title: 3`mRNA sequencing of splenic RNA (MACE) at the 30h time point after acetaminophen (APAP) 300mg/kg administration

summary: Splenic RNA from mice (C57BL/6) of 2 groups (vehicle treated, n=5; APAP-treated (300mg/kg), n=11) were pooled at equal shares. Thereafter, pooled RNA underwent analysis by 3`mRNA sequencing (MACE, GenXPro, Frankfurt, Germany)

overall_design: Examination of APAP induced liver injury at 30h and crosstalk to the spleen

first: Sina

last: Gonther


title: Cancer EVP Uptake in Lung Interstitial Macrophages Enhances Vascular Permeability and Metastatic Potential (in vitro)

status: Public on Jun 26 2024

city: new york

first: David

last: Lyden

state: NY

address: 413 East 69th Street, Room BB1228

department: Pediatrics

country: USA

institute: Weill Cornell medical College

type: Expression profiling by high throughput sequencing

summary: Enhanced vascular permeability in the pre-metastatic niche facilitates tumor cell extravasation and metastasis. Extracellular vesicles and particles (EVPs) are pivotal mediators of cancer progression, including induction of vascular permeability. We identify a novel mechanism whereby melanoma and osteosarcoma EVPs (B16F10 and K7M2) enhance endothelial cell permeability, tumor extravasation and lung metastasis.In contrast, EVPs from breast tumors (4T1 and 67NR) elicited only mild vascular permeability, tumor cell extravasation, and metastasis. EVP induced vascular leakiness is observed within 48h following tumor implantation and as early one hour following direct injection of the B16F10 or K7M2 derived EVPs in non-tumor bearing mice. Rather than acting directly on endothelial cells, EVPs activated interstitial macrophages (IMs) anddepletion of IM with a CSF1R antibody significantly reduced vascular leakiness and metastatic potential.Subsequent activation of JAK/STAT signaling in IMs induces IL-6 secretion which in turn induces endothelial permeability.B16F10 and K7M2 EVPs highly expressed integrin-α5 compared to breast tumors, and knock down ofITGα5impairs IM signaling, vascular permeability and metastasis. Furthermore, in patients Il-6 expression is elevated in tumor-adjacent IMs compared to distant tissues. Our findings identify a key role for IMs in mediating tumor type-specific EVP-driven vascular permeability and metastasis, offering promising targets for therapeutic intervention.

overall_design: To evaluate the effect of ITGA5 IN EVPs on interstitial machrophages (IMs), we sorted IMs from naïve mice,  and treat them with EVPs from B16F10 CON KO, B16G10 ITGA5 KO, K7M2 CON KO and K7M2 ITGA5 KO cell line.. We then performed gene expression profilling anaylsis.

first: Shani

last: Dror


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]

city: New York

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We determined the gene expression profiles during conversion of EpiSCs to DE using scRNA-seq. We used dTAG13 to deplete OTX2 at two timepoints of differentiation

overall_design: Mouse EpiSCs were differentiated to DE with or without dTAG13 added at primitive streak or 24hr DE stage to deplete OTX2 for further 24hrs. Cells were harvested and live cells sorted by flow cytometry.

first: Matthias

last: Stadtfeld

first: Daniel

last: Medina-Cano


title: Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used ATAC-seq to identify open chromatin regions in OTX2-depleted definitive endoderm cells and identify sites with changed accessibility during DE differentiation

overall_design: Mouse EpiSCs were differentiated to DE with or without dTAG13 added at primitive streak stage to deplete OTX2 for 24hrs. Cells were harvested and live cells sorted by flow cytometry. Open chromatin regions were mapped by ATAC-seq on three technical replicates per sample.


title: Effect of TWIST1 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells

city: Stanford

first: Sahin

last: Naqvi

state: CA California

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

institute: Stanford University

summary: To assess the effects of quantitative TWIST1 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag TWIST1 with FKBPV36 and V5, Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different TWIST1 concentrations, as measured by V5 intracellular staining and flow cytometry. We then profiled chromatin accessibility in each of these TWIST1 concentrations

overall_design: Genome-wide chromatin accessibility profiling (ATAC-Seq) of TWIST1-tagged H9 hESC-dervied cranial neural crest cells (CNCCs)


title: Mi-2 and E93 coordinate robust cell cycle exit with terminal differentiation through enhancer decommissioning [RNA-seq]

city: Ann Arbor

first: Laura

last: Buttitta

state: MI

address: 1105 N University Ave

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

summary: Many postmitotic tissues coordinate robust cell cycle exit with the progression of terminal differentiation. While the signals involved in initiating cell cycle exit during terminal differentiation for some tissues have been described, less is known about the mechanisms that maintain a stable, non-cycling state. We previously found that chromatin accessibility changes at a subset of rate-limiting cell cycle genes occurs during maintenance of cell cycle exit, suggesting chromatin remodelers may play a key role in maintaining a robust postmitotic state during terminal differentiation. Here we show that the chromatin remodeler Mi-2 is required to ensure a stable, postmitotic state in Drosophila eyes and wings. Mi-2 alters chromatin accessibility and gene expression during cell cycle exit and terminal differentiation. Mi-2 and a transcription factor involved in tissue maturation, E93, close chromatin accessibility at an overlapping subset of potential enhancers that include the rate-limiting mitotic regulator string (cdc25c) and genes involved in the progression of terminal differentiation. E93 is also required for a stable, postmitotic state and we verified in vivo that Mi-2 and E93 cooperate to decommission an enhancer for the essential mitotic regulator string, to coordinate the transition to a postmitotic state with terminal differentiation. Enhancer decommissioning at the string locus provides a molecular explanation for the long-term, nearly irreversible postmitotic state observed in many tissues as terminal differentiation progresses.

overall_design: RNA-seq for Mi-2, E93 manipulations with controls in 24h and 44h APF Drosophila eyes

first: Elli

middle: M

last: Buchert

first: Elizabeth

middle: A

last: Fogarty

first: Yiqin

last: Ma

first: Matthew

last: Neiderhuber

middle: J

last: McKay


title: Comparison of the expression profile between PDLIM2-knockdown and control LLC cells.

city: Miaoli County

first: Jingxing

last: Yang

address: 35, Keyan Road, Zhunan Town

department: Immunology Research Center

country: Taiwan

institute: National Health Research Institutes

summary:
Lung cancer is one of the most commonly diagnosed and deadliest forms of cancer. PDLIM2 has been shown to regulate the stability and activity of different transcription factors, including STATs and NF-kB, and it plays a role in various biological processes such as inflammation and cancer.
To understand the role of PDLIM2 in lung cancers, we employed microarray analysis to identify differentially expressed genes, delineating both up-regulated and down-regulated ones in PDLIM2-knockdown LLC cells.

overall_design: Murine LLC-shEmpty and LLC-shPDLIM2 cells were utilized for RNA extraction and subsequent hybridization on Affymetrix microarrays. The objective was to identify genes that were up- and down-regulated in PDLIM2 knockdown cells.

first: Jing-Xing

first: Yu-Chen

last: Chuang

first: Tsung-Hsien


title: Mi-2 and E93 coordinate robust cell cycle exit with terminal differentiation through enhancer decommissioning [ATAC-seq]

overall_design: ATAC-seq for Mi-2 manipulations with controls in 24h and 44h APF Drosophila eyes


title: Effect of human recombinent Annexin A5 on gene expression of bone marrow derived macrophages polarizaionn with LPS and IFN-gama

city: Shanghai

first: Zhuoxuan

last: Jia

state: Shanghai

country: China

institute: Shanghai 9th People’s  Hospital, Shanghai Jiao Tong University School of Medicine

summary: Primary BMDMs were obtained from male C57BL/6 mice aged 4-6 weeks. The mice were euthanized, and femurs and tibias were removed. BMDMs were flushed out of the bones using a cold culture medium, filtered through a 70-um cell strainer , and centrifuged at 1500 rpm for 5 min. The cells were suspended in cold culture medium supplemented with 20 ng/ml M-CSF and cultured for five days, with half of the medium being replaced on day three and full replacement on day 5 before being used for subsequent experiments.The culture medium was alpha-MEM supplemented with 10% FBS and 1% penicillin-streptomycin-gentamicin solution. Mature BMDMs were double-stained using flow cytometry antibodies CD16/32 and F4/80 for identification. The recombinant protein AnxA5 used in this study was produced by SEME Cell Technology Co., Ltd, China. To investigate the role of AnxA5 in regulating macrophage polarization in an inflammatory environment, 100000 BMDMs were seeded in 12 well plates. After 24 hours of cell seeding, the regular medium was replaced with culture medium (control group, 1-1, 1-2 and 1-3), culture medium containing 1 ug/mL lipopolysaccharide and 30 ng/mL interferon gama (model group, 2-1, 2-2 and 2-3), culture medium containing 1 ug/mL LPS, 30 ng/mL IFN gama, and different 2 ug/mL of AnxA5 (Treat group, 4-1, 4-2 and 4-3) for 6 hours

overall_design: Total RNA was extracted using Trizol from BMDMs after LPS and IFN-gamma treatment with or without AnxA5 (n = 3) for six hours.

first: Wenjie

last: Zhang


title: hsa-miRNA-548v controls the viscoelastic properties of human cardiomyocytes and improves their relaxation rates

city: PARIS

first: Jean-Sebastien

last: Hulot

address: 56 Rue Leblanc

department: PARCC

country: France

institute: Universite Paris Cite

summary: The impairment of left ventricular (LV) diastolic function with inadequate increase in myocardial relaxation velocity directly results in lower LV compliance, increased LV filling pressures and heart failure symptoms. The development of agents facilitating the relaxation of human cardiomyocytes requires a better understanding of the underlying regulatory mechanisms. We performed a high-content microscopy-based screening in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) using a library of 2565 human miRNA mimics and measured relaxation kinetics via high-computing analyses of motion movies. We identified hsa-miR-548v, a primate specific miRNA, as the miRNA producing the largest increase in relaxation velocities. This positive lusitropic effect was reproduced in engineered cardiac tissues generated with healthy and BRAF T599R mutant hiPSC-CMs, and was independent of changes in calcium transients. Consistent with improvements in viscoelastic responses to mechanical stretch, RNA-sequencing showed that hsa-miR-548v down-regulated multiple targets, especially components of the mechano-sensing machinery. The exogenous administration of hsa-miR-548v in hiPSC-CMs notably resulted in a significant reduction of ANKRD1/CARP1 expression and localization at the sarcomeric I-band. This study suggests that the sarcomere I-band is a critical control center of the ability of cardiomyocytes to relax and a target for improving relaxation and diastolic dysfunction.

