title: TL1A and IL-18 synergy promotes GM-CSF dependent thymic emergency granulopoiesis

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

summary: The current model of hematopoiesis only resolves the thymus around the production and establishment of the peripheral T cell pool. However, the role and in situ development of other immune subsets has been overlooked. We aim to demonstrate that during TL1A and IL-18 induced inflammation, the thymus is capable of producing other cell types such as neutrophils, monocytes, and macrophages and that these potentially have other functions aside from supporting T cell development as scavengers. Here we have proven that ex vivo and in vivo treatment with TL1A and IL-18 results in acute thymic atrophy by a massive loss of DP T cells and shrinking of the thymic lobe. By electron microscopy, flow cytometry and single cell we demonstrate that neutrophils are able to maturate inside the thymus lobe in a NOTCH-independent manner. We used fate-mapping tools to elucidate the origin of thymic neutrophils since we observed a great expansion in our culture that is isolated from the influx of BM progenitors. The Rag1-Cre Rosa26-YFP fate mapping model revealed that neutrophils share a common progenitor with T cells, while monocytes/macrophages do not. Furthermore, we found that most of the thymic GMPs (defined as Lin-Sca-1-c-Kit+CD16/32+CD34+) show history of Rag1 expression in comparison with bone marrow GMPs. Additionally, by using Ms4a3-Cre Rosa26Tdtomato fate mapping model we observed that there was not difference in Tdt labeling between the thymus and bone marrow, suggesting that thymic neutrophils still undergo conventional neutrophils pathway arising from GMPs. Moreover, we show that thymic-derived neutrophils are functional and are capable of forming extracellular neutrophils traps (NETs) similarly to benchmark peritoneal neutrophils. We found that the expansion of thymic neutrophils is GM-CSF dependent by using Csf2rb KO mice.  Additionally, we identified DR3+ and IL-18Rα+ expressing subsets of ILCs and gdT cells as the cellular source GM-CSF. Lastly, in vivo treatment with TL1A+IL-18 lead to emergency granulopoiesis and an increase of neutrophils in all the organs investigated, including the thymus.

overall_design: There are two sets of samples. The first set consists of two samples both originating from murine neonatal thymus organ cultures 6 days post treatment, one treated with TL1A, the other sample treated with TL1A + IL-18.The second set consists of seven 5' scRNA sequencing samples all derived from murine neonatal thymus organ cultures that were treated with mock or a combination of cytokines across three timepoints. The first is a reference sample taken on day 0. Samples 2 to 7 are all taken from the lobes of a neonatal thymus organ culture.The treatments of samples 2,3 and 4 are, respectively, mock treatment, IL-12+IL-18 and TL1A+IL-18. The samples were taken 1.5 days post treatment. Samples 5,6 and 7 have the same respective treatments but were taken 3 days post treatmentSample 8 is taken from the supernatant of a neonatal thymus organ culture 3 days post treatment with IL-12+IL-18.

first: Mario

last: Ruiz Pérez

first: Christian

last: Maueroder

first: Wolf

last: Steels

first: Jelle

last: Huysentruyt

first: Sahine

last: Lameire

first: Ria

last: Roelandt

first: Amanda

last: Gonçalves

first: Riet

last: De Rycke

first: Bart

last: Lambrecht

first: Tom

last: Taghon

first: Georges

last: Leclerq

first: Peter

last: Vandenabeele

last: Tougaard


title: RNA-seq of AML12 cells treated with PA+si-NC/PA+si-circ-SLC9A6

status: Public on Sep 05 2024

city: Dalian

first: Jihong

last: Yao

address: 9 West Section, Lvshun South Road, Lvshunkou District, Dalian 116044, China

country: China

institute: Dalian medical university

type: Expression profiling by high throughput sequencing

summary: We analyzed the global RNA expression profile in circ-SLC9A6-deficient AML12 cells under PA stimulation，and found that 84 mRNAs are up-regulated and 307 are down-regulated.

overall_design: In the study, to elucidate the underlying molecular mechanism of circ-SLC9A6,we profiled mRNA expression in AML12 cells of 3 PA +si-NC group and 3 PA+si-circ-SLC9A6 group.

first: Yue

last: Wang

first: Xinyao

last: Tian

first: Zhecheng

first: Yan

last: Zhao


title: Comprehensive Profiling of Peripheral Blood Mononuclear Cells Reveals Monocyte-CD8+ T cell-B cell Communication as Central Cell-cell Interaction and pathogenesis in IgA Vasculitis

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

summary: IgA vasculitis (IgAV) is a common vasculitis which often occurs in children. IgAV is characterized by the vasculitis caused by IgA deposition in the walls of small vessels. The mechanisms of immune disorders in IgAV, as well as the innmue network regulation between immune cells is still unclear. Dissecting the IgA-secreting B cells is crucial for understanding the pathegenesis mechanisms of IgA deposition in IgA vasculitis (IgAV). Here, we used single-cell RNA sequencing to profile immune cells in peripheral blood mononuclear cells of IgAV. MIF induced IgA secretion in IgAV, and monocyte-CD8+ T cell-B cell communication regulated MIF pathway. ICAMs pathway regulated monocyte-CD8+ T cell-B cell communication, and promoted B cells adhension in IgAV. CD8+ T cell was the key cell in monocyte-CD8+ T cell-B cell communication. TCR repertoire analysis identified a specific CD8+ Temra cluster with specific TCR clonetypes. BCR repertoire analysis revealed the existence of IgA Fc-specific IgG in serum of IgAV nephritis. These findings reveals complicated immune regulation in IgAV, emphrazing the importance of MIF and ICAMs pathways in cell-cell interaction, discovering CD8+ T cells’ crucial function for IgAV pathogenesis, and bringing new insights into the pathegenesis of IgA deposition in IgAV.

overall_design: Both IgAV patients and controls were collected from Wuhan Children's Hospital.

