature on transcriptome and energy metabolism of porcine myotubes

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,880 probe-sets were screened

overall_design:
RNAs of porcine myoblasts were hybridized to Affymetrix Porcine Snowball Array.
MIXED procedure in SAS (Version 9.4, SAS Institute Inc.). The pool (pool 5 or pool 20), temperature (35°, 37°, 39° or 41 °C) and the interaction of temperature and pool were used as fixed factors.

first: Klaus

last: Wimmers


title: Disease modeling and gene correction of LGMDR21- iPSCs elucidates the role of POGLUT1 in skeletal muscle maintenance, regeneration and satellite cell niche

city: Houston

first: Annie

middle: W.

last: Shieh

state: Texas

address: 1825 Pressler St

department: Brown Foundation Institute Of Molecular Medicine

institute: University of Texas Health Science Center

summary: LGMDR21 is a recessive limb girdle muscular dystrophy caused by mutations in the protein O-glucosyltransferase 1 gene (POGLUT1). This enzyme is responsible for O-glucosylation of specific epidermal growth factor-like (EGF) repeats found in ~50 mammalian proteins, including the Notch receptors. Previous data from patient biopsies indicated impaired Notch signaling, reduction of muscle stem cells and accelerated differentiation of myoblasts as possible pathologic mechanism. Using patient iPSCs and their corrected isotypes, we showed that patient iPSC-derived myogenic progenitors demonstrate dysregulation of gene clusters related to POGLUT1, NOTCH, muscle development, ECM, cell adhesion and migration (MET signaling). They also exhibited reduced in vitro enzymatic activity and NOTCH signaling, defective myogenesis, proliferation, migration and differentiation. In vivo studies demonstrated significant reductions in engraftment, muscle stem cell formation, PAX7 expression and maintenance, along with increased percentage of PAX7 positive cells in the interstitial space between myofibers. Remarkably, gene corrected cells were able to rescue in vitro and in vivo phenotypes. These results describe novel mechanistic insights for LGMDR21 pathology and the efficacy of site-specific gene correction in disease modeling and rescue of the phenotypes and paving the way toward gene therapies for LGMDs.

overall_design: NOT PROVIDED; REQUESTED

first: Jose

last: Ortiz-Vitali

first: Jianbo

last: Wu

first: Nasa

last: Xu

first: Nima

last: Niknejad

first: Megumi

last: Takeuchi

first: Carmen

last: Paradas

first: Chunru

last: Lin

first: Hamed

last: Jafar-Nejad

first: Robert

last: Haltiwanger

first: Sidney

middle: H

last: Wang

first: Radbod

last: Darabi


title: Human mast cell gene expression in psoriasis and normal skin

city: Manchester

first: Silvia

last: Bulfone-Paus

address: 46 Grafton Street

department: Lydia Becker Institute of  Immunology & Inflammation

institute: University Of Manchester

summary: Comparison of gene expression profiles of mast cells isolated from lesional psoriatic and healthy volunteer skin

overall_design: Bulk RNAseq, 2 conditions, mast cells isolated from skin of 7 healthy volunteers and 7 psorisis patients (2 psoriasis patients pooled in one sample). Total 7 healthy vs 6 psoriasis samples

first: Peter

last: West

first: Rajia

last: Bahri

first: Chiara

last: Tontini

first: Haris

last: Atmoko

first: Christopher

last: Griffiths

first: Richard

last: Warren


title: Expression data from donor lungs of cardiac death and brain death donors (re-analysis)

city: Toronto

first: Ricardo

last: Zamel

address: 101 College St.

institute: University Health Network

type:
Expression profiling by array
Third-party reanalysis

summary:
Ischemia reperfusion induced injury contributes to poor lung transplant outcomes.Microarrays were used to study the biological response of human lungs to the ischemia reperfusion process. Samples were
collected from lung transplant cases at Toronto General Hospital. Lungs were donation after brain death (DBD)

overall_design: We reanalyzed a subset of samples previously deposited in GEO under Series GSE18995 (see meta.txt for reanalysis details).  The samples were used for validation purposes in the present study.

first: Aaron

last: Wong

first: Jonathan

last: Yeung

first: Gary

last: Bader

first: Claudia

last: Dos Santos

first: Xiaohui

last: Bai

first: Yubo

first: Shaf

last: Keshavjee

first: Mingyao

last: Liu


title: Molecular Dysregulation Underlying Racial Disparity in Hepatocellular Carcinoma (HCC)