overall_design:
To investigate the changes in gene expression levels in response to hsa-miR-548v as compared to miR negative control
We performed gene expression profiling analysis using data obtained from RNA-seq of hiPSC-CMs transfected with hsa-miR-548v vs.miR negative control, 4 preparations per conditions, one time point

first: Eva

last: Vermersch

first: Andrea

last: Ruiz Velasco


title: Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

summary: Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM), which participates in gene expression and various metabolic processes. Nannochloropsis, a significant oleaginous microalgae of economic significance, demonstrates a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted ChIP-seq and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2,057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions, comprising 853 upregulated genes and 1,204 downregulated genes. Moreover, a total of 5,375 differential Kla peaks were identified, including 5,331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (<= 1 kb) (71.07%), 5’UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research reveals the regulatory functions of lactylation in lipid metabolism and gene expression in Nannochloropsis, offering a new perspective for the investigation of lipid biosynthesis.

overall_design: Examination of lactylation modifications under nitrogen repletion and nitrogen deprivation in Nannochloropsis oceanica cells.

first: Lingyu

last: Ouyang

first: Jiao

last: Wang

first: Han

last: Zhu

first: Yikai

last: Wu


title: Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica [RNA-Seq]

overall_design: mRNA profiles of Nannochloropsis oceanica under nitrogen repletion and nitrogen deprivation.

last: Wei


title: RIG-I sensing of self-RNA in aged endothelial cells links cellular senescence with an interferon gene signature

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Contribution of crosstalk of mesothelial and tumoral epithelial cells in pleural metastasis of lung cancer

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Tumor metastasis commonly affects pleura in advanced lung cancer and is related to poor prognosis, but without systematic investigation on different cell types and their crosstalk at single cell resolution. Here, by integrating 180785 single cells from lung cancer and control samples, the most distinctive transcriptome profiles between tumor and control were revealed in mesothelial cells, which is the predominate cell type of pleura. Four subtypes were divided, including one predominately identified in malignant pleural effusion which was characterized by enriched cancer related pathways (e.g., cell migration) along evolutionary trajectory from normal mesothelial cells. Cancer-associated mesothelial cells exhibited varied interactions with different subtypes of malignant epithelial cells, and multiple ligands/receptors exhibited significant correlation with poor prognosis. Experimentally, mesothelial cells can increase the migration ability of lung cancer cells through co-culturing assay, and EGFR was the only affected gene in cancer cells that exhibited interaction with mesothelial cells and was associated with poor prognosis. Using EGFR antagonist cetuximab prevented the increased invasiveness of lung cancer cells induced by mesothelial cells. Moreover, EPGN-EGFR interaction was supported through spatial distribution analysis, revealing the significant proximity between EPGN+ mesothelial cells and EGFR+ epithelial cells. Our findings highlighted the important role of mesothelial cells and their interactions with cancer cells in pleural metastasis of lung cancer, which may facilitate cancer progression.

overall_design: After co-culture, the RNA of A549 and MET-5A cells of control group and co-culture group was respectively extracted, which were further sequenced

first: Pei-Heng

last: Li

first: Yang

last: Shu


title: RIG-I sensing of self-RNA in aged endothelial cells links cellular senescence with an interferon gene signature [RIP-seq]

summary: Senescent endothelial cells accumulate in blood vessels during aging and contribute to age-related cardiovascular disease. Identification of senescent cells is challenging as molecular changes are cell-type specific. Here, we established, benchmarked, and validated a new gene signature EndoSEN that pinpoints senescent endothelial cells. The EndoSEN signature was enriched for interferon stimulated genes (ISG) and correlated with the senescence-associated secretory phenotype (SASP) signature. SASP establishment is classically attributed to DNA damage and cGAS activation, but our results revealed a pivotal role for RNA accumulation and sensing. Mechanistically, we showed that endothelial senescence hallmarks include self-RNA accumulation, RNA sensor RIG-I upregulation, and an ISG signature. Moreover, a virtual model of RIG-I knockout in endothelial cells underscored senescence as an impacted pathway. We tested and confirmed that RIG-I knockdown was sufficient to extend the lifespan and decrease the SASP in endothelial cells. Our evidence suggests that targeting RNA sensing is a potential strategy to delay vascular aging.

overall_design: RNA was immunoprecipitated from senescent ECFCs using RIG-I antibody, including positive and negative controls

first: Jasenka

last: Guduric-Fuchs

first: Pietro

last: Bertelli

first: Shannon

last: McDonnell

first: Varun

last: Pathak

first: Kiran

last: McLoughlin

first: Christina

middle: L

last: O’Neill

first: Alan

middle: W

last: Stitt

first: Reinhold

last: Medina


title: RIG-I sensing of self-RNA in aged endothelial cells links cellular senescence with an interferon gene signature I

overall_design: Cell suspensions for scRNA-seq were obtained from mouse retinas at 3 ages: 3, 12, and 23 months. Enrichment for CD31+ cells was performed using the AutoMACS.

last: O'Neill


title: Iron chelation therapy elicits innate immune control of metastatic ovarian cancer

city: New York City

first: Tito Alejandro

last: Sandoval Medina

email: tas2037@med.cornell.edu, tito@wustl.edu

state: New York

address: 1300 York Avenue E907

department: OBGyN

institute: Weill Cornell Medine

summary: Iron accumulation in cancer cells contributes to malignant progression and chemoresistance. While disrupting this process can influence various hallmarks of cancer, the immunomodulatory effects of chelating iron in tumors remain undefined. Here, we report that treatment with deferiprone, an FDA-approved iron chelator, elicits innate immune responses that control metastatic ovarian cancer. Deferiprone reprogrammed ovarian cancer cells towards an immunostimulatory state characterized by enhanced production of type I interferon (IFN) and surface overexpression of molecules that activate natural killer (NK) cells. Mechanistically, this reprogramming was driven by innate sensing of mitochondrial DNA in the cytosol and concomitant activation of nuclear DNA damage responses evoked upon iron chelation. Deferiprone administration synergized with chemotherapy and prolonged the survival of mice bearing metastatic ovarian cancer by bolstering intratumoral NK cell infiltration and type I IFN responses. Iron chelation may represent an alternative immunotherapeutic approach for malignancies that are normally refractory to T cell-centric modalities.

overall_design: This is a sample of cell infiltrate from ovarian cancer ascites

first: Juan

middle: R

last: Cubillos-Ruiz


title: Regulatory role of echinochrome A in cancer-associated fibroblast-mediated lung cancer cell migration

city: Busan

first: Chaeyoung

last: Lee

address: 40, Jwadong-gil, Jangan-eup, Gijang-gun

country: South Korea

institute: Dongnam Institute of Rediological & Medical Sciences

summary: Echinochrome A (Ech A), a marine biosubstance isolated from sea urchins, is a strong antioxidant,  and its clinical form, histochrome, is being used to treat several diseases, such as ophthalmic,  cardiovascular, and metabolic diseases. Cancer-associated fibroblasts (CAFs) are a component  of the tumor stroma and induce phenotypes related to tumor malignancy, including epithelial–mesenchymal transition (EMT) and cancer stemness, through reciprocal interactions with cancer cells. Here, we investigated whether Ech A modulates the properties of CAFs and alleviates CAF-induced lung cancer cell migration. Interestingly, the secretion of several cytokines and chemokines stimulating cancer cell metastasis was reduced in CAF-like MRC5 cells treated with Ech A compared to untreated MRC5 cells. Moreover, while conditioned medium from MRC5 cells enhanced the migration of non-small cell lung cancer cells, conditioned medium from MRC5 cells treated with Ech A suppressed cancer cell migration. In conclusion, we suggest that Ech A might be a potent adjuvant that increases the efficacy of cancer treatments to mitigate lung cancer progression.

overall_design: To characterize the regulatory effect of Ech A on gene expression, we performed mRNA transcriptome analysis in MRC5 cells treated with or without Ech A. Samples were collected at both the 24 h and 72 h time points under each experimental condition, and differences in gene expression were analyzed by comparing the values at 72 h with those at 24 h.

first: Da-Young

last: Eum

first: Yoo

last: Choi

first: Hwayoung

last: Yun

first: Kyu

last: Heo


title: Unraveling the Role of Srsf1 in Brown Adipose Tissue Thermogenic Function through Single-Nucleus RNA Sequencing.

first: Yuan

middle: Ning

last: Yang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,CAS

summary: Single-nucleus RNA sequencing reveals that Srsf1 absence alters the cell type composition and differentiation trajectories of BAT.

overall_design: Interscapular brown adipose tissue was harvested from 8-week-old control and adipose tissue-specific Srsf1-knockout mice for experiment. In order to obtain single-cell suspension, fresh tissue samples were cut and lysed in nucleus lysis solution. The nuclei obtained were subsequently used for sequencing.

first: Ningyang

last: Yuan

first: Ying

last: Feng


title: Mediator Kinase Inhibition Impedes Transcriptional Plasticity and Prevents Resistance to Sustained MAPK-Targeted Therapy in KRAS-Mutant Cancers

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways.  KRAS, for example, is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses.  Here, we developed multiple models of acquired resistance to second-generation MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, then probed the long-term events enabling survival against this class of drugs.  These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and tumor-specific.  Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to sustained MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, tumor-specific resistance programs.

overall_design: ChIP-Seq for H3K27ac (antibody from Active Motif: 39133) was performed on KRAS-mutant pancreatic cancer cells (MIA PaCa-2 cells) in biological duplicates in 3 treatment populations: 1) 0.01% DMSO 2) treated for 1 week with ERK inhibition (1 µM SCH772984) and 3) following the development of stable resistance to ERK inhibition (treated weekly with 1 µM SCH772984 and split weekly until growth rate exceeded 50% of that of %0.01 DMSO treated controls).