first: Chaohong

last: Liu

first: Jingzhi

last: Yang

first: Lu


title: Correlation with Apoptosis Process through RNA-Seq Data Analysis of Hep3B Hepatocellular Carcinoma Cells Treated with Glehnia littoralis Extract (GLE)

status: Public on Sep 04 2024

city: Jinju-si

first: Minyeong

last: Park

address: Jinju-daero

country: South Korea

institute: Gyeongsang National University

summary: Glehnia littoralis is a perennial herb found in coastal sand dunes throughout East Asia. This herb has been reported to have hepatoprotective, immunomodulatory, antioxidant, antibacterial, antifungal, anti-inflammatory, and anticancer activities. It may be effective against hepatocellular carcinoma (HCC). However, whether this has been proven through gene-level RNA-seq analysis is still being determined. Therefore, we are attempting to identify target genes for the cell death process by analyzing the transcriptome of Hep3B cells among HCC treated with GLE (Glehnia littoralis extract) using RNA-seq. Hep3B was used for the GLE treatment, and the MTT test was performed. Hep3B was then treated with GLE at a set concentration of 300 μg/mL and stored for 24 h, followed by RNA isolation and sequencing. We then used the data to create a plot. As a result of the MTT analysis, cell death was observed when Hep3B cells were treated with GLE, and the IC50 was about 300 μg/mL. As a result of making plots using the RNA-seq data of Hep3B treated with 300 μg/mL GLE, a tendency for the apoptotic process was found. Flow cytometry and annexin V/propidium iodide (PI) staining verified the apoptosis of HEP3B cells treated with GLE. Therefore, an increase or decrease in the DEGs involved in the apoptosis process was confirmed. The top five genes increased were GADD45B, DDIT3, GADD45G, CHAC1, and PPP1R15A. The bottom five genes decreased were SGK1, CX3CL1, ZC3H12A, IER3, and HNF1A. In summary, we investigated the RNA-seq dataset of GLE to identify potential targets that may be involved in the apoptotic process in HCC. These goals may aid in the identification and management of HCC.

overall_design: To determine whether GLE has any function in Hep3B, we sequenced mRNA from GLE-treated Hep3B and normal Hep3B.

first: Sujin

last: Lee

first: GonSup

last: Kim


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration

city: Cambridge

first: Jessica

last: Whited

state: MA

address: 7 Divintiy Street, Sherman Fairchild - Whited Lab

country: USA

institute: Harvard University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify whether the proliferating cells of the systemically-activated limbs are epigenetically different from those of homeostatic limbs. identify which cells drive systemic-activation response in the limbs distant to the amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed bulk ATAC seq of the dividing, 4C population.

first: Steven

middle: J

last: Blair

middle: L


title: Exercise promotes peripheral glycolysis through miR-204 induction in skeletal muscle

city: Daejeon

first: Eui-Ju

last: Hong

state: Not Applicable

address: 99 Dahak-ro, #412, Veterinary Building, Daejeon, 34134

institute: Chungnam National University (CNU)

type: Non-coding RNA profiling by high throughput sequencing

summary: Mechanisms underlying exercise induced insulin sensitization are of interest as exercise is a clinically critical option as a lifestyle intervention for diabetic patients. Some of microRNAs (miRNAs), which can be secreted from skeletal muscle after exercise, regulate insulin sensitivity and are used for diagnostic marker for diabetic patients. MiR-204 is well-known for its involvement in development, cancer, and metabolism. However, it is still unknown whether miR-204 associates with exerciseinduced glycemic control. In preliminary data, we found that endurance exercise of mice increases miR-204 expression levels in skeletal muscle. In chronic exercise mice model, miR-204 expression levels were increased with glycolytic enzymes in skeletal muscle. When hypoxia induced hypoxia inducible factor 1 alpha (HIF1α), miR-204 expression levels were increased. HIF1α overexpression also increased miR-204 expression levels. To corroborate the causality between miR-204 and glycolysis, miR-204 mimic was introduced to myoblast cell line, C2C12 myoblast cell line. After exposure to miR-204 mimic, C2C12 cells could increase the glycolysis rate measured by extracellular acidification rate. miR-204 mimics also increased mRNA expression levels of glycolytic enzymes. In vivo intravenous miR-204 administration to mice also increased the glucose clearance rate after refeeding of mice. MiR-204 increased blood glucose surge on earlier point of refeeding but promoted the blood glucose lowering on later point of refeeding. Skeletal muscle glycolytic enzymes were increased in mRNA expression levels by miR-204 injection. This finding suggests the novel physiological role of miR-204 in skeletal muscle glycolysis where insulin action is limited.

overall_design: For control and test RNAs, the library construction was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, for each library, total RNA was prepared, and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA, and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified using magnetic beads to remove all reaction components. The library was amplified to add complete adapter sequences required for cluster generation. The final library was purified from the PCR components. High-throughput single-end 75 sequencing was performed using NextSeq 550 (Illumina, Inc., USA). RNA sequencing (RNA-seq) analysis of differentially expressed genes (DEGs) was performed using the Excel-based Differentially Expressed Gene Analysis (ExDEGA) software package provided by EBIOGEN Inc. (Korea). Heatmap generation and G0 functional analysis were performed using EdgeR [PMID19910308] and comparisons were performed with DEG master file production using ExDEGA (EBIOGEN Inc, Korea).

first: Sang R.


title: GPR158 in pyramidal neurons mediates social novelty behavior  via modulating synaptic transmission in male mice

city: Shenzhen

first: Shoupeng

last: Wei

state: Guangdong

address: 628 Zhenyuan Rd

institute: The Seventh Affiliated Hospital, Sun Yat-Sen University

summary: Impairment in social communication skills is a hallmark feature of autism spectrum disorder (ASD). The role of G-protein coupled receptor 158 (GPR158) in ASD remains largely unexplored. In this study, we observed both constitutive and cell/tissue-specific knockouts of Gpr158 in pyramidal neurons or medial prefrontal cortex (mPFC) result in impaired novelty preference, while sociability remains unaffected in male mice. Notably, loss of GPR158 leads to a significant decline in excitatory synaptic transmission, characterized by the reduction in glutamate vesicles, as well as the expression and phosphorylation of GluN2B in the mPFC. We successfully rescue the phenotype of social novelty deficits either by reintroducing GPR158 in the mPFC of Gpr158 deficient mice or by chemogenetic activation of pyramidal neurons where Gpr158 is specifically ablated. Our findings indicate that GPR158 in pyramidal neurons plays a specific role in modulating social novelty, and may represent a potential target for treating social disorder.

overall_design: To elucidate the molecular basis underlying glutamate vesicle shortage induced by loss of glutamatergic GPR158, we conducted RNA-sequencing analysis in the mPFC tissues from CamK2A-Cre;Gpr158fl/fl (CaKO) and Gpr158fl/fl control mice (4 mice each group). Total RNA was extracted from the mPFC of adult male CaKO mice and the littermate Gpr158fl/fl controls with Tripure Isolation Reagent (Roche, Germany). RNA-sequencing analysis was carried out using the Illumina NovaSeq 6000 platform (Novogene, China). Paired-end clean reads were aligned to the mouse reference genome (Ensemble_GRCm38.90) with TopHat (version 2.0.12), and HTSeq-count (version 0.6.1) was used to quantify the mRNA levels.

