title: Inter-chromosomal contacts of the 16p11.2 locus connect with gene expression changes of Pcdh genes in autism spectrum disorder

city: Berlin

first: Ana

last: Pombo

address: Hannoversche Strasse 28

institute: Max Delbrueck Center for Molecular Medecine

summary: Differentiation experiment of mouse embryonic stem cells (ESCs) to neuronal precursor (NPC) and immature dopaminergic neurons (NEU) commited to ventral midbrain lineage. Controls and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus which is synteny conserved with human 16p11.2 locus. Mice harbouring CNVs in this locus display behavioural phenotypes and distinct changes in brain architecture resembling ASD-like traits. Mouse models are described in Guy Horev et al., 2011 (doi: 10.1073/pnas.1114042108). Samples with same numeric identifier were differentiated in parallel.

overall_design: RNA-seq and Hi-C on controls and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus. Cell types include embronic stem cells, neuronal progenitor cells, dopaminergic neurons.

first: Kempfer

last: Rieke

first: Szabo

last: Dominik

first: Alexander

last: Kukalev

first: Marta

last: Slimak-Mastruoboni

first: Julietta

last: Ramirez

first: Christoph

last: Thieme


title: Inhibition of Rho-associated, coiled-coil-containing protein kinase 2 in murine podocytes

status: Public on Mar 20 2024

city: Minato City

first: Kensuke

last: Sekiguchi

state: Please Select

address: 3-19-18 Nishishinbashi

country: Japan

institute: Jikei University

type: Expression profiling by high throughput sequencing

summary: Focal segmental glomerulosclerosis (FSGS) is characterized by damage to podocytes, a crucial pathological feature. While several mechanisms of podocyte injury have been suggested, many questions remain unanswered. Rho-associated, coiled-coil-containing protein kinase 2 (ROCK2), a serine/threonine kinase with diverse cellular functions, appears to play a significant role. We observed activation of ROCK2 in podocytes of mice with FSGS induced by adriamycin (ADR), as well as in cultured podocytes exposed to ADR. To delve deeper, we used conditional knockout mice where the ROCK2 gene was specifically disrupted in podocytes (PR2KO). These mice showed resistance to ADR-induced albuminuria, glomerular sclerosis, and podocyte damage. Additionally, pharmacological inhibition of ROCK2 significantly improved podocyte loss and kidney sclerosis in a mouse model of FSGS by counteracting profibrotic factors. RNA sequencing of podocytes treated with a ROCK2 inhibitor confirmed ROCK2's role as a regulator of the cyclic nucleotide signaling pathway. Our findings underscore the potential of ROCK2 inhibition as a therapeutic avenue for FSGS.

overall_design: To explore the involvement of ROCK2 in podocyte damage, we used a chemical inhibitor of ROCK2 in murine podocytes.

first: Keiichiro

last: Matoba

first: Yosuke

last: Nagai

first: Shinji

last: Ohashi

first: Etsuko

last: Mitsuyoshi

first: Masayuki

last: Shimoda

first: Toshiaki

last: Tachibana

first: Daiji

last: Kawanami

first: Tamotsu

last: Yokota

first: Kazunori

last: Utsunomiya

first: Rimei

last: Nishimura


title: Mutant p53 alters gene expression in human acute myeloid leukemia cells [patients]

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

country: USA

institute: Northwestern University

summary: We found that Mutant p53 alters gene expression in human acute myeloid leukemia cells .

overall_design: To determine whether mutant p53 alters gene transcription in human leuemia cells, we performed RNA-seq using primary AML cells with missense TP53 mutations and control cells from lymphoma patients who have normal hematopoiesis and no TP53 mutations.

first: Madina

last: Sukhanova


title: Phlorizin ameliorates cognitive and behavioral impairments via the microbiota-gut-brain axis in diet-induced obese mice

city: Xi'an

first: Shuqing

last: Zhang

address: West Changan Avenue

country: China

institute: Shaanxi Normal University

summary:
Background: The long-term high-fat, high-sugar diet exacerbates type 2 diabetes mellitus (T2DM)-related cognitive impairments. The negative impact of poor dietary patterns on brain development and neurological function may be related to gut microbiota disturbance. The role of phlorizin in mitigating glucose and lipid metabolism disorders is well documented. However, the protective effect of phlorizin on diabetes-related cognitive dysfunction is unclear. Therefore, the present study aimed to investigate the effect of dietary supplementation of phlorizin on high-fat and high-fructose diet (HFFD)-induced cognitive dysfunction and evaluate the crucial role of the microbiota-gut-brain axis.
Results: Dietary supplementation of phlorizin for 14 weeks effectively prevented glucolipid metabolism disorder, spatial learning impairment, and memory impairment in HFFD mice. In addition, phlorizin improved the HFFD-induced decrease in synaptic plasticity, neuroinflammation, and excessive activation of microglia in the hippocampus. Transcriptomics analysis shows that the protective effect of phlorizin on cognitive impairment was associated with increased expression of neurotransmitters and synapse-related genes in the hippocampus. Phlorizin treatment alleviated colon microbiota disturbance, mainly manifested by an increase in gut microbiota diversity and the abundance of short-chain fatty acid (SCFA)-producing bacteria. The level of microbial metabolites, including SCFA, inosine 5'-monophosphate (IMP), and D (-)-beta-hydroxybutyric acid (BHB) were also significantly increased after phlorizin treatment. Moreover, integrating multiomics analysis observed tight connections between phlorizin-regulated genes, microbiota, and metabolites. Furthermore, removal of the gut microbiota via antibiotics treatment diminished the protective effect of phlorizin against HFFD-induced cognitive impairment, underscoring the critical role of the gut microbiota in mediating cognitive behavior. Importantly, supplementation with SCFA and BHB alone mimicked the regulatory effects of phlorizin on cognitive function.
Conclusions: These results indicate that gut microbiota and their metabolites mediate the ameliorative effect of phlorizin on HFFD-induced cognitive impairment. Therefore, phlorizin can be used as an easy-to-implement nutritional therapy to prevent and alleviate metabolism-related neurodegenerative diseases by targeting the regulation of the microbiome-gut-brain axis.

overall_design: Eighteen male C57BL/6J mice were randomly assigned to three groups: the control group fed with a standard diet_AIN-93M, the HFFD group fed with a HFFD （TP 23100 45% kcal from fat, 10% fructose in drinking water), and HFFD+HPH group (TP 23100 45% kcal from fat, 10% fructose in drinking water, high-dose phlorizin were orally fed 20 mg/kg/day of phlorizin) for 14 weeks.


title: Effect of PD0325901 on gene expression during inner ear organoids differentiation

city: Shanghai

first: Jiaoyao

last: Ma

state: Shanghai

address: No. 130, Dong'an Road, Xuhui District

institute: Fudan University

summary: To determine the mechanism through which PD0325901(PD) promotes inner ear hair cells generation, we cultured the inner ear organoids in 1 μM PD or the same volume of DMSO for 10 days, after which we used RNA-seq to establish a database to analyze differentially expressed genes .

overall_design: To determine the mechanism through which PD0325901(PD) promotes inner ear hair cells generation, we cultured the inner ear organoids in 1 μM PD or the same volume of DMSO for 10 days, after which we used RNA-seq to establish a database to analyze differentially.

first: Ma

last: Jiaoyao

first: Xia

last: Mingyu

first: Chen

last: Bing

first: Sun

last: Shan


title: Unraveling the Transcriptome Profile of Pulsed Electromagnetic Field (PEMF) Stimulation in Bone Regeneration Using an In Vitro Investigation Platform Based on a Perfusion Bioreactor and 3D Printed Bone Tissue-Like Scaffolds

status: Public on Mar 21 2024

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

summary: A global transcriptome profiling was performed by RNA-seq on human BM-MSCs exposed to biomechanical stimulation (perfusion) and biophysical stimulation (PEMF stimualtion) and the set of pathways and upstream regulators were  detected using bioinformtic tools to determine how biophysical stimulation induce biological effects.

overall_design: RNA-Seq technology was implemented to compare the gene transcription induced in human BM-MSCs stimulated by PEMF in a bone tissue-like physiological environment.

first: Farah

last: Daou

first: Andrea

last: Cochis

first: Lia

last: Rimondini


title: FUS reads histone H3K36me3 to regulate alternative polyadenylation

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Title: Profiling Small RNA from Brain Extracellular Vesicles in Individuals with Depression

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary: Major depressive disorder (MDD) is a leading cause of disability with significant mortality risk. Despite progress in our understanding of the etiology of MDD, the underlying molecular changes in the brain remain poorly understood. Extracellular vesicles (EVs) are lipid-bound particles that can reflect the molecular signatures of the tissue of origin. We aimed to optimize a streamlined EV isolation protocol from post-mortem brain tissue and to determine whether EV RNA cargo, particularly microRNAs (miRNAs) have an MDD-specific profile. EVs were isolated from post-mortem human brain tissue. Quality was assessed using western blots, transmission electron microscopy, and microfluidic resistive pulse sensing. EV RNA was extracted and sequenced on Illumina platforms. Functional follow up was performed in silico. Quality assessment showed an enrichment of EV markers, as well as a size distribution of 30-200 nm in diameter, and no contamination with cellular debris. Small RNA profiling indicated the presence of several RNA biotypes, with miRNAs and transfer RNAs (tRNAs) being the most prominent. Exploring miRNA levels between groups revealed decreased expression of miR-92a-3p and miR-129-5p, which was validated by qPCR and was specific to EVs and not seen in bulk tissue. Finally, in silico functional analyses indicate potential roles for these two miRNAs in neurotransmission and synaptic plasticity. We provide a streamlined isolation protocol that yields EVs of high quality that are suitable for molecular follow up. Our findings warrant future investigations into brain EV miRNA dysregulation in MDD.

overall_design: EVs were isolated from post-mortem human brain tissue of individuals who had MDD and died by suicide as well as psychiatrically healthy individuals who died naturally or by accident. RNA was isolated from EVs and small RNA libraries were constructed and sequenced. Isolations took place in 2 batches, the first batch was sequenced on Illumina HiSEQ, the second on Illumina NOVASEQ.