first: Cecilia

middle: B

last: Levandowski

first: Daniel

middle: P

last: Nussbaum

first: Alejandro

last: Barrera


title: TORSEL, a 4EBP1-based mTORC1 live-cell sensor, reveals nutrient-sensing targeting by histone deacetylase inhibitor

city: Shenzhen

first: Canrong

last: Li

state: Guangdong

address: No.66,Gongchang Road,Guangming District,Shenzhen,Guangdong 518107,P.R.Chinan

institute: Sun yet-sen University

summary: Mammalian or the mechanistic target of rapamycin complex 1 (mTORC1) is an effective therapeutic target for diseases such as cancer, diabetes, aging, and neurodegeneration. However, an efficient tool to monitor mTORC1 inhibition in living cells or tissues is lacking. We developed a genetically encoded mTORC1 sensor called TORSEL. This sensor changes its fluorescence pattern from diffuse to punctate when 4EBP1 dephosphorylation occurs and interacts with eIF4E. TORSEL can specifically sense physiological, pharmacological, and genetic inhibition of mTORC1 signaling in living cells and tissues. Importantly, TORSEL is a valuable tool for imaging-based visual screening of mTORC1 inhibitors. Using TORSEL, we identified histone deacetylase inhibitors that selectively block nutrient-sensing signaling to inhibit mTORC1. Therefore, TORSEL is a unique living cell sensor that efficiently detects the inhibition of mTORC1 activity, and histone deacetylase inhibitors such as panobinostat target mTORC1 signaling through amino acid sensing.

overall_design: To elucidate the mechanism by which Panobinostat inhibits the mTOR pathway, we investigated the gene expression profile of 293T cells treated with Panobinostat.

first: Xiaoduo

last: Xie

first: Yingyi

last: Ouyang

first: Yuguo

last: Yi

first: Fengzhi

last: Chen


title: Enhancer-AAVs allow genetic access to diverse populations of astrocytes and oligodendrocytes across species

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes. These oligodendrocyte and astrocyte enhancer-AAVs were highly specific, showed variable expression levels, and our astrocyte enhancer-AAVs showed multiple distinct expression patterns that reflected the spatial distribution of astrocyte subtypes. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.

overall_design: Single-cell RNA-seq on flow-sorted enhancer-AAV-labeled transgene-expressing cells from 47 mouse brains. For each mouse brain up to 48 individual cells were profiled by SMARTer single-cell RNA-seq.

middle: K

first: Smrithi

last: Sunil

first: Nelson

last: Johansen

first: Refugio

last: Martinez

first: Mckaila

last: Leytze

first: Bryan

last: Gore

first: Joseph

middle: T

last: Mahoney

first: Yoav

last: Ben-Simon

first: Yemeserach

last: Bishaw

first: Victoria

last: Omstead

first: Jazmin

last: Campos

first: Ryan

last: Canfield

first: Tamara

last: Casper

first: Nick

last: Dee

first: Deja

last: Monet

first: Amanda

last: Gary

first: Shane

last: Gibson

first: Jeff

last: Goldy

first: Melissa

last: Reding

first: Ximena

last: Opitz-Araya

first: Erin

last: Groce

first: Adriana

middle: E

last: Sedeño-Cortés

first: Nadiya

middle: V

last: Shapovalova

first: Michael

last: Taormina

first: Naz

last: Taskin

last: Tieu

first: Nasmil

last: Valera Cuevas

first: Natalie

last: Weed

first: Sharon

last: Way

first: Zizhen

last: Yao

first: Delissa

last: McMillen

last: Kunst

first: Medea

last: McGraw

first: Bargavi

last: Thyagarajan

first: Jack

last: Waters

first: Trygve

last: Bakken

first: Shenqin

first: Kimberly

last: Smith

first: Karel

last: Svoboda

first: Kaspar

last: Podgorski


title: Sexual differences in the gonochoristic tardigrade Paramacrobiotus metropolitanus,

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

summary: Sex dimorphism is a diversification that can be observed in single species of gonochoristic animals. Phylum Tardigrada exhibits remarkable diversity in sex dimorphism in its morphology and behavior. Despite the wealth of genomic and zoological knowledge accumulating, sexual genetic differences of tardigrades have been identified yet. In this study, we focused on the gonochoristic species Paramacrobiotus metropolitanus, employing omics analyses to unravel the basis of sex differences. Approximately 2,000 male-biased expression genes were concentrated in 29 non-male-specific genomic loci, of which two paralogs of a new Doublesex-Mab-3-related (DM) subfamily specific to Macrobiotidae were discovered. We also identified several tardigrade specific anhydrobiosis genes exhibiting sex-biased　expression, suggesting a potential role in protecting sex-specific gametes. The existence of male-biased, but not male specific genomic loci and the limited conservation of the newly identified dimorphically-expressed DM subfamily would provide the foundation for understanding the diverse sex determination cascade in tardigrades.

overall_design: RNA-Seq of adult males and females

first: Kenta

last: Sugiura

first: Yoshida

last: Yuki

first: Hayashi

last: Kohei

first: Arakawa

last: Kazuharu

first: Kunieda

last: Takekazu

first: Matsumoto

last: Midori


title: Investigating the RNAs bound by Malate Dehydrgenase 2

city: Heidelberg

first: Thileepan

last: Sekaran

address: Mayerhoffstarsse

country: Germany

institute: EMBL

summary: Mitochondrial Malate Dehydrogenase 2 has been identified as an RNA-binding protein in several RNA-interactome capture studies. Here, we used eCLIP to identify the RNA targets bound by human MDH2. We identify  cytosolic RNA targets for MDH2, as well as several mitochondrial tRNAs.

overall_design: MDH2 was immunopurified from UV-crosslinked cell lysates to identify RNAs co-purified with it. We followed the eCLIP protocol for library preparation and used size matched input (SMI) and a control IgG immunopurification to identify MDH2's RNA targets

first: Michelle

last: Noble

first: Aindrila

last: Chatterjee

first: Thomas

last: Schwarzl

first: Matthias

last: Hentze


title: The Transcriptional Cofactor SKI Regulates Medullary Thymic Epithelial Cell Differentiation and Peripheral T Cell Responses

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary:
The thymus is an important site for the establishment and maintenance of an appropriate immune response through positive and negative selection of developing T cells. During selection, developing T cells interact with cortical and medullary thymic epithelial cells (TECs), termed cTECs and mTECs respectively. Our lab found that TEC-specific deletion of Ski decreased the mTEC compartment in the thymus and that tissue restricted antigen (TRA) expression in mTECs was also altered.
Interestingly, these mice were significantly protected from developing experimental autoimmune encephalomyelitis (EAE) disease compared to the control mice and naïve CD4 T cells purified from Ski-deleted mice showed a defect in proliferation in vitro after global T cell receptor (TCR) stimulation.  Overall, our findings suggest that SKI signaling in the thymus regulates mTEC differentiation and function as well as downstream peripheral T cell responses and provide evidence for targeting SKI in T cell driven autoimmune diseases such as multiple sclerosis.

overall_design: comparison of mTECs amd cTECS regarding TEC specific deletion of SKI

first: Chiu

last: Honyin

first: Sabine

last: Spath

first: Alex

last: Hu

last: Varela

first: Kristin

last: Weinstein

first: Kazushige

last: Ninomiya

first: Steven

middle: F

last: Ziegler


title: The Janus kinase 1 is critical for the postnatal development of the pancreas and cancer progression

city: Detroit

first: Kay-Uwe

last: Wagner

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

summary:
Inflammatory cytokines promote the development of pancreatic ductal adenocarcinoma (PDAC), but the functions of specific intracellular signaling mediators in this process are less well-defined. In this study, we discovered that the Janus kinase 1 (JAK1) is critical for the early postnatal growth of the exocrine pancreas.
Using a ligand-controlled and pancreas-specific knockout in adult mice, we demonstrate that JAK1 deficiency prevents the formation of KRASG12D-induced pancreatic tumors, and we established that JAK1 is essential for the constitutive activation of STAT3 whose activation is a prominent characteristic of PDAC.
We identified C/EBPδ as a biologically relevant downstream target of JAK1 signaling, which is upregulated in human PDAC. Reinstating the expression of C/EBPδ was sufficient to rescue the growth of JAK1-deficient tumorspheres.
Collectively, the findings of this study suggest that JAK1 executes important functions of inflammatory cytokines through C/EBPδ and may serve as a molecular target for PDAC prevention and treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data forsix isogenic pairs of mouse pancreatic cancer cell lines before and after Cre-mediated deletion of JAK1.

first: Hridaya

last: Shrestha

first: Patrick

middle: D

last: Rädler


title: Transcriptomic analysis of human naive B cells stimulated by CD40L, CpG, anti-IgM IgG, IL-4 or combinations

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: B-lymphocytes play major adaptive immune roles, producing antibody and driving cell mediated responses. However, how B-cells acutely differentiate in response to receptor signaling codes, including T-cell dependent versus independent cues, remains incompletely understood. To gain insights, we used multi-omic profiling to characterize ex vivo primary human B-cell transcriptomic, proteomic and metabolomic remodeling by B-cell receptor (BCR), Toll-like receptor 9 (TLR9), CD40-ligand (CD40L), interleukin-4 (IL4) or combinations thereof, highlighting  key stimulus-specific phenotypes.

overall_design:
Primary human B-cells were treated in culture in the absence of stimulation or stimulated by, CD40L only, CpG only, IL4 only, aIgM only, CD40L+CpG, CD40L+IL4, CpG+ aIgM, CD40L+ aIgM, and CD40L+ aIgM+IL4. Cells were treated for 24 hours. For each experiment, cells from 3 donors were isolated and treated separately.
Primary human B-cells knocked out for BCAT1.

first: Benjamin

last: Gewurz


title: Transcriptome Analysis of CD9-overexpressing SEM Cells after Dexamethasone Treatment

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
Purpose: This study aimed to study the expression changes of CD9-overexpressing SEM cells after Dexamethoasone treatment
Methods: RNA-seq data were generated by deep sequencing using Illumina. The sequence reads that passed quality filters were analyzed.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the human genome (buildhg38) and annotated with ensemble release 100.

