title: Exploration of miRNAs in diabetic foot ulcers of mice

status: Public on Aug 31 2024

city: Shanghai

first: Meijie

last: Yuan

state: --- Select One ---

address: 528 Zhangheng Road, Pudong New Area

country: China

institute: Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the expression of miRNAs in C57 diabetic ulcer mice by Small RNA sequencing

overall_design: Comparative gene expression profiling analysis of Small RNA-seq data for normal ulcer and diabetic ulcer in C57 mice

first: Jian

last: Sun


title: Study on the effect and mechanism of c-Maf liquid-liquid separation in promoting MM cellular proliferation and drug resistance through Mtbp/c-Myc axis

city: nanjing

first: wang

last: ze

address: qixia

institute: Nanjing University Of Chinese Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Previous experiments have demonstrated that c-Maf can undergo liquid-liquid phase separation (LLPS) in MM. In order to search for the downstream target genes of c-Maf based on its LLPS regulation, we successfully constructed three kinds of cells with EV, c-Maf and already c-Maf-IDR mutation, and simultaneously subjected the three kinds of cells to ChIP sequencing (selecting the FLAG-tagged antibody), and then analysed them for the differential genes, thus screening the downstream targets of c-Maf based on its LLPS regulation.

overall_design: Cells were human multiple myeloma cell line (ARP1). Group: EV, c-Maf, c-Maf-IDR mutation.  Antibody: FLAG.

first: Wang

last: Ze


title: Decidual natural killer cells promote extravillus trophoblast developmental pathways: evidence from trophoblast organoid co-cultures

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

type: Expression profiling by high throughput sequencing

summary: The placenta an essential extra-embryonic organ that supports the fetus throughout gestation. The interactions between the placenta and the maternal immune system during the first trimester have not been completely characterized, despite their close physical association and hem-allogeneic relationship to each other. The most abundant type of immune cell found in the uterus in the first trimester is the decidual natural killer cell (dNK). Despite their name, dNKs play supportive roles during pregnancy by remodelling uterine spiral arteries. We present evidence suggesting that the matrix metalloproteinases (MMPs) that dNKs secrete to promote this remodelling also drive placental development. This study was performed using a novel co-culture system of dNKs and trophoblast organoids, which are mini-organs that represent two to three different cell types of the human placenta. We found that co-cultures for one week led to significant (p=0.020) increases in organoid area. Through bulk RNA sequencing and immunohistochemical examinations we also observed significant decreases in trophoblast stemness markers, and upregulation of gene sets associated with extravillous trophoblast (EVT) development. These changes were accompanied by significant (p<0.001) increases in collagen subunit gene expression in the organoids, with simultaneous significant decreases (p<0.001) in the proportion of organoid area occupied by collagen as determined through Masson’s Trichrome. Cultures containing dNKs also contained significantly higher levels of MMP1, 3, 9, and 10 in their culture media, each of which can break down collagen. Collectively, these findings demonstrate that dNKs promote changes concordant with trophoblast differentiation towards EVTs and villous branching morphogenesis.

overall_design: organoids grown under maintenance conditions in the presence or absence of decidual natural killer cells from allogenic donors

first: Morgan

last: Zych


title: A plastidial lipoyl synthase LIP1p plays a crucial role in phosphate homeostasis in Arabidopsis

city: Zhe jiang

first: Shenghong

last: Ge

address: No. 2318, Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Hangzhou Normal University

summary: Phosphate (Pi) homeostasis is important for plant growth and adaptation to dynamic environment, which requires the precise regulation of phosphate transporter (PHT) trafficking from endoplasmic reticulum to plasma membrane. LIPOYL SYNTHASE 1p (LIP1p) is known as a key enzyme in plastids to catalyze lipoylation of pyruvate dehydrogenase complex for de novo fatty acid synthesis. It is unknown whether this process is involved in regulating Pi homeostasis. Here, we demonstrate a new role of LIP1p in controlling Pi homeostasis by regulating PHT1 trafficking. We recovered a weak mutant allele of LIP1p in Arabidopsis that accumulates much less Pi and has enhanced expression of phosphate starvation induced genes. Lipidomics analysis revealed that LIP1p mutation alters lipid profile and compromises vesicle trafficking of PHT1 to the plasma membrane to impair Pi uptake. Beside phosphorus, the homeostasis of a series of mineral nutrients was also perturbed in lip1p mutant. Our findings provide powerful genetic evidences to support the linkage between lipoylation and ion homeostasis in plant.

overall_design: Total RNAs were extracted from 8-day-old seedlings under HP or LP conditions using a RNeasy Plant Mini Kit (Qiagen, R415102) according to the instruction manual. Three biological replicates were performed for each genotype. The genes that were up-regulated or down-regulated with a twofold or higher change with an adjusted P value of ≤0.05 were regarded as DEGs. Venn diagrams were created using Venny (2.1.0). GO enrichment analysis was performed using clusterProfiler (v.4.0.5)(Yu et al., 2012).

first: Shenhong

first: Mingguang

last: Lei


title: Reproductive biomarker response to PFAS-contaminated groundwater [liver]

city: Gainesville

first: Christopher

last: Martyniuk

state: Florida

address: 2063 Mowry

department: Physiological Sciences

country: USA

institute: University of Florida

summary:
The use of aqueous film-forming foams (AFFF) at fire-training areas (FTAs) has introduced into ground- and surface waters a complex mixture of per- and poly-fluorinated alkyl substances (PFAS). The toxicity of environmental PFAS mixtures to wildlife is not well understood and presents a knowledge gap that limits accurate risk assessment. To evaluate reproductive biomarker responses to complex environmental PFAS mixtures, we conducted a series of on-site experiments using flow-through mobile laboratories exposing fish to groundwater impacted by a legacy FTA and an adjacent reference site
A 60K fathead minnow microarray was used to quantify gene expression patterns in the testis and liver of fish exposed to water from Fire Training Area 1 and 2 relative to a reference site.

overall_design: Fathead minnows were exposed to ground water in a mobile laboratory at the fire training areas. Sample sizes included the following: Reference site (n=6), Control effluent (n=8), FTA-1 (n=5), FTA-2 (n=6) and FTA-2/Ref (50/50 mix) (n=6).

first: A

middle: M

last: Vajda

first: J

middle: A

last: Jenkins

first: D

middle: W

last: Bertolatus

first: S

middle: H

last: Keefe

middle: R

last: LeBlanc

first: Abigail

last: Dethloff

first: C

middle: J

middle: S

last: Miller

first: R

last: Lohman

first: L

middle: B

last: Barber


title: Reproductive biomarker response to PFAS-contaminated groundwater [testis]

overall_design: Fathead minnows were exposed to ground water in a mobile laboratory at the fire training areas.    Sample sizes included the following: Reference site (n=5), Control effluent (n=7), FTA-2 (n=5) and FTA-2/Ref (50/50 mix) (n=5).


title: Single-cell RNA sequencing of murine kidneys for ischemia-reperfusion induced renal injury and fibrosis

city: Wuhan

first: Yinzheng

last: Li

address: No. 1095, Jiefang Avenue, Wuhan, China. 430030

institute: Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology,

summary: Using single-cell RNA sequencing (scRNA-seq), we isolated approximately 100,000 cells from mouse kidneys and generated a large-scale transcriptomic dataset corresponding to time points of 4 hours, 12 hours, 1 day, 5 days, 14 days, and 28 days after IR. Our preliminary analysis identified 16 distinct cell types, providing a robust database to study the changes and evolution of renal IRI from early to late stages.

overall_design: C57BL/6 mice were euthanized at 4 hours, 12 hours, 1 day, 5 days, 14 days, and 28 days after IR, and analyzed using scRNA-seq.

first: Rui

last: Zeng

first: Ying

last: Yao

first: Gang

last: Xu


title: Effect of Adgrd1 or Gpr39 knockdown during differentiation of adipose progenitor cell

city: Beijing

first: Chuan

last: Ye

address: 38 Xueyuan Road, Haidian District

institute: Peking University

summary:
Purpose: To explore the effect of Adgrd1 or Gpr39 knockdown in mouse primary adipose progenitor cell.
Method: Primary adipose progenitor cell were isolated from inguinal white adipose tissue of mice. siRNA transfection was employed to achieve knockdown of Adgrd1 or Gpr39. 48 hours after differentiation induction, RNA were collected for sequencing.
Results: cAMP and ERK pathway were significantly enriched by Adgrd1 and Gpr39 knockdown, respectively.

overall_design: Expression profiling by RNA-seq, profiling of mouse primary adipose progenitor cell after knockdown of Adgrd1 or Gpr39.

first: Changtao

last: Jiang

first: Dongyu

last: Zhao


title: Flame retardant tetrabromobisphenol A (TBBPA) disrupts histone acetylation and zygotic transcription during zebrafish embryogenesis

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

summary: 3,3’,5.5’-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant utilized in the production of electronic devices and plastic paints. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures (0, 10, 20 and 40μM) at 0.75 h post fertilization (hpf) and monitored early developmental events such as cleavage, blastula and epiboly that encompass maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). Our data revealed that TBBPA exposures induced onset of developmental delays by 3 hpf (blastula). By 5.5 hpf (epiboly), TBBPA-exposed (10-20 μM) embryos showed concentration-dependent developmental lag by up to 3 stages or 100% mortality at 40 μM. Interestingly, while continued 0.75- 48 hpf TBBPA exposures (10 μM) led to severely deformed embryos, replacing exposure solution with chemical-free media at 6 hpf mitigated this effect, with 100% normal embryos at 48 hpf. To examine the genetic basis of TBBPA-induced delays, we conducted mRNA-sequencing on embryos exposed to 0 or 40 μM TBBPA from 0.75 hpf to 2, 3.5 or 4.5 hpf. Read count data showed that while TBBPA exposures had no overall impacts on maternal or maternal-zygotic genes, collective read counts for zygotically activated genes were lower in TBBPA treatment at 4.5 hpf compared to time-matched controls, suggesting that TBBPA delays ZGA. Gene ontology assessments for both time- and stage-matched differentially expressed genes revealed TBBPA-induced inhibition of chromatin assembly- a process regulated by histone modifications. Since acetylation is the primary histone modification system operant during early ZGA, we hypothesized that TBBPA inhibits histone acetylation, resulting in lack of open chromatin within promoters of zygotic genes and delaying ZGA. Therefore, we co-exposed embryos to 20 μM TBBPA and 100 μM N-(4-Chloro-3-(trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB) -a histone acetyltransferase activator that promotes histone acetylation- and showed that TBBPA-CTB co-exposures from 0.75- 3 hpf significantly reversed TBBPA-only developmental delays, suggesting that TBBPA-induced phenotypes are indeed driven by repression of histone acetylation. Collectively, our work demonstrates that TBBPA disrupts ZGA and early developmental morphology, potentially by inhibiting histone acetylation. Future studies will focus on mechanisms of TBBPA-induced chromatin modifications.