first: Pascal

last: Ibrahim

first: Ryan

last: Dennistion

first: Haruka

last: Mitsuhashi

first: Jennie

last: Yang

first: Laura

middle: M

last: Fiori

first: Dariusz

last: Zurawek

first: Naguib

last: Mechawar

first: Corina

last: Nagy


title: FUS reads histone H3K36me3 to regulate alternative polyadenylation [RIP-seq]

summary: Complex organisms are able to generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates how cells behave in tissues. However, little is known about how chromatin, especially the histone modifications, regulates RNA polyadenylation. Here, we find that FUS is recruited to chromatin by H3K36me3 at gene bodies. Once H3K36me3 is abolished, FUS is dissociated from chromatin to increase the binding with RNA, resulting in increased distal polyadenylation selections that are far from the stop codon. The H3K36me3 recognition of FUS is mediated by the proline residues in ZNF domain, mutations of which lead to reduced chromatin association of FUS, increased RNA binding of FUS, and distal polyadenylation selections. Proline mutation, which corresponds to the mutation in amyotrophic lateral sclerosis, contributes to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal FUS as an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.

overall_design: RIP-seq of ES-E14 ESCs (WT, Setd KO, Fus KO, Fus P423L, Smyd5 KO)

first: Junqi

last: Jia

first: Haonan

last: Fan


title: Effect of Fusarium sp. strain K-23-infection on the gene expression in Arabidopsis thaliana plants under control and salt stress conditions

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

country: Spain

institute: CBGP (UPM-INIA/CSIC)

summary: Several fungi have been reported to form intimate bonds with plants. These close mutual relationships can provide physiological benefits to the interacting organisms, including the improvement of nutrient assimilation or enhanced stress tolerance. The root-colonizing fungus Fusarium sp. strain K-23 is known to successfully colonize tomato roots. Previous studies highlighted the promotion of plant biomass production and stress tolerance of tomato plants infected with the K-23. However, up to data, nothing is known about the effect of this fungus on the model plant Arabidopsis thaliana. We here report the comparative analysis of the effect of mock- and K-23-infected wild-type Arabidopsis plants (Col-0) in the abscence and presence of moderate salt stress conditions (50 mM NaCl). Our data provide evidence for a profound effect of K-23 on root hair elongation through the activation of a regulatory network that includes several plant hormones. Intriguingly, the fungus suppresses gibberellic acid biosynthesis which, in turn, promotes root hair elongation.

overall_design: To investigate differential gene expression in mock- (M) and Fusarium sp. strain K-23-infected (F) Arabidopsis wild-type plants (Col-0) under control (0) and salt stress (50) conditions (50 mM NaCl) in shoots (S) and roots (R).


title: Title: Profiling Small RNA from Brain Extracellular Vesicles in Individuals with Depression [NovaSeq]


title: Single cell transcriptome analysis of decidua macrophages in normal and recurrent spontaneous abortion patients

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: We isolated CD14+CD45+ dMΦ from the normal or RSA decidua by flow cytometry, followed by single cell RNA sequencing (scRNA-seq). In total, 23,062 single-cell transcriptomes of macrophage were profiled (12,470 Normal and 10,592 RSA), which were divided into 13 major clusters via T-distributed stochastic neighbor embedding (t-SNE) visualization.

overall_design: Our study redefined the polarization state and physiological characteristic of dMΦ in early normal and RSA pregnancy

first: Qingliang

last: Zheng

first: Liping

last: Jin


title: Mutant p53 dysregulates gene transcription in human CD34+ cells [RNA-seq 3]

first: Yan

last: Liu

summary: We found that mutant p53 alters gene transcription in human hematopoietic stem and progenitor cells (CD34+).

overall_design:
To determine the mechanisms by which mutant p53 enhances the repopulating potential of human HSPCs, we performed RNA-seq sequencing in CD34 cells expressing either GFP or mutant p53.
We introduced GFP or p53R248W into human CD34+ cells.
We sorted GFP+ cells and isolate RNAs from thes ecells for RNA-sequencing.


title: FUS reads histone H3K36me3 to regulate alternative polyadenylation [PolyA-seq]

first: Dong

last: Fang

overall_design: PolyA-seq of ES-E14 ESCs (WT, Setd2 KO, Fus KO, Fus P421A, Fus P423L)


title: Coactivator-independent vitamin D receptor signaling impairs intestinal calcium transport in mice, leading to severe rickets, which is not prevented by a diet high in calcium, phosphate, and lactose.

city: Leuven

first: Annemieke

last: Verstuyf

address: Herestraat 49 box 902

country: Belgium

institute: KU Leuven

summary: The vitamin D receptor (VDR) plays a critical role in the regulation of mineral and bone homeostasis. Upon binding of 1α,25-dihydroxyvitamin D3 to the VDR, the activation function 2 (AF2) domain repositions and recruits coactivators for the assembly of the transcriptional machinery required for gene transcription. In contrast to coactivator-induced transcriptional activation, the functional effects of coactivator-independent VDR signaling remain unclear. In humans, mutations in the AF2 domain are associated with hereditary vitamin D-resistant rickets, a genetic disorder characterized by impaired bone mineralization and growth. In the present study, we used mice with a systemic or conditional deletion of the VDR-AF2 domain (VdrΔAF2) to study coactivator-independent VDR signaling. We confirm that ligand-induced transcriptional activation was disabled because the mutant VDRΔAF2 protein was unable to interact with coactivators. Systemic VdrΔAF2 mice developed short, undermineralized bones with enlarged growth plates, a bone phenotype that was more pronounced than that of systemic Vdr knockout (Vdr-/-) mice. Interestingly, a rescue diet that is high in calcium, phosphate, and lactose, normalized this phenotype in Vdr-/-, but not in VdrΔAF2 mice. Our findings in osteoblast- and osteoclast-specific VdrΔAF2 mice did not recapitulate this bone phenotype indicating coactivator-independent VDR effects are more important in other organs. On the other hand, RNA-seq analysis of duodenum and kidney revealed a repression of VDR  target genes in systemic VdrΔAF2 mice, which was not observed in Vdr-/- mice. These genes could provide new insights in the compensaory (re)absorption of minerals that are crucial for bone homeostasis. In summary, coactivator-independent VDR effects contribute to mineral and bone homeostasis.

overall_design: To investigate the differential effects of co-activator independent VDR signaling versus absent VDR signaling on mineral homeostasis, we performed RNA seq analysis in duodenum and kidney samples of Vdr-/- and VdrAF2 mice. Herefor, we used 8-week-old female mice to obtain 6 Vdr wildtype samples, 4 Vdr-/- samples and 4 Vdr AF2 samples of two different tissues, duodenum and kidney, which makes 28 samples in total. Mice were maintained on a diet high in calcium, phosphate and lactose (Inotiv, TD.96348) to circumvent effects of hypocalcemia and hypophosphatema, at least in the Vdr-/- mice.


title: FUS reads histone H3K36me3 to regulate alternative polyadenylation [CUT&Tag]

overall_design: CUT&Tag of ES-E14 ESCs (Fus KO, Setd2 KO, WT, Fus P423L)


title: Chromatin profiling reveals many transcriptional regulators of proliferation and differentiation of bovine satellite cells

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: Litton Reaves Hall

department: School of Animal Sciences

institute: Virginia Tech

summary: Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle repair, remodeling, and maintenance. Like myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study we aimed to identify the enhancers and the transcription factors binding to these enhancers that control gene expression in proliferating and differentiating bovine satellite cells. Using ChIP-seq, we identified 56,973 and 54,470 active enhancers, genomic regions marked with both H3K4me1 and H3K27ac, and 50,956 and 59,174 repressed enhancers, genomic regions marked with H3K27me3, in proliferating and differentiating bovine satellite cells, respectively. Motif enrichment analyses revealed many transcription factors including the AP-1 family transcription factors that regulate gene expression in proliferating bovine satellite cells and many transcription factors besides MyoG that regulate gene expression in differentiating bovine satellite cells.

overall_design: In this study we isolated satellite cells from skeletal muscle from two Angus-crossbred steers and cultured them in growth medium or differentiation medium. We used ChIP-seq to identify genomic regions marked with H3K4me1, H3K27ac, and H3K27me3 in both proliferating and differentiating bovine satellite cells.

first: Pengcheng

last: Lyu


title: Effect of in vivo culture condition on the proliferation and differentiation of rat adipose-derived stromal cells

city: chongqing

first: Chao

last: Wang

address: 136 zhongshan NO.2 road,yuzhong

institute: Children's hospital of chongqing medical university

summary: Adipose-derived stromal cells (ADSCs) represent a promising stem cell source for tissue engineering and cell based therapy. However, long-term in vitro expansion of ADSCs impede stemness maintaining, partly attributed to deprivation of their original microenvironment. Incompetent cells largely limit the therapeutic effects in ADSCs based clinical use. Therefore, reconstructing a more physiologically and physically relevant niche is an ideal strategy to settle this issue and therefore facilitates their extensive applications in clinical. Here, we transplanted separated ADSCs to local subcutaneous adipose tissues of nude mice as an in vivo cell culture model. We found transplanted ADSCs maintained the primitive morphologies, showed improved proliferation and delayed senescence when compared to cells in conventional incubator. Significantly increased expression of stemness-related markers and multi-lineage differentiation abilities were further observed in in vivo cultured ADSCs. At last, sequencing results revealed different expression genes between ADSCs obtained from in vivo and in vitro conditions mainly located in extracellular matrix and extracellular space, which participated in regulating transcription and protein synthesis. Moreover, we found an Egr1 involved signaling pathway might exert a crucial impact on controlling stemness properties. Our findings might collectively pave the way between the bench and beside in regard of ADSCs based application.

overall_design: To evaluate the effect of in vivo culture condition on the stemness property of ADSCs, we cultured rat primary ADSCs in two different conditions, and ADSCs were divided in three groups in our study: Con-ADSCs: the 4th passage ADSCs isolated from GFP transgenic rat adipose tissue. Vitro-ADSCs: the 4th passage ADSCs traditionally cultured and passaged in a incubator, and collected at the same time point of the Vivo-ADSCs group. Vivo-ADSCs: the 4th passage ADSCs injected into adipose tissues of nude mice and re-isolated after 7 day of injection. Subsequently,  we performed gene expression profiling analysis using data obtained from RNA-seq of  cells from the above three groups. Comparative gene expression profiling analysis of RNA-seq data for Con-ADSCs, Vitro-ADSCs and Vivo-ADSCs.