overall_design: To analyze the differentially expressed genes between control CD9-low and experimental CD9-overexpressing SEM cell line after exposure to Dexamethasone.

first: K

last: Leung


title: gene expression analysis of the rat prefrontal cortex following psilocybin or ketanserin administration

city: Philadelphia

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

summary: We report mRNAs differentially expressed in the prefrontal cortex of adult male rats 24 hours following administration of ketanserin and/or psilocybin

overall_design: mRNA profiles in the prefrontal cortex of animals injected intraperitoneally with ketanserin alone, psilocybin alone or ketanserin and psilocybin simultaneously. Animals were euthanized 24 hours after the last injection.

last: Sillivan


title: Ancestralization of the modern human aryl hydrocarbon receptor by genome editing

city: Leipzig

first: Svante

last: Paabo

address: Deutscher Platz 6

department: Department of Evolutionary Genetics

institute: Max-Planck-Institute for Evolutionary Anthropology

summary: The aryl hydrocarbon receptor (AHR) is a transcription factor that upon binding ligands induces the expression of cytochrome P450 genes, which encode enzymes that metabolize aromatic hydrocarbons. The AHR carries an amino acid substitution at position 381 in all present-day humans that occurred after the divergence of modern humans from Neandertals and Denisovans. Here, we use genome editing to revert position 381 back to the ancestral state in human cells. Cells were treated with ligands for 4 h followed by RNA extraction and RNA-Seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9 hESC with ancestralized AHR and modern human wild type controls. Cells treated with 50 nM benzo(a)pyrene, 100 nM kynurenic acid, 10 nM indirubin or 5 µM CH-223191 for 4 h. 6 replicates per genotype and treatment.

first: Nelly

last: Helmbrecht

first: Martin

last: Lackner

first: Tomislav

last: Maricic

last: Pääbo


title: Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells (Series4- chromatin profiles, MINT-ChIP)

city: Jerusalem

first: Milan

last: Patra

address: Hadassah Ein Kerem

department: Faculty of Medicine, Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Using a unique model of cultured human beta cell senescence we show that chromatin reorganization leads to activation of enhancers regulating functional maturation genes, concomitantly with acquisition of glucose-stimulated insulin secretion capacity. Interferon-response genes are elevated in senescent beta cells, but cytokine-encoding senescence-associated secretory phenotype (SASP) genes are not. Human beta cell senescence thus involves chromatin-driven upregulation of a functional maturation program and of interferon-stimulated genes, changes that could increase both insulin secretion and immune reactivity.

overall_design: Chromatin modifiction profiles of non-senescent and senescent state of human pancreatic beta cell line

first: Ittai

last: Ben-Porath

first: Yuval

last: Dor


title: Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells (Series2 - chromatin sccessibility, ATAC-seq)

overall_design: Chromatin accessibility profiles of non-senescent and senescent state of human pancreatic beta-like cells in culture.


title: Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells (Series1 - Transcriptome)

overall_design: Expression profiles of non-senescent and senescent  human pancreatic beta-like cells in culture.


title: RIG-I sensing of self-RNA in aged endothelial cells links cellular senescence with an interferon gene signature II

first: Edoardo

last: Pedrini

address: Via Olgettina 60

institute: Hospital San Raffaele

overall_design: Total RNA from endothelial cells ECFCs was isolated at 4 different status: early passage proliferating, early passage quiescent, mid passage, and senescent.

first: Jasenka

last: Guduric-Fuchs

first: Pietro

middle: M

last: Bertelli

first: Shannon

last: McDonnell

first: Varun

last: Pathak

first: Kiran

last: McLoughlin

first: Christina

last: O'Neill

first: Alan

last: Stitt

first: Reinhold

last: Medina


title: Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells (Series3 - Chromatin profiles, ChIP-seq)

overall_design: Chromatin modifiction profiles of non-senescent and senescent state of human pancreatic beta cell line by employing Chromatin immunoprecipitation DNA-sequencing (ChIP-seq).


title: Distinct DNA methylation landscape between pediatric brain and adult brain

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: Epigenetics tightly regulates gene expression during brain development, which ensemble distinct cell types and form complicated functional brain organ. DNA methylation is an important mark which undergo dramatically changes during brain development. The disturb of this process will lead to various brain tumors. To study the concordant DNA methylation changes during normal brain development, we sequenced DNA methylome of pediatric brain tissues from autopsy with various ages. We systematically compared the DNA methylome of pediatric brain and adult brain and identified candidate DMRs that contribute to normal brain development. This comprehensive analysis will provide important epigenetic reference for human brain development which will be a valuable data to study the epigenetic mechanism of pediatric brain tumor.

overall_design: We sequenced DNA methylomes of pediatric brain tissues from autopsy; We systematically compared DNA methylome between pediatric and adult brain.

first: Yun

last: Huang

first: Xiaonan


title: Timecourse RNA Sequencing of three CHO cell lines: non-producing CHOZN®GS-/-, an IgG1 producer, and an EPO-Fc producer

city: Newark

first: Mark

middle: A.

last: Blenner

state: Delaware

department: Chemical and Biomolecular Engineering

institute: University of Delaware

summary: We analyzed the transcriptomic response in three distinct CHO cell lines: a non-producing host cell line (CHOZN®GS-/-), an immunoglobulin G1 (IgG1) producer, and an erythropoietin Fc fusion (EPO-Fc) producer. We compared the growth and production characteristics of all three cell lines during fed-batch culture. High throughput RNA sequencing (RNASeq) and quantitative polymerase chain reaction (qPCR) were used to study differential gene expression analysis of the timecourse dataset with the host cell line CHOZN®GS-/- as the reference. The objective of this analysis was to study the common and unique responses of cell lines producing different protein products. This analysis showed enrichment and transient upregulation of mRNAs involved in ER stress, the UPR, and oxidative protein folding and processing in both protein producers. Analysis of temporal differential expression profiles led to the identification of novel engineering targets.

overall_design: Comparative gene expression analysis of RNASeq data for a non-producing host CHO cell line (CHOZN®GS-/-, denoted ZN) and two protein-producing CHO cell lines (an IgG1 producer, denoted I23 and an EPO-Fc producer, denoted E33). Samples were collected in biological triplicate for each cell line from four different days of fed-batch culture (days 0, 1, 3, and 5). For example, sample "ZN_D0_1" is read as "host, day 0, replicate 1". Thirty-six samples were submitted for RNASeq. Samples of the non-producing host cell line were considered reference in this study.

first: Dyllan

last: Rives

first: Molly

last: Wintenberg

first: Tara

last: Richbourg

first: Caroline

last: Peak


title: CMS121 partially attenuates disease progression in mouse models of Huntington's disease

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: To investigate the effects of the drug candidate CMS121 on transcrptional changes in the striatum of the R6/2 mouse model of Huntington's disease at 14 weeks of age.

overall_design: Comparative gene expression profiling of striata taken from WT (control) and R6/2 mice (hemi) either untreated (control) or treated with 200 or 400 ppm CMS121 in the diet from 6 to 14 weeks of age.

first: Pamela

last: Maher

first: Gamze

last: Ates


title: lncRNA expressions of the kidney tissues of DKD patients and controls

city: zhengzhou

first: Guo

last: Jia

address: 1 Jianshe Dong Lu, Erqi District,

institute: The First Affiliated Hospital of Zhengzhou University

summary: A total of 35 samples of renal tissues (15 DN, 10 DM, and 10 CON) were selected randomly from archived deidentified formalin-fixed paraffin-embedded DN biopsy tissue specimens. Normal control kidney tissues were obtained from kidneys that had been refused for use in transplantation due to vascular anomalies or from preimplant biopsy samples. Three random samples from each group were used for lncRNA microarrays

overall_design: The assay was completed with assistance from Aksomics Biotech. Co., Ltd, (Shanghai, China), using Arraystar human LncRNA Chip V3.0 to analyze various biological samples (plasma, urine, kidney tissue). Sample labeling and chip hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology), and the hybrid chip was finally scanned using an Agilent DNA Microarray Scanner (part number G2505C). The raw data were analyzed following quantile standardization, using GeneSpring GX v12.1 software (Agilent Technologies). The differentially expressed LncRNAs or mRNAs between the two groups was screened based on the P-value/FDR (P< 0.05, fold of change >2.0).

last: Guo


title: RNA-Seq  of WT and UBQLN1 KO hESCs treatment with 5%O2 or NAC

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

summary: We aimed to investigate the transcriptional change after treatment with NAC or 5% O2

overall_design: The Wild type and UBQLN1-/- hESCs treatment with NAC or 5% O2

first: Lin

last: Liu

first: Shuang

last: Zhao

first: Jie

first: Songqi

last: Duan


title: Effect of FL-Fc-DM1 drug on gene expression of THP-1 cells pretreated with cytarabine.

status: Public on Jun 25 2024

first: Dengyang

last: Zhang

address: Zhenmei road, guangming district

department: Scientific research center

institute: Seventh affiliated hospital, Sun Yat-sen University

summary:
Cytarabine is one of the first line chemo drugs to treat acute myeloid leukemia (AML).
However, cytarabine can induce AML cell cell cycle arrest at G0/G1 phase. These cell-cycle-arrested AML cells resist cytarabine, show a senescence-like phenotype or stem-cell like phenotype.
To eliminate these cell-cycle arrested cells, we developed a FL-Fc-DM1 drug by conjugating FLT3 liangd Fc fusion protein and mertansine. We used the THP-1 cells as a AML model.
The total mRNA of THP-1 cells treated with different drugs (cytarabine, FL-Fc-DM1, FL-Fc) were sequenced.

overall_design:
THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS.
In the control group, THP-1 cells were cultured for 4 days. In the cytarabine group, THP-1 cells were treated with 20 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, THP-1 cells were treated by cytarabine for 3 days and then treated with FL-Fc-DM1 (5 nM) for another 24 hours in the absence of cytarabine. In the FL-Fc treatment group, THP-1 cells were treated by cytarabine for 3 days and then treated with FL-Fc (5 nM) for another 24 hours in the absence of cytarabine.
We than analyze the transcriptome differences between different groups.