overall_design: Zebrafish embryos were exposed to 0 or 40 uM TBBPA from 0.75 to 2, 3.5 or 4.5 hpf, followed by sample collection, RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 (Illumina, San Diego, CA) (2x150 bp, ~40m reads/sample).

first: Rosemaria

last: Serradimigni

first: Alfredo

last: Rojas

first: Madeline

last: Bryan

first: Connor

last: Leong

first: Uttam

last: Pal

first: Sunil

last: Sharma

first: Maria

last: Baltazar


title: Menin orchestrates macrophage reprogramming to maintain the pulmonary immune homeostasis [RNA-seq]

city: Xiamen

first: Bin

address: Room 112, Chengzhi building, School of Medicine, Xiamen University, Xiang'an South Road, Xiang'an District

institute: Xiamen University

summary: Menin is a scaffold protein encoded by the Men1 gene, and it interacts with a variety of chromatin regulators to activate or repress cellular processes. The potential importance of menin in immune regulation remains unclear. Here, we report that myeloid deletion of Men1 results in the development of spontaneous pulmonary alveolar proteinosis (PAP). This is strongly correlated with impaired development of alveolar macrophages (AM) and epigenetic inactivation of the GM-CSF pathway caused by Men1 deficiency. Mechanistically, menin directly interacts with SETD2 through the NTD and Palm domains to maintain protein stability and chromatin recruitment. SETD2 and menin collectively maintain GM-CSF expression through H3K36me3, which orchestrates AM reprogramming and pulmonary immune homeostasis.

overall_design: To explore the target genes of Men1 in macrophage, we isolated the  alveolar macrophages from WT and Men1 knockout(KO) mice and performed gene expression profiling analysis by RNA-seq.

first: Xinwen

last: Zhu

first: Guanghui

last: Jin


title: Expression data from BBEE-treated SH-SY5Y cell

city: Tsukuba

first: sharmin

last: Aktar

state: Ibaraki Prefecture

department: Life and Environmental Science

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals anti-inflammatory effects of BBEE on lipopolysaccharide (LPS)-induced Human neuronal SH-SY5Y cells
We evaluated the pretreatment effect of BBEE on LPS-induced inflammation in SH-SY5Y cells. Pretreatment with BBEE could significantly attenuate nitric oxide (NO) production and LPS-induced release of inflammatory mediators in SH-SY5Ycells.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Clariom S assay system (Thermo Fisher, Japan) was used on duplicate RNA samples of each group. In accordance with the user manual, complementary DNA (cDNA) for microarray was generated using the GeneChip WT Plus Reagent kit (Thermo Fisher Science, Japan). Samples were hybridized using Clariom S GeneChip microarray kit (Thermo Fisher Science, Japan). After washing and staining, images were captured, and then CEL data were generated using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan). The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the SST-robust multichip average (SST-RMA) algorithm (Thermo Fisher Scientific, Japan).

first: Aktar

last: Sharmin


title: miRNA profile of C2C12 myoblasts with TGF-β stimulation

first: laimeng

last: song

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

institute: University of Shanghai for Science and Technology

summary: Myoblasts are supposed to participate in skeletal muscle fibrosis. In this dataset, myoblasts were treated with TGF-β and then miRNA sequencing was performed to identify potential targets.

overall_design: According to the miR expression profile of myoblast stimulated by tgf-β, the role of myoblast in skeletal muscle fibrosis can be determined

first: Luze

last: Shi

first: Laimeng

last: Song


title: Dynamic phosphorylation of FOXA1 by Aurora B guides post-mitotic gene reactivation

city: hefei

first: 张

last: 婷

state: Select an option…

address: 安徽省合肥市蜀山区黄山路443号中国科学技术大学西校区生命科学学院547室

institute: 中国科学技术大学

summary: FOXA1 serves as a crucial pioneer transcription factor in developmental processes, and plays a pivotal role as a mitotic bookmarking factor to perpetuate gene expression profiles and maintain cellular identity. During mitosis, the majority of FOXA1 dissociates from specific DNA binding sites and redistributes to non-specific binding sites, however, the regulatory mechanisms governing FOXA1's molecular dynamics in mitosis remain elusive. Here we show that mitotic kinase Aurora B regulates FOXA1's different DNA binding modes and the formation of the biomolecular condensate. Mechanistically, Aurora B kinase phosphorylates FOXA1 at Serine 221 (S221) to disrupt the specific, but not the non-specific, DNA binding. The phosphorylation of S221 also negatively regulates the FOXA1 condensates that require specific DNA binding. Importantly, perturbation of the dynamic phosphorylation impairs accurate gene reactivations and cell proliferation, suggesting that reversible mitotic protein phosphorylation emerges as a fundamental mechanism for the spatiotemporal control of mitotic bookmarking.

overall_design: CUT&Tag sequencing for FOXA1 wild-type and FOXA1 S221A in interphase and mitotic stably expressing GFP-FOXA1 wild-type and S221A HeLa cell

first: Ting

last: Zhang

first: Shuaiyu

last: Liu

first: Xing

first: Xuebiao

last: Yao


title: Trancriptome profiling of medial frontal cortices of P28 offspring from breeding of Dnmt3l conditional knockin and Emx1-cre mice

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

summary: The objective of the study was to examine the gene expression changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J.  There were 12 samples in total- A-1, A-2, A-3, B-1, B-2, B-3, C-1, C-2, C-3, D-1, D-2, and D-3. A-1 to A-3 and B-1 to B-3 were medial frontal cortices from the male and female Emx1-cre mice respectively, which were used as the control groups (CON). C-1 to C-3 and D-1 to D-3 were medial frontal cortices from the male and female Dnmt3l overexpression mice respectively, which were used as the experimental groups (OE). The total RNA of each sample was extracted from the medial frontal cortices by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 119414 cleaned mRNAs, 3015 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with  GO and KEGG enrichment revealed the top functional groups including ATP binding, zinc ion binding, glutamatergic synapse, dopaminergic synapse, MAPK signaling pathway, and PI3K-Akt signaling pathway.  Among 23698 lncRNAs, 658 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 10673 circRNAs, 49 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold). Among 1821 microRNAs,  101 were differentially expressed in OE group compared with CON group (p value ≤ 0.05 and expression change ≥2 fold).

overall_design: Transcriptome profiling of 6 control (3 males and 3 females, medial frontal cortices of P28 offspring from the Emx1-cre mice, strain of C57BL/6J.) and 6 experimental (3 males and 3 females, medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J.) samples.

first: Jie

last: Lu

first: Ruida

last: Xing


title: ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma [MUG-Chor RNA-seq]

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Chordoma, a rare and challenging primary bone malignancy, currently lacks effective targeted therapies. Despite surgical resection and adjuvant radiotherapy, prognosis remains poor. Recent preclinical studies have highlighted potential therapeutic targets, including the transcription factor TBXT, although clinical outcomes have been modest. In this study, we investigated the therapeutic potential of tRNA synthetase inhibitors, specifically halofuginone and halofuginol, in chordoma treatment. We conducted extensive drug screening, identifying these compounds as effective in reducing cell viability in chordoma cell lines through an ATF4-mediated stress response rather than TBXT regulation. Our findings were validated using RNA sequencing, which revealed significant upregulation of ATF4 and associated stress response genes. Additionally, halofuginone demonstrated significant tumour growth inhibition in an in vivo patient-derived xenograft model. These results suggest that targeting metabolic stress pathways via ATF4 activation presents a novel therapeutic approach for chordoma, warranting further clinical investigation.

overall_design: Examination of gene expression differences in MUG-Chor cell line in response to DMSO control, Halofuginone and Halufuginol over 0, 6, 24 and 72 hours

middle: P


title: ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma

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

overall_design: Refer to individual Series


title: WGBS of medial frontal cortices of P28 offspring from breeding of Dnmt3l conditional knockin and Emx1-cre mice

type: Methylation profiling by high throughput sequencing

summary: The objective of the study was to examine the genomic DNA methylation changes in the medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, the strain of C57BL/6J.  There were 12 samples in total- CC1rest, CC3rest, CF2rest, B-3, B-4, and B-5  were medial frontal cortices from the male and female Emx1-cre mice, respectively, which were used as the control groups (CON). CC2rest, CD5rest, CF1rest, D-1, CD6rest, and CD16rest were medial frontal cortices from the male and female Dnmt3l overexpression mice, respectively, which were used as the experimental groups (OE). The genomic DNA of each sample was extracted from the medial frontal cortices. We analyzed methylation level changes across the genome using methylation-capture followed by bisulfite sequencing. Overall, among the more than 1.7 million captured CpG sites, 16.38% had significant differences in methylation levels; the overall methylation rate of the genome was slightly increased (~5%); the methylation level distribution of all CpG sites did not change significantly. In different functional regions of the genome, most of the differentially methylated CpG sites were mildly increased (β value difference <0.2), and most of the methylation difference sites were concentrated in the intergenic and intron regions.

overall_design: WGBS of 6 control (3 males and 3 females, medial frontal cortices of P28 offspring from the Emx1-cre mice, strain of C57BL/6J.) and 6 experimental (3 males and 3 females, medial frontal cortices of P28 offspring from the breeding of Dnmt3l conditional knockin and Emx1-cre mice, strain of C57BL/6J.) samples.


title: ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma [PDX RNA-seq]

overall_design: The antitumor activity of DMSO control and halofuginone  was tested in a Patient-Derived Xenograft (PDX) model, designated SF8894


title: RNA binding protein Pcbp1 maintains mitochondria integrity to promote antibody production and germinal center response[RNA-seq]

city: Xihu District, Hangzhou

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: B cells are crucial for adaptive immunity, orchestrating humoral responses by producing antibodies essential for pathogen clearance. Here, we show that Poly(rC) binding protein 1 (Pcbp1), a multifunctional RNA-binding protein, is a key regulator of antibody production in B cells. Pcbp1 deficiency in B cells resulted in significant reductions in IgM expression at steady state and compromised differentiation of germinal center B cells and production of high-affinity antibodies upon immunization. These effects result from compromised mitochondrial integrity in Pcbp1-deficient B cells, including compromised mitochondrial electron transport chain (ETC) complex I and increased mitochondrial ROS production. Blocking mitochondrial ROS production rescued IgM production and improved germinal center responses caused by Pcbp1 deficiency. Mechanistically, Pcbp1 promotes the expression of Fdxr, a critical component of ETC complex I, via binding to its 3’UTR. Overall, our findings reveal a novel role for Pcbp1 in regulating mitochondrial function, protein synthesis, and antibody responses in B cells, providing novel insight into post-transcriptional regulation and mitochondrial functions.