title: Atractylenolide II Suppresses Glycolysis and Induces Apopto-sis by Blocking the PADI3-ERK Signaling Pathway in Endo-metrial Cancer Cells

city: Jinzhou

first: shuang

last: tian

state: Liaoning

address: No.40，Section 3,Songpo Road

institute: Jinzhou Medical University

summary: Atractylenolide II (AT-II), the major bioactive compound of Atractylodes macrocephala exhibits anticancer activity against many types of tumors, but the roles and the potential mechanisms in endometrial cancer remain unclear. To explore a novel therapeutic target of AT-II for the clinical therapy of endometrial cancer,  the high-throughput sequence was performed.

overall_design: The RL95-2 cells were treated with AT-II or DMSO for 48h. RNA was extracted using TRIzol reagent, and the samples were sent to Genechem (Shanghai, China) for RNA-seq. Three samples were supplied in each group. The differential ex-pressed genes (DEGs) were defined based on the following criteria: |log2FoldChange| > 1 and p < 0.05.

first: Shuang

last: Tian

first: Lili

last: Ren

first: Zhe


title: Mass spectrometry imaging and single-cell transcriptome reveal metabolic profiles of the postauricular glands of the Bufo gargarizans, and hypothesize Bufotoxin biosynthesis pathways

city: Chengdu

first: Lingyu

last: zhang

address: No.1166, Liutai Avenue, Wenjiang District, Chengdu, Sichuan, China

institute: Chengdu University of TCM

summary: bufotoxin, which contain alkaloids, small peptides and bufadienolides (BDS), are neurotoxic and cardiotoxic, they are promising medical drugs, but the unclear specifics of bufotoxin in the postauricular glands (PG) and the biosynthetic routes of BDS are unknown. We used MALDI/MS to visualize 1872 components of PG, and established the expression profiles of 9316 cells by single-cell sequencing, which were classified into nine clusters by marker genes. We analyzed the expression differences of key genes for alkaloid, terpene backbone and steroid synthesis, identified optimal and silenced genes involved in key enzymes encoding bufotoxin biosynthesis, and hypothesized the full route of BDS synthesis via by analyzing the cholesterol metabolic pathway. BDS was enriched in EP, FB, and GG2 cells, and genes were expressed mainly in EP and FB cells. Combined with the bulk-RNA transcriptome we suggest that BDS synergistically synthesized by the liver and PG. metabolic mapping of toxin components in the PG of the toad, as demonstrated by our data.

overall_design: The Bufo gargarizans' postauricular glands were separating into single-cell suspensions.

last: Zhang

first: Feixia

last: Hou

first: Jihai

last: Gao


title: SARS-CoV-2 infection response in iPSC-derived alveolar epithelial cell type-2

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: The coronavirus disease 2019 (COVID-19) pandemic has affected nearly 700 million and claimed more than 6 million lives. However, the large heterogeneity in disease susceptibility and severity of illness (SOI) remains poorly understood.  A growing body of evidence suggests that alveolar epithelial cell type 2 (AT2), which constitute 10-15% of all alveolar cells and are critical for alveolar homeostasis, are the primary targets of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and damage to AT2s may directly contribute to disease severity and poor prognosis in COVID-19 patients. Our in-vitro modeling of SARS-CoV-2 infection, in well-characterized, highly uniform, (r2 at 95% CI = 0.92 ± 0.03), induced pluripotent stem cell (iPSC) derived AT2s from 10 participants of our Mexican American Family Study, showed interindividual variability in infection susceptibility and the post-infection cellular viral load. To understand the underlying mechanism of the AT2’s capacity to regulate SARS-CoV-2 infection and cellular viral load, we performed a systematic characterization of the pre- and post-SARS-CoV-2 challenged AT2 transcriptomes. A total of 1,393 genes were found significantly (Oneway ANOVA FDR corrected p ≤ 0.05; FC abs ≥ 2.0) differentially expressed (DE)  between pre- and post-SARS-CoV-2 infection-challenged AT2 and suggest significant upregulation of viral infection-related cellular innate immune response pathways (p-value ≤ 0.05; activation z-score ≥ 3.5), whilst the cholesterol and xenobiotic related metabolic pathways were significantly downregulated (p-value ≤ 0.05; activation z-score ≤ - 3.5). Interestingly, pre-infection expression of 238 DE genes showed a high correlation with the post-infection SARS-CoV-2 viral load (FDR corrected p-value ≤ 0.05, and r2-absolute ≥ 0.57). The 85 genes whose expression was negatively correlated with the viral load showed significant enrichment in viral recognition and cytokine-mediated innate immune GO biological processes (p-value range: 4.65x10-10 to 2.24x10-6). The 153 genes whose expression was positively correlated with the viral load showed significant enrichment in cholesterol homeostasis, extracellular matrix, and MAPK/ERK pathway-related GO biological processes (p-value range: 5.06x10-5 to 6.53x10-4). Overall, our results strongly suggest that AT2s pre-infection innate immunity and metabolic state affects their susceptibility to SARS-CoV-2 infection and viral load.

overall_design: Well-characterized AT2 lines generated from validated iPSCs of 10 different individuals were SARS-CoV-2 infection-challenged in in-vitro monolayer cultures.  The pre- (vehicle-treated) and post- SARS-CoV-2 infection challenged AT2s were then analyzed by immunocytochemistry, RT-PCR, and genome-wide comparative gene expression analysis to understand the mechanisms of the AT2’s capacity to regulate SARS-CoV-2 infection and cellular viral load.

first: Joanne

middle: E

last: Curran

first: John

last: Blangero


title: NR4A2 and NR4A3 selectively modulate elements of the monocyte response to buffered hypercapnia

city: Dublin

first: Eoin

middle: P

last: Cummins

state: Dublin

address: UCD Conway Institute of Biomolecular and Biomedical Research, UCD Belfield

department: Conway Institute/School of Medicine

country: Ireland

institute: University College Dublin

summary: In wild type, NR4A2-deficient, and NR4A3-deficient monocytes we used RNA-sequencing to investigate the effect of 4hrs of exposure to buffered hypercapnia (10% CO2) compared to normocapnia (5% CO2) with and without the pro-inflammatory stimulus LPS (2.5ug/ml) for the final 2hrs. Buffered hypercapnia causes transcriptional  changes associated with altered metabolic function in both the basal and stimulated states.

overall_design: To investigate the effect of NR4A2 ot NR4A3 depletion on the hypercapnic response in monocytes, we exposed NR4A2-deficient and NR4A3-deficient monocytes to 10% CO2 or 5% CO2 for 4 hours in the presence or absence of LPS (2.5ug/ml) for the final 2 hours.

first: David

last: Phelan


title: Plasma extracellular vesicle microRNAs reflecting the therapeutic effect of the CBP/β-catenin inhibitor PRI-724 in patients with liver cirrhosis

city: Tokyo

first: Juntaro

last: Matsuzaki

address: 1-5-30 Shibakoen, Minato-ku

institute: Keio University Faculty of Pharmacy

summary: Plasma extracellular vesicle (EV) miRNA profile before and after the administration of PRI-724 in patients with liver cirrhosis

overall_design: 18 patients with liver cirrhosis received PRI-724. Plasma samples were obtained before and after the administration of PRI-724 and plasma EVs were collected using the TIM4 method (Wako). Comprehensive miRNA microarray analysis was performed for the collected EVs using 3D-Gene (Toray).

first: Yoshida

last: Mayu

first: Matsuzaki

last: Juntaro

first: Fujita

last: Koji

first: Kimura

last: Masamichi

first: Tokuda

last: Noi

first: Yamaguchi

last: Tomoko

first: Kuroda

last: Masahiko

first: Ochiya

last: Takahiro

first: Saito

last: Yoshimasa

last: Kiminori


title: Liver tissue miRNA profile before and after the administration of PRI-724 in patients with liver cirrhosis

summary: The dataset analyzed in the report entitled Plasma extracellular vesicle microRNAs reflecting the therapeutic effect of the CBP/β-catenin inhibitor PRI-724 in patients with liver cirrhosis

overall_design: 13 patients with liver cirrhosis received PRI-724. Biopsy samples of the liver were obtained before and after the administration of PRI-724.

first: Umezu

last: Tomohiro


title: The impact of endurance exercise on human skeletal muscle transcriptome

city: Tübingen

first: Thomas

last: Beiter

address: Hoppe-Seyler-Str. 6

department: Sports Medicine

country: Germany

institute: Eberhard-Karls-University Tübingen

summary: The aim of this study was to elucidate the transcriptional signatures that distinguish the endurance-trained and the untrained muscle in healthy adult young males, both at baseline as well as in response to an acute bout of exercise.

overall_design: We characterized baseline differences as well as acute exercise-induced transcriptome responses in vastus lateralis biopsy specimen of endurance-trained athletes (ET; n = 8; age, 25.4 ±3.8; VO2max, 67.2 ±8.9 ml/min/kg) and sedentary untrained volunteers (SED; n = 8; age, 22.6 ±2.8; VO2max, 40.3 ±7.6 ml/min/kg) using Human Genome U219 (HG-U219) microarray platform. The acute exercise protocol that consisted of 60 min of high intensity cycling exercise on a cycle ergometer at a power requiring 80% of the individual VO2max (including 10 min of initial warm-up cycling at 60% VO2max). Baseline samples of the resting muscle were obtained 24 hours before the acute exercise protocol was started. Post exercise biopsies were taken at 30 min (+30') and at 3 hours (+3 h) after cessation of acute cycling exercise.

first: Martina

last: Zügel

first: Andreas

last: Nieß

first: Frank

middle: C

last: Mooren

first: Jürgen

last: Steinacker


title: The Wnt co-receptor PTK7/Otk in Neurogenesis and Patterning

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: Wnt signaling is a highly conserved metazoan pathway that plays a crucial role in cell-fate determination and morphogenesis during development. Wnt ligands can induce disparate cellular responses. The exact mechanism behind these different outcomes is not fully understood but may be due to interactions with different receptors on the cell membrane. PTK7/Otk is a transmembrane receptor that is implicated in various developmental and physiological processes including cell polarity, cell migration, and invasion. Here we examine two roles of Otk1 and Otk2 in patterning and neurogenesis. We find that Otk1 is a positive regulator of signaling and Otk2 functions as its inhibitor. We propose that PTK7/Otk functions in signaling and in particular cell migration and polarity contributing to the diversity of cellular responses seen in Wnt-mediated processes.