last: Chen


title: PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

first: Marina

last: Volegova

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: MYCN-amplified neuroblastoma cells exhibit upregulation of translation initiation factors as a result of MYCN-driven transcriptional amplification, including the RNA helicase eIF4A1. Here, we treated MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells with a novel translation initiation inhibitor, amidino-rocaglate CMLD12824, to  analyze the impact on the global pattern of eIF4A1 binding to mRNA compared to the naive condition.

overall_design: MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells (COG-N-415) were treated for 1 hour with 10 nM CMLD12824 amidino-rocaglate compound and photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of eIF4A1 was performed to analyze the patterns and changes in eIF4A1 binding of cellular RNAs. Corresponding bulk RNA-sequencing was also performed as control.

first: Ushashi

last: Banerjee

first: Lauren

last: Brown

first: Porco

last: John Jr

first: Rani

last: George


title: Polyopes affinis Suppressed IFN-γ- and TNF-α-Induced  Inflammation in Human Keratinocytes via Down-Regulation of the NF-κB and STAT1 Pathways

city: Incheon

first: Youn-Jung

last: Kim

address: Academyro 119

institute: Incheon National University

summary: Polyopes affinis is a red algal species commonly found on the South coast and near Jeju Island, Korea. This study aimed to determine whether P. affinis extracts can inhibit the pathogenesis of T-helper-2 (Th2)-mediated inflammation in a human keratinocyte cell line of atopic dermatitis (AD). Cells were incubated with 10 ng/mL of interferon gamma (IFN-γ) and 10 ng/mL of tumor necrosis factor-alpha (TNF-α) at various concentrations of PAB (10, 30, and 60 µg/mL) and PAA (100, 500, and 1,000 µg/mL) extracts. A gene-ontology (GO)-enrichment analysis revealed that PAB significantly enriched the genes associated with biological processes such as cell adhesion, immune response, inflammation, and chemokine-mediated pathways. PAB suppressed the ex-pression of the secretory proteins and mRNAs that are associated with the thymus and the production of activation-regulated chemokines (TARC/CCL17) and macrophage-derived chemo-kines (MDC/CCL22). The effect of the extract on mitogen-activated protein kinases (MAPKs) was related to its inhibition of TARC/CCL17 and MDC/CCL22 production by blocking NF-κB and STAT1 activation. These results suggest that seaweed extract may improve AD by regulating pro-inflammatory chemokines. In conclusion, we first confirmed the existence of phloroglucinol, a polyphenol formed from a precursor called phlorotannin, which is present in PAB, and this result proved the possibility of PAB being used as a treatment for AD.

overall_design: To investigate target genes and mechanism related to anti-inflammation by Polyopes affinis extract in HaCaT cell line stimulated with IFN-γ and TNF-α, we performed gene expression profiling analysis using data obtained from RNA-Seq of 3 groups(solvent control group, IFN-γ and TNF-α treated group, Polyopes affinis extract with IFN-γ and TNF-α treated group). Each group was treated with three dishes, and the RNA obtained from each dish was pooled after adjusting the concentration for RNA sequencing.

first: Yuna

last: Ha

first: Won-Hwi

last: Lee

first: Jang-Kyun

first: Hee-Kyung

last: Jeon

first: Jongsung


title: Comprehensive target engagement by EZH2 inhibitor CPI-0209 allows for preferential targeting of ARID1A mutant urothelial carcinoma

city: Cambridge

first: Patrick

last: Trojer

address: 215 First Street, Suite 200

institute: Constellation Pharmaceuticals

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

overall_design: Refer to individual Series


title: Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells

first: Milan

last: Patra


title: Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

summary: MYCN-amplified neuroblastoma cells exhibit upregulation of translation regulation factors and ribosome biogenesis proteins as a result of MYCN-driven transcriptional amplification. Here, we treated MYCN-amplified and non-amplified neuroblastoma cells with a novel translation inhibitor, amidino-rocaglate CMLD12824, to compare the defects in translational efficiency.

overall_design: MYCN-amplified (Kelly) and non-amplified (SK-N-AS) neuroblastoma cells were treated for 1 hour with 10 nM CMLD12824 amidino-rocaglate compound and analyzed for changes in translational efficiency using ribosome profiling and bulk RNA sequencing.


title: The effect of constitutive root isoprene emission on root phenotype and physiology under control and salt stress conditions

city: Lubbock

first: Mostafa

middle: ABDELWAHED NOURELDEIN

last: ABDELRAHMAN

state: TX

address: 3120 4th Street, Lubbock, TX, USA

institute: TEXAS TECH UNIVERSITY

summary: Isoprene, a volatile hydrocarbon, is typically emitted from the leaves and other aboveground plant organs; isoprene emission from roots is not well studied. Given its well-known function in plant growth and defense aboveground, isoprene may also be involved in shaping root physiology to resist belowground stress. We used isoprene-emitting transgenic lines (IE) and a non-emitting empty vector and/or wild type lines (NE) of Arabidopsis to elucidate the roles of isoprene in root physiology and salt stress resistance. We assessed root phenotype and metabolic changes, hormone biosynthesis and signaling, and stress-responses under normal and saline conditions of IE and NE lines. We also analyzed the root transcriptome in the presence or absence of salt stress. IE lines emitted isoprene from roots, which was associated with higher primary root growth, root biomass, and root/shoot biomass ratio under both control and salt stress conditions. Transcriptome data indicated that isoprene altered the expression of key genes involved in hormone metabolism and plant responses to stress factors. Our findings reveal that root constitutive isoprene emission sustains root growth also under salinity by regulating and/or priming hormone biosynthesis and signaling mechanisms, amino acids biosynthesis, and expression of key genes relevant to salt stress defense.

overall_design: To investigate the root transcriptome changes in Isoperene overexpression lines compared with Wild-type plants in response to different salinity stress conditions.

first: Tom

last: Sharkey

last: Abdelrhman


title: RET overexpression leads to increased brain metastatic competency in luminal breast cancer patients

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

summary: Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge significantly from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastasis and provide a rationale for targeting the receptor in this patient cohort. Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalised counts per million (CPM) (log2(TMM-CPM +1) gene expression values for the patients described in this study (n=19,622 protein coding genes; N=16 tumour samples).

overall_design:
Exome capture RNA sequencing  was carried out on a cohort of patient breast cancer brain metastatic tumor samples.
>>> Submitters state "Raw RNA sequencing data for the breast cancer brain metastatic samples are not published openly in order to protect participant identities, but will be made available upon request and under regulatory compliance via a data usage agreement (DUA). Please contact the corresponding author with data access requests that will be granted once the DUA is signed" <<<

first: Petra

last: Jagust

first: Mihaela

last: Ola

first: Aoibhin

last: Powell


title: Single-cell transcriptome analysis of tumor infiltrated CD45+ immune cells isolated from ctrl- or thonzonium bromide- treated mice

city: Shang Hai

first: Ping

middle: Ping

last: Nie

address: Songhu Road 2005

institute: Fudan University

summary: As a monocationic detergent, thonzonium bromide (TB) has been approved as an additive to pharmacologic formulations, serving to promote tissue contact of the administered drugs by dispersion and penetration of the cellular debris and exudate, but has not been used for cancer treatment. In this study, we performed single-cell RNA sequencing (scRNA-Seq) to identify the composition of the immune microenvironment after TB  treatment.

overall_design: Tumor infiltrated CD45+ immune cells were isolated by Fluorescence-activated cell sorting (FACS) from PBS or thonzonium bromide treated tumor-bearing mice.

first: Zhaocai

last: Zhou

first: Shi

last: Jiao


title: STING1 orchestrates the injurious neuronal stress response

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

summary: In this study we investigated the neuronal stress response in the experimental autoimmune encephalomyelitis (EAE), the animal model of MS.

overall_design: We used Glt25d2 BacTRAP which allowed to analyze the translatome of layer 5 motoneurons from the cortex of EAE animals. We compared healthy mice, acute phase (15 days after immunization), and chronic phase (30 days after immunization). We sequenced the input and the immunoprecipitated RNA.

middle: S

first: Christina

last: Mayer

first: Manuel

middle: A

last: Friese


title: The Rubicon-WIPI axis regulates exosome biogenesis during aging

city: Suita

first: Ryuya

last: Edahiro

institute: Osaka University

type: Non-coding RNA profiling by high throughput sequencing

summary: Cells release intraluminal vesicles (ILVs) in multivesicular bodies as exosomes to communicate with other cells. Although recent studies suggest an intimate link between exosome biogenesis and autophagy, the detailed mechanism is not fully understood. Here we employed comprehensive RNAi screening for autophagy-related factors and discovered that Rubicon, a negative regulator of autophagy, is essential for exosome release. Rubicon recruits WIPI2d to endosomes to promote exosome biogenesis. Interactome analysis of WIPI2d identified the ESCRT components that are required for ILV formation. Notably, we found that Rubicon is required for an age-dependent increase of exosome release in mice. In addition, small RNA sequencing of serum exosomes revealed that Rubicon determines the fate of exosomal microRNAs associated with aging and longevity pathways. Taken together, our current results suggest that the Rubicon-WIPI axis functions as a key regulator of exosome biogenesis and is responsible for the age-dependent changes in exosome quantity and quality.

overall_design: Exosomes isolated from young and aged mice with or without Rubicon knockout

first: Kyosuke

last: Yanagawa

first: Tamotsu

last: Yoshimori


title: The male pachynema-specific protein MAPS drives phase separation in vitro and regulates sex body formation in vivo

first: Dongliang

last: LI

state: Hong Kong S.A.R. of China

address: 21 SASSOON ROAD, POKFULAM

department: Obstetrics & Gynaecology Department

institute: The University of Hong Kong

summary: Highly dynamic chromosome remodeling and extensive nuclear compartmentalization occur during mammalian meiotic prophase I. We report here that mouse spermatocytes lacking MAPS, the male pachynema-specific protein, exhibit multiple pachytene defects, including disordered chromatin accessibility, interrupted nucleosome composition, and globally altered transcription, accompanied by disturbed nucleus phase formation. Adult Maps−/− pachytene spermatocytes lack sex body formation and exhibit improper autosomal chromatin condensation, which can be attributed to the feature of MAPS to mediate phase separation through its unique intrinsically disordered regions (IDRs), amino acids 2-9. MAPS protein with deletion of IDR failed to form a distinguishable phase in vitro and in cultured cells, and remarkably, MAPS IDR-deleted male mice suffer from pachytene arrest and sterility, with a typical absence of sex body and less condensed autosomal chromosomes, similar to Maps−/− mice. Thus, the nucleus phase separation mediated by MAPS may be essential for male pachynema progression in mice.