overall_design:
To investigate the role of Pcbp1 in B cell development and function, we generated Pcbp1 floxed (fl/fl) Mb1-Cre mice (Pcbp1 BKO) and induced germinal center B cell differentiation using the 40-LB system (iGCB). We then conducted gene expression profiling analysis based on RNA-seq data obtained from naive B cells and iGCB cells.
we performed a comparative gene expression profiling analysis of RNA-seq data for naive B cells (2 pairs of WT vs KO) and iGCB cells (3 pairs of WT vs KO).

first: Lizhen

first: Geng

last: Li

first: Li

last: Ling


title: Regulation of IL-33 alarmin production from lung epithelial cells via CLEC-2:Podoplanin interactions

city: Boston

first: Vijay

last: Kuchroo

address: 25 Shattuck Street

institute: Harvard Medical School

summary: Lung epithelial cells produce alarmins that promote allergic inflammation, however, the molecular mechanisms that regulate alarmin expression and production have not been fully elucidated. We constructed an integrated single-cell RNA-seq atlas of murine airways, lung, and vagal nerves, which we use to characterize novel lung cell subsets and infer intercellular interactions, including an interaction between podoplanin (PDPN) on alveolar epithelial cells and C-type Lectin-like Receptor-2 (CLEC-2/Clec1b) on alveolar macrophages that controls the expression of IL-33. Clec1b-/- mice spontaneously develop allergic airway inflammation with increased Il33 expression in alveolar epithelial type 2 (AT2) cells and airway-associated fibroblasts; this airway inflammation is ameliorated by co-deletion of the IL-33 receptor, Il1rl1 (ST2). Myeloid cell-specific deletion of Clec1b and acute blockade of endogenous CLEC-2:PDPN interactions in vivo also promote type 2 immune responses in airway inflammation. Organoid experiments reveal that the regulation of AT2 Il33 expression by CLEC-2:PDPN interactions is directly mediated by alveolar macrophages. Single-cell characterization of house dust mite (HDM)-induced asthma reveals a smaller population of Clec1b expressing alveolar macrophages and increased Il33 expression by AT2 cells.  Thus, our study has identified the CLEC-2:PDPN pathway as an important regulator of epithelial alarmin production and induction of type 2 immunity.

overall_design: C57BL/6J, C57BL/6-Tg(Pf4-icre)Q3Rsko/J (PF4-Cre) and B6.129P2-Lyz2tm1(cre)Ifo/J (LysM-Cre) mice were from the Jackson Laboratory. Clec1b-/- mice on 129/Sv background were provided by Shannon Turley (Dana-Farber Cancer Institute, Boston, Massachusetts, USA) and backcrossed with C57BL/6J for 5 generations in house. Clec1b fl/fl mice on 129/Sv background were provided by Mark Kahn (University of Pennsylvania, Philadelphia, Pennsylvania, USA) and crossed with PF4-Cre or LysM-Cre in house. Il1rl1-/- mice on C57BL/6J background were originally generated by Andrew McKenzie and provided by Diane Mathis (Harvard Medical School, Boston, Massachusetts, USA). Littermates were used as controls for all experiments using genetically modified mice and experimental and control mice were co-housed. Mice were age-matched for experiments and between 6 weeks and 4 months of age. To induce allergic airway inflammation, mice were treated intranasally with 10 μg house dust mite (HDM) extract (Greer Laboratories) on day 0, 7, 8, and 9, and then euthanized on day 10. For some experiments 25 μg Podoplanin-Fc fusion protein (PDPN-Fc; Biolegend, 551704) or isotype control (Biolegend, 403502) was administered intranasally on the same day as HDM. All mice were maintained in specific pathogen-free conditions at the Hale Building of Transformative Medicine. All animal experiments were performed in compliance with the approved BWH IACUC protocols.

first: Daniel

middle: T

last: Montoro

first: Patrick

last: Burkett

first: Antonia

last: Wallrapp

first: Karthik

last: Jagadeesh

first: Hee

middle: s

last: Choi

first: Se-Jin

last: Kim

first: Tanush

last: Kumar

first: Samantha

last: Riesenfeld

first: Elena

last: Christian

first: Raja-Elie

middle: E

last: Abdulnour

first: Bruce

middle: D

last: Levy

first: Aviv

last: Regev

middle: K


title: Macrophages modulate MSC function via TNF-α in tooth extraction model

city: Okayama

first: Kentaro

last: Akiyama

address: 2-5-1 Shikata Cho

department: Department of Oral Rehabilitation and Regenerative Medicine

institute: Okayama University

summary: We performed differentially expressed genes (DEGs) analysis data obtained from RNA-seq of bone marrow mesenchymal stem cells (MSCs) with TNF-α stimulated and unstimulated to investigate the TNF-α stimulation-specific MSC transcriptomes.

overall_design: Differentially expressed genes analysis of RNA-seq data for TNF-α unstimulated bone marrow-derived MSCs from wild-type mice as control and TNF-α stimulated MSCs for 24hr from wild-type mice

first: Aung

last: Mun

first: Ziyi

last: Wang

first: Jiewen

last: Zhang

first: Wakana

last: Kitagawa

first: Teisaku

last: Kohno

first: Ryuji

last: Tagashira

first: Kei

last: Ishibashi

first: Naoya

last: Matsunaga

first: Tingling

last: Zou

first: Mitsuaki

last: Ono

first: Takuo

last: Kuboki


title: Identify WT and p53 3KR target in basal progenitor cells of epidermis

city: New York

first: Zhe

last: Ying

state: NY

address: 1428 Madison Avenue

department: Department of Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: Unbalanced and growth promoting cell fate dynamics that follow p53 loss, and the inability of canonical p53 functions to restrict clonal expansion, suggest the existence of a non-canonical p53 transcriptional program that controls key cell fate regulators. We hypothesized that these cell fate genes are among the shared targets of p53WT and p533KR.

overall_design: p53 ChIP-seq performed in isolated epidermal basal progenitor cells of  p53WT and p533KR animals, 25uM of Nutlin-3a were added to digestion medium to stabilize p53

first: Slobodan

last: Beronja


title: The impact of USP30-AS1 knockdown on gene expression in MDA-MB-231 cell line

city: SHENZHEN

first: Yapei

last: JIANG

state: Guangdong

address: Tsinghua University campus, Shenzhen University Town, Xili Street,  Nanshan District，Shenzhen city，Guangdong

institute: Tsinghua University

summary: We discovered that USP30-AS1 is significantly upregulated in breast cancer tissues and is closely associated with the cell proliferation signaling pathway. Knockdown of USP30-AS1 notably inhibits cell proliferation in MDA-MB-231 breast cancer cells. USP30-AS1 inhibits the expression of the cell cycle inhibitor p21.

overall_design: To explore the impact of USP30-AS1 on gene expression in MDA-MB-231 cells, we knocked down the expression of USP30-AS1 by siRNA and performed transcriptome analysis.

first: Jiang

last: Yapei

first: Xin

last: Qilei

first: Liao

last: Weije

first: Xu

last: Naihan


title: The impact of HnRNPF knockdown on gene expression in MDA-MB-231 cell line

summary: We discovered that HnRNPF is significantly upregulated in breast cancer tissues and is closely associated with the cell proliferation signaling pathway. Overexpression of HnRNPF notably inhibits cell proliferation in MDA-MB-231 breast cancer cells. HnRNPF promotes the expression of the cell cycle inhibitor p21.

overall_design: To explore the impact of HnRNPF on gene expression in MDA-MB-231 cells, we knocked down the expression of HnRNPF by siRNA and performed transcriptome analysis.


title: Type 2 Diabetes Specific Spatial Differential Gene Expression in Pancreas Visium Data

city: Bethesda

first: Neelam

last: Sinha

state: Maryland

address: 4998, BATTERY LN, APT 206

department: NHGRI

institute: NIH

summary: Understanding the spatial distribution of gene expression in the pancreas could provide new insights into its function and islet biology. Visium spatial gene expression is a powerful tool for quantifying gene expression of cells within their spatial context. We describe the generation and analysis of spatial transcriptomics data from six pancreas samples from healthy donors. Our analysis revealed high expression of INS within islets. However, we also identified a bleed of highly abundant islet genes (e.g., INS, GCG) into surrounding tissue areas. Through computational analyses, we successfully corrected for this bleed. We then identify genes which are spatially differentially expressed in the Type 2 Diabetes samples.  We provide these data for researchers to study the organization of the pancreas and islets.

overall_design:
human pancreatic tissue flash frozen with isopentane; tissue sections prepared and processed with the 10X Genomics Visium Spatial Gene Expression Reagent kit
>>>Raw data were deposited in dbGaP under phs001188.v3.p1 due to patient privacy concerns.<<<<

first: Lori

middle: L

last: Bonnycastle

first: Mike

last: Erdos

first: Caleb

last: Grenko

first: Zoe

last: Weiss

first: Cassie

last: Robertson

first: Narisu

last: Narisu

first: Leland

last: Taylor

first: Francis

last: Collins


title: RNA binding protein Pcbp1 maintains mitochondria integrity to promote antibody production and germinal center response[scRNA-seq]

first: Xing

last: Chang

overall_design: To elucidate the mechanism of Pcbp1 regulation in GCB development, NP+ GCB cells (CD19+ B220+ NP+ GL7+ CD95+) were isolated from wild-type (WT) or Pcbp1 fl/fl AID-Cre mice (Pcbp1 GCB KO) and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Lizhen

last: Zhu

first: Geng

last: Li

first: Li

last: Ling


title: Ribotag-RNA sequencing data using Csde1-KD dorsal root ganglion(DRG) neurons

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

summary: We found that the expression of various ribosomal protein genes is regulated at the translation level, and the post-transcriptional regulator CSDE1 controls their association with ribosomes after sciatic nerve injury. This sequencing data shows neurons without CSDE1 exhibit a deficiency in the recruitment of ribosomal protein mRNAs to ribosomes.

overall_design: Adult DRG neurons from the RiboTag;Advillin-Cre mice were cultured after giving the pre-conditioning effects induced by sciatic nerve injury 24 hours prior to DRG tissue dissection. Cultured DRG neurons were infected with AAV-control or AAV-shCsde1 four hours after plating. Neurons were collected at DIV3, and their RNAs were extracted from the anti-HA immunoprecipitated lysates.