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Hepatocellular carcinoma (HCC) is a highly fatal disease with mortality running parallel to its incidence. For HCC patients, there is a statistically significant increase in incidence and mortality and a decrease in 5-year survival rates in African American (AA)/Black patients compared to non-Hispanic (white) patients. There is a gap of knowledge in our understanding of the molecular mechanism underlying the HCC racial disparity between AA/Black and white patients. To address this issue, we analyzed existing RNA-sequencing (RNA-seq) data from HCC patients in the TCGA database, and performed RNA-seq in 14 white and 19 AA/Black HCC patients from Virginia Commonwealth University. In both analysis the only pathway which showed statistically significant activation in AA/Black patients, compared to white patients, was type I interferon (IFN-I) signaling. A four gene signature of IFN-I-stimulated genes (ISGs) showed increased expression in AA/Black HCC tumors compared to their white counterparts. HCC is a disease of chronic inflammation and IFN-I function as a pro-inflammatory and immunosuppressive cytokine. These findings suggest a potential role of IFN-I in conferring disparity in AA/Black HCC patients.

overall_design: We compared gene expression profiles of AA/Black and white HCC patients using TCGA and in-house-generated data.

first: Saranya

last: Chidambaranathan Reghupaty

first: Rachel

last: Mendoza

first: Zhao

last: Lai

first: Devanand

last: Sarkar


title: Regulation of human interferon signaling by transposon exonization

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to prevent autoimmunity. Here, we found that the alternative splicing of exons derived from transposons is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

overall_design: Transcriptional profiling (RNA-seq) of HeLa cells cells (wild-type, IFNAR2-S KO, IFNAR2-L KO and IFNAR2-E7 KO) that were either untreated or stimulated with 10U/mL human recombinant interferon beta  (IFNb) for 4hrs.

first: Giulia

middle: I

last: Pasquesi


title: Gene expression profile of luminal breast cancer samples from FFPE sample of primary luminal breast cancer from patient who had a loco-regional recurrence [cohort B]

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: We aimed at finding a gene signature able to discriminate patients who had a loco-regional recurrence either at early time after surgery or late (< 2 yrs, early;  >2 and <5 yrs, intermediate; < 5 yrs, late)

overall_design: We performed gene expression profile using Clariom D platform from FFPE sample of primary luminal breast cancer from patient who had a loco-regional recurrence at different time after surgery (cohort B)

first: Mario

middle: P

last: Colombo

last: Chiodoni


title: Gene expression profile of luminal breast cancer samples from FFPE sample of primary luminal breast cancer from patient who had a loco-regional recurrence

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

overall_design: Refer to individual Series


title: Differential transcription network analysis for Fusarium head blight disease of barley in combination with drought stress

city: Freising

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

institute: Technische Universität München

summary: For improvement of stress and disease resistance of barley, this global transcriptomic study focuses on how drought conditions affect Fusarium head blight (FHB) severity in spring barley. In general, drought-stress prior to Fusarium culmorum infection reduced FHB-susceptibility. This study gives evidence, that FHB-severity and strength of drought responses is variety-dependent under complex stress situations.

overall_design: Global gene expression study of 3’-RNAseq for the four different Barley cultivars Barke, Grace, Morex and Palmella Blue. Flowering plants were irrigated or exposed to drought stress for 7days before expected mid of flowering (growth stage 65) and then inoculated either with Fusarium culmorum spores, Fusarium avenaceum spores or mock and whole spikes were harvested 48 and 96 hours post-infection.

first: Christine

last: Wurmser

first: Felix

last: Hoheneder

first: Christina

last: Steidele


title: Transcriptome analysis of the kidney of socially stressed male C57 BL/6 mice

city: Beijing

first: yuchen

last: lu

address: Yard 27, Taiping Road

institute: Beijing Institute of Basic Medical Sciences

summary: To investigate the difference of gene expression between kidneys of groups with different treatments, We performed gene expression profiling analysis using data obtained from RNA-seq of kidney from socially stressed male C57 BL/6 mice with different treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different kidney comimg from different treatment groups

first: Jiyan

last: Zhang

first: Hailong

last: Jin

first: Guanglei

last: Xu

first: Yuchern

last: Lu


title: Expression profiles of perihematomal brain tissues of intracerebral hemorrhage (ICH) mice treated with or without TEPP-46