overall_design: To check the MSCI status of pachytene cells after MAPS protein deletion, pachytene cells from WT, MAPS-/- and MAPSEE;MAPS-/- groups (postnatal date ~80 day) were purified by STA-PUT method. Three mice with identical genotypes for each group were used for pachytene cell purification. RNA-seq were conducted with two independent experiments.

first: Jiahuan

last: ZHENG

first: Zexiong

last: LIN

first: Kui

last: LIU


title: RET overexpression leads to increased brain metastatic competency in luminal breast cancer

first: Leonie

last: Young

summary: In the present study we aimed to explore the role of tyrosine kinase receptor, RET, in promoting breast cancer brain metastasis. Using patient-derived brain metastatic models, we found RET significantly enriched in brain metastasis originating from estrogen receptor positive breast cancer where it played a key role in promoting cancer cell adhesion, survival, and outgrowth in the brain.

overall_design: To model the RET overexpression observed in patients and ex vivo models of BCBM, ER+ve brain metastatic breast cancer cells (T347) were transduced with Luc-GFP as a control (Ctrl) or the Luc-GFP-RET overexpression vector, generating a stable RET overexpression T347 cell line (RET+). We performed a comparative gene expression profiling analysis of RNA-seq data for T347-Ctrl and T347-RET+ cell lines.

first: Arnold

last: Hill

first: Damir

last: Varešlija


title: Investigation of corneal limbal stem cells and immune repertoires in human infant cornea by multi-omics solution

city: Wuhan

first: jian

last: guan

state: China

address: Aier eye hospital,Wuhan

institute: wuhan aier eye hospital

summary: This project aims to study two key points related to keratoplasty resistance. LSCs (limbal stem cells), which are crucial for the growth and repair of the cornea, have not been identified by specific markers. Furthermore, the characterization of corneal T/B cells has been rarely studied, even though they play a vital role in transplant rejection. To optimize donated corneas, researchers have utilized single-cell multi-omics methods such as single-cell 5’ mRNA and single-cell V(D)J sequencing to explore both LSCs and T/B immune repertoires (IR) simultaneously. Potential LSCs and dominant V(D)J types were analyzed, and the location of the cell marker was determined by RNA in situ sequencing. From the single-cell transcriptomics of 17,218 whole corneal cells, 20 cell subtypes were observed. A subcluster (0.3% of total cells) was identified as putative epithelial LSCs based on the known markers stating stem cells in the G0 cell cycle. TCR/BCR were rarely found in the cornea. The results suggest that GPHB5 could be a potential marker for limbal stem cells, but high-throughput single-cell VDJ sequencing is not the ideal method for analyzing corneal immune repertoires due to the rare presence of T/B cells.

first: Jian

last: Guan

first: Yiqiao

last: Xing


title: Ago and Fkbp project

city: Memphis

first: Mario

last: Halic

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: S. pombe nucleophosmin proteins have other functions in addition to the established role in ribosome biogenesis. Indeed, Fkbp39 contributes to silencing of centromeric and subtelomeric heterochromatic transcripts and displays a negative genetic interaction with the RNAi pathway. While the mechanisms of Fkbp39 action on heterochromatin and the negative genetic interaction with RNAi require further investigation, in this study we show that argonaute deletion cells have defects in transcription, shedding light on previously uncharacterized roles of RNAi.

overall_design: ChIP sequencing, nascent, total RNA and small RNA sequencing in wild type cells and different S. pombe mutants

first: Ilaria

last: Ugolini


title: Bacterial rapid adaptation to alkaline environments

status: Public on Jun 24 2024

city: Beijing

first: Qi

last: PENG

address: No.2 Yuan Ming Yuan West Road

institute: IPPCAAS

summary: To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.

overall_design: Bt HD73 strain was cultured in LB at 30 °C and 220 rpm. NaOH was added at a concentration of 28 mM to the cultures when the OD600 reached 0.7. After 10 minutes of incubation, total RNA was extracted

first: Fuping

last: Song

last: Peng


title: Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease

first: Christian

last: Krebs

address: Martinistraße 52

summary: Although it is well established that microbial infections predispose to autoimmune diseases, the underlying mechanisms remain poorly understood. After infection, tissue-resident memory T (TRM) cells persist in peripheral organs and provide immune protection against reinfection. However, whether TRMcells participate in responses unrelated to the primary infection, such as autoimmune inflammation, is unknown. By using high-dimensional single-cell analysis, we identified CD4+TRMcells with a TH17 signature (termed TRM17 cells) in kidneys of patients with ANCA-associated glomerulonephritis. Experimental models demonstrated that renal TRM17 cells were induced by pathogens infecting the kidney, such asStaphylococcus aureus,Candida albicans, and uropathogenicEscherichia coli, and persisted after the clearance of infections. Upon induction of experimental glomerulonephritis, these kidney TRM17 cells rapidly responded to local proinflammatory cytokines by producing IL-17A and thereby exacerbate renal pathology. Thus, our data show that pathogen-induced TRM17 cells have a previously unrecognized function in aggravating autoimmune disease.

overall_design: scRNA-seq of human samples from the kidney and peripheral blood, specifically from individuals with ANCA-associated glomerulonephritis, was performed from FACS-sorted CD3 positive T cells using Single Cell 3' v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina HiSeq4000.

first: Yu

last: Zhao

first: Ulf

last: Panzer

first: Stefan

last: Bonn


title: Prenatal inflammation remodels lung immunity and function by programming ILC2 hyperactivation

city: Salt Lake Ciy

first: Anna

last: Beaudin

state: Utah

address: 2001 Circle of Hope Drive

department: Hematology/HCI

institute: University of Utah

summary: We examined how prenatal inflammation shapes tissue function and immunity in the lung by reprogramming tissue-resident immune cells from early development. Maternal, but not fetal, type I interferon-mediated inflammation provoked expansion and hyperactivation of group 2 innate lymphoid cells (ILC2s) seeding the developing lung.  Hyperactivated ILC2s produced increased IL-5 and IL-13, were associated with acute Th2 bias, decreased Tregs, and persistent lung eosinophilia into adulthood. ILC2 hyperactivation was recapitulated by adoptive transfer of a fetal liver precursor following prenatal inflammation, indicative of developmental programming at the fetal progenitor level. Reprogrammed ILC2 hyperactivation and subsequent lung immune remodeling, including persistent eosinophilia, was associated with worsened histopathology and increased airway dysfunction equivalent to papain exposure, indicating increased asthma susceptibility in offspring. Our data elucidate a potential mechanism by which early-life inflammation results in increased asthma susceptibility, driven by hyperactivated ILC2s that drive persistent changes to lung immunity during perinatal development.

overall_design: Single-cell RNA sequencing of ILC2s sorted from neonatal (postnatal day 14) mouse lung after prenatal saline or poly(I:C) treatment (embryonic day E14.5).

first: Diego

last: López

first: Aleah

last: Griffin

first: Lorena

last: Aguilar

first: Cassandra-Deering

last: Rice

first: Elizabeth

middle: J

last: Myers

first: Kristi

last: Warren

first: Robert

last: Welner


title: scRNA-seq of aortas from mice with Wnk1 deletion in vascular smooth muscle cells (experiment 1)

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

summary: scRNA-seq of total cells from aortas of mice with Wnk1 deletion in vascular smooth muscle cells

overall_design:
We performed single-cell RNA-seq analysis of total cells viable cells from aortas of mice with Wnk1 deletion in vascular smooth muscle cells
-------------------------------------
MultiSeq Barcode     Barcode Sequence     Hashtagged Sample
BC8     CCTTGGCACCCGAGAATTCCACGAGATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(-)Wnk1(lox/lox) 1
BC9     CCTTGGCACCCGAGAATTCCAGTAGCACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(-)Wnk1(lox/lox) 2
BC10     CCTTGGCACCCGAGAATTCCACGACCAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(-)Wnk1(lox/lox) 3
BC11     CCTTGGCACCCGAGAATTCCATTAGCCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(+)Wnk1(lox/lox) 1
BC13     CCTTGGCACCCGAGAATTCCACCAACCGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(+)Wnk1(lox/lox) 2
BC14     CCTTGGCACCCGAGAATTCCATGACCGATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(+)Wnk1(lox/lox) 3
BC15     CCTTGGCACCCGAGAATTCCAGCAACGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     Sm22Cre(+)Wnk1(lox/lox) 4

first: Clement

last: Cochain

first: Antoine-Emmanuel

last: Saliba


title: Interuption of Klf5 acetylaiton at K358 affects tumor microenvironment in Pten deficient mouse prostates

city: Shenzhen

first: Jin-Tang

last: Dong

address: 1088 Xueyuan Blvd

department: Human Cell Biology and Genetics

institute: Southern University of Science and Technology

summary: PTEN deficiency induces KLF5 acetylation; and the interruption of KLF5 acetylation orchestrates intricate interactions between cancer cells and CAFs that enhance FGFR1 signaling and promote tumor growth. Deacetylated KLF5 promotes tumor cells to secrete TNF, which stimulates inflammatory CAFs to release FGF9. Single-cell transcriptomic analysis reveals an enhanced FGF signaling from fibroblasts to cancer cells after the interruption of Klf5 acetylation.