first: Jian

last: Jiang

first: Dilong

first: Jinlong

last: Chang


title: RIPK4 promotes oxidative stress and ferroptotic death through the downregulation of ACSM1

city: Shanghai

first: Jing

last: Zhang

address: NO. 280 South Chongqing Road

institute: Shanghai Jiaotong University

summary: One of the most critical axes for cell fate determination is how cells respond to excessive reactive oxygen species (ROS)-oxidative stress. Extensive lipid peroxidation commits cells to death via a distinct cell death paradigm termed ferroptosis. However, the molecular mechanism regulating cellular fates to distinct ROS remains incompletely understood. Through siRNA against human receptor-interacting protein kinases (RIPK) family members, we discovered that RIPK4 is crucial for oxidative stress and ferroptotic death. Upon ROS induction, RIPK4 is rapidly activated and the kinase activity of RIPK4 is indispensable to induce cell death. Specific ablation of RIPK4 in kidney proximal tubules protects mice from acute kidney injury induced by cisplatin and renal ischemia/reperfusion. RNA sequencing revealed the dramatically decreased expression of acyl-CoA synthetase medium-chain (ACSM) family members induced by cisplatin treatment which is compromised in RIPK4 deficient mice. Among these ACSM family members, suppression of ACSM1 strongly augments oxidative stress and ferroptotic cell death with induced expression of ACSL4, an important component for ferroptosis execution. Our lipidome analysis revealed that over-expression of ACSM1 leads to the accumulation of monounsaturated fatty acids (MUFAs), attenuation of polyunsaturated fatty acids (PUFAs) production, and thereby cellular resistance to ferroptosis. Hence, knock-down ACSM1 re-sensitizes RIPK4 KO cells to oxidative stress and ferroptotic death. In conclusion, RIPK4 is a key player involved in oxidative stress and ferroptotic death, which is potentially important for a broad spectrum of human pathologies. The link between RIPK4-ASCM1 axis to PUFAs and ferroptosis reveals a novel mechanism to oxidative stress induced necrosis and ferroptosis.

overall_design: Ripk4 WT and cKO mice were mice were intraperitoneally injected with 15 mg/kg cisplatin. Four days later, mice were sacrificed, the samples of kidney tissues were harvested to extract RNA for sequencing


title: RNA-Seq of Primary HSCs of Wild-type and Cyp1b1 Knockout Mice with Thioacetamide Treatment

city: Pittsburgh

first: Wen

last: Xie

state: Pennsylvania

address: 335 Sutherland Dr

department: Center for Pharmacogenetics and Department of Pharmaceutical Sciences

institute: University of Pittsburgh

summary: The goal of this study was to compare transcriptomes of mouse primary HSCs isolated from wild-type or Cyp1b1 knockout mice with PBS or thioacetamide (TAA) treatment.

overall_design: RNA-Seq analysis of primary HSCs isolated from wild-type or Cyp1b1 knockout mice treated with 3 doses of PBS or TAA for every 3 days.

first: Hung-Chun

last: Tung

first: Sihan

last: Li


title: Polo like kinase 2 (PLK2) promotes microglial activation via regulation of the HSP90α/IKKβ pathway

city: Hangzhou

first: Junjie

last: Cheng

address: Huancheng East 208

department: Pharmacy

institute: Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine

summary: Microglial overactivation is actively involved in the pathogenesis of neurodegenerative diseases. Polo-like kinase 2 (PLK2) is a serine/threonine protein kinase associated with the regulation of synaptic plasticity and centriole duplication. Here, we identified PLK2 as an important early response gene in lipopolysaccharide (LPS)-stimulated microglial cells. Knockdown or inhibition of PLK2 remarkably attenuated LPS-induced expression of pro-inflammatory factors such as IL-1β, IL-6, COX2, TNF-α, and iNOS in microglial cells via suppressing the IKKβ-NF-κB signaling pathway. Notably, overexpression of PLK2 induced expression of pro-inflammatory factors and NF-κB transcriptional activation in the absence of inflammatory stimuli. Mechanistically, co-immunoprecipitation experiments revealed association between PLK2 and IKKβ, whereas GST pull-down assay showed no direct interaction between PLK2 and IKKβ. Proteomic analysis and in vitro kinase assay identified heat shock protein 90 alpha (HSP90α), a regulator of IKKβ activity, as a novel PLK2 substrate. Knockdown or pharmacological inhibition of HSP90α abolished PLK2-mediated activation of NF-κB transcriptional activity and microglial inflammatory activation. Furthermore, phosphoproteomic analysis pinpointed Ser252 and Ser263 on HSP90α as novel phosphorylation targets of PLK2. Subsequent functional studies demonstrated that re-expression of phosphor-dead mutation of these two phosphorylation sites on HSP90α failed to rescue the PLK2-induced activation of the NF-κB signaling. Lastly, conditional knockout of PLK2 in microglial cells dramatically ameliorated neuroinflammation and subsequent dopaminergic neuron loss in an intracranial LPS-induced mouse PD model. The present study revealed, for the first time, that PLK2 promoted microglial activation through the phosphorylation of HSP90α and subsequent activation of the IKKβ-NF-κB signaling pathway. Consequently, PLK2 emerges as a potential therapeutic target for the amelioration of neuroinflammation-related diseases.

overall_design: BV2 microglial cells were stimulated with LPS (200 ng/ml) for 0, 1, 12 h followed by RNA extraction and RNA-Seq

first: Lei

last: Wu

first: Xiaowan

last: Chen

first: Shuai

first: Zhirou

last: Xu

first: Renjuan

last: Sun

first: Yiwei

last: Huang

first: Huicui

first: Guanghui

last: Wang

first: Xuechu

last: Zhen

first: Long-Tai

last: Zheng


title: Polo like kinase 2 (PLK2) promotes microglial activation via regulation of the HSP90α/IKKβ pathway [II]