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

summary: To investigate the expression changes in the mRNAs of perihematomal brain tissues of ICH mice treated by TEPP-46.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of perihematomal brain tissues of mice at 5 days after ICH treated with or without TEPP-46.
Comparative gene expression profiling analysis of RNA-seq data for TEPP-46 treated and Vehicle treated mice.


title: Single cell RNA-seq for human and bovine PBMCs stimulated with M. tuberculosis

city: Gliwice

first: Anna

last: Papiez

address: Akademicka 16

department: Department of Data Science and Engineering

institute: Silesian University of Technology

summary: We propose a custom pipeline for combining data from experiments on multispecies studies tested on data from human and bovine peripheral blood mononuclear cellssamples, stimulated with Mycobacterium tuberculosis.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: PBMC samples from cattle and human were isolated using pancoll (Pan-Biotech) gradient density centrifugation following the manufacturer’s protocol and analysed using scRNAseq.


title: Endothelial Cell Cycle Responses to Laminar Shear Stress

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

institute: Medical College of Wisconsin

summary: Quiescence is a tempoary arrest from the cell cycle that can be induced by many methods, including contact inhibition, fluid shear stress, and serum starvation. p27 is important to inhibit cell cycle progression. Here we evaluate transcriptional differences between three different methods of quiescence induction, flow, contact inhibition and serum starvation, in the presence or depletion of p27.

overall_design: Comparative gene expression analysis for RNA-seq data for HUVEC exposed to 72h shear stress or static conditions, or low density or high density conditions, or normal serum or low serum conditions, as well as control and p27 KD (siRNA depletion).

first: Natalie

last: Tanke

first: Ziqing

last: Liu

first: Morgan

last: Oatley

first: Victoria

last: Bautch


title: Gene expression profile of luminal breast cancer samples from FFPE sample of primary luminal breast cancer from patient who had a loco-regional recurrence [cohort A]

first: Loris

last: De Cecco

overall_design: We performed gene expression profile using Clariom D platform from FFPE sample of primary luminal breast cancer from patient who had a loco-regional recurrence at different time after surgery (cohort A)

first: Mario

last: Colombo

first: Claudia

last: Chiodoni


title: Regulation of cardiomyocyte hypertrophy through dynamic regulation of type I collagen

city: Cincinnati

first: Jeffery

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Communications between cardiomyocytes and fibroblasts in the heart are thought to occur through both secreted growth factors and via alterations in the structural properties of the extracellular matrix that each of the cell types helps generate. While perturbations in fibroblast activity are known to impact development of cardiomyocyte hypertrophy, the specific role played by collagen in this intercellular communication remains unknown. In this study we addressed this knowledge gap through differential regulation of collagen 1a2 using mouse hearts. The microarray assays reported here were carried out to assess the effects of collagen 1a2 ablation on cardiac transcriptional profiles.

overall_design:
We used microarrays to generate information about transcriptional profiles of hearts lacking collagen 1a2
Hearts were harvested from 2-month old control and experimental mice. Total RNA was isolated using the Trizol protocol and submitted to Affymetrix Clariom S array pipeline after quality control analysis using Agilent 2100 Bioanalyzer.

first: Qinghang

last: Meng

first: Vikram

last: Prasad


title: Target sites of SWO1 and their expression under salt stress

city: Shanghai

first: Zhidan

last: Wang

address: Chenhua Road 3888

institute: Chinese academy of sciences

sample_organism:
Arabidopsis
Arabidopsis thaliana

platform_organism:
Arabidopsis
Arabidopsis thaliana


title: RNA-seq analysis of WT, swo1-2 with or without salt treatment in Arabidopsis

summary: RNA-seq was performed to detect differentially expressed genes between WT and swo1 mutant under salt stress

overall_design: Total RNAs were extracted from 7-day-old seedlings grown during long days with or without NaCl treatment for indicated time using a RNeasy Plant Mini kit (Qiagen)

first: Li

last: Peng

first: Chunzhao

last: Zhao


title: The role of DOT1L in ovarian cancer growth and progression

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: Disruptor of telomeric silencing 1-like (DOT1L) expression is elevated in many cancer types including ovarian cancer. Therefore, we analyzed the role of DOT1L in ovarian cancer. Pharmacological inhibition of DOT1L expression in ovarian cancer cell lines resulted in decreased proliferation, and increased cell death.