first: Eunsu

last: Jang

first: Yewon

last: Jeon

first: Jinyoung

last: Lee

first: Yeonsoo

last: Oh

first: Hoyong

last: Jin

first: Bohm

first: Jung

last: Shin


title: Genomic Characterization of Papillary Thyroid Carcinoma: Age Differences in Tumor Aggressiveness and Immune Infiltration

city: Fuzhou

first: Bo Wang

last: Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

institute: Fujian Medical University Union Hospital

summary: Adolescents and Young Adults (AYA) with papillary thyroid carcinoma (PTC) tend to exhibit more aggressive metastatic features compared to Adults (AD), despite low overall tumor proliferation. This study statistically analyzed clinical data from 501 PTC patients in The Cancer Genome Atlas (TCGA), categorized as Adolescents and Young Adults (AYA) and Adults (AD), to uncover differential clinical features between the two age groups.An independent cohort of 13 patients (7 AYA, 6 AD) was used to screen for differentially expressed genes (DEGs) through RNA sequencing. Functional enrichment and topology analyses identified core molecules associated with the heightened aggressiveness of age-related tumors, which were subsequently validated using immunohistochemistry (IHC). Among the 239 core DEGs identified between AYA and AD PTC, key genes such as CXCR4, OPCML, and S100A2 were upregulated in AYA, while ATP1A3, CHL1, HLA-DRA, and IL-1 Beta were downregulated. These genes play a crucial role in tumor invasion and are linked to immune cell infiltration. These findings suggest that integrating age-specific molecular markers into clinical management could enhance diagnostic accuracy and enable personalized treatment strategies for AYA patients, with further research needed to validate these results in larger cohorts and explore their therapeutic potential.

overall_design: An additional cohort of 13 PTC patients was recruited. Patients were categorized as AYA (n=7) or AD (n=6).

first: Wei

last: Ao

first: Bo

first: Wen-Xin

last: Zhao


title: Comparative cell free salivary miRNA profile in Bubalus bubalis between diestrus and estrus stages

city: Karnal

first: Suneel

middle: Kumar

last: Onteru

state: HARYANA

address: Lab No 154, Animal Biochemistry Division, NDRI, Karnal

department: Animal Biochemistry

country: India

institute: NDRI

summary: Despite buffaloes being primary farm animals, their reproductive performance remains poor mainly due to inaccurate estrus detection methods that ultimately has an economic impact on dairy industry as well as farmers. Recently, numerous studies showed potential of miRNAs as estrus biomarker. However, a miRNA profile of buffalo cell free saliva, a non-invasive fluid, at estrus and diestrus stages is missing. Hence, the present study was planned to identify differential levels of salivary cell free miRNAs in estrus as compared to the diestrus phase of buffalo oestrous cycle (n=3) in order to discover a possible estrus specific miRNAs as biomarkers. miRNA-Seq data analysis showed that in total 10 miRNAs i.e bta-miR-375, bta-miR-200c, bta-miR-30d, bta-let-7f, bta-miR-200a, bta-miR-12034, bta-let-7b, bta-miR-142-5p, bta-miR-2467-3p, bta-miR-30a-5p are significantly altered (log2foldchange >3 and p<0.05) during estrus in comparison to the diestrus phase in buffaloes, suggesting their estrus biomarker potential. Overall, 8 miRNAs i.e bta-miR-375 (6.87 Fold; p-value 0.003), bta-miR-200c (5.98 Fold; p-value 0.003), bta-miR-30d (4.17 Fold; p-value 0.015), bta-let-7f (3.34 Fold; p-value 0.022), bta-miR-200a (4.92 Fold; p-value 0.024), bta-miR-12034 (3.58 Fold; p-value 0.0025), bta-let-7b (3.06 Fold; p-value 0.031),  bta-miR-30a-5p (4.7 Fold; p-value 0.036) were upregulated, whereas bta-miR-142-5p (-3.4 Fold; p-value 0.032) and bta-miR-2467-3p (-5.24 Fold; p-value 0.035) were downregulated during estrus. However, further validation study using qPCR is required in a large sample size in order to determine their estrus biomarker potential. In summary, our results revealed differential salivary cell free miRNAs profile during the oestrous cycle that may lead to the development of estrus specific miRNAs based point-of-care test applicable for the reproductive management of buffaloes in the field condition in the near future.

overall_design: Saliva samples were collected from three healthy murrah buffaloes at estrus and diestrus phase of an oestrous cycle.

first: Dheer

last: Singh

first: Rajeev

last: Chandel


title: The impact of mild episodic ketosis on microglia and hippocampal long-term depression in 5xFAD mice

city: Sacramento

first: Jacopo

last: Di Lucente

state: CA

address: 2805 50th Street

department: Pathology and Laboratory Medicine

institute: UC Davis

summary: In Alzheimer’s disease, dysfunctional microglia possess abnormal immunometabolic features that cause neuronal/synaptic damage and aggravate pathology. A critical question is how to reverse or fine-tune abnormal microglial metabolism towards beneficial immunometabolic outcomes. A major metabolic intervention strategy to raise circulating ketone levels for health benefits, such as by consumption of a ketogenic diet 1, fasting, or other approaches collectively called ketotherapeutics, has raised a great deal of interest, but its effects on microglia are not well understood. Our previous in vitro study showed that β-hydroxybutyrate (BHB), a major ketone body, reverses multiple pathological features of amyloid-β oligomer (AβO)-activated human microglia. In the current study, we tested the in vivo effects of BHB on microglia and synaptic plasticity in the 5xFAD Alzheimer’s disease mouse model. To capture the metabolic impact of BHB on microglia, we employed a “subacute” 1-week regimen of daily intraperitoneal injection of BHB (250 mg/kg), which induced brief and mild episodic (daily) ketosis. This short regimen was able to mitigate pro-inflammatory microglia activation linked to NLRP3 inflammasome formation, and reduce brain amyloid-β deposition by enhancing phagocytosis. Remarkably, this regimen mitigated the deficits of hippocampal long-term depression but not long-term potentiation, and this effect was linked to suppression of the inflammasome-generated cytokine IL-1β. Our results suggest that short-term BHB treatment may ameliorate microglial abnormalities and microglia-regulated synaptic deficits in Alzheimer’s disease. Because beneficial results were achieved with mild episodic BHB elevation alone without diet restriction and without the need of feeding a KD, our results have significant implications to human ketotherapeutics. As KDs are known for poor compliance and low sustainability due to their restrictive nature, our study opens the possibility for alternative ketogenic approaches that are less restrictive, potentially safer, and easier for compliance than a KD, such as short-term BHB injections or dietary ketone esters, a translatable form of induced ketosis.

overall_design: In this study, we tested the effects of BHB on microglia in vivo using 5xFAD mice, which harbor five familial mutations of APP and PSEN1 genes and show robust Aβ production and Aβ‐associated microglia activation and neuroinflammation. we employed a “subacute” 1-week regimen of daily injection of BHB, which induces episodic ketosis similar to that induced by daily strenuous exercise, exercise or fasting. The subacute course was expected to allow a metabolic shift to develop. Freshly isolated microglia was use for RNAseq and analysis.

first: Lee-Way

first: Izumi

last: Maezawa


title: GLABRA2 Transcription Factor integrates Arsenic tolerance with cell differentiation in Epidermal Cells [Exp2]

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Arsenic poses a global threat to living organisms, compromising crop security and yield. Limited understanding of the transcriptional network integrating arsenic tolerance mechanisms with plant developmental responses hinders the development of strategies against this menace. Here, we employed an integrative genomic approach in Arabidopsis thaliana, involving a high-throughput yeast one-hybrid assay, and a transcriptomic analysis coupled with a transcription factor binding site enrichment analysis in gene expression clusters, to uncover novel transcriptional regulators of the arsenic response. We identified the GLABRA2 (GL2) transcription factor as a novel regulator of arsenic tolerance, revealing a wider regulatory role beyond its established function as a repressor of root hair formation. Furthermore, we found that ANTHOCYANINLESS2 (ANL2), a GL2 subfamily member, acts redundantly with this transcription factor in the regulation of arsenic signaling. Both transcription factors act as repressors of arsenic response. gl2 and anl2 mutants exhibit enhanced tolerance and reduced arsenic accumulation. Transcriptional analysis in the gl2 mutant unveils potential regulators of arsenic tolerance. These findings highlight GL2 and ANL2 as novel integrators of the arsenic response with developmental outcomes, offering insights for developing safer crops with reduced arsenic content and increased tolerance to this hazardous metalloid.

overall_design: 2 replicates for mock and As(V)-treated samples, 3 time points

first: Micaela

last: Navarro

first: Cristina

first: Luis

last: Eduardo Hernández

first: María

last: Garnica

first: José

last: Manuel Franco-Zorrilla

first: Yogev

last: Burko

last: García-Mina

last: Pruneda-Paz

first: Joanne

last: Chory

first: Antonio

last: Leyva


title: GLABRA2 Transcription Factor integrates Arsenic tolerance with cell differentiation in Epidermal Cells [Exp1]


title: ZEB2 orchestrates a transcriptional program to safeguard the integrity of human CD4+ Th1 EM cells

city: North Adelaide

first: Simon

last: Barry

state: SA

address: Women’s and Children’s Hospital, Clarence Rieger Building, floor 2, 72 King William Rd

department: Robinson Research Institute

country: Australia

institute: University of Adelaide

summary: CD4+ Th1 cells migrate to sites of inflammation, where they are indispensable for eliminating intracellular pathogens. The lineage defining transcription factor T-bet establishes the Th1 transcriptional programme, directing IFNG to drive effector responses and inducing subordinate transcription factors to shape their phenotype. Aberrant Th1 cell activity drives the pathogenesis of multiple autoimmune diseases, but the detailed mechanisms by which Th1 cells maintain or lose their integrity remain largely uncharacterised. Using immunogenomics and high resolution immune phenotyping in human CD4+ cells, we discovered that the transcription factor ZEB2 is lineage restricted to Th1EM cells. Detailed molecular validation using CRISPR/Cas9 deletion of ZEB2, whole genome transcriptomics and pathway mapping has revealed that ZEB2 is a signalling hub for multiple pathways, stabilising the integrity and function of human CD4+ Th1EM cells. Furthermore, our disease linked pathway mapping suggests that ZEB2 is implicated in the control of Th1-mediated autoimmune disease.

overall_design: To investigate the role of ZEB2 in Tconv cells, we utilized CRISPR/Cas9 technology for gene deletion in human Th1 Tconv cells. The procedure began with the resuspension of three sgRNAs targeting ZEB2 and a non-targeting control sgRNA to a final concentration of 100µM, following which the ZEB2-targeting sgRNAs were mixed to achieve a 40µM concentration. Ribonucleoprotein (RNP) complexes, comprising the sgRNAs and 2NLS Cas9 nuclease, were prepared and incubated with Nucleofection™ buffer. Purified Th1 cells (CD4+ CD25lo CD127hi CD45RA-,CXCR3+, CCR6-), previously activated and then washed, were resuspended in Human T Cells Nucleofector™ Solution and electroporated using the Amaxa® Nucleofector® 2b device with a T-020 pulse setting for activated T cells. Post-electroporation, cells were allowed to recover in prewarmed Complete X-VIVO T cell medium supplemented with IL-2 and then cultured in a 24-well plate. Medium replacement occurred 24 hours post-electroporation to facilitate optimal cell recovery, and after 48 hours, viable cells were sorted for Th1 central memory (CD62L+) and Th1 effector memory (CD62L-) and RNA sequencing were performed.