overall_design: To investigate the function of Wnt4, Otk1 and Otk2 in Drosophila embryos, we used the UAS and RNAi systems in Drosophila to upregulate and downregulate the expression of these target genes. Two replicates were sequenced per condition.

first: Tan

middle: Q

last: Hui

first: Agimaa

last: Otgonbataar

first: Nicholas

last: Tolwinski

first: Nathan

last: Harmston


title: cGAS-STING axis activation drove inflammatory phenotype acquisition of senescent nucleus pulposus cells via p65-mediated transcriptional modulation

city: Wuhan

first: Cao

last: Yang

state: Hubei

address: Jiefang average

institute: Wuhan Union Hospital

summary: Given the leading cause of disability worldwide, low back pain (LBP) is recognized as a pivotal socio-economic challenge to the aging population, which is importantly attributed to intervertebral disc degeneration (IVDD), a highly prevalent affliction of aging. Elastic nucleus pulposus (NP) tissue is essential for maintenance of IVD structural and functional integrity. Native NP cells exhibit crucial functions for regulating extracellular matrix homeostasis, constructing an accommodating biomechanical environment and maintaining the gelatinous property of NP tissue. The accumulation of senescent NP cells with inflammatory hypersecretory phenotype due to aging and other damaged factors is a distinctive hallmark of IVDD initiation and progression. In this study, we revealed a mechanism of IVDD progression in which aberrant genomic DNA damage promotes NP cell inflammatory senescence via activation of cGAS-STING axis. cGAS-STING axis activation drove inflammatory phenotype acquisition and inflammatory hypersensitivity to damaged signals of senescent NP cells via p65-mediated transcriptional modulation. And STING pharmacological inhibitor notably suppressed p65-mediated inflammatory response formation and senescence-associated screctory phenotype (SASP) acquisition of senescent cells.

overall_design: The CUT&Tag-seq (Cleavage under targets and tagmentation sequencing) in nucleus pulposus (NP) cells from degenerated and no-degenerated human NP tissues via using specific anti-p65 antibody. The p65-binding CUT&Tag-seq in P8 senescent NP cells after treated with STING pharmacological inhibitor (H-151) or vehicle (DMSO) for 24 hours.

first: Weifeng

last: Zhang

first: Gaocai

last: Li

first: Xingyu

last: Zhou


title: RNA-seq profiling in Arabidopsis thaliana wild-type and cpl2-2

city: Singapore

first: Yu

state: Singapore

address: 1 Research Link national university of singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: To investigate the function of CPL2 in flowering time control, we collected 9-day-old wild type and cpl2-2 seedlings to perform RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 9-day-old wild-type Col and cpl2-2 seedlings. Each sample has three biological replicates.

first: Lisha

last: Shen


title: Gene expression data from HepG2  cell treated with glutathione (GSH)

city: Inashiki

first: Yoshiaki

last: Uchida

state: Ibaraki

summary:
Gene expression profiling reveals multiple tissue-specific functionality of GSH.
We evaluated the effects of GSH against hydrogen peroxide (HP) on HepG2 cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of GSH.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and GSH-treated HepG2 samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space) were considered as differentially expressed genes (DEGs).


title: CytoDNA triggered NP cell inflammatory senescence via cGAS-STING axis sensing but not AIM2 inflammasome activation

summary: Given the leading cause of disability worldwide, low back pain (LBP) is recognized as a pivotal socio-economic challenge to the aging population, which is importantly attributed to intervertebral disc degeneration (IVDD), a highly prevalent affliction of aging. Elastic nucleus pulposus (NP) tissue is essential for maintenance of IVD structural and functional integrity. Native NP cells exhibit crucial functions for regulating extracellular matrix homeostasis, constructing an accommodating biomechanical environment and maintaining the gelatinous property of NP tissue. The accumulation of senescent NP cells with inflammatory hypersecretory phenotype due to aging and other damaged factors is a distinctive hallmark of IVDD initiation and progression. In this study, we revealed a mechanism of IVDD progression in which aberrant genomic DNA damage promoted NP cell inflammatory senescence via activation of cGAS-STING axis. cGAS-STING axis activation drove inflammatory phenotype acquisition and inflammatory hypersensitivity to damaged signals of senescent NP cells via NF-ÎºB pathway-mediated transcriptional modulation. And the administration of H-151 revealed that STING pharmacological inhibitor notably suppressed the inflammatory response formation and senescence associated screctory phenotype (SASP) acquisition of senescent cells. Furthermore, blocking STING activation could suppress NF-ÎºB pathway-mediated transcriptional remodeling and inflammatory phenotype acquisition in senescent NP cells.

overall_design: The transcriptional profiles of nucleus pulposus (NP) cells from three degenerated and three no-degenerated human NP tissues. The transcriptional profiles of NP cells at passage 2 (P2) generation and passage (P8) generation via serial passage.  The transcriptional profiles of P8 senescent NP cells treated with H-151 or DMSO.


title: Prenatal screening for miRNAs in fetal diseases

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

summary: Distinct miRNA expression patterns may reflect anomalies related to fetal  malformations such as spinal bifida (SB) or congenital diaphragmatic hernia (CDH), which could shed light on novel pathomechanism determination and subsequent diagnostic significance evaluation. The aim of this study was to determine the miRNA maternal expression profile in plasma and amniotic fluid samples of women carrying fetuses with SB and CDH.

overall_design: Women carrying fetuses with SB, women carrying fetuses with CDH, and women with euploid healthy fetuses were enrolled for this study. miRNA profile in amniotic fluid and matched plasma samples was analyzed using NanoString miRNA assay.

first: Monika

last: Zbucka-Krętowska


title: B cells mediate lung ischemia-reperfusion injury by recruitment of CCR2+-classical monocytes via synergistic BCR-TLR4 signaling

city: Saint Louis

first: Ruben

last: Nava

state: MO

address: 4590 Children’s Place

department: Department of Surgery

institute: Washington University in St Louis

summary: Ischemia reperfusion injury (IRI)-mediated primary graft dysfunction (PGD) adversely impacts both short- and long-term outcomes after lung transplantation, a procedure which remains the only treatment option for patients suffering from end-stage respiratory failure. While B cells can regulate adaptive immune responses through antibody production, antigen presentation and secretion of cytokines, their role in lung IRI is not well understood. Here, we demonstrate by intravital imaging that B cells are rapidly recruited to injured lungs, where they extravasate into the parenchyma. Using hilar clamping and transplant models, we observe that lung-infiltrating B cells produce the monocyte chemokine CCL7 in Toll-like receptor 4 (TLR4)-TRIF-dependent fashion, a critical step contributing to classical monocyte (CM) recruitment and subsequent neutrophil extravasation, resulting in worse lung function. We find that synergistic BCR-TLR4 activation on B cells is required for the recruitment of CMs to the injured lung. Finally, we corroborate our findings in reperfused human lungs, where we observe a correlation between B cell infiltration and CM recruitment after transplantation. This study uncovers a role for B cells as critical orchestrators of lung IRI. As B cells can be depleted with currently available agents, our study provides a rationale for clinical trials investigating B cell-targeting therapies.

overall_design: We performed syngeneic orthotopic murine left lung transplants from CD45.2+ C57BL/6J to CD45.1+ C57BL/6J mice with 60 minutes of cold ischemia at 4˚C then 45 minutes of warm ischemia at 28˚C followed by either 2 hours (WT2H) or 3 days (WT3D) of reperfusion and created single cell suspensions. Additionally, we also collected single cells from a naïve C57BL/6J mouse (CTRL). From each sample (CTRL, WT2H, WT3D), we pooled cells from two mice and sorted recipient CD45.1+ cells. We then performed single-cell RNA sequencing on these three samples.

first: Khashayar

last: Farahnak

first: Yun

middle: Z

last: Bai

first: Yuhei

last: Yokoyama

first: Deniz

middle: B

last: Morkan

first: Zhiyi

last: Liu

first: Junedh

last: Amrute

first: Alejandro

last: De Filippis Falcon

first: Yuriko

last: Terada

first: Fuyi

last: Liao

first: Wenjun

first: Hailey

last: Shepherd

first: Ramsey

middle: R

last: Hachem

first: Varun

last: Puri

first: Kory

middle: J

last: Lavine

first: Andrew

last: Gelman

first: Ankit

last: Bharat

first: Daniel

last: Kreisel


title: Dabrafenib alters MDSC differentiation and function by activation of GCN2

city: Toronto

first: Tracy

last: McGaha

state: Ontario

address: 610 University Ave

department: Immunology

institute: University Health Network

summary: The BRAF inhibitor dabrafenib has been reported to activate the integrated stress response (ISR) kinase GCN2, and the therapeutic effect has been partially attributed to GCN2 activation. Since ISR signaling is a key component of myeloid-derived suppressor cell (MDSC) development and function, we measured the effect of dabrafenib on MDSC differentiation and suppressive activity. Our data showed that dabrafenib attenuated MDSC ability to suppress T cell activity, which was associated with a GCN2-dependent block of the transition from monocytic progenitor to polymorphonuclear (PMN)-MDSCs and proliferative arrest resulting in PMN-MDSC loss. Transcriptional profiling revealed that dabrafenib-driven GCN2 activation altered metabolic features in MDSCs enhancing oxidative respiration, and attenuated transcriptional programs required for PMN development. Thus, ourdata reveals transcriptional networks that govern MDSC developmental programs, and the impact of GCN2 stress signaling on the innate immune landscape in tumors, providing novel insight into potentially beneficial off target effects of dabrafenib.

overall_design: Bone marrow was flushed out of the tibia and femur of C57BL/6 mice. Red cells were depleted with ACK lysing buffer. Cells were seeded at concentration 6x10^5 cells/mL in RPMI 1640 medium supplemented with 10% FBS, 100 units/mL of penicillin, 100 µg/mL of streptomycin and 55 µM 2-Mercaptoethanol. GM-CSF (50 ng/mL) and IL-6 (50 ng/mL) were used to drive MDSC differentiation in vitro in presence of 1.5 μM Dabrafenib or matching volume of Dimethyl sulfoxide (DMSO). On day 4, cells were harvested and processed for scRNA-seq using Chromium Next GEM Single Cell 5’ Kit v2 workflow (10x Genomics).