overall_design: The mouse prostates of 16-week-old PBCre;Pten-/-;Klf5KR/KR (KR) and PBCre;Pten-/-;Klf5+/+ (WT) were dissected and minced for scRNA-seq

first: Baotong

last: Zhang

first: Mingcheng

last: Liu

first: Fengyi

last: Mai

first: Weijian

last: Ding


title: Precise RNA knockdown of smn1,or tardbp and tarbpl by CRISPR-QKD and transcription activation of lin28a and sox9b by CRISPR-Qa in zebrafish

first: Youngnam

middle: N

last: Jin

state: Hubei

address: 115 Donghu Road, Wuchang District

department: Medical Research Institute

institute: Wuhan University

summary: CRISPR-Cas systems have revolutionized gene regulation technologies in various organisms, including zebrafish. However, most zebrafish studies rely on transient injections of CRISPR components, with limited use of transgenic models, primarily for Cas9-mediated knockouts. This is largely due to challenges in achieving sustained and effective expression of Cas effectors. To address these challenges, we introduce the CRISPR-Q system, which integrates the QFvpr/QUAS binary expression system with CRISPR-Cas effectors. This approach overcomes limitations associated with transient mRNA or protein delivery and circumvents the toxicity and silencing issues typical of other binary systems, such as Gal4/UAS. The CRISPR-Q system enables robust expression of CasRx or dCas9vpr, facilitating efficient transcript knockdown (CRISPR-QKD) and gene activation (CRISPR-Qa). Using this system, we successfully achieved significant knockdown of smn1 and the simultaneous knockdown of the paralogs tardbp and tardbpl, modeling phenotypes of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS), respectively. Furthermore, CRISPR-Qa effectively activated the endogenous genes lin28a and sox9b, demonstrating the system's broad applicability. The CRISPR-Q system represents a significant advancement in zebrafish genetic manipulation, providing a robust and versatile platform for studying gene function and modeling human diseases, with potential extensions to other model organisms

overall_design: To investigate the efficiency and specificity of CRISPR-Q induced KD or transcriptional activation, we established triple transgenic (3Tg) zebrafish which contains CRISPR-Q components and guide RNAs (gRNAs or sgRNAs), and double transgenic (2Tg) zebrafish which lacks gRNA, served as a control. gRNA targeting smn1 and gRNA array targeting tardbp and tardbpl were used to test CRISPR-QKD, while sgRNAs targeting lin28a and sox9b were used for CRISPR-Qa. We then performed RNA-seq analysis for smn1, tardbp, lin28a and sox9b from 3Tg embryos and their respective 2Tg siblings.

first: Miaoyuan

last: Shi

first: Weigi

last: Ge

first: Liu

last: Bin

first: Xiaoyi

last: Deng

first: Chengjie

first: Meijun

last: Zheng

first: Pu

first: Li

last: Lei

first: Changheng

last: Li

first: Ying

last: Guo

first: Yanxun

last: Yu


title: Impaired fatty acid import and metabolism in macrophages restricts intracellular growth of Mycobacterium tuberculosis

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

summary: Mycobacterium tuberculosis (Mtb) infection of macrophages reprograms cellular lipid metabolism to promote the formation of cytosolic lipid droplets. While it is clearly known that intracellular Mtb utilize host derived fatty acids and cholesterol to fuel a majority of its biosynthetic demands, the role of macrophage lipid metabolism on the bacteria’s ability to access the intracellular lipid pool remains controversial. We have utilized a CRISPR genetic knockdown approach to, systematically and comprehensively, characterize the role of macrophage fatty acid metabolism on the intracellular growth of Mtb. Our analyzes demonstrate that knockdown of lipid import, sequestration and metabolism genes collectively impair the intracellular growth of Mtb in macrophages. We further demonstrate that modulating fatty acids homeostasis in macrophages impair Mtb replication by enhancing production of pro-inflammatory cytokines, restricting the bacteria access to nutrients and increasing oxidative stress in a manner which is surprisingly divergent. We also demonstrate that impaired macrophage lipid droplet biogenesis is restrictive to intracellular Mtb growth. However, increased induction of lipid droplet formation by downstream blockade of fatty acid oxidation does not rescue the impaired Mtb growth phenotypes. Our work provides a characterization of macrophage fatty acid homeostasis and how its modulation impacts Mtb intracellular growth.

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: Analysis of the transcriptional profile of both the host and Mtb in  Mtb infected macrophages with impaired fatty acid metabolism genes (Scramble (SC), PLIN2, FATP1 and CPT2)

first: N

first: E

last: Jaecklein

first: C

last: Sassetti

first: D

middle: G

last: Russell


title: Complete Genome Sequencing and Transcriptome Analysis of aniline-degrading strain T1

city: 长春

first: 金涛

last: 茹

state: 中国

address: 吉林省长春市解放大路理化楼

department: 新能源与环境

institute: 吉林大学

summary: The aniline-degrading strain T1 can efficiently degrade aniline, however, it is not clear which key genes are associated with aniline degradation, and we have adopted a genome-wide and transcriptomic approach to fully understand the microbial degradation mechanism of aniline.

overall_design: Pseudomonas veronii T1 cells are cultured in LB medium. After approximately 6-9 hours of incubation in LB medium, when the nutrients in LB are depleted, substrate aniline(200mg/L) is added for induction. After 3 hours of induction, blank samples were taken and measured with samples from the induction group.


title: Distinct localization, transcriptional profiles, and functionality in early life tonsil regulatory T cells

city: New York

first: Thomas

last: Connors

state: New York

address: 3595 Broadway CHN 10-24

institute: Columbia University Medical Center

summary: CD4+ regulatory T cells (Tregs) are key orchestrators of the immune system, fostering the establishment of protective immunity while preventing deleterious responses. Infancy and childhood are crucial periods of rapid immunologic development but how Tregs mediate immune responses at these earliest timepoints of human life is poorly understood. Here we compare blood and tissue (tonsil) Tregs across pediatric and adult subjects to investigate age related differences in Treg biology. We observed increased FoxP3 expression and proportions of Tregs in tonsil compared to paired blood samples in children. Within tonsil, early life Tregs accumulated in extrafollicular regions with cellular interactions biased towards CD8+ T cells. Tonsil Tregs in both children and adults expressed transcriptional profiles enriched for lineage defining signatures and canonical functionality compared to blood, suggesting tissue as the primary site of Treg activity. Early life tonsil Tregs transcriptional profiles were further defined by pathways associated with activation, proliferation, and polyfunctionality. Observed differences in pediatric tonsil Treg transcriptional signatures were associated with phenotypic differences, high proliferative capacity and robust production of IL-10 compared to adult Tregs. These results identify tissue as a major driver of Treg identity, provide new insights into developmental differences in Treg biology across the human lifespan and demonstrate unique functional properties of early life Tregs.

overall_design: In this study, we applied  high dimensional flow cytometry, RNAsequencing, and immunofluorescent imaging to  blood and tonsil Tregs obtained from pediatric and adult donors to reveal distinct properties of early life Tregs. Sequencing data was generated by sorting conventional CD4 T cells and regulatory (CD25+/CD127-) T cells with comparisons made across tissue (tonsil/blood) and age (infant vs adult) to define transcriptional differences in regaulatory T cells. These results were then validated using high dimensional flow cytometry with additional insights generated by the use of imaging of tonsil tissue.

first: Shivali

last: Verma

first: Marissa

middle: C

last: Bradley

first: Joshua

last: Gray

first: Pranay

last: Dogra

first: Daniel

middle: P

last: Caron

first: Sarah

last: Maurrasse

first: Eli

last: Grunstein

first: Minyoung

last: Jang

first: Kalpana

last: Pethe

first: Donna

middle: L

last: Farber


title: Interuption of Klf5 acetylaiton at K358 affects gene expression profiles in Pten deficient mouse prostates

first: Jin-Tang

last: Dong

state: Guangdong

summary: Cancer associated fibroblasts (CAFs) play a pivotal role in tumor progression, but it remains elusive whether and how PTEN-deficient prostate cancers reprogram CAFs to overcome the barriers for tumor progression. Herein, we report that PTEN deficiency induces KLF5 acetylation; and interruption of KLF5 acetylation orchestrates intricate interactions between cancer cells and CAFs that enhance FGFR1 signaling and promote tumor growth. Deacetylated KLF5 promotes tumor cells to secrete TNF-α, which stimulates inflammatory CAFs to release FGF9. CX3CR1 inhibition blocks FGFR1 activation triggered by FGF9 and sensitizes PTEN-deficient prostate cancer to AKT inhibitor capivasertib.

overall_design: Differential gene expression caused by Klf5-K358R (KR) knockin in Pten-loss mouse prostates were determined by RNA-seq in anterior prostates (AP) and dorsal prostates (DP). The prostates were dissected from 16-week mice with the genotypes of PB-Cre::Pten F/F::Klf5 W/W (WW); PB-Cre::Pten F/F::Klf5 KR/W (KRW); PB-Cre::Pten F/F::Klf5 KR/KR (KRKR).

first: Baotong

last: Zhang


title: scRNA-seq of aortas from mice with Wnk1 deletion in vascular smooth muscle cells (experiment 2)

first: Alexander

last: Leipold

overall_design: We performed single-cell RNA-seq analysis of total cells viable cells from aortas of mice with Wnk1 deletion in vascular smooth muscle cells

first: Clement

last: Cochain

first: Antoine-Emmanuel

last: Saliba


title: Type VI Collagen Deficiency Causes Enhanced Periodontal Tissue Destruction in Induced Periodontitis

city: Bethesda

first: Taishi

last: Komori

state: Maryland

address: 30 CONVENT DR RM 125

institute: NIH

summary:
Single cell analysis of PDL cells in ligature-induced periodontitis:
The periodontal ligament (PDL) is a fibrillar connective tissue that lies between the alveolar bone and the tooth and is composed of highly specialized extracellular matrix (ECM) molecules and a heterogeneous population of cells that are responsible for collagen formation, immune response, bone formation, and chewing force sensation. Type VI collagen (COL6), a widely distributed ECM molecule, plays a critical role in the structural integrity and mechanical properties of various tissues including muscle, tendon, bone, cartilage, and skin. However, its role in the PDL remains largely unknown. Our study shows that deficiency of COL6 impairs PDL fibrogenesis and exacerbates tissue destruction in ligature-induced periodontitis (LIP).  We found that COL6 deficient mice exhibited increased bone loss and degraded PDL in LIP and that fibroblasts expressing high levels of Col6α2 are pivotal in ECM organization and cell-ECM interactions. Moreover, COL6 deficiency in the PDL led to an increased number of fibroblasts geared towards the inflammatory response. We also observed that cultured COL6 deficient fibroblasts from the PDL exhibited decreased expression of genes related to collagen fiber metabolism and ECM organization, and migration and proliferation. Our findings suggest that COL6 plays a crucial role in the PDL, influencing fibroblast function in fibrogenesis and affecting the immune response in periodontitis. These insights could advance our understanding of the molecular mechanisms underlying PDL maturation and periodontal disease.