first: Soon

last: Wong

first: Cheryl

middle: Y

last: Brown

middle: C


title: Optimisation of the self-transcribing active regulatory region sequencing massively parallel reporter assay for the functional interrogation of cis-regulatory regions

city: Singapore

first: Lee

last: Siggens

address: 14 medical drive, MD6, level 8

country: Singapore

institute: National University of Singapore

summary: H3K27ac chromatin was captured and cloned into a modified STARR-seq vector. The captured CREs were assayed for regulatory activity.

overall_design: HEK293T cells were used to capture H3K27ac enriched genomic regions using ChIP-seq and then transfected with the library to measure CRE activity.


title: ORAI2 promotes BMP9-induced osteogenic differentiation via the MAPK/ERK1/2 and PI3K/AKT pathways in MEFs

city: Yuzhong district

first: Xiang

last: Gao

state: Chongqing

address: No. 1 Yixueyuan Road, Yuzhong Chongqing, China 400016

institute: Chongqing Medical University

summary: Bone morphogenetic protein (BMP)9 is crucial for osteogenic differentiation. Our RNA-sequencing results revealed that calcium release-activated calcium modulator 2 (ORAI2) was upregulated in mesenchymal stem cells (MSCs) in which osteogenic differentiation was induced by BMP9. ORAI2 is a subunit of store-operated Ca2+ (SOC) channels, which is associated with the second messenger Ca2+. In this study, we found that ORAI2 was downregulated in the bone tissue of ovariectomy (OVX) rats. Subsequently, we examined the impact of ORAI2 on BMP9-induced MSC osteogenic differentiation. Exogenous ORAI2 expression promoted osteogenic differentiation in vitro and bone repair in vivo, whereas silencing ORAI2 inhibited them. Similar results were also revealed using the SOC entry inhibitor SKF96365. Mechanistically, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the effects of ORAI2 may involve the PI3K/AKT signaling pathway. Consistent with the KEGG analysis results, western blotting results further revealed that exogenous expression of ORAI2 increased the levels of phosphorylated-Akt in cells undergoing BMP9-induced osteogenic differentiation, whereas silencing of ORAI2 reduced them. Furthermore, mass spectrometry results suggested that ORAI2 may bind to IQGAP1, which was confirmed by co-immunoprecipitation and western blotting; notably, ORAI2 could interact with IQGAP1 and then facilitate mitogen-activated protein kinase/ERK1/2 signaling. Our results demonstrated that ORAI2 may promote osteogenic differentiation and play an important role in osteogenesis.

overall_design: To investigate the role of ORAI2 in the regulation of osteogenic differentiation. We established MEFs cells lines in which ORAI2 has been exogenous expressed by recombinant adenovirus. We then performed gene expression profiling analysis using data obtained from RNA-seq.


title: RNA-seq in Cpeb4 knockdown RAW264.7 cells three days after RANKL stimulation

city: Noda

first: Yasuhiro

last: Arasaki

state: Chiba

address: Yamazaki, 2641

department: Molucular Phamacology

institute: Tokyo University of Science

summary: To identify the changes of mRNA expressions by Cpeb4 knockdown in RAW264.7 cells treted with RANKL for three days, we performed RNA-sequencing.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of Cpeb4 knockdown RAW264.7 cells treated with RANKL.

first: Tadayoshi

last: Hayata


title: ILC2s directly activate anti-tumor cytotoxic CD8+ T lymphocytes by internalizing, processing, and presenting exogenous antigens

city: Seoul

first: Jihyun

last: Kim

state: Seoul

address: 103 Daehak-ro, Jongno-gu, Seoul, Republic of Korea, 융합관 312

institute: Seoul National University

summary: Type-2 innate-lymphoid cells (ILC2s) associate with both tumor promotion and inhibition. We found that ILC2s may induce anti-tumor immunity by a hitherto-unrealized mechanism: they may internalize, process, and present exogenous tumor antigen on major-histocompatibility-complex class-I (MHCI) molecules with costimulatory molecules to CD8+ T cells. This converts the T cells into cytotoxic-T-lymphocytes (CTLs). Specifically, transferring ILC2s into tumor-bearing mice inhibited tumor growth in a CD8+ T cell-dependent manner. Moreover, co-culturing human or murine CD8+ T cells with ILC2s upregulated T-cell expression of cytotoxic molecules. The resulting CTLs efficiently killed tumor cells in vitro and upon transfer into tumor-bearing mice. ILC2s were found to internalize exogenous antigens via clathrin-dependent endocytosis and to process/present them as efficiently as professional antigen-presenting cells for CD8+ T cells (type-1 conventional dendritic cells). Thus, ILC2s can present antigen to CD8+ T cells and induce their tumor-killing activity. This novel finding has promising implications for anti-tumor strategies.

overall_design: Isolated CD8+ T cells and ILC2s were co-cultured with 5:1 ratio for 3 days. Bulk RNA sequencing was performed on co-cultured CD8+ T cells and ILC2s, with individually cultured CD8+ T cells or ILC2s serving as control groups. A total of 1x106 cells from each group were isolated using BD FACSAria™ III through flow cytometry. Each group included 2 replicates.

first: Hye


title: Targeting LYPLAL1-mediated cGAS depalmitoylation enhances the response to anti-tumor immunotherapy

city: Xi'an

first: Yizeng

last: Fan

address: Yanta West Road

institute: Xi'an Jiaotong University

summary: Cyclic GMP-AMP synthase (cGAS) binds pathogenic and other cytoplasmic double-stranded DNA (dsDNA) to catalyze the synthesis of cyclic GMP-AMP (cGAMP), which serves as the secondary messenger to activate the STING pathway and innate immune responses. Emerging evidence suggests that activation of the cGAS pathway is crucial for anti-tumor immunity, however, no effective intervention method targeting cGAS is currently available. Here we report that cGAS is palmitoylated by ZDHHC9 at cysteines 404/405, which promotes the dimerization and activation of cGAS. We further identified that lysophospholipase-like 1 (LYPLAL1) depalmitoylates cGAS to compromise its normal function. As such, inhibition of LYPLAL1 significantly enhances cGAS-mediated innate immune response, elevates PD-L1 expression and enhances anti-tumor response to PD-1 blockade. Our results therefore reveal that targeting LYPLAL1-mediated cGAS depalmitoylation contributes to cGAS activation, providing a potential strategy to augment the efficacy of anti-tumor immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4T-1 wild-type cells and Lyplal1 knockout cells.

first: Gao

last: Yang

first: Wenyi

last: Wei

first: Lei

last: Li


title: Impaired glycosylation drives golgi stress-mediated gastric tumorigenesis that can be targeted by lectin-drug conjugates

city: Bunkyo-ku

first: Junya

last: Arai

state: Tokyo

address: Clinical reserch center A #422 7-3-1 Hongo

institute: University of Tokyo

summary: Downregulation or gene mutation of MUC6, a major component of gastric mucin, is often identified in human gastric cancers. However, the mechanistic role of MUC6 alteration in gastric carcinogenesis remains unclear. Here, using Muc6-deficient mice, we revealed that dysregulated glycosylation in Muc6-deficient gastric epithelium causes aberrant golgi stress responses, resulting in spontaneous gastric cancer development. Muc6-deficient tumor growth is dependent on MAPK activation, which is mediated by golgi stress-induced golph3 upregulation. Glycomic analysis and lectin-binding assays revealed abnormal expression of mannose-rich N-type glycans in Muc6-deficient gastric tumors. Banana lectin-drug conjugates, which bind to mannose-rich glycans, dramatically suppress mannose-rich murine and human gastric cancer growth. Thus, we propose golgi stress responses and aberrant sugar chains as promising therapeutic targets in gastric cancers accompanied with mucin expression disorder.

overall_design: To investigate the assciation between golph3 and gastric carcinogenesis, we experimented Golph3 shRNA adenovirus treatment in MKN45 (Muc6 negative) and compared gene expression by RNA sequence with control shRNA adenovirus treatment group.

first: Yoku

last: Hayakawa


overall_design: To investigate the assciation between muc6 and gastric carcinogenesis, we newly generate Muc6-/- mice and compared gene expression by RNA sequence between WT and MUC6-/- mice.


title: Location matters – how the cytoskeletal protein Leiomodin 1 controls myogenic differentiation by modulating Sirtuin 1 localization

city: Jena

first: Ellen

last: Spaeth

state: Thuringia

address: Beutenbergstraße 11

country: Germany

institute: FLI - Leibniz Institute on Aging

summary: During myogenic differentiation the architecture and proteome of muscle stem cells undergo extensive remodelling. These processes are only partially understood and display impairments in age and disease. Using mass spectrometry to analyse protein dynamics during myogenic differentiation, we identified the actin nucleator Leiomodin 1 (LMOD1) increasing in abundance in early phases of myogenic differentiation. Knockdown of LMOD1 in primary myoblasts severely affected myogenic differentiation and fusion of myotubes, while overexpression had the opposite effect. Mechanistically, we show that LMOD1 interacts with Sirtuin1 (SIRT1) and that both follow similar changes in nuclear/cytoplasmic localization during differentiation. We demonstrate that LMOD1 influences SIRT1 localization and the expression of a subset of its target genes. Consistently, depletion or pharmacological inhibition of SIRT1 partially rescues the effects of LMOD1 knockdown. Our work identifies a novel regulator of myogenic differentiation that might be a potential target to improve muscle regeneration in aging and disease.

overall_design: To identify downstream effectors that could explain the observed rescue effect after siLmod1/siSirt1 double knockdown, an RNA-Seq experiment was conducted. Therefore, siRNA against Lmod1 and Sirt1 was performed in 5 different primary myoblast cell lines, and primary myoblasts were differentiated for one day. Differential gene expression analysis of RNASeq Data was used to understand the early transcriptional changes in the myogenic program under the different knockdown conditions (siSirt1 vs siCtrl and siLmod1 vs siCtrl).