summary: Microglial overactivation is actively involved in the pathogenesis of neurodegenerative diseases. Polo-like kinase 2 (PLK2) is a serine/threonine protein kinase associated with the regulation of synaptic plasticity and centriole duplication. Here, we identified PLK2 as an important early response gene in lipopolysaccharide (LPS)-stimulated microglial cells. Knockdown or inhibition of PLK2 remarkably attenuated LPS-induced expression of pro-inflammatory factors such as IL-1β, IL-6, COX2, TNF-α,and iNOS in microglial cells via suppressing the IKKβ-NF-κB signaling pathway.Notably, overexpression of PLK2 induced expression of pro-inflammatory factors and NF-κB transcriptional activation in the absence of inflammatory stimuli. Mechanistically,co-immunoprecipitation experiments revealed association between PLK2 and IKKβ, whereas GST pull-down assay showed no direct interaction between PLK2 and IKKβ. Proteomic analysis and in vitro kinase assay identified heat shock protein 90 alpha (HSP90α), a regulator of IKKβ activity, as a novel PLK2 substrate. Knockdown or pharmacological inhibition of HSP90α abolished PLK2-mediated activation of NF-κB transcriptional activity and microglial inflammatory activation. Furthermore,phosphoproteomic analysis pinpointed Ser252 and Ser263 on HSP90α as novel phosphorylation targets of PLK2. Subsequent functional studies demonstrated that re-expression of phosphor-dead mutation of these two phosphorylation sites on HSP90α failed to rescue the PLK2-induced activation of the NF-κB signaling. Lastly, conditional knockout of PLK2 in microglial cells dramatically ameliorated neuroinflammation and subsequent dopaminergic neuron loss in an intracranial LPS-induced mouse PD model. The present study revealed, for the first time, that PLK2 promoted microglial activation through the phosphorylation of HSP90α and subsequent activation of the IKKβ-NF-κB signaling pathway. Consequently, PLK2 emerges as a potential therapeutic target for the amelioration of neuroinflammation-related diseases.

overall_design: To determine the gene expression profile regulated by PLK2, we overexpressed PLK2, PLK2(D223N), or a control vector in HEK293T cells. RNA-Seq was then performed to compare the changes in gene expression following PLK2 overexpression.There were three groups（Vector/PLK2/PLK2D223N), each with three biological replicates.


title: Single cell RNA seq of 8 week old wild-type mouse choroid-RPE tissue

city: Chicago

first: Benjamin

middle: R

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Whole choroids/RPE complexes were dissected from wildtype ICR mice at 8 weeks of age, dissociated and subjected to single cell RNA sequencing using the 10x Chromium platform

overall_design: Enucleated eyes from 8 week old mice were dissected to collect Choroid-RPE complexes. Each sample consists of pooled eyes from 1 male and 1 female mouse.


title: RNA-sequencing analysis gene expression changes of H9C2 treated with CIRBP  in response to oxygen-glucose deprivation/reperfusion

city: shenzhen

first: Qiang

address: 628 Zhenyuaan Rd.

department: Emergency medicine

institute: The seventh Affiliated Hospital of Sun Yat sen University

summary: Cardiac arrest (CA) represents a significant public health concern, placing a substantial burden on the healthcare system. Post-restoration of autonomous circulation, a majority of patients encounter myocardial dysfunction, a primary cause of death in individuals with cardiac arrest. Hence, the identification of novel therapeutic approaches to enhance myocardial resilience in high-risk cardiac arrest patients holds immense clinical importance. Cold-inducible RNA-binding protein (CIRBP) serves as a vital player in cellular protection and stress resistance, induced by cold conditions. Studies have indicated that the elevation of CIRBP through its agonists can impede the progression of heart failure. However, its role in cardiac toxicity prompted by cardiac arrest remains ambiguous. This study delves into investigating the protective mechanism of CIRBP on cardiac function post-cardiac arrest and sheds light on potential target genes regulated by CIRBP via transcriptome sequencing. Our research outcomes highlight the robust cardioprotective impact of CIRBP on cardiac dysfunction triggered by cardiac arrest and resuscitation.

overall_design: H9C2 were used as the research subjects. Comparative gene expression profiling analysis of RNA-seq data was performed on H9C2s  treated with CIRBP after oxygen-glucose deprivation/reperfusion (OGD/R) . Each group consisted of three duplicate samples. The divided experimental groups was as follows: OGD/R + NC rep1  ,OGD/R+ NC  rep2,OGD/R + NC rep3, OGD/R + CIRBP  rep1, OGD/R + CIRBP rep2,OGD/R + CIRBP rep3,  OGD/R + si-NC  rep1,OGD/R + si-NC  rep2, OGD/R + si-NC  rep3,OGD/R + si- CIRBP  rep1,OGD/R + si- CIRBP  rep2,OGD/R + si- CIRBP  rep3

first: Keke

last: Liu


title: Gene expression file at single cell level of nerve cells in damaged areas of the cerebral cortex in mice with traumatic brain injury

city: Xi'an

first: xiangyu

last: Gao

address: Changle Xi Road

department: Department of Neurosurgery, Xijing Hospital

institute: Fourth Military Medical University

summary: Endothelial cells-derived extracellular vesicles can promote nerve function in mice with traumatic brain injury. We used snRNAseq to analyze the effects of extracellular vesicles derived from endothelial cells on nerve cells in mice with traumatic brain injury.

overall_design: Extracellular vesicles derived from endothelial cells or PBS were injected into mice with traumatic brain injury. We extracted tissue from injured areas of the cerebral cortex in mice and analyzed using snRNAseq.


title: Exosomes from Hypoxia Preconditioned BMSCs Improve Peri-implant Osteogenesis under Type II Diabetes Condition via miR-106b-5p/HIF-1α Signaling Axis

first: Ximeng

last: Cao

address: No.371 Yanqiao Rd.

summary: Rationale：Poor peri-implant osseointegration of dental implants in patients with type II diabetes has become a major clinical challenge in recent years. MSC (Mesenchymal stem cell)-derived exosomes may play an important role in peri-implant osseointegration, but the mechanism remains unclear. Enhancing the therapeutic effect of MSC-derived exosomes and exploring the potential mechanism can help provide a new therapeutic strategy to improve the clinical outcome of dental implant restorations in patients with type II diabetes. Methods：The exosomes derived from hypoxia (Hypo-exos) or normoxia (Nor-exos) preconditioned bone marrow mesenchymal stem cells (BMSCs) were co-cultured with BMSCs and human umbilical vein endothelial cells (HUVECs). The effect of exosomes on BMSCs cell proliferation was detected by CCK-8 assay and EdU assay, and the effect on angiogenesis ability of HUVECs was detected by wound healing assay, transwell migration assay, tube formation assay, enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. A diabetic rat dental implant model was also established and the effect of exosomes on implant osseointegration was evaluated through micro-CT scanning and histological analysis. The differentially expressed miRNAs between Hypo-exos and Nor-exos were identified by high-throughput miRNA sequencing. Subsequently, the target genes and their roles in regulating angiogenesis were predicted and analyzed by bioinformatics analysis and dual luciferase reporter assay. Results：In vitro experiments indicated that hypoxia preconditioning could elevate exosome production and promote cell proliferation of BMSCs and angiogenesis of HUVECs. Moreover, Hypo-exos promoted peri-implant osteogenesis in rats with diabetes. Further investigation revealed the vital involvement of the miR-106b-5p/HIF-1α axis in promoting peri-implant osseointegration.  Conclusion: Exosomes derived from hypoxia-preconditioned BMSCs could improve the peri-implant osseointegration in rats with diabetes by promoting cell proliferation and angiogenesis, and the miR-106b-5p/ HIF-1α axis could be the underlying mechanism.