first: M

middle: T

last: Ciudad

first: R

last: Quevedo

first: S

last: Lamorte

last: Jin

first: N

last: Nzirorera

last: Koritzinsky

first: T

middle: L


title: Effect of vesicles produced after apoptosis induction therapy on tumor cells

city: Guangzhou

first: Xiaotian

last: He

state: Guangdong

address: Dongfeng Road

institute: Sun Yat-sen University Cancer Center (SYSUCC)

summary: Understanding the mechanism by which cancer derived apoEVs regulate tumor cells is imperative for enhancing our knowledge of tumor metastasis and recurrence. Herein, we conducted a series of in vivo and in vitro experiments, and we report that tumor-derived apoEVs promoted lung adenocarcinoma (LUAD) metastasis, self-renewal and chemoresistance. Mechanistically, we demonstrated that apoEVs facilitated tumor metastasis and stemness by initiating the epithelial-mesenchymal transition program and upregulating the transcription of the stem cell factor SOX2. In addition, we found that ALDH1A1, which was transported by apoEVs, activated the NFκB signaling pathway by increasing aldehyde dehydrogenase enzyme activity in recipient tumor cells. Furthermore, targeting apoEVs-ALDH1A1 significantly abrogated these effects. Collectively, our findings elucidate a novel mechanism of apoEV-dependent intercellular communication between apoptotic tumor cells and live tumor cells that promotes the formation of cancer stem cell-like populations, and these findings reveal that apoEVs-ALDH1A1 may be a potential therapeutic target and biomarker for LUAD metastasis and recurrence.

overall_design: A549 cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml).Apoptosis was induced by Staurosporine or cisplatin. After co-culture with tumor cells for 96 h, RNA was extracted and mRNA sequencing was performed.

first: Lanjun

last: Zhang


title: Transcriptional responses of the fetal lung after intra-amniotic LPS injection in rats [placenta]

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary: We evaluated the transcriptional responses of the placenta to intra-amniotic inflammation induced by intra-amniotic LPS injections.

overall_design: Pregnant rats were randomized to receive ultrasound-guided intra-amniotic injections of placebo (PBS) or LPS (E. coli O55:B5, 10 micrograms) on gestational day 18. Tissue samples were collected 24 hours after injection.

first: April

middle: W

last: Tan

first: Xiaoying

last: Tong

first: Silvia

last: Alvarez-Cubela

first: Pingping

last: Chen

first: Vanessa

last: Nunes de Paiva

first: Juan

last: Dominguez-Bendala

first: Claudia

last: Rodrigues


title: Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program [RNA-seq]

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

summary: Tissue resident macrophages play important roles in tissue homeostasis and repair. However, how macrophages monitor and maintain tissue integrity is not well understood. The extracellular matrix (ECM) is a key structural and organizational component of all tissues. Here, we find that macrophages sense the mechanical properties of the ECM in order to regulate a specific tissue repair program. We show that macrophage mechanosensing is mediated by cytoskeletal remodeling and can be performed in three-dimensional environments through a non-canonical, integrin-independent mechanism analogous to amoeboid migration. We find that these cytoskeletal dynamics also integrate biochemical signaling by CSF1 and ultimately regulate chromatin accessibility to control the mechanosensitive gene expression program. This study suggests a distinct mode of ECM mechanosensing and growth factor signaling through which macrophages may regulate tissue repair and fibrosis.

overall_design: RNA-seq of IL-4 stimulated and unstimulated murine bone-marrow derived macrophages (BMDMs) in a 3-dimensional collagen gel.

middle: D

first: Matthew

last: Mezlish

first: Yoshitaka

last: Kimura

first: Ruslan

last: Medzhitov


title: Transcriptional responses of the fetal lung after intra-amniotic LPS injection in rats

summary: We evaluated the transcriptional responses of the fetal lung to intra-amniotic inflammation induced by intra-amniotic LPS injections.

middle: N

last: de Paiva


title: Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program [ATAC-seq]

overall_design: ATAC-seq of unstimulated, IL-4 stimulated, IL-4 stimulated+MCSF, and IL-4 stimulated+LatA murine bone-marrow derived macrophages (BMDMs).


title: The interaction of MLE with CLAMP zinc finger domains is important for dosage compensation in Drosophila melanogaster

city: Moscow

first: Anastasia

last: Revel-Muroz

address: 34/5 Vavilov St.

country: Russia

institute: Institute of Gene Biology, Russian Academy of Sciences

summary: The Drosophila male-specific lethal (MSL) complex binds to the male X chromosome to activate transcription, and consists of five proteins, MSL1, MSL2, MSL3, MOF, MLE, and two roX RNAs. The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. MSL2 is expressed only in males and interacts with the N-terminal zinc-finger of the transcription factor CLAMP that is important for specific recruitment of the MSL complex on the male X chromosome. Here we found that the unstructured C-terminal region of MLE interacts with 6-7 zinc-finger domains of CLAMP. In vitro 4-5 zinc fingers are critical for specific DNA-binding of CLAMP with GA-repeats, which constitute the core motif at the high affinity binding sites for MSL proteins. Deletion of the Clamp Binding Domain (CBD) in MLE results in decreasing of MSL proteins association with male X chromosome and increasing of male lethality. These results suggest that interactions of unstructured regions in MSL2 and MLE with CLAMP zinc finger domains are important for the specific recruitment of the MSL complex on the male X chromosome.

overall_design: ChIP-seq signal of the MSL1, MSL2 and MSL3 proteins occupancy in MLEwt and MLEΔCBD transgenic fly lines

first: O

last: Maksimenko

first: A


title: Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation

city: Villigen

first: Shivashankar

last: GV

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institut

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

overall_design: Refer to individual Series


title: NSUN6 is a prognostic indicator and therapeutic target in esophageal squamous cell carcinoma

city: guangzhou

first: hui

last: han

state: guangdong

address: yuexiu

institute: the first affiliated hospital，sun yat-sen university

summary: We performed polyribosome-bound mRNAs sequencing (polyribosome-seq) using the samples from NSUN6 depleted K150 cells and control cells and calculated the translation efficiency (TE) for each sample.

overall_design: Translation efficiency (TE) of individual transcript from K150 cells with or without NSUN6 knockdown was calculated by dividing its FPKM (Fragments Per Kilobase of transcript per Million mapped reads) in polyribosome-seq by its FPKM in corresponding input RNA-seq

first: Hui

last: Han


title: Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program


title: Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (RNA-Seq)

summary: Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional  changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state. In addition, the rejuvenated cells contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

overall_design: To investigate gene expression differences among the aged fibroblast we establisehed young 10 year age GM09503 and 75 year aged GM08401 human dermal fibroblast. On ther hand we allow to grow the 75 year aged fibroblast on fixed micropatterns to achieve partial reprogramming state up until 8 day. At 8 day spheroid formation cells were then re-differerntiated called rejuvenation using collagen gel with 1 mg/ml for 48 hours. Cells after 48 hours were isolated as single cells using collaginase enzyme treatment followed by culture them on normal cell culture dish. We then purified total RNA from all three samples in replicates and subjected to sequencing.

first: Trinadharao

last: Sornapudi

first: Luezhen

last: Yuan

first: Jana

last: Braunge

first: Caroline

last: Uhler

first: G

middle: V

last: Shivashankar


title: Endothelial cell-derived extracellular vesicles promote sepsis-related acute lung injury by targeting and reprogramming monocytes

city: Nanjing

first: Lu

last: Wang

address: 87 Dingjiaqiao Road

department: Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine

institute: Zhongda Hospital, School of Medicine, Southeast University

summary: Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a common life-threatening critical syndrome with no effective pharmacotherapy. Extracellular vesicles (EVs) are considered as a new way of long-distance communication between cells. Our previous research using an ex vivo perfused human ALI model suggested that endothelial cell-derived EVs (EC-EVs) mediate the development of ALI/ARDS. However, how EC-EVs aggravate lung injury remains largely unknown. Here we demonstrated that EC-EVs released under inflammatory stimulation are preferentially taken up by monocytes and reprogram the differentiation of monocytes towards M1 type macrophage. These findings demonstrate a previously unidentified mechanism by which distant infections could lead to ALI/ARDS, providing novel targets and strategies for the prevention and treatment of sepsis-related ALI/ARDS.

overall_design: To further clarify the role of EC-EVs in the development of sepsis-related ARDS, we isolated normal mouse endothelial cell-derived EVs (N-EC-EVs) and used LPS stimulation to simulate the in vivo environment of sepsis (the derived EVs were named L-EC-EVs). The extracted primary mouse bone marrow-derived monocytes were co-incubated with N-EC-EVs or L-EC-EVs for 24 h, and subjected to RNA sequencing.

last: wang

first: Ying

last: Tang

first: Haibo

last: Qiu


title: Inter-Organ Steroid Hormone Signaling Promotes Myoblast Fusion via Direct Transcriptional Regulation of a Single Key Effector Gene

city: DALLAS

first: Zhi-Rong

last: Ruan

address: 6000 Harry Hines Blvd. NA8.102

department: Molecular Biology

institute: UTSouthwestern Medical Center

summary: Steroid hormones regulate tissue development and physiology by modulating the transcription of a broad spectrum of genes. In insects, the principal steroid hormones, ecdysteroids, trigger the expression of thousands of genes through a cascade of transcription factors (TFs) to coordinate developmental transitions such as larval molting and metamorphosis. However, whether ecdysteroid signaling can bypass transcriptional hierarchies to exert its function in individual developmental processes is unclear. Here, we report that a single non-TF effector gene mediates the transcriptional output of ecdysteroid signaling in Drosophila myoblast fusion, a critical step in muscle development and differentiation. Specifically, we show that the 20-hydroxyecdysone (commonly referred to as “ecdysone”) secreted from an extraembryonic tissue, amnioserosa, acts on embryonic muscle cells to directly activate the expression of antisocial (ants), which encodes an essential scaffold protein enriched at the fusogenic synapse. Not only is ants transcription directly regulated by the heterodimeric ecdysone receptor complex composed of Ecdysone receptor (EcR) and Ultraspiracle (USP) via ecdysone response elements, but more strikingly, expression of ants alone is sufficient to rescue the myoblast fusion defect in ecdysone signaling-deficient mutants. We further show that EcR/USP and a muscle-specific transcription factor Twist synergistically activate ants expression in vitro and in vivo. Taken together, our study provides the first example of a steroid hormone directly activating the expression of a single key non-TF effector gene to regulate a developmental process via inter-organ signaling and provides a new paradigm for understanding steroid hormone signaling in other developmental and physiological processes.