last: Späth

first: Svenja

last: Schüler

first: Julia

last: von Maltzahn

first: Alessandro

last: Ori


title: Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation in Arabidopsis

city: Gainesville

first: Jeremy

middle: Robert Barker

last: Newman

state: FL

address: 2033 Mowry Road

department: Genetics Institute

institute: University of Florida

summary: There is increasing interest in the effects of low-dose ionizing radiation (IR) on plants as might occur during spaceflight, or as a consequence of human activities, such as nuclear power generation, that may result in the release of radioactive materials into the environment. High doses of IR have long been used for the induction of mutations in plants with the goal of generating desirable traits for agribusiness. However, less is known about the responses of plants to acute low doses of IR exposure. Here, we take a multi-omics approach to characterize the response to low dose IR in A. thaliana. We adapt the Methyltransferase Accessibility Protocol for individual templates (MAPit) technique for use in plants allowing us to assay the epigenetic response to acute low-dose IR (10 cGy and 100 cGy) 72 hr after exposure, and, in parallel, use RNA sequencing to profile the transcription response at 1, 3, 24 and 72 hr after exposure. We observe that IR exposures as low as 10 cGy elicit robust genetic responses in Arabidopsis thaliana detectable as early as 1 hr after exposure. Examination of these responses revealed dose-dependent changes in gene expression, chromatin accessibility and DNA methylation that implicate the ethylene signalling pathway and response to abiotic stress as underlying the transcriptional and epigenetic changes associated with IR. These changes are observable up to 72 hr after exposure suggesting that they are maintained well after the initial acute exposure. Our findings indicate that A. thaliana executes a coordinated, multi-modal response to low-dose IR through induction and regulation of the ethylene response pathway.

overall_design:
To investigate the effect of low-dose ionizing radiation on gene expression in Arabidopsis thaliana (Col-0 ecotype), A. thaliana seeds were sown in autoclaved soil and cold-treated at 4°C for 3 days to promote uniform germination (Zhou et al., 2017). Plants were grown under a short-day condition (8 hr light, 16 hr dark) at 22°C for 1 week, followed by transplantation of each seedling to individual cells in 36-cell trays
At 4 weeks of growth, plants were placed in a 137Cs irradiator and exposed to gamma IR at 1.4 cGy per second. Plants were irradiated for 7 sec (10 cGy equivalent), 71 sec (100 cGy equivalent) or not exposed (0 cGy or “Mock”).
Gene expression profiling was performed using RNA-seq from whole rosettes collected at 1 h, 3 h, 24 h, 72 h post-exposure. Analysis of gene expression was carried out comparing IR-exposed (10 cGy, 100 cGy) to mock-treated plants at each time point

first: Mingqi

last: Zhou

first: Chris

last: Pires

first: Rhonda

last: Bacher

first: Michael

last: Kladde

first: Patrick

last: Concannon


title: Impaired glycosylation drives golgi stress-mediated gastric tumorigenesis that can be targeted by lectin-drug conjugates II


title: P14 T cells from C57BL6J draining lymph node after vaccinia-GP33

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

summary: CD90.1 T cells were isolated from draining lymph nodes of vaccinia-GP33 infected ears 45 days post infection

overall_design: P14 T cells from draining lymph nodes were MACS enriched for CD90.1, then flow sorted on CD90.1+, CD8+, CD44+, Live (DAPI-), CD45 IV- (extravascular). Enriched cells were then submitted to NYU genomics center for single cell RNA sequencing

first: Heim

last: Taylor

first: Schultz

last: Austin

first: Delclaux

last: Ines

first: Lund

last: Amanda


title: miRNA expression data in plasma from women with breast cancer and healthy volunteers with or without alterations associated to metabolic syndrome [sequencing]

city: Buenos Aires

first: Adriana

last: De Siervi

state: Buenos Aires

address: Vuelta de Obligado 2490

department: Instituto de Biología y Medicina Experimental

country: Argentina

institute: CONICET

summary: Breast cancer (BCa) is the leading cause of death by cancer in women worldwide. Early diagnosis is improving the survival of BCa patients but more sensitive and specific tools are still necessary. We propose the use of miRNAs as a biomarker alternative in BCa diagnosis. MiRNAs are small non-coding RNAs that regulate gene expression.  Circulating miRNAs can be detected in body fluids. Aberrant expression of miRNAs in both tissues and fluids are linked to several pathologies. Furthermore, metabolic syndrome (MeS) is a risk factor for BCa. Molecular mechanisms underlaying this association have not been fully elucidated.  The aim of this work was to identify the circulating miRNAs in plasma of BCa patients and healthy donors with or without clinical features linked to MeS. MiRNAs were isolated from plasma of woman. BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. Healthy women (HD) (N=36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). We hybridized miRNAs of each group using GeneChip® miRNA 4.0 Array (Affymetrix). miRNA expression profile was also determined by miRNA sequencing from 6 BC patients and 4 HD. Data analysis revealed 11 miRNAs upregulated in the plasma from BCa patients compared to HD. Meanwhile, 24 miRNAs were altered in plasma of women with MeSL compared to control.

overall_design:
BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. In addition, healthy women (36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). Four samples of healthy women (2 control and 2 AAMS) were generated by pooling miRNAs from 9 donors. Samples were hybridized to the GeneChip® miRNA 4.0 Array (Affymetrix). Data normalization and analysis were performed using Expression Console™ Software 1.3.1 and Affymetrix® Transcriptome Analysis Console (TAC) Software. For miRNA sequencing, from 6 BC patients and 4 HD was sent to GenoHub (Real Seq Bioscience INC, USA). They performed miRNA isolation using Quick-cfRNA Serum and Plasma (Zymo Research, USA) and sequencing was performed using the NextSeq platform (Illumina, USA). The analysis comparing BC versus HD followed the pipeline and their versions: Ubuntu 18.04.2 LTS x86_64-pc-linux-gnu (64-bit), R version 3.6.0 -- "Planting of to Tree", FastQC v0.11.5, cutadapt version 2.3, bowtie version 1.2.2, DESeq2_1.22.2, Rsubread_1.32.4, BiocParallel_1.16.6, Ggplot2_3.1.0.

submitter states that raw data files are no longer available.

first: Paula

last: Farré

first: Rocío

last: Belén Duca

first: Guillermo

middle: N

last: Dalton


title: sptaial transcriptomics of high intraocular pressure and WT rats.

city: Beijing

first: Shen

last: Wu

state: - 选择州/省 -

address: No.17 hougou hutong, Dongcheng district，Beijing

institute: institute of ophthalmology

summary: Previous studies indicated that activation of glial cells and inflammatory responses are triggering factors of glaucomatous optic neuropathy. In particular, neurotoxic reactive astrocytes have been found to play a significant role in retinal ganglion cell damage. Furthermore, research showed that activation of glial cells is not dependent on retinal ganglion cell injury, but rather a direct response to pathological elevation of intraocular pressure. However, the molecular mechanism by which elevated intraocular pressure triggers glial activation through mechanical forces remains unknown. By spatial transcriptome sequencing, our study revealed that the neurotoxic astrocyte would rapidly be reactivated in the optic nerve head under elevated intraocular pressure in vivo.

overall_design: we established the high IOP animal model by injecting hydrogel into the anterior chamber. 7 days after hydrogel injection, 2 different eyes from high IOP and wt animals were collect for cryosection.  For spatial transcriptomic, two sagittal sections passing through the ONH region were selected as technical replicates, with a minimum distance of 20 μm between the two sections.


title: miRNA expression data in plasma from women with breast cancer and healthy volunteers with or without alterations associated to metabolic syndrome [array]

summary: Breast cancer (BCa) is the leading cause of death by cancer in women worldwide. Early diagnosis is improving the survival of BCa patients but more sensitive and specific tools are still necessary. We propose the use of miRNAs as a biomarker alternative in BCa diagnosis. MiRNAs are small non-coding RNAs that regulate gene expression.  Circulating miRNAs can be detected in body fluids. Aberrant expression of miRNAs in both tissues and fluids are linked to several pathologies. Furthermore, metabolic syndrome (MeS) is a risk factor for BCa. Molecular mechanisms underlaying this association have not been fully elucidated.   The aim of this work was to identify the circulating miRNAs in plasma of BCa patients and healthy donors with or without clinical features linked to MeS. MiRNAs were isolated from plasma of woman. BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. Healthy women (HD) (N=36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). We hybridized miRNAs of each group using GeneChip® miRNA 4.0 Array (Affymetrix). miRNA expression profile was also determined by miRNA sequencing from 6 BC patients and 4 HD. Data analysis revealed 11 miRNAs upregulated in the plasma from BCa patients compared to HD. Meanwhile, 24 miRNAs were altered in plasma of women with MeSL compared to control.

overall_design: BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. In addition, healthy women (36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). Four samples of healthy women (2 control and 2 AAMS) were generated by pooling miRNAs from 9 donors. Samples were hybridized to the GeneChip® miRNA 4.0 Array (Affymetrix). Data normalization and analysis were performed using Expression Console™ Software 1.3.1 and Affymetrix® Transcriptome Analysis Console (TAC) Software.  For miRNA sequencing, from 6 BC patients and 4 HD was sent to GenoHub (Real Seq Bioscience INC, USA). They performed miRNA isolation using Quick-cfRNA Serum and Plasma (Zymo Research, USA) and sequencing was performed using the NextSeq platform (Illumina, USA). The analysis comparing BC versus HD followed the pipeline and their versions: Ubuntu 18.04.2 LTS x86_64-pc-linux-gnu (64-bit), R version 3.6.0 -- Planting of to Tree, FastQC v0.11.5, cutadapt version 2.3, bowtie version 1.2.2, DESeq2_1.22.2, Rsubread_1.32.4, BiocParallel_1.16.6, Ggplot2_3.1.0.


title: miRNA expression data in plasma from women with breast cancer and healthy volunteers with or without alterations associated to metabolic syndrome

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: CFH1 tethers the circadian clock to red light dependent photomorphogenesis

city: New Haven

first: Chun Chung

last: Leung

state: CT

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

summary: Investigating the differential expression genes in cfh1 mutants, CFH1 decoys, and PIF3 over-expression lines.

overall_design: Col-0, cfh1-1 mutant, CFH1 decoy line, and PIF3 over-expression line were grown in 12L:12D for 7 days and then transferred to constant red light. Samples were collected on day 12 ZT1.

first: Wei

last: Liu

first: Harper

last: Lowrey

first: Joshua

middle: M

last: Gendron


title: RNA sequencing facilitates quantitative analysis of mBBZ CAR and CXCR4 CAR T cell transcriptomes

city: Shanghai

first: RUIXIN

last: SUN

address: No.25/Ln2200, XieTu Road Shanghai 200032, P.R.China

institute: Shanghai Cancer Institute

summary: Purpose: Analyzing the cytokine transcription and associated signalings of h8E5(2I)-mBBZ and h8E5(2I)-mBBZ-CXCR4 CAR T cells.Methods: Mouse h8E5(2I)-mBBZ and h8E5(2I)-mBBZ-CXCR4 CAR T cells were stimulated with antigen peptides for four hours.Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome

overall_design: The mRNA profiles of h8E5(2I)-mBBZ and h8E5(2I)-mBBZ-CXCR4 CAR T cells upon stimulation with antigen peptides for four hours. There are two sample replicates for the h8E5(2I)-mBBZ and h8E5(2I)-mBBZ-CXCR4 CAR T cells.

first: Ruixin

last: Sun

first: Yansha

first: Chuanlong

first: Yifan


title: Cytochrome P450 monooxygenase eicosanoid pathway mediates the colon cancer-enhancing effects of dietary linoleic acid