overall_design: examing 2 conditions(hypoxia and normoxia), each with 3 replicates

first: Yingying

first: Chun


title: CRISPR Screen of Venetoclax Response-Associated Genes Identifies Transcription Factor ZNF740 as a Key Functional Regulator [CUT&Run]

city: Birmingham

first: Changde

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary: BCL-2 inhibitors such as venetoclax offer therapeutic promise in acute myeloid leukemia (AML) and other cancers, but drug resistance poses a significant challenge. It is crucial to understand the mechanisms that regulate venetoclax response. While correlative studies have identified numerous genes linked to venetoclax sensitivity, their direct impact on the drug response remains unclear. In this study, we targeted around 1,400 genes upregulated in venetoclax-sensitive primary AML samples and carried out a CRISPR knockout screen to evaluate their direct effects on venetoclax response. Our screen identified the transcription factor ZNF740 as a critical regulator, with its expression consistently predicting venetoclax sensitivity across subtypes of the FAB classification. ZNF740 depletion leads to increased resistance to venetoclax, while its overexpression enhances sensitivity to the drug. Mechanistically, our integrative transcriptomic and genomic analysis identifies NOXA as a direct target of ZNF740, which negatively regulates MCL-1 protein stability. Loss of ZNF740 downregulates NOXA and increases the steady state protein levels of MCL-1 in AML cells. Restoring NOXA expression in ZNF740-depleted cells re-sensitizes AML cells to venetoclax treatment. Furthermore, we demonstrated that dual targeting of MCL-1 and BCL-2 effectively treats ZNF740-deficient AML in vivo. Together, our work systematically elucidates the causal relationship between venetoclax response signature genes and establishes ZNF740 as a novel transcription factor regulating venetoclax sensitivity.

overall_design: We performed Cut&Run-seq to profile ZNF740 binding sites in Cas9-positive OCI-AML2 and MOLM-13 cells expressing guide RNAs targeting either Luciferase or ZNF740.

first: Lixia

last: Zhang

first: Rui

last: Lu


title: Knockdown of HSPA13 inhibits TGFβ1-induced epithelial-mesenchymal transition of RPE by suppressing the PI3K/Akt signaling pathway

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: To investigate the effect of HSPA13 on TGFβ1-induced EMT of RPE cells, we performed bulk RNA sequencing (RNA-seq). Gene set enrichment analysis (GSEA) revealed that gene signatures associated with EMT and cell migration were significantly downregulated in the shHSPA13+TGFβ1 group relative to the shScramble+TGFβ1 group.  PI3K/Akt signaling-related gene levels were repressed as well.

overall_design: We compared the transcriptomic profiles of shHSPA13 and shScramble human embryonic stem cells (hESCs) -derived retinal pigment epithelium (RPE) cells treated with or without TGFβ1. To induce EMT, hESC-RPE cells were seeded in 1% Matrigel-coated 12-well plates at a density of 5 x 10^5 cells/well. Following 24 hours of cell plating, the cells underwent 24-hour serum deprivation. Subsequently, the cells were subjected to incubation with a concentration of 10 ng/ml of recombinant human TGFβ1 for 48 hours.

first: Furong


title: Non-coding cause of congenital heart defects: Abnormal RNA splicing with multiple isoforms as a mechanism for heterotaxy

city: Indianapolis

first: John

middle: Robert

last: Wells

state: IN

address: 1044 W Walnut St

department: Department of Medical & Molecular Genetics

institute: Indiana University School of Medicine

summary: Heterotaxy is a disorder characterized by severe congenital heart defects (CHDs) and abnormal left-right patterning in other thoracic or abdominal organs. Clinical and research-based genetic testing has previously focused on evaluation of coding variants to identify causes of CHDs, leaving non-coding causes of CHDs largely unknown. Variants in the transcription factor Zinc finger of the cerebellum 3 (ZIC3) cause X-linked heterotaxy. We identified an X-linked heterotaxy pedigree without a coding variant in ZIC3. Whole genome sequencing revealed a deep intronic variant (ZIC3 c.1224+3286A>G) predicted to alter RNA splicing. An in vitro minigene splicing assay confirmed the variant acts as a cryptic splice acceptor. CRISPR/Cas9 served to introduce the ZIC3 c.1224+3286A>G variant into human embryonic stem cells demonstrating pseudoexon inclusion caused by the variant. Surprisingly, Sanger sequencing of the resulting ZIC3 c.1224+3286A>G amplicons revealed several isoforms, many of which by-pass the normal coding sequence of the third exon of ZIC3, causing a disruption of a DNA binding domain and a nuclear localization signal. Short- and long-read mRNA sequencing confirmed these initial results and identified additional splicing patterns. Assessment of four isoforms determined abnormal functions in vitro and in vivo while treatment with a splice-blocking morpholino partially rescued ZIC3. These results demonstrate that pseudoexon inclusion in ZIC3 can cause heterotaxy and provide functional validation of non-coding disease causation. Our results suggest the importance of non-coding variants in heterotaxy and the need for improved methods to identify and classify non-coding variation that may contribute to CHDs.

overall_design: CRISPR/Cas9 was used in H1-OCT4-eGFP cells (a male human embryonic stem cell line) to produce two cell clones containing the ZIC3 intronic variant (NM_003413.4:c.1224+3286A>G) termed ZIC3 AtoG_C1 and ZIC3 AtoG_C2. Two ZIC3 knockout cell clones were also produced (ZIC3 KO_C1: NM_003413.4:c.190_200delinsG; ZIC3 KO_C2: NM_003413.4:c.200_201del). Unedited H1-OCT4-eGFP cells were termed ZIC3 WT. Short-read RNA sequencing was completed for ZIC3 WT ( n=1), ZIC3 AtoG_C1 (n=1), ZIC3 AtoG_C2 (n=1), ZIC3 KO_C1 (n=1), and ZIC3 KO_C2 (n=1) H1-OCT4-EGFP cells using the Illumina sequencing platform. Long-read RNA sequencing was completed in ZIC3 WT (n=3), ZIC3 AtoG_C1 (n=3), and ZIC3 KO_C1 (n=3) H1-OCT4-EGFP cells using the Oxford Nanopore sequencing platform.