overall_design:
Cells were dissociated from the PDL of 11-week-old mice ligature-induced periodontitis (LIP) mice. 1-day and 3-day post-LIP mice were used in this study. Cells from 5 mice were pooled and analyzed by scRNAseq using the 10x Genomics platform.
contributor: NIDCD/NIDCR Genomics and Computational Biology Core

last: Martin

first: Changyu

last: Zheng

first: Marian

last: Young


title: Actication of alpha7 nicotinic receptor regulates herpes simplex virus infection in the central nervous system

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
mRNA isolated from a mouse microglia cell line, BV2 cells, treated with or without α7 nicotinic receptor agonist, choline, before HSV-1 infection.
mRNA expression was examined with the NanoString© platform (www.nanostring.com) utilizing the Mouse Neuropatholgy codeset (NS_Mm_neuropath_V1.0) that measures 760 endogenous and 10 housekeeping (HK) RNAs.

overall_design: RNA from mouse microglia cell line, BV2 cells, treated with (1) mock, (2) α7 receptor agonist, choline, (3) Herpes simplex virus type 1 (HSV-1), and (4) HSV-1 + choline.

first: Shih-Heng

last: Chen

first: Kevin

middle: E

last: Gerrish

first: Rickie

last: Fannin


title: Activation of alpha7 nicotinic receptor regulates herpes simplex virus infection in the central nervous system.

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

overall_design: Refer to individual Series


title: Activation of alpha7 nicotinic receptor regulates herpes simplex virus infection in the central nervous system

summary:
mRNA isolated from a mouse microglia cell line, BV2 cells, treated with or without α7 nicotinic receptor agonist PNU-282987 before HSV-1 infection.
mRNA expression was examined with the NanoString© platform (www.nanostring.com) utilizing the Mouse Neuropatholgy codeset (NS_Mm_neuropath_V1.0) that measures 760 endogenous and 10 housekeeping (HK) RNAs.

overall_design: RNA from mouse microglia cell line, BV2 cells, treated with (1) mock, (2) α7 receptor agonist, PNU-282987, (3) Herpes simplex virus type 1 (HSV-1), and (4) HSV-1 + PNU-282987.


title: Occupancy profiling of IRF2BP2, MYCN, AP-1 and SOX11 by CUT&Tag from Neuroblastoma cells

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: MYCN and SOX11 are master transcription factors (TFs) in neuroblastoma by directly occupying each other's and their own super-enhancers (SEs). Additionally, Master TFs cooperatively co-occupy the same SE components, which promotes the expression of IRF2BP2 involved in cell survival. We also observed the significant enrichment of the AP-1 family at the binding sites of IRF2BP2. In the present study, CUT&Tag (Cleavage Under Targets and Tagmentation) analysis was performed to explore the target of IRF2BP2, MYCN, AP-1 and SOX11 in NB cells.

overall_design: CUT&Tag using antibody against IRF2BP2, MYCN, AP-1 and SOX11 in SK-N-BE(2) cells.

first: Yanling

first: Jian

last: Pan


title: Cochlear single-cell gene expression profiles in mice with noise-induced hidden hearing loss and noise-induced hearing loss.

city: Xi 'an

first: Yihong

last: Jiang

state: Shaanxi

address: West Changle Road, Xincheng District

department: Center of Clinical Aerospace Medicine, School of Aerospace Medicine

institute: Air Force Medical University

summary: Noise-induced hidden hearing loss (HHL) is a new type of hearing loss that has been identified in recent years and leads to insidious damage to the cochlea, unlike the well-known noise-induced hearing loss (NIHL). However, the cellular and molecular basis for it remains to be elucidated. Here, we established a single-cell transcriptome profile of the C57BL/6J mouse cochlea, in which we describe the transcriptome changes of individual cell types within the cochlea with HHL and NIHL. Mice in the HHL group were exposed to 110 dB of noise for 2 hours, and those in the NIHL group were exposed to 115 dB of noise for 4 hours for 3 days. The cochlea was taken 6 hours after the last noise exposure. The control group was not exposed to noise, with other conditions being the same as those in the noise-exposed group. The results of sequencing at the single-cell level help us gain a deeper understanding of the mechanisms of the development of HHL and NIHL.

overall_design: Gene expression in individual cells of the cochlea of mice with HHL and NIHL was analyzed by single-cell sequencing.

first: Jiang

last: Yihong

first: Zheng

last: Zeyu

first: Zhang

last: Min

first: Zhu

last: Jing

first: Ruan

last: Bai

first: Wang

last: Xiaocheng


title: IRF2BP2 promotes neuroblastoma progression

last: Zhang

summary: We report a previously unrecognized role of IRF2BP2 in neuroblastoma. To explore IRF2BP2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the IRF2BP2-knockdown SK-N-BE(2) cells in comparison to control group. We find that IRF2BP2 contributes to maintenance ADRN signature of neuroblastoma cell.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-Scb) or sh-IRF2BP2 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.


title: IRF2BP2 Modulates Chromatin Accessibility in Neuroblastoma

summary: Chromatin accessibility of SK-N-BE(2) cells without or with IRF2BP2 depletion were profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.

overall_design: SK-N-BE(2) cells treated with lentivirus delivering control shRNAs or shRNAs against IRF2BP2. Stable gene-knockdown cells were screened by puromycin selection. About 50,000 cells were obtained for ATAC-seq libraries.


title: Expression data from cultured human acute megokaryblastic myeloid leukemia and acute myeloid leukemia cell lines

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: The genetic lesions that drive acute megakaryoblastic leukemia (AMKL) have not been fully elucidated. To search for AMKL gene, we subjected 9 AMKL cell lines and 39 non-AMKL acute myeloid leukemia cell lines to microarray gene expression analysis.

overall_design: 9 AMKL and 39 non-AMKL acute myeloid leukemia cell lines expression data

first: Seiichi

last: Mori

first: Motomi

last: Osato

first: Jie

middle: Y

last: Lau

first: Tuan

middle: Z


title: Transcriptomic profiling of human orbital fat and differentiating orbital fibroblasts

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

summary: Bulk RNA-Seq and snRNA-Seq of human orbital aft

overall_design: orbital fat from human were collected for bulk RNA-Sequencing; patient's fibroblasts were differenciated into adipocytes in vitro and collected for snRNA-Seq

first: Dong

middle: W

first: Kamil

last: Taneja

first: Thanh

last: Hoang

first: Clayton

last: Santiago

first: Timothy

last: McCulley

first: Shannath

last: Merbs

first: Nicholas

middle: R

last: Mahoney

first: Seth

last: Blackshaw

first: Fatemeh

last: Rajaii


title: Gene expression data from 1 year old SAMR1 mouse brain cortex after 5 mg/kg daily oral administration of TCQA for 1 month

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling study of normally-aging SAMR1 mice brain cortex with TCQA treatment
We used microarrays to detail the global gene expression of SAMR1 mouse brain with TCQA treatment as a control for the senescence-acCELerated mouse prone 8 (SAMP8) model of aging mice

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 TCQA-treated SAMR1 mouse brain cortex 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 (Mouse; 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 > 2 (in linear space) were considered as differentially expressed genes (DEGs).

first: Ashley


title: Hepatic insulin resistance promotes fructose-enriched diet-induced fatty liver diseases.

status: Public on Jun 23 2024

city: Boston

first: rongya

last: tao

state: Ma

address: 300 longwood ave

institute: Boston children's hospital

summary: Understanding mechanisms causing MAFLD (Metabolic Associated Fatty Liver Disease) and its progression to MASH (metabolic dysfunction-associated steatohepatitis) is clinically important and scientifically challenging. Hepatic insulin resistance is a common component in the progression of MAFLD in patients and experimental animals; however, hepatic steatosis caused by the HFD45% (high-fat diet) decreases during chronic hepatic IR generated by inactivation of Irs1/2 (LDKO), AKT1/2, or InsR 1-3—which is inconsistent with the expected relationship between IR and MAFLD in humans4. Here we found that complete hepatic insulin resistance promotes the fructose-enriched GAN diet-induced MAFLD, including acute inflammation and MASH in LDKO mice. Unexpectedly, fructose phosphorylation catalyzed by hepatic Khk (ketohexokinase) was not required as acute MAFLD progressed strongly in LDKOKhkL/L mice fed the GAN diet. FoxO1 activated during hepatic IR induces Fst (Follistatin) expression and secretion from the liver of LDKO mice. Inactivation of hepatic FoxO1 in LTKO mice (LDKO•FoxO1L/L) or Fst in LDKOFstKO mice prevented acute MAFLD during the GAN diet. Consistently, overexpression of hepatic Fst promoted GAN diet-induced MAFLD/MASH and hepatic carcinoma. Mechanistically, circulating Fst promoted adipose tissue IR and lipolysis, which can deliver FFA (free fatty acid) to the liver for esterification with excess Gro3P (glycerol 3-phosphate) generated by fructose metabolism, although hepatic DNL (de novo lipogenesis) decreased strongly in LDKO mice while. Since circulating FST correlates positively with both T2D and MAFLD in humans, our results suggests that hepatic FST induced by progressive hepatic IR might promote MAFLD/MASH during the consumption of sugar-sweetened food and beverages consumed frequently by people and animals with T2D.

overall_design: We generated the LDKO (Irs1L/L:Irs2L/L:CreAlb)  as previously described.  Male Cntr and LDKO mice were fed HFD, GAN, or HFruD between 5-15 wks (n=2). Gene expression was determined by RNAseq. Moreover,  C57BL/6 mice were fed chow, HFD or GAN diet  and infected at 33 weeks without or with Fst315AAV-TBG (Fst315 mice) or GFPAAV-TBG (GFP mice.Liver samples were collected after 5 hours fasting

first: Rongya

last: Tao

first: Morris

last: White

first: Kyle

last: Copps

first: Oliver

last: Stöhr