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

institute: Centenary Institute

summary: CYP monooxygenase-mediated conversion of LA to EpOMEs plays critical roles in the health effects of dietary LA, implicating a unique mechanistic linkage between dietary fatty acid intake and cancer risks.

overall_design: We determine the specific lipid metabolic pathways and metabolites involved in its colon cancer-enhancing effects. Using a LC-MS/MS-based lipidomics, we find that the previously unappreciated cytochrome P450 (CYP) monooxygenase pathway is a major pathway to metabolize LA in vivo. Furthermore, CYP monooxygenase is required for the colon cancer-promoting effects of LA, since LA-rich diet fails to exacerbate colon cancer in CYP monooxygenase-deficient mice.

first: Guodong

last: Zhang

first: Jianan

first: Jun

last: Yang

first: Darryl

last: Zeldin


title: RNA sequencing facilitates quantitative analysis of glioma stem cells with or without dbcAMP treatment transcriptomes

city: Guangzhou

first: Zixi

last: Qin

address: Department of Pathology, Medical College, Jinan University, Guangzhou, 510632, P. R. China

institute: Jinan university

summary: Purpose: The goals of this study are to compare control with dbcAMP treatment GSC11 cells transcriptome profiling (RNA-seq).

overall_design: GSC11 mRNA profiles of control and dbcAMP treatment.

first: Fan

last: Xing


title: Hexokinase 3 enhances myeloid cell survival via non-glycolytic functions

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
Purpose: The goal was to compare transcriptome profiles of HL60 HK3-null and Cas9 expressing control cells treated with either ATRA or DMSO using RNA sequencing. In addition, to find accessible DNA regions by probing open chromatin with hyperactive mutant Tn5 Transposase using ATAC sequencing.
Methods: HL60 HK3-null and Cas9 expressing control cells were treated with 1µM of ATRA or DMSO (0.01%) for 36h. Treated cells were then harvested for RNA-Seq and ATAC-Seq analysis.
Results: We mapped sequence reads per sample to the human genome (GRCh38 - hg38) and identified differentially expressed transcripts as well as open chromatin peaks in AML HL60 HK3-null and Cas9 expressing cells upon treatment with ATRA or DMSO as control. Differentially expressed genes, were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our results show that HK3 knockout (HK3-null) AML cells had an accumulation of reactive oxygen species (ROS) as well as DNA damage during ATRA-induced differentiation. RNA sequencing analysis confirmed pathway enrichment for programmed cell death, oxidative stress and DNA damage response in HK3-null AML cells. These signatures were confirmed in ATAC sequencing, showing that loss of HK3 leads to changes in chromatin configuration and increases accessibility of genes involved in apoptosis and stress response.

overall_design: HL60 HK3-null and Cas9 expressing control cells were treated with ATRA or DMSO. Next, RNA-Seq and ATAC-Seq analyses was perfomred and differences between control and HK3-null as well as ATRA and control treated HL60 cells were assessed.

first: Kristina

last: Seiler

first: Mario

last: Tschan

first: Bruce

last: Torbett


title: Bulk RNA-seq of intestinal epithelial cells from Ctrl and Fzd5KO

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: General gene profiles change after Fzd5 knockout

overall_design: 3 replicates for each group

first: Lu

last: Deng

first: Linheng

last: Li


title: Gene expression profiling and developmental outcomes reveals early toxicological mechanisms of lead effects in an early-life stage amphibian, Xenopus laevis

city: Saskatoon

first: Natacha

last: Hogan

state: SK

address: 51 Campus Drive

institute: University of Saskatchewan

summary: Lead (Pb) is a widespread environmental toxicant that can elicit a wide variety of adverse effects in aquatic species. In fish, exposure to Pb can induce oxidative stress and reduce antioxidant capacity and there is evidence that Pb-induced developmental abnormalities are the result of dysregulated metabolism pathways but to date, no studies have characterised the molecular mechanisms of lead toxicity in amphibians. To investigate this, we coupled transcriptomic responses and early-life stage toxicity testing to identify specific molecular mechanisms that drive the adverse effects of lead, in Xenopus laevis. Embryos were exposed to one of the concentrations (0, 70, 210 and 630 ng/L) of lead (II) nitrate starting from 2 days post fertilization (dpf) until 6 dpf and 21 dpf to examine the transcriptomic and apical responses, respectively. We observed common dysregulated pathways and with similar magnitude at medium and high lead concentrations, but a phenotypic response only with the highest lead level. RNA Seq analysis showed about ~250 differentially expressed genes that could be further categorized into KEGG pathways based on their involvement in key biological processes. The most dysregulated pathways were Glutathione metabolism, Cytochrome P450 (drug/ xenobiotic metabolism) and Steroid hormone biosynthesis. Developmental studies showed that tadpoles exposed to the highest Pb concentration (630 ug/L) had significantly decreased total length and higher proportion of developmental abnormalities. Therefore, evaluating gene expression responses can provide early indication of toxicological mechanisms of lead effects in amphibians. As with fish, dysregulated metabolic pathways are most likely the molecular mechanisms underlying lead toxicity in ELS amphibians and contribute to the altered growth and developmental abnormalities observed in this study.

overall_design: In this study we analyzed the gene expression profiles of  whole body Xenopus laevis embryos exposed to either of the treatments, water control, 210 ng/L, 630 ng/L of lead (II) nitrate starting from 2 days post-fertilization until 6 days post fertilization. Each treatment had 5 replicates and each replicate had 3 individuals.

first: Shreyas

last: Jois

first: Summer

last: Selinger

first: Anita

last: Masse

first: Jessica

last: Ewald

first: Jeff

last: Xia

first: Doug

last: Crump

first: Niladri

last: Basu

first: Markus

last: Hecker


title: Simultaneous Detection of Gene Expression of insects, nematode and bacterial specific genes to monitor the infection.

city: Bengaluru

first: Nagesh

last: Mandadi

state: Karnataka

address: Bellary Road, H.A. Farm Post, Hebbal, Bengaluru, Karnataka

department: Division of Genomics Resource

institute: ICAR-National Bureau of Agricultural Insect Resources

summary:
In this study, NanoString technology gene expression quantification platform was used to study the expression of toxin genes causing infections from Bacteria (Photorhabdus and Xenorhabdus), Nematode (H.indica, S.riobrave , S.carpocapsae) specific genes for detection and Immune related genes from the infected insects (Spodoptera frugiperda and Galleria mellonella).
The study revealed the expression of different immune related genes from the infected insects (Spodoptera frugiperda and Galleria mellonella) and helped in understanding the trend of expression of gene in the samples from the healthy condition to the death stage. Variations in gene expression were seen as per the expectation.

platform_organism:
Xenorhabdus
Bombyx mori
Spodoptera frugiperda
Galleria mellonella
Drosophila melanogaster
Photorhabdus
Heterorhabditis bacteriophora

overall_design: The worms were infected with bacteria from genus of Photorhabdus and Xenorhabdus. The experiment included samples in three stages, Uninfected, Infected and Dead. Uninfected samples were taken as control. Sufficient amount of RNA was extracted suitable for NanoString custom assay and after subjecting to quantity and quality check it was proceeded for NanoString custom multiplexed assay. Total samples- 10.

first: Savithri

last: Handanahal

first: Sindhu

last: Madhusudhan

first: Arpitha

last: Ghosh

first: Manju

last: Murthy

first: Narasimha

first: Swagat

last: Patra


title: DDX17-regulated alternative splicing that produced a novel oncogenic isoform of PXN-AS1 to promote HCC metastasis [tissues]

city: Chongqing

first: Hongzhong

last: Zhou

institute: ChongQing Medical University/.

summary: Alternative splicing (AS) events have been considered one of the critical hallmarks of cancer progression. However, the significance of ASE in HCC metastasis is not fully revealed. This study aims to investiage the important role of differential splicing events in HCC metastasis.

overall_design: To reveal the significance of ASE in HCC metastasis, we have analyzed the RNA-seq data of 9 pairs of EHMH and 9 pairs of MFH.  We found increased differentially spliced events covering A3SS, A5SS, MXE, IR and SE in EHMH relative to MFH.Moreover, HCC tissues with extrahepatic metastasis showed more significant differentially spliced events on metastasis-associated genes with preferential increase in A3SS, A5SS, IR and SE, suggesting that splicing of these genes might represent an alternate mechanism for HCC metastasis.

first: Juan

last: Chen

first: Hong-Zhong

first: Sheng-Tao

last: Cheng

first: Hai-Jun

last: Deng

first: Yu-Jiao

first: Min-Li

last: Yang

first: Ji-Hua

last: Ren


title: RNA Sequencing of RNA profiles from BHMT Overexpression (OE) and BHMT knockout (KO)

city: Salt Lake City

first: Gregory

last: Ducker

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

summary:
Purpose: Betaine-Homocysteine Methyltransferase (BHMT) catalyzes the conversion of betaine to dimethylglycine and homocysteine to methionine. We were interested in both overexpressing and knocking out BHMT and examining the global effects of RNA transcription. We did this in both in vivo and in vitro models.
Methods: Tumors: 1,000,000 HepG2 BHMT OE or BHMT KO cells were injected to the left and right flank of nude mice (n = 5), respectively, as a xenograft.  Once tumors reached the appropriate size, they were harvested. The tissue was homogenized and RNA was extracted. Cells: HepG2 BHMT OE and KO cells (n = 3/group) were grown in Human Plasma-Like Medium (HPLM) for 48 hours. Then, cells were harvested and RNA was extracted. Both: Samples were submitted to the University of Utah sequencing core, who performed library prep and sequencing. Total RNA was taken from samples and run on an illumina sequencer.
Note: OE2 and KO2 were large outliers, and therefore remove from the data analysis. They came from the same mouse.

overall_design: Tumors: RNA profile of the tumor created from a xenograft of HepG2 BHMT OE and KO cells in nude mice Cells: RNA profile from HepG2 BHMT OE and KO cells in HPLM for 48 hr.

first: Chase

last: Neumann

first: Kyle

last: Dunlap


title: Gene Expression Data from Human Peripheral Blood

city: Richmond

first: Adam

last: Dempsey

state: VA

address: 8751 Park Central Drive, Suite 200

institute: StageZero Life Sciences

summary:
Early diagnosis of cancer has been shown to substantially improve 5-year survival rates for many cancer types. With current methodologies early diagnosis has proven difficult for cancers of deep tissues, such as the pancreas and lung. However, whole peripheral blood has been demonstrated to be a promising non-invasive surrogate tissue for the detection of many types of cancer.
Blood samples were collected in EDTA blood collection tubes from 2,485 human volunteers and gene expression profiled with the goal to develop a classification model that differentiations patients with cancer from those without cancer.