first: Maria

middle: B

last: Padua

first: Allison

middle: M

last: Haaning

first: Amanda

last: Smith

first: Shaine

middle: A

last: Morris

first: Muhammad

last: Tariq

first: Stephanie

last: Ware


title: A cis-regulatory atlas of rice single cells

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. Within syntenic regions shared with four other grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, and Urochloa fusca), we identified 10,219 cell-type-specific accessible chromatin regions (ACRs), serving as sources for investigating divergence of these species. To elucidate the roles of cell-type-specific ACRs in species divergence, we focused on leaf cells in O. sativa and the aforementioned grass species. We observed species-specific candidate CREs (cCREs) potentially associated with cell differentiation, especially in epidermal cells across species. These data also revealed presence of H3K27me3-associated ACRs in the majority of cell types across different organs and species, potentially harboring silencer cCREs. Together, this study significantly advances our understanding of the role of cCREs during cell differentiation, shedding light on their contribution to species divergence in plants

overall_design: All samples were integrated into a single all vs. all analysis. Several organs (axillary buds, seedlings, seminal roots, crown roots, panicles, seeds, etc) were profiled with biological replicates.

first: Haidong

last: Yan


title: CRISPR Screen of Venetoclax Response-Associated Genes Identifies Transcription Factor ZNF740 as a Key Functional Regulator [RNA-Seq]

last: Cheng

overall_design: We performed RNA-seq to profile transcriptional changes in Cas9-positive OCI-AML2 and MOLM-13 cells expressing guide RNAs targeting either Luciferase or ZNF740.


title: RNA sequencing of murine NK cells treated with PGE2

city: Munich

first: Anna-Marie

last: Pedde

address: Ismaningerstr. 22

department: Institute of Molecular Immunology

country: Germany

institute: Klinikum rechts der Isar, TU Munich

summary: RNA sequencing was used to determine the impact of PGE2 signaling on NK cell function. Our analysis revealed that PGE2 induces a dysfunctional program in NK cells characterized by the inability to produce cytokines and chemokines upon their activation. Mechanistically, this program is governed by transcriptional changes downstream of the PGE2 receptors EP2 and EP4.

overall_design: Murine NK cells were isolated from spleens of C57BL/6J, Ptger2-/-Ptger4fl/fl or GzmbCrePtger2-/-Ptger4fl/fl mice and cultured for 5 days in low doses of IL-2 and IL15:IL15Ra. In vitro cultured NK cells were treated for 5h with PGE2 (100ng/ml) or conditioned medium (CM) from PGE2-producing control BRAFV600E cells. To assess the transcriptional changes upon activation, NK cells were treated for 1h with PGE2 or CM from control BRAFV600E and stimulated for the last 4h through the activating receptor NK.1.1.

first: Jan

middle: P

last: Böttcher

first: Sainitin

last: Donakonda

first: Rupert

last: Öllinger


title: ATAC sequencing of murine NK cells treated with PGE2

summary: ATAC sequencing was used to determine the impact of PGE2 signaling on NK cell function. Our analysis revealed that PGE2 induces a dysfunctional program in NK cells characterized by the inability to produce cytokines and chemokines upon their activation. Mechanistically, this program is governed by epigenetic changes downstream of the PGE2 receptors EP2 and EP4.

overall_design: Murine NK cells were isolated from spleens of C57BL/6J or GzmbCrePtger2-/-Ptger4fl/fl mice and cultured for 5 days in low doses of IL-2 and IL15:IL15Ra. In vitro cultured NK cells were treated for 5h with PGE2 (100ng/ml) or conditioned medium (CM) from PGE2-producing control BRAFV600E cells. To assess the transcriptional changes upon activation, NK cells were treated for 1h with PGE2 or CM from control BRAFV600E and stimulated for the last 4h through the activating receptor NK.1.1.

first: Hyunu

last: Kim


title: Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer (RNA-seq)

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: To elucidate the regulation of NSD2 in metastatic castration-resistant prostate cancer(CRPC), we performed ChIP-seq of H3K36me2, H3K27me3, H3K4me1, H3K4me3,H3K27ac and NSD2 against castration-sensitive prostate cancer cell line LNCaP and metastatic castration-resistant prostate cancer cell lines, PC3 and DU145, respectively. In metastatic CRPC, we found specific regions of activation with epigenetic changes.

overall_design: Expression profile by RNA-seq for prostate cancer cell lines

first: Sanji

last: Kanaoka

first: Atushi

last: Kaneda


title: Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer

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

overall_design: Refer to individual Series


title: Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer (Hi-C)

summary: To elucidate the regulation of NSD2 in metastatic castration-resistant prostate cancer(CRPC), we performed Hi-C against castration-sensitive prostate cancer cell line LNCaP and metastatic castration-resistant prostate cancer cell lines, PC3 respectively. In metastatic CRPC, we found specific regions of activation with epigenetic changes.

overall_design: Hi-C seq for prostate cancer cell lines


title: RNA-binding protein IGF2BP1 is required for spermatogenesis in an age-dependent manner

status: Public on Sep 03 2024

first: Shuai

last: Xu

state: Shanghai

address: Wujin Road 85, Shanghai, China

institute: Shanghai General Hospital, Shanghai Jiaotong university of  Medicine

summary: Post-transcriptional regulation mediated by RNA binding proteins is crucial for male germline development. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), an RNA binding protein, is specifically expressed in human and mouse male gonads and is involved in manifold biological processes and tumorigenesis. However, the function of IGF2BP1 in mammalian spermatogenesis remains poorly understood. Herein, we generated an Igf2bp1 conditional knockout mouse model using Nanos3-Cre. Germ cell deficiency of Igf2bp1 in mice caused spermatogenic defects in an age-dependent manner, resulting in decreased numbers of undifferentiated spermatogonia and increased germ cell apoptosis. Immunoprecipitation-mass spectrometry analysis revealed that ELAV-like RNA binding protein 1, a well-recognized mRNA stabilizer, interacted with IGF2BP1. Single cell RNA-sequencing showed distinct mRNA profiles in spermatogonia from conditional knockout versus wide type mice. Further research showed that IGF2BP1 plays a vital role in the modulation of spermatogenesis by regulating Lin28a mRNA, which is essential for clonal expansion of undifferentiated spermatogonia. Thus, our results highlight the crucial effects of IGF2BP1 on spermatogonia for the long-term maintenance of spermatogenesis

overall_design: We profiled cells using 8-month-old Igf2bp1 cKO and WT testes from 2mice.