overall_design: To identify the downstream targets of ecdysone signaling, three independent mRNA libraries of ∼stage 14 wild-type and spo mutant Drosophila embryos were sequenced and analyzed.

first: Ze

last: Yu

first: Chao

last: Xing

first: Elizabeth

last: Chen


title: Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

summary: Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

overall_design: To investigate chromatin interaction frequencies differences among the aged fibroblast we establisehed young 10 year age GM09503 and 75 year aged GM08401 human dermal fibroblast. On ther hand we allow to grow the 75 year aged fibroblast on fixed micropatterns to achieve partial reprogramming state up until 8 day. At 8 day spheroid stage cells were then re-differerntiated called rejuvenation using collagen gel with 1 mg/ml for 48 hours. Cells after 48 hours were isolated as single cells using collaginase enzyme treatment followed by culture them on normal cell culture dish. We then prepare three cell types for HiC DNA preparation using standarad in-nucleus HiC procedure.

middle: M


title: Coactivator condensation drives lineage specification

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: During development, cells make switch-like decisions to activate the expression of new gene programs leading to lineage specification1. The mechanisms underlying these decisive choices remain unclear2. Here we find that Myocardin (MYOCD), a cardiomyocyte and smooth muscle cell-specific transcriptional coactivator3-6, activates lineage-specific gene programs by concentration-dependent and switch-like formation of nuclear condensates. While compartmentalization of the transcriptional machinery by condensates has been associated with gene activation7,8, directly linking the two processes has been a major challenge for the field9,10. By modeling the natural changes in MYOCD concentration during development, coupled with quantitative fluorescence microscopy, single-cell resolution reporter assays, and cellular differentiation assays, we demonstrate that condensate formation is directly linked to transcriptional activation and lineage specification. During cardiomyocyte and smooth muscle cell differentiation, the formation of MYOCD condensates precedes activation of cell identity genes and these condensates are present at sites of cell identity gene transcription. MYOCD condensates form, activate gene expression, and specify cell state at critical concentration thresholds, dependent upon the C-terminal disordered region of MYOCD. Disrupting condensate formation by manipulating the sequence of this region impairs gene activation which can be rescued by replacing this region with condensate-forming disordered regions from functionally unrelated proteins. These results demonstrate that coactivator condensation at critical concentrations enables switch-like changes in gene expression programs crucial for lineage specification.

overall_design: Comparative gene expression profiling analysis of RNA-seq data and MYOCD chromatin occupancy by ChIP-seq data for undifferentiated hiPSCs and meso-stage differentiation of smooth muscle (D8) and cardiomyocytes (D5)

first: Peiheng

last: Gan

first: Mikayla

last: Eppert

first: Nancy

last: De La Cruz

first: Reshma

last: Veettil

first: Akansha

last: Shah

first: Prashant

last: Pradhan

first: Svetlana

last: Bezprozvannaya

first: Ning

last: Liu

first: Eric

last: Olson


title: H3K4 methylation regulates development, DNA repair, and virulence in Mucorales

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

institute: University of Murcia

summary: Mucorales are basal fungi that opportunistically cause a fatal infection known as mucormycosis (black fungus disease), which poses a significant threat to human health due to its high mortality rate and its recent association with SARS-CoV-2 infections. On the other hand, histone methylation is a regulatory mechanism with pleiotropic effects, including the virulence of several pathogenic organisms. However, the role of epigenetic changes at the histone level never has been studied in Mucorales. Here, we dissected the functional role of Set1, a histone methyltransferase that catalyzes the methylation of H3K4, which is associated with the activation of gene transcription and virulence. A comparative analysis of the Mucor lusitanicus genome (previously known as Mucor circinelloides f. lusitanicus) identified only one homolog of Set1 from Candida albicans and Saccharomyces cerevisiae that contains the typical SET domain. Knockout strains in the gene set1 lacked H3K4 monomethylation, dimethylation, and trimethylation enzymatic activities. These strains also showed a significant reduction in vegetative growth and sporulation. Additionally, set1 null strains were more sensitive to SDS, EMS, and UV light, indicating severe impairment in the repair process of the cell wall and DNA lesions and a correlation between Set1 and these processes. During pathogen-host interactions, strains lacking the set1 gene exhibited shortened polar growth within the phagosome and attenuated virulence both in vitro and in vivo. Our findings suggest that the histone methyltransferase Set1 coordinates several cell processes related to the pathogenesis of M. lusitanicus and may be an important target for future therapeutic strategies against mucormycosis.

overall_design: RNA-seq experiment to analyze the differences in gene expression caused by Set1 KO in M. lusitanicus. Total RNA was extracted from MU636 and MU1350 (set1 KO) for 24 hours on YPG media (solid) at 26 ºC. For each strain, we performed three biological replicates

first: José

last: Cánovas-Márquez


title: PanCancer Immune panel on infiltrating memory CD8 T cells purified from the allografts subjected to prolonged cold ischemic storage  in mice cardiac heart transpalnatation model.

city: cleveland

first: Hidetoshi

last: Tsuda

state: ohio

address: 9500 euclid ave

institute: cleveland clinic

summary: We testd differences in hetelogous memory CD8 T cells and donor specific memory CD8 T cells  infiltrating A/J heart allografts from of CTLA-4Ig non- or conditioned B6 recipients.Transcroptome analysis using memory CD8 T cell lysates isolated from the allografts showed differential expression of transcripts in this model.

overall_design: To test differences in heterologous memory CD8 T cells and donor specific memory CD8 T cells infiltrating A/J heart allografts  subjected to 8 hours cold ischemic storage (CIS),  we purified CD45.2+CD44+CD8 cells from the grafts on day2 post-transplant or at the time of rejection by flow sorting. To generate donor reactive memory CD8+ T cells, wild type (CD45.2+) B6 recipients received A/J skin allografts. After 8 weeks, recipient spleen suspensions were prepared from the mice and total CD8+ T cells were enriched by a negative selection mouse T cell isolation kit. Then, purified CD8 T cell populations were transferred intravenously (2x106/mouse) to congenic (CD45.1+) B6 recipients. After 72 hours, recipient mice received cardiac allografts subjected to prolonged CIS, were injected CTLA-4 Ig at 0.25 mg i.p. daily on days 0 and +1 and the allografts were harvested on days 2 post-transplant. Then, we performed transcriptomic analysis of heterologous or donor specific memory CD8 T cells using a PanCancer immune-profiling gene panel for the NanoString platform.

first: Karen

middle: S

last: Keslar

first: Peter

last: Heeger

first: Anna

last: Valujskikh

first: Robert

last: Fairchild


title: Senescent cell elimination modifies features of Alzheimer’s disease in 3xTg-AD mice

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: Cellular senescence has been associated with neurodegenerative disease and clearance of senescent cells using genetic or pharmaceutical strategies (senolytics) has demonstrated beneficial effects in mouse models investigating individual disease etiologies of Alzheimer’s disease (AD). However, it has remained unclear if senescent cell clearance in a mouse model exhibiting both plaque and tau pathologies modifies the disease state (3xTg). Here, we show that treatment with senolytics (ABT263 (navitoclax) or a combination of dasatinib and quercetin (D+Q)) or transgenic removal of p16-expressing cells (via INK-ATTAC) reduced microgliosis and ameliorated both amyloid and tau pathology in 3xTg mice. Using RNA sequencing, we found evidence that synaptic dysfunction and neuroinflammation was attenuated with senescent cell removal. Unfortunately, these beneficial effects were not seen with short-term senolytic treatment in mice with more advanced disease. Overall, our results further corroborate the beneficial effects senescent cell clearance could have on AD and highlight the importance of early intervention for treatment of this debilitating disease.

overall_design: Gene expression profiling analysis using data obtained from bulk RNA-seq of WT and 3xTg-AD mice treated with vehicle or ABT263, or dasatinib+quercetin.

first: Pei

last: Ng

first: Hu

last: Li

first: Darren

last: Baker


title: Epigenome analysis of control and mTORC2-suppressed glioblastoma cells

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

institute: Tokyo Women's Medical University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of control and mTORC2-suppressed glioblastoma cells (U87-EGFRvIII cells). The Illumina Infinium HumanMethylation EPIC BeadChip Array was used to obtain DNA methylation profiles with 865,918 probes in glioblastoma cell line samples. Samples included 2 control U87-MG cells without mTORC2 suppresion, and mTORC2-knockdown U87-MG cells with lentivirus-mediated suppression of mTORC2.

overall_design: DNA methylation profiles of U87-EGFRvIII glioblastoma cell lines with lentivirus-mediated scramble or Rictor (a core component of mTORC2) knockdown were generated by the Illumina Infinium HumanMethylation EPIC BeadChip Array.

first: Masui

last: Kenta


title: Compared with the Mock group, FGF8+10 treatment mature the differentiated LPM-like cells to form LM-like cells [RNA-seq]

city: Chengdu

first: Zhonghan

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

summary: When treated with FGF8+10, LM makers were upregulated and the expression levels were higher than that of the Mock cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hPSC-derived Msx1+Pdgfra+ and Msx1+Pdgfralow cells from FGF8+10 and Mock groups.

first: Yuansong

last: Liao

first: Fanchen

last: Kang

first: Jingfei

last: Xiong

first: Ling

last: Yu

first: Kun

last: Xie

first: Yuqing

last: Wang

first: Hanyi

last: Chen

first: Guogen

last: Ye

first: Yike

last: Yin

first: Weihua

last: Guo

first: Qing

last: Zhu


title: Compared with the Mock group, FGF8+10 treatment mature the differentiated LPM-like cells to form LM-like cells, and gene expression profile at single cell level of Msx1+ mesenchymal progenitors from mouse E10.5 embryos

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profile at single cell level of Msx1+ mesenchymal progenitors from mouse E10.5 embryos [scRNA-seq]

summary: Lateral plate mesoderm and limb mesenchyme are the major subsets.

overall_design: Msx1+ cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of tdTomato signal and analyzed using scRNAseq.


title: Customized PanCancer Immune panel on heart allografts subjected to 8hrs cold ischemic storage in mice cardiac heart transpalnatation model.

first: Hidetoshi

last: Tsuda

summary: We tested the impact of prolonged graft cold storage on graft injury.Transcroptome analysis using total RNA isolated from the allografts showed differential expression of transcripts in this model.