overall_design: IGROV-1 and SK-OV-3 cells were treated with  DOT1L inhibitor (10 micomolar) EPZ-5676 for 48 hours, samples were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.


title: Genome-wide occupancy of SWO1 in Arabidopsis [ChIP-seq]

summary: ChIP-seq was performed to detect genome-wide binding sites of SWO1

overall_design: Arabidopsis wild-type Col-0 and SWO1-GFP plants were subject to ChIP-seq analysis using the GFP antibody.


title: GATA2 tumor suppressive role revealed in ERG - AML mouse model, unveiling a preleukemic phenotype

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: The transcription factor (TF) GATA2, is crucial for the formation, and lifelong homeostasis of hematopoietic stem cells. Mono-Allelic germline disruptions of GATA2, result in haploinsufficiency syndromes. These disorders display variable manifestations, including immune deficiency, lymphedema, pulmonary proteinosis, and bone marrow failure. The later is presented by myelodysplastic changes (MDS), that subsequently evolve to leukemia (AML). MDS/AML are the most devastating, yet most consistent outcomes, designating GATA2 deficiency as one major predisposing condition to AML development.

overall_design: To date, biomolecular trajectories of GATA2 deficiency, just vaguely delineated explanatory mechanisms. Experimental models recapitulating the disease evolution are meager, and functional studies are thus hampered. Here, we created murine models, reflecting the evolution of GATA2 deficiency, from gestational stage, to malignancy. We imposed the oncogenic driving force of TF ERG, upon Gata2 heterozygote and WT mice, to create a credible model. Both ERG/Gata2WT, and ERG/Gata2het mice developed leukemia, yet ERG/Gata2het, sustained an accelerated disease, resulting in diminished survival (p<0.0001). Subsequently, we obtained expression profiles of pre-leukemic blood precursors, using high throughput genomics, followed by functional assessments of self-renewal and cycling capacities. These studies elucidated a unique proliferative phenotype held by ERG/Gata2het progenitors. Additional expression analyses, metabolic assays, and electrons-microscopy inspections, suggested ERG/Gata2het progenitors uniquely relay on oxidative phosphorylation, and harbor alterations in mitochondrial structure and function. Excitingly, similar expression signature and morphological features were observed in human GATA2+/R396W cells, and in profiles of Inv(3)/GATA2MUT AML’s. We here provide new insights into GATA2 deficiency evolutionary course, underscoring the need to deconvolute pre-malignant stages in translational studies.

first: Avigail

last: Rein

first: Shai

last: Izraeli


title: Preimplantation embryo ketone body exposure exerts sex-specific effects on mouse fetal and placental transcriptomes

city: Parkville

first: David

middle: K

last: Gardner

state: VIC

address: University of Melbourne

department: School of BioSciences

country: Australia

institute: University of Melbourne

summary: Ketogenic diet consumption elevates circulating levels of the ketones β-hydroxybutyrate (βOHB) and acetoacetate (AcAc). In vitro ketone exposure perturbs preimplantation mouse embryo viability and female-specific fetal development post-transfer. Here we assessed whether transient exposure of preimplantation embryos to ketones impacts post-implantation fetal and placental gene expression. Blastocysts cultured in vitro with or without 2 mmol/L βOHB alone (‘βOHB’) or combined with 0.8 mmol/L AcAc (‘Keto’) underwent embryo transfer. Transcriptional profiles of sexed E14.5 placentae, liver, and brain were examined via RNA-Seq and DAVID functional analysis, revealing a sexually dimorphic transcriptomic response. βOHB and Keto exposure both downregulated genes related to oxidative phosphorylation specifically in female liver. βOHB downregulated female placental steroid biosynthetic processes, while Keto treatment upregulated genes relevant to blood vessel formation and cell migration in male placentae. Brain transcriptomes were minimally affected. X-linked genes and chromatin modifiers were identified as differentially expressed, alluding to a sex-specific regulatory mechanism. Transient preimplantation ketone exposure therefore perturbs sex-specific fetal liver and placental gene expression demonstrating a developmental programming effect that warrants future investigation of male and female offspring postnatal metabolic health.