first: Jiaqiang

last: Luo

first: Chao

last: Yang

first: Chencheng

last: Yao


title: Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues

city: Kensington

first: Yolanda

last: Colino Sanguino

state: NSW

address: C25/9 High St

country: Australia

institute: Children's Cancer Institute

summary: Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of three well-established high throughput 3’-scRNAseq platforms: Drop-seq, 10x Chromium and BD Rhapsody; using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar but higher gene sensitivity than Drop-seq, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.

overall_design: PyMT mouse tumours were digested, and analyzed using scRNAseq (Drop-seq, Chromium 10x and BD Rhapsody). Artifically damaged samples were digested and left overnigh at 4ºC

last: Colino-Sanguino

first: Fatima

last: Valdes-Mora

first: David

last: Gallego-Ortega


title: Kidney fibroblasts but not pericytes are involved in fibrogenic and cell plasticity changes that lead to long-term kidney fibrosis and kidney dysfunction associated to dysfunctional telomeres [2021]

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: Tubulointerstitial fibrosis associated to chronic kidney disease represents a global healthcare problem. We showed previously that short and dysfunctional telomeres lead to interstitial renal fibrosis, however, the cell-of-origin of kidney fibrosis associated to telomere dysfunction was unknown to date. To identify the specific cell type responsible for this type of renal fibrosis, we induced telomere dysfunction by deleting the Trf1 telomere-binding factor both in renal fibroblasts and pericytes both in short-term and long-term life-long experiments in mice. Short-term Trf1 deletion in renal fibroblasts and pericytes was not sufficient to trigger kidney fibrosis. However, long-term persistent deletion of Trf1 in fibroblasts, triggered inflammation, cell cycle arrest, fibrogenesis, and vascular rarefaction. These cellular responses lead to macrophage-to-myofibroblast transition (MMT), Endothelial-to-mesenchymal transition (EndMT), and epithelial-to-mesenchymal transition (EMT), ultimately causing kidney fibrosis at humane-endpoint when deletion of Trf1 in fibroblasts was maintained throughout the lifespan of mice. In contrast, Trf1 deletion in pericytes did not lead to any kidney phenotypes both in short-term and long-term experiments.

overall_design: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to six-to eight-week-old male and female Trf1+/+ KFP+/t Cre+/t and Trf1lox/lox KFP+/t Cre+/t mice for three times a week for 8 weeks. Fibroblasts were isolated.

first: Sarita

last: Saraswati

last: Graña-Castro

first: María

last: Blasco


title: Global transcriptional profiles in peripheral blood mononuclear cell during classical swine fever virus infection

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: Classical swine fever virus (CSFV) is an etiologic agent that causes a highly contagious disease in pigs. Laying a foundation to solve problems in its pathogenic mechanism, microarray analysis was performed to detect the gene transcriptional profiles in peripheral blood mononuclear cells (PBMC) following infection with a Chinese highly virulent CSFV strain Shimen. Three susceptible pigs were inoculated intramuscularly with a lethal dose (1.0 × 106 TCID50) of CSFV. Pigs showed classical CSF signs, depletion of lymphocytes and monocytes consistent with CSFV infection, and the CSFV genome was also confirmed in the PBMC. The PBMC were isolated at 1, 3, 6 and 9 days post-inoculation (dpi). Total RNA were extracted and subjected to microarray analysis. Data showed that expression of 847 genes wherein 467 genes were known function and the remaining 380 genes were unknown function, and 541 up- and 306 down-regulation, altered after infection. There were 54, 181, 438 and 354 up- and 61, 120, 218 and 145 down-regulated genes presented on 1, 3, 6 and 9 dpi, respectively. These genes were involved in immune response (14.5%), apoptosis (3.3%), signal transduction (7.6%), transcription (4.4%), metabolism (11%), transport (3.9%), development (6.8%) and cell cycle (3.7%). Results demonstrated its usefulness in exploring the pathogenic mechanisms of CSFV.

overall_design: A total of 12 samples were analyzed in this study. Peripheral blood mononuclear cells (PBMC) were isolated from three susceptible pigs that were inoculated intramuscularly with a lethal dose (1.0 × 10⁶ TCID₅₀) of the highly virulent Chinese Classical Swine Fever Virus (CSFV) strain Shimen. Each pig served as a biological replicate, and samples were collected at four different time points: 1, 3, 6, and 9 days post-inoculation (dpi). RNA was extracted from the PBMCs and subjected to microarray analysis to determine the gene transcriptional profiles. No separate control or reference samples were included, as each pig's pre-inoculation state was used as the baseline for comparison. Gene expression changes were analyzed across the time points, revealing a dynamic response to CSFV infection. The data showed that 847 genes were differentially expressed, with 541 up-regulated and 306 down-regulated genes across the different time points.

first: Jun

last: Li


title: Transcriptome of mouse renal cortices without or with acute kidney injury, and without or with renal tubular epithelial cell-specific deficiency of the glucocorticoid receptor

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

institute: German Cancer Research Center

summary: Microarray expression data of the renal cortex of mice without or with myoglobinuric acute kidney injury, and without or with renal tubular epithelial cell-specific deficiency of the glucocorticoid receptor

overall_design: RNA was extracted from the renal cortex of healthy mice and of mice 24 hours after induction of myoglobinuric acute kidney injury (intramuscular injection of glycerol). Mice with tubular epithelial cell-specific deficiency of the glucocorticoid receptor (genotype Pax8-Cre;nr3c1 flox/flox) were compared to controls (genotype nr3c1 flox/flox).

first: Hermann-Josef

last: Gröne


title: Preimplantation Genetic Testing Analysis for a Chinese Family with Hereditary Spherocytosis Caused by a Novel Splicing Variant of SPTB

first: Yiming

last: Wu

address: No.500 Furonghua Rd

institute: We-health BioTech

summary: In this study, we recruited a patient with Hereditary spherocytosis (HS) detected to have a novel heterozygous variant in the SPTB in the proband. Sanger sequencing of variant alleles and haplotype linkage analysis were performed simultaneously. Five embryos were identified with one heterozygous and four not carrying the SPTB variant. Single-cell amplification and whole genome sequencing showed that three embryos had varying degrees of trisomy mosaicism.