overall_design: To identify the transcriptome signature of the allografts with low- vs. high risk, we performed transcriptomic analysis of allografts subjected either 30min or 8hrs cold ischemic storage using  a customized PanCancer immune-profiling gene panel for the NanoString platform.We also used the allograft in the recipient received  p40 homodimers.

first: Karen

last: Keslar

first: Peter

last: Heeger

first: Anna

last: Valujskikh

first: Robert

last: Fairchild


title: Alzheimer’s disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs [lncRNA]

city: Kuopio

first: Flavia

last: Scoyni

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary:
To detect total RNA in microglia derived from AD mice (5xFAD) brain we single cell sorted Cd11b+ and Cd45+ cells divided by Methoxy-X04 staining (Ab aggregates) positivity
We performed differentially expression analysis of RNA-seq of wild-type microglia (Me-X04 neg), non-phagocytic AD microglia (Me-X04 neg), phagocytic AD microglia (Me-X04 positive)

overall_design: Comparative gene expression analysis of RNA-seq data for wild-type microglia (Me-X04 neg), non-phagocytic AD microglia (Me-X04 neg), phagocytic AD microglia (Me-X04 positive)(n= 6-7 biological replicates)

first: Luca

last: Giudice


title: Exosomal microRNA sequencing in Nicorandil pretreated and non-treated mesenchymal stem cell-derived exosomes

city: Beijing

first: Zhaoting

last: Gong

address: No.167 North Lishi Road, Xicheng District

institute: Fuwai Hospital

summary: To investigate the specific miRNA conducting the cardioprotective effect of Nicorandil pretreated MSC-derived exosomes (MSCNIC-Exo) in cardiac repair, we performed microRNA sequencing on exosomes secreted from nicorandil pretreated MSCs and non-treated MSCs to identify differentially expressed miRNA.

overall_design: MSCNIC-Exo was isolated from conditioned medium of MSCs pretreated by 200uM of nicorandil for 24 hours. Three isolated samples for each group(MSCNIC-exo and MSC-exo) were collected and RNA isolated from exosomes were analyzed using Illumina HiSeqTM 2500 platform.

first: Yang

last: Yuejin


title: Alzheimer’s disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs [BV-2 cells]

summary:
To detect miRNA targets in glioblastoma cell line (BV-2) we stimulate the cells with LPS 10ng/ml or vehicle and then transfect them with miRNA mimics or scrable control
We performed differentially expression analysis of RNA-seq BV-2 cells vehicle or LPS stimulated overexpressing miRNA mimic or scramble mimic

overall_design: Comparative gene expression analysis of RNA-seq data for Vehicle BV-2 cells overexpressing scramble mimic, miR-7a, miR-29a or miR-146a or BV-2 induced with LPS overexpressing scramble mimic, miR-7a, miR-29a or miR-146a (n= 4)


title: Alzheimer’s disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs [short RNA]

summary:
To detect miRNAs in microglia derived from AD mice (5xFAD) brain we single cell sorted Cd11b+ and Cd45+ cells divided by Methoxy-X04 staining (Ab aggregates) positivity
We performed differentially expression analysis of RNA-seq of wild-type microglia (Me-X04 neg), non-phagocytic AD microglia (Me-X04 neg), phagocytic AD microglia (Me-X04 positive)

overall_design: Comparative gene expression analysis of RNA-seq data for wild-type microglia (Me-X04 neg), non-phagocytic AD microglia (Me-X04 neg), phagocytic AD microglia (Me-X04 positive)(n= 5 biological replicates)


title: Knockdown of ribosome RNA processing protein 15 (RRP15) suppresses metastasis of hepatocellular carcinoma via LAMC2/FAK pathway

city: Wenzhou

first: Liang

last: Xu

state: Zhejiang

address: Chashan Higher Education Zone

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

summary: Collectively, RRP15 is highly expressed in HCC tissues and is positively correlated with OS% and DSS% of HCC patients. Knockdown of RRP15 notably prevented the proliferation of HCC cells in vitro and the growth of ectopic transplanted tumors in vivo. Moreover, RRP15 knockdown suppressed the cells migration, invasion and adhesion through reducing the activation of laminin 5/integrin β4/FAK signaling pathway. The findings of the current study revealed the role of RRP15 in the progression of HCC, and laid a theoretical basis for RRP15 as a potential target for HCC diagnosis or/and treatment.

overall_design: The expression of RRP15 in normal liver tissues and HCC tissues were analyzed by   using database. RT-qPCR, western blotting, proliferation assay, flow cytometry, transwell   assay, cell scratch assay, cell adhesion assay and subcutaneous tumor-formation assay in   nude mice were used to detect the effects of RRP15 on the proliferation, migration,   invasion and adhesion of HCC cells. The underlying mechanism of RRP15 regulating the   progression of HCC was further determined by RNA-seq and bioinformatics analysis.

first: Ouyang

last: Zhang

first: Yuqin

first: Yanwen

last: Yu


title: Upregulation of VEGF-Hypoxia Signature in Balck Women with Breast Cancer

city: Chicago

first: Olufunmilayo

middle: I

last: Olopade

state: IL

address: 900 E. 57th Street

institute: University of Chicago

summary: Expression of 110 genes were analyzed in breast tumors from African Americans, European Americans and Nigerians

overall_design:
Total RNA were isolated from FFPE breast tumor samples and subjected to NanoString nCounter gene expression array containing 110 genes
abbrebiations: Nig,Nigerians; AA, African Americans; Cau, Caucasians; Lum, Luminal Subtype; Basal, Basal-like Subtype

first: Yoo

last: Han


title: Alzheimer’s disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs

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

overall_design: Refer to individual Series


title: Glutamine inhibited hyperglycolysis to curb lactylation of AMPKα to accelerate extracellular matrix synthesis and autophagy and restrain senescence in nucleus pulposus cell

city: Guangzhou

middle: yang

address: 107 Yanjiang West Road

institute: Sun Yat Sen Memorial Hospital

summary: IDD (Intervertebral disc degeneration) is an important cause of low back pain which has become a global public health problem. We aimed to determine the role of glutamine in the development of IDD and evaluate its mechanism to prevent IDD.

overall_design: Nucleus pulposus cells and SD rats are devided into 3 group under the stimulation of control, TNF-α/puncture and glutamine

first: Yangyang

first: Wei

last: Ye


title: Role of MYC acetylated lysine residues in cell transformation and gene-selective regulation [MCF10A]

city: Riverside

first: Ernest

last: Martinez

address: 900 University Ave.

department: Biochemistry

institute: University of California Riverside

summary: The functions of MYC acetylation have remained unclear. In this study we identified the major lysine residues of MYC that are acetylated by p300 and GCN5 in cancer cell lines and established the requirment of three specific acetyl-lysine (AcK) residues for MYC transformation of Rat1a fibroblasts and MCF10 mammary epithelial cells. We further uncovered gene-selective regulatory functions and conserved genetic programs and biolofical processes regulated by MYC AcK residues in both cell types.

overall_design: We generated stable cell lines (MCF10A) expressing empty vector, mouse MYC wild type (WT), MYC K149R (R149), MYC K158R (R158), or MYC K323R (R323). We performed stranded mRNA sequencing (mRNA-seq) on three biological replicates for each cell line.

first: Jeffrey

last: Pino

first: Ryan

last: Gates

first: Victoria

last: Seewaldt


title: Role of MYC acetylated lysine residues in cell transformation and gene-selective regulation [Rat1A]

overall_design: We generated stable cell lines (Rat1a) expressing empty vector, mouse MYC wild type (WT), MYC K149R (R149), MYC K158R (R158), or MYC K323R (R323). We performed stranded mRNA sequencing (mRNA-seq) on three biological replicates for each cell line.

first: Matthew

last: Hurd

first: Michael

last: Hamilton

first: Thomas

last: Girke


title: Extramedullary hematopoiesis and immune training drive systemic inflammation and associated organ damage in Systemic Lupus Erythematosus

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

type: Methylation profiling by high throughput sequencing


title: Role of MYC acetylated lysine residues in cell transformation and gene-selective regulation

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Transcriptomic analysis of the bone marrow from RNase L-/- mice following total body irradiation.

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

summary: Ionizing radiation is capable of mediating damage on DNA, RNA, proteins and other intracellular biomolecules. The OAS/RNase L pathway, an intracellular RNA sensor that senses exogenous or endogenous dsRNA, plays an important role in the antiviral infection and innate immunity. RNase L is an essential endonuclease that regulates the degradation and translation of RNA during exogenous stimuli. Therefore, we hypothesized that ionizing radiation-induced RNA damage activates the RNA sensor in response to exogenous stresses. RNase L-/- mice were performed to explore the effect of RNase L in radiation-induced damage repair in the bone marrow, a radiation-sensitive organ.

overall_design: Bone marrow derived from RNase L-/- or wildtype mice, which were performed total-body irradiation at a dose of 6Gy by a 60Co irradiator, was analyzed for transcriptome. This experiment is divided into four groups: (1)Wildtype mice with non-treatment, (2)RNaseL-/- mice with non-treatment, (3)Wildtype mice exposed to irradiation, and (4) RNaseL-/- mice exposed to irradiation.

first: Kexin

last: Ding

first: Hanjiang

last: Fu

first: Xiaofei

last: Zheng


title: Induction of fatty acid oxidation underlies DNA damage-induced cell death and ameliorates obesity-driven chemoresistance

city: Seoul

first: Seung Min

last: Jeong

address: 222, Banpo-daero, Seocho-gu

department: Department of Biochemistry

country: South Korea

institute: College of Medicine, The Catholic University of Korea

summary: The DNA damage response is essential for preserving genome integrity and eliminating damaged cells. Although cellular metabolism plays a central role in cell fate decision between proliferation, survival or death, the metabolic response to DNA damage remains largely obscure. Here, we show that DNA damage induces fatty acid oxidation (FAO), which is required for DNA damage-induced cell death. Mechanistically, FAO induction increases cellular acetyl-CoA levels and promotes N-alpha-acetylation of caspase-2, leading to cell death. Whereas chemotherapy increases FAO related genes through PPARα, accelerated hypoxia-inducible factor-1α stabilization by tumor cells in obese mice impedes the upregulation of FAO, which contributes to its chemoresistance. Finally, we find that improving FAO by PPARα activation ameliorates obesity-driven chemoresistance and enhances the outcomes of chemotherapy in obese mice. These findings reveal the shift toward FAO induction is an important metabolic response to DNA damage and may provide effective therapeutic strategies for cancer patients with obesity.