overall_design: mRNA profiles of male and female D14.5 murine fetal liver, fetal brain and placental tissues cultured in vitro with 2 mM βOHB versus control, or 0.8 mM AcAc + 2 mM βOHB versus control.

first: Emma

last: Whatley

first: Thi

middle: T

last: Truong

first: Alexandra

last: Harvey


title: Directed Evolution of an Adenine Base Editor with Increased Activity and Context Compatibility

status: Public on Sep 14 2023

city: CHICAGO

first: Yuan

last: Wu

state: Illinois

address: 929 E 57th St, GCIS E535

department: Chemistry

institute: University of Chicago


title: Metabolic engineering of oleaginous yeast in lipogenic phase enhances production of nervonic acid

first: Xiaoqiang

last: Ma

address: 800 DONG CHUAN ROAD

institute: Shanghai Jiaotong University

summary: Insufficient biosynthesis efficiency can be a major obstacle to engineer oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs) during the lipogenic phase. Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic preferences of three plant-derived ketoacyl-CoA synthases rationally guided reconstructing efficient NA biosynthetic pathway in R. toruloides. More importantly, a genome-wide transcriptional analysis endowed clues to strengthen the fatty acid elongation (FAE) module and identify/use lipogenic phase-activated promoter, collectively addressing the stagnation of NA accumulation during the lipogenic phase. The best-designed strain exhibited a high NA content (major component in total fatty acid [TFA], 46.3%) and produced a titer of 44.2 g/L in a 5 L bioreactor. The strategy developed here provides an engineering framework to establish the microbial process of producing valuable VLCFAs in oleaginous yeasts.

overall_design: To understand the underlying mechanism of the weakening productivity of the VLCFA biosynthesis during the lipogenic phase, we first conducted a genome-wide comparative transcriptomic analysis using  Rhodosporidium toruloides strains  grown at 48h and 120h, respectively.

first: Feixiang

last: Liu

first: Erzheng

last: Su


title: Directed Evolution of an Adenine Base Editor withIncreased Activity and Context Compatibility [sgRNA-target library]

summary: Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. ABEs function most effectively when the target A is in a TA context. Deficient ABE processing of RA (R = A or G) is most evident when the target A is outside the comfortable editing window or when delivery is suboptimal. In the current study, we report directed evolution of TadA8r, a new variant of the Escherichia coli tRNA-specific adenosine deaminase (TadA) with ultra-fast deoxyadenosine deamination and no context bias.

overall_design: To systematically evaluate the editing performance of ABE8r, we prepared a library wherein target sites were individually paired with their cognate sgRNAs. Similar paired sgRNA-target libraries have previously been used to characterize CRISPR nucleases and base editors. To bridge our high-throughput characterization with future applications of ABEs in disease-relevant contexts, we randomly chose 12,000 NGG-adjacent target sites from the ClinVar database, each hosting a potentially pathogenic G:C-to-A:T transition at protospacer positions 3-10. These G:C-to-A:T transitions are evenly distributed across protospacer positions and XA contexts. The library was stably integrated into HEK293T cells with ABEs transiently expressed to facilitate editing. The entire sgRNA-target cassettes were subsequently amplified and deep sequenced. Consistent editing levels were observed across two biological replicates for all ABEs

first: Xiao

last: Yu-Lan

first: Wu

last: Yuan

first: Tang

last: Weixin


title: The role of SMC3 in heart development  by regulating super-enhancer associated genes

city: shanghai

first: bowen

last: zhang

state: shanghai

address: dongan road

institute: Fudan university

summary: Abnormal cardiac development has been observed in individuals with Cornelia de Lange Syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. But the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed an association between SMC3 mutations and congenital heart disease (CHD) in CdLS patients. To further explore this relationship, we utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which displayed varying degrees of outflow tract (OFT) abnormalities. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. Employing single nucleus RNA sequencing and 3C-high-throughput genome-wide translocation sequencing, we unveiled that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SE) and promoters. Notable, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research uncovers a novel role for SMC3 in heart development by regulating SE-associated genes, suggesting its potential relevance as one of the CHD-related genes and providing crucial insights into the molecular basis of cardiac development.

overall_design: Transcriptome profiles and pair-wise chromatin interactions of diverse cell types were examined from  different viewpoints respectively before or/and after SMC3 knock down (duplicates), respectively.

first: Bowen

last: Zhang

first: Yongchang

last: Zhu

first: Ranran

last: Dai