overall_design: A set of 1,013 unique patient blood samples spanning 11 types of cancer or pre-cancer (colorectal polyps) of interest and 1,832 unique control samples, including those with autoimmune and cardiovascular disease, were collected and profiled on Affymetrix U133 Plus 2.0 GeneChips. A multi-cancer classification model was generated using logistic regression to classify sample profiles into the 11 different cancer classes.

first: Samuel

last: Chao

first: Tanya

last: Pilcz

first: Dimitri

last: Stamatiou

first: Jay

last: Ying

middle: A


title: Single-cell RNA-sequencing of human intestinal organoid cells

status: Public on Aug 30 2024

city: Utrecht

first: Daisong

last: Wang

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We focused on a rare cell population of human intestine, the M cells. Using human intestinal organoid as a model, the M cells could be differentiated, FACS-sorted from organoids and analyzed by scRNA-seq.

overall_design: Human intestinal organoids were cultured in M cell differentiation medium. Cells derived from the differentiated M cell orgnaoids were FACS sorted and individally collected in the 384 well plates for SORT-seq based scRNA-seq analysis.

first: Sangho

last: Lim


title: Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

institute: Montreal Heart Institute

summary: Heart maturation and remodelling during the foetal and early postnatal period are critical for proper survival and growth of the foetus, yet our knowledge of the molecular processes involved are lacking for many cardiac cell types. To gain a deeper understanding of the transcriptional dynamics of the heart during the perinatal period, we performed single-cell RNA-seq on E14.5, E16.5, E18.5, P0, P4 and P7 mouse hearts to establish a catalogue of 49,769 cells. Gene regulatory network and pathway activity analyses underscored that heart maturation is strongly associated with regulation of cell growth and proliferation via pathways such as TGFβ. We additionally identified a common, cell type-independent signature for imprinted genes over time. Surprisingly, bioinformatics analyses and confirmation with RNAscope confirmed that while lncRNA H19 expression decreased over time in multiple cardiac cell types, it remained stably expressed in endocardial cells between E14.5 and P7. This suggests a differential requirement for H19 in the endocardium, and points towards an endocardium-specific maturation process when compared to other cardiac cell types. We envision this dataset to serve as a resource for better understanding perinatal heart maturation at the transcriptomic level, and to help bridge the gap between early developmental and adult heart stages for single-cell transcriptomics.

overall_design: Drop-seq was performed on single-cell suspensions from a total of 30 mouse hearts. We sampled 5 different time points during the perinatal period (E16.5,E18.5,P0,P4,P7) with 6 biological replicates per time point, from mice on a C57Bl/6NJ background. The raw UMI matrix contains a further 6 replicates from a previous study for E14.5 hearts (GSE109247).

first: Gregor

last: Andelfinger

first: Lara

last: Feulner


title: Bulk RNA-sequencing of human intestinal organoid cells

summary: We focused on a rare cell population of human intestine, the M cells. Using human intestinal organoid as a model, the M cells could be differentiated, FACS-enriched and analyzed by RNA-seq.

overall_design: Human intestinal organoids were cultured in M cell differentiation medium. Cell subpopulations derived from the differentiated M cell orgnaoids were FACS sorted and collected in TRIzol for bulk RNA-seq analysis.


title: RNA-seq analyses of pathogenic Burkholderia glumae under in vivo rice panicle condition

city: Busan

first: Jungwook

last: Park

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

department: Microbiology

institute: Pusan National University

summary: RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns of B. glumae BGR1 under infected rice panicle tissue.

overall_design: Three libraries constructed for Burkholderia glumae BGR1 infected in rice panicles.

first: Hyun-Hee

last: Lee

first: Hyejung

last: Jung

first: Young-Su

last: Seo


title: Succinate diminishes biological activity and mitochondrial function of human adipose-derived stem cells

city: shanghai

first: bo

last: wang

address: 130 Meilong Rd.

institute: East China University of Science and Technology

summary: Alterations in succinate levels have been associated with various metabolic and inflammatory diseases. However, little is currently known about whether adipose-derived stem cells (ADSCs) undergo changes when exposed to succinate. Here, we investigate the biological properties, mitochondrial function and immunophenotype of ADSCs treated with succinate. We observed that reduced biological activity of ADSCs following by succinate stimulated. Of note, succinate treated-ADSCs exhibit mitochondrial dysfunctions, including increased mitochondrial fragments, decreased mitochondrial mass, increased ROS production, reduced Oxidative phosphorylation (OXPHOS). Furthermore, transcriptome analysis revealed that the downregulation of genes involved in cell proliferation, OXPHOS and metabolism, whereas the signaling pathways related to cancer, apoptosis, inflammation were upregulated upon succinate treatment. The findings indicate that ADSCs exposed to succinate exhibit signs of mitochondrial dysfunction, inflammation, and a significant decrease in biological activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Adipose stem cells treated with DMS and DMM versus control.

first: Bo

first: xinxin

first: Meijin

last: Guo

first: Huiming

last: Xu


title: CUT&Tag Profiling Reveals Arid3a-Dependent Epigenetic Control in Vascular Smooth Muscle Cells

city: guiyang

first: Dijie

last: Zheng

address: No.8 beijing road

institute: guizhou medical universuty

summary: This study employs CUT&Tag technology to meticulously map the chromatin-binding landscape of the transcription factor Arid3a in Vascular Smooth Muscle Cells (VSMCs), thereby highlighting its crucial function in the intricate regulation of gene expression. The CUT&Tag assay illuminates Arid3a's presence at key promoter regions, exerting a profound impact on transcriptional modulation and suggesting the epigenetic governance of 260 genes. By integrating RNA-seq with sophisticated bioinformatic analyses, our research elucidates Arid3a's integral role in fundamental cellular activities, particularly in the dynamics of actin filaments, as well as its potential regulatory nexus with critical pathways, including cAMP signaling and calcium signaling. These insights unveil the intricate molecular choreography of Arid3a in the functioning of VSMCs and shed new light on its role in the development of abdominal aortic aneurysm (AAA).

overall_design: We utilized RNA interference technology to knockdown Arid3a in Vascular Smooth Muscle Cells (VSMCs), successfully establishing several Arid3a knockdown cell lines.In this study, we utilized CUT&Tag technology to functionally map the Arid3a protein-DNA interactions within the chromatin of Vascular Smooth Muscle Cells (VSMCs). The CUT&Tag assay was performed on Arid3a knockdown cells to specifically capture and sequence the DNA fragments associated with Arid3a binding sites. This method allows for the identification of direct genomic targets regulated by Arid3a, providing a detailed view of its chromatin architecture role.

first: Yazhu

last: Deng

first: Mo

last: Zhang


title: Epigenetic Regulation of VSMCs by Arid3a: Insights from RNA-seq Analyses

summary: This study employs RNA-seq to investigate the transcriptional effects of Arid3a in Vascular Smooth Muscle Cells (VSMCs), revealing a comprehensive signature of gene expression. We identified 394 genes that were downregulated and 227 that were upregulated in response to Arid3a knockdown, shedding light on its regulatory network. The RNA-seq data highlighted the key role of Arid3a in controlling the dynamics of actin filaments, which has implications for processes such as cell adhesion and the cAMP signaling pathway.

overall_design: We utilized RNA interference technology to knockdown Arid3a in Vascular Smooth Muscle Cells (VSMCs), successfully establishing several Arid3a knockdown cell lines. Subsequently, we conducted RNA sequencing to explore the alterations in gene expression profiles following the reduction of Arid3a levels. Our aim was to elucidate the downstream effects of Arid3a depletion on the transcriptome of VSMCs, providing insights into its regulatory mechanisms in these cells.


title: GeneQuery RNA Profile of Trigeminal Ganglia from Tumor Burden and Tumor Naïve Mice

city: Sioux Falls

first: Paola

middle: Drapkin

last: Vermeer

state: SD

address: 2301 East 60th street north

department: Cancer Biology and Immunotherapies Group

institute: Sanford Research

summary: Cancer patients often experience changes in mental health, prompting an exploration into whether nerves infiltrating tumors contribute to these alterations by impacting brain functions. Using a mouse model for head and neck cancer and neuronal tracing we show that tumor-infiltrating nerves connect to distinct brain areas. The activation of this neuronal circuitry altered behaviors (decreased nest-building, increased latency to eat a cookie, and reduced wheel running). Tumor-infiltrating nociceptor neurons exhibited heightened calcium activity and brain regions receiving these neural projections showed elevated Fos as well as increased calcium responses compared to non-tumor-bearing counterparts.

overall_design: A total of 8 PCR plates were utilized in this study. Four of the plates were four biological replicates from the tumor burden experimental group. The other four plates were four biological replicates for the non-tumor burden controls. One trigeminal ganglia from an individual mouse was used to isolate RNA for each plate that was run.

first: Jeffery

last: Barr

first: Austin

last: Walz

first: Anthony

last: Restaino

first: Moran

last: Amit

first: Sarah

last: Barclay

first: Elisabeth

middle: G

last: Vichaya

first: William

last: Spanos

first: Robert

last: Dantzer

first: Sebastien

last: Talbot


title: Tumor-Associated Microglia Secrete Extracellular ATP to Support Glioblastoma Progression

city: Stanford

first: Caren

middle: Yu-Ju

last: Wu

state: CALIFORNIA

address: 1201 Welch Rd, Stanford, CA 94305

department: Department of Neurosurgery

institute: Stanford University

summary: Glioblastoma (GBM) is a highly aggressive brain tumor with poor prognosis and high recurrence rates. The complex immune microenvironment of GBM is highly infiltrated by tumor-associated microglia and macrophages (TAMs). TAMs are known to be heterogeneous in their functional and metabolic states and can transmit either pro-tumoral or anti-tumoral signals to glioma cells. Here, we performed bulk RNA-seq and single-cell RNA-seq on GBM patient samples, which revealed increased ATP synthase expression and oxidative phosphorylation (OXPHOS) activity in TAMs located in the tumor core relative to the tumor periphery. Both in vitro and in vivo models displayed similar trends of augmented TAM mitochondrial activity, along with elevated mitochondrial fission, glucose uptake, mitochondrial membrane potential, and extracellular ATP (eATP) production by TAMs in the presence of GBM cells. Tumor-secreted factors, including GM-CSF, induced the increase in TAM eATP production. Elevated eATP in the GBM microenvironment promoted glioma growth and invasion by activating the P2X purinoceptor 7 (P2X7R) on glioma cells. Inhibition of the eATP-P2X7R axis attenuated tumor cell viability in vitro and reduced tumor size and prolonged survival in glioma-bearing mouse models. Overall, this study revealed elevated TAM-derived eATP in GBM and provided the basis for targeting the eATP-P2X7R signaling axis as a therapeutic strategy in GBM.

first: Kwang-Yu

last: Chang

first: Jian-Ying

last: Chuang

first: Yiyung

last: Chen