overall_design: mRNA expression profiles of the allograft tumors from lean control mice and leptin-deficient ob/ob mice pre and post chemotherapy.

first: Seung


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ca(OH)2 Nanoparticles Effect

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

institute: Emory University

summary: The goal of this study is to investigate the effect of Ca(OH)2 nanoparticles on the transcriptome profiles of bone marrow derived dendritic cells (BMDCs) of mice

overall_design: Examination of mRNA profiles in bone marrow derived dendritic cells of mice with or without Ca(OH)2 nanoparticles treatment

first: Jin

last: Xie

first: Yong

last: Teng

first: Zhengwei

last: Cao

first: Shuyue

last: Zhan


title: Extramedullary hematopoiesis and immune training drive systemic inflammation and associated organ damage in Systemic Lupus Erythematosus (RNA-seq)

summary:
Extramedullary hematopoiesis (EMH) is an emerging player in peripheral tissue injury in autoimmune disorders. Here, we use the NZBW/F1 lupus mouse model to explore the contribution of EMH to disease pathogenesis of SLE.
We demonstrate that EMH takes place in the spleen of F1-L mice and show it is correlated with the activity of lupus nephritis (LN).
Transcriptomic analysis demonstrated that splenic hematopoietic stem and progenitor cells (HSPC) carry a higher inflammatory potential than their bone marrow counterparts. Administration of β-glucan, an inducer of innate immunity, exacerbated splenic EMH, increased neutrophil production and worsened LN.
Transcriptomic signatures of HSPCs in SLE patients with high disease activity show changes similar to the ones observed in the lupus-prone mouse model.
Overall, EMH and trained immunity are ubiquitous in SLE, contributing to disease pathogenesis by sustaining and amplifying the inflammatory response and increasing the risk for flare of the disease.

overall_design: RNA-seq dataset

first: Eleni

last: Zervopoulou

first: Maria

last: Grigoriou

first: Anastasia


title: Extramedullary hematopoiesis and immune training drive systemic inflammation and associated organ damage in Systemic Lupus Erythematosus (RRBS)

overall_design: RRBS dataset


title: Transcriptional remodeling of primary human monocytes exposed to Leishmania braziliensis

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Trained immunity is a phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled the transcriptome of human monocytes trained with Leishmania braziliensis and then re-exposed to lipopolysaccharide.

overall_design: Human primary monocytes were isolated using Ficoll and Percoll gradient separation. Baseline monocytes were collected after 1 hour in culture (attached). Monocytes were exposed to media alone or Leishmania braziliensis for 24 hours, allowed to differentiate to macrophages for 5 days and then re-exposed to LPS for 4 hours. RNA was collected at baseline (day 0), 24 hours (day 1), day 6 and day 6 with 4hr LPS.

first: Jessica

last: Dos Santos

first: Leo

last: Joosten


title: Serological mechanisms driving cardiotoxicity in COVID-19

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: The aim of the study is to investigate the effects of serum from COVID-19 patients on pluripotent stem cells derived cardiomyocytes (PSC-CMs)

overall_design:
To investigate the effects of serum, PSC-CMs were treated for 4 days in the presence of serum coming from control, mild or severe COVID-19 patients.
To investigate COVID-19 specific pathways, PSC-CMs were also treated with plasma coming from ARDS patients

last: Colzani

first: Eleanor

middle: C

last: Williams

first: Sanjay

last: Sinha


title: Quercetin regulates gene expression in  airway basal cells obtained from pateints with chronic obstructive pulmonary diesease

city: Philadelphia

first: Umadevi

last: Sajjan

state: PA

address: 3500 N Broad street, 1157 MERB, 115, 1157 MERB,

country: USA

institute: Temple University

summary: Quercetin treated cells showed differential regulation of 1527 genes and the upregulated genes were involved in epithelium and tissue development and differentiation.

overall_design: Airway basal cells from patients with COPD were treated with quercetin, isolated total RNA and subjected to Affymatrix gene expression analysis.


title: Glioblastoma and its treatment are associated with extensive accelerated brain aging

city: Groningen

first: Anna

middle: Pilar

last: Ainslie

address: Antonius Deusinglaan, 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

summary: Neurocognitive dysfunction is the leading cause of a reduced quality of life in patients with primary brain tumors. However, how the human brain responds to the tumor and its treatment remains largely unknown. Here we show that the brain of patients with glioblastoma shares features with Alzheimer’s disease and displays hallmarks of accelerated ageing, mitochondrial and neuronal dysfunction, and proteostasis deregulation, thus revealing new targets for managing cancer-related side effects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brain tissue from GBM patients (three regions: two near the tumour and one far from the tumour), five unaffected control individuals (three regions: region-matched to the GBM patient samples), and five AD patients (one region: region-matched to one near region of the GBM patient samples).

first: A

first: M

last: Klaver

first: D

last: Voshart

first: E

last: Gerrits

first: W

last: den Dunnen

first: B

last: Eggen

first: S

last: Bergink

first: L

last: Barazzuol


title: G4 quadruplex landscape and its regulation revealed by a new antibody capture method

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

summary: Currently, the identification of G4 quadruplexes in vivo depends on a published and widely used G4-ChIP protocol (PMID: 29470465) that uses the anti-G4 antibody to captures the quadruplexes like regular chromatin. This method is challenged by some false positives and false negatives in G4-quadruplex capture. We have developed an antibody capture G4-ChIP  (AbC G4-ChIP) method to overcome these challenges. The AbC G4-ChIP achieves (i) minimized in vitro artifacts during the incubation steps, and (ii) capture of G4-quadruplexes which are not protein-bound. We have applied the AbC G4-ChIP to study the regulatory effect of a CGG-repeat binding protein CGGBP1 on G4-quadruplex formation. The AbC G4-ChIP identifies inter-strand G/C-skew as a sequence property associated with CGGBP1-regulated G4-quadruplexes.

overall_design: The antibody capture G4-ChIP (AbC G4-ChIP) employs permeabilization of fixed cells in presence of a buffer (Tris-KCl-Triton X100) such that 1H6 antibody could capture endogenous DNA G4-quadruplexes. The antibody-G4-quadruplex interaction is then crosslinked and pulled down. The AbC G4-ChIP ensures (i) minimization of the presence of in vitro G4-quadruplex artifacts (as false positives) formed during the assay, and (ii) loss of endogenous-formed G4-quadruplex (as false negatives) due to melting during crosslinking. The AbC G4-ChIP profile has been compared against both in vitro and conventional G4-ChIP profiles. The regulatory effect of CGG-repeat binding protein CGGBP1 has been studied in presence and absence of endogenous levels of CGGBP1. The functional relevance of genome-wide profile of CGGBP1-dependent G4-quadruplex regions has been analyzed.

first: Subhamoy

last: Datta

first: Manthan

last: Patel

first: Divyesh


title: RNA microarray of mRNA after after hypoxia or glucose deprivition compared to controls.

city: Shanghai

first: Qing-Wei

last: Zhang

address: Pujian Road 160

country: China

institute: Renji Hospital

summary: We report a total of 402 upregulated genes and 197 downregulated genes (2-fold) were detected after hypoxia treatment  and 386 upregulated genes and 245 downregulated genes (2-fold) were detected after glucose deprivation in HUVEC cells

overall_design: Examination of differently mRNA, lcnRNA, cirRNA expression in HUVEC cells after hypoxia or glucose deprivition compared to controls.

first: Zhi-Zheng

last: Ge


title: RNA sequence of mRNA after silencing of HGDILnc1 compared to controls.

summary: We report a total of 692 downregulated genes and 916 upregulated genes (2-fold) were detected after knockdown of HGDILnc1 in HUVEC cells

overall_design: Examination of differently mRNA expression in HUVEC cells after HGDILnc1 silencing compared to controls.


title: Impact of endogenous IL-27 on innate and adaptive responses during acute and chronic toxoplasmosis

first: Jonathan

last: Hill

state: MA

address: 50 Hampshire St 8th floor

institute: Surface Oncology

summary: In mice infected with the parasite Toxoplasma gondii the cytokine IL-27 limits the development of T cell mediated pathology but it is unclear if IL-27 acts early to constrain the expansion of pathological T cells or acts late to limits their activities. Analysis of infected mice revealed the production of IL-27p28 by a subset of inflammatory monocytes and sustained IL-27p28 production at sites of acute and chronic infection.  Administration of anti-IL-27p28 prior to infection resulted in the development of immune pathology associated with increased levels of macrophage and granulocyte activation and enhanced effector T cell responses.  However, IL-27 blockade that started on 4 dpi still resulted in enhanced numbers of parasite specific effector T cells but did not result in adverse systemic pathology. Neutralization of IL-27p28 during the chronic phase of infection did not alter peripheral T cell responses but manifested as enhanced T cell responses in the brain. Thus, IL-27 has distinct suppressive effects that impact innate and adaptive immunity during acute and chronic phases of infection.

overall_design: Mouse splenocytes were prepared by mechanical dissociation of whole spleens, followed by ACK lysis of red blood cells. After staining with antibody cocktails, total CD45+ cells (day 5; n=5 per treatment) and tetramer positive T-cells (day 10; n=5 per treatment) were sorted by FACS directly into lysis buffer. Total RNA was extracted from sorted cells with the RNeasy® Mini Kit (Qiagen, Cat. No: 74104) and adjusted to 20 ng/ul in nuclease free water (Qiagen, Cat. No: 19101). Gene expression profiling on was performed on Affymetrix GeneChip™ Mouse Gene 2.0 ST Arrays (Applied Biosystems, Cat. No: 902118). Processing of RNA samples, hybridization and array scanning were carried out using standard Affymetrix GeneChipTM protocols at the Boston University Microarray and Sequencing Resource (BUMSR). All CEL files were normalized by Robust Multi-array Average (RMA) (Irizarry et al., 2003) and gene expression data were preprocessed by removing unexpressed probes and discarding transcripts with high inter-replicate coefficient of variance. Subsequent analyses (mean expression, fold change, t.test) were performed in R.

first: Jeongho

last: Park

first: Devapregasan

last: Moodley

first: Daniel

last: Albridge

first: Anthony

last: Phan

first: Enrico

last: Radaelli

first: Ross

last: Kedl

first: Pamela

last: Holland

middle: A

first: Christopher

last: Hunter