overall_design:
whole genome amplication DNA of 5 embryos and parents' gDNA were genotyped on Illumina ASA SNP array.
contributor: Fudan University


title: Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer (ChIP-seq)

first: Masaki

last: Fukuyo

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for prostate cancer cell lines

first: Sanji

last: Kanaoka

last: Kaneda


title: dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development

city: Oxford

first: Amélie

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

summary: Wnt signaling plays a fundamental role in the initial patterning and development of the embryo, including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further, Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled, however, the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study, we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis, revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension, with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single-cell RNAseq and gpc4-/- zebrafish, a convergent extension mutant with an opposite craniofacial phenotype, we identified dact1/2 specific roles during early development. Using this subtractive approach, we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain, capn8, suggesting a previously unappreciated role of calcium-dependent proteolysis during embryogenesis. Taken together, our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development, providing new insights into the multifaceted regulation of Wnt signaling.

overall_design: Single-cell RNA sequencing (scRNA-seq) analyses were performed on 10 zebrafish embryos (4 WT, 3 dact1-/-;dact2-/- compound mutant, and 3 gpc4-/- mutant embryos) harvested at the 3 somite stage, to assess transcriptomic perturbations during development induced by deletion of dact1/2.

first: Shannon

middle: H

last: Carroll

first: Sogand

last: Schafer

first: Kenta

last: Kawasaki

first: Casey

last: Tsimbal

first: Shawn

last: Hallett

first: Edward

first: Eric

middle: C

last: Liao


title: A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [Mouse_RNAseq_bulk]

city: Leuven

first: Maurilio

last: Sampaolesi

address: Herestraat 49, ON4 - box 804

department: Department of Development and Regeneration

institute: KU Leuven

summary: Rhabdomyosarcoma (RMS), the most common soft-tissue sarcoma occurring in the pediatric population, arises from the skeletal muscle compartment. Several transcriptional and post-transcriptional regulators lock the tumor in a continuous undifferentiated state and prevent the cells from returning to quiescence.  MicroRNAs (miRNAs) are short non-coding RNAs that modulate cell identity by means of post-transcriptional regulation of messenger RNAs. In this study, we aimed at identifying miRNAs that could affect FN-RMS cell identity. Thus, we analyzed publicly available datasets and identified miR-449a and miR-340 as the main regulators of cell cycle and p53 signaling. Using miR-eCLIP technology, we identified the direct effects of miRNAs in FN-RMS cell lines, and an overall rewiring of cell identity at the transcriptomic, epigenetic and metabolic level. We observed that miR-449a+340 directly and indirectly targeted glycolysis and pyruvate entry into mitochondria by inhibiting mitochondrial pyruvate complex (MPC) inhibition. The pharmacological inhibition of MPC resulted in a similar metabolic shift with cell cycle exit and a significant reduction in metastatic potential of FN-RMS models.  In conclusion, the combination of miR-449 and miR-340 play a pivotal role in orchestrating the cell identity of FN-RMS, and the modulation of MPC emerges as a key factor in redirecting FN-RMS towards a quiescent, non-tumorigenic state.

overall_design: Murine fusion-negative rhabdomyosarcoma (FN-RMS) cell line KMR46 was transfected with either lipofectamine or miR-449a + miR-340 for 60 hours, and subsequently bulk RNAseq was performed

first: Enrico

last: Pozzo


title: Sex- and age-associated factors drive the pathophysiology of MASLD

first: Núria

last: Morral

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is strongly associated with obesity. The use of animal models fed Western-style diets is vital for investigating the molecular mechanisms contributing to metabolic dysregulation and for facilitating novel drug target identification. However, the sex- and age-associated mechanisms underlying the pathophysiology remain poorly understood. Here we show distinct responses to a HFD between males and females. Our study underscores the need for utilizing both sexes in drug target identification studies, and characterizing the molecular mechanisms contributing to the MASLD pathophysiology in aging animals. Hepatology Communications 2024

overall_design: Young (7 weeks) and aged (52 weeks), male and female mice were fed a high-fat diet (HFD) or low-fat diet (LFD). Liver metabolome (>600 molecules) and transcriptome profiles were analyzed


title: Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [smRNA-seq]

city: Urbana

first: Natalia

middle: Julianna

last: Krawczynska

state: illinois

address: 407 South Goodwin Ave

department: MIP

institute: UIUC

summary: Small extracellular vesicles (sEVs) are emerging as critical mediators of intercellular communication in the tumor microenvironment. Here, we investigate the mechanisms by which sEVs derived from neutrophils treated with the cholesterol metabolite, 27-hydroxycholesterol (27HC), influence breast cancer progression. sEVs released from 27HC treated neutrophils enhance epithelial-mesenchymal transition (EMT) and stem-like properties in breast cancer cells, resulting in loss of adherence and increased migratory capacity. Decreased miRs within the sEVs resulted in activation of the WNT/ β-catenin signaling pathway in recipient cells and suggest that this may be a predominant pathway for stem-like phenotype and EMT. Our findings underscore a novel mechanism by which 27HC-modulated neutrophils contribute to breast cancer pathophysiology through EV-mediated intercellular communication, suggesting potential therapeutic targets in cancer treatment.

overall_design: Total RNA isolated form sEVs was used for small-RNA-Seq. sEVs were isolated, using comercial SBI kit, from primary neutrophils (Ly6G+ cells; from WT BALB/c female mice) treated with DMSO or 10uM 27HC for 48h. Total RNA from extracellular vesicles was isolated using miRNeasy Micro kit (Qiagen) according to the manufacturer’s protocol with supported modification for small RNA quantities. The quantity and quality of isolated RNA were determined with Qubit Fluorometer (Thermo Fisher Scientific), Bioanalyzer 2100 and Fragment Analyzer (Agilent).

first: Erik

last: Nelson

first: Jenny

last: Drnevich


title: Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [RNA-seq]

overall_design: Total RNA was used for bulk RNA-Seq from 2D culture of 4T1 cells in complete media with EVs depleted FBS (Gibco). Cells were treated with small extracellular vesicles (sEVs) for 48h and 72h. sEVs were isolated, using comercial SBI kit, from primary neutrophils (Ly6G+ cells; from WT BALB/c female mice) treated with DMSO or 10uM 27HC for 48h. Cells after 27HC_sEVs lost adherence and started to float. Two subpopulation of cells after that treatment was used: adherent and non-adherent. 5 replicates from each treatment group was performed.


title: Inhibition of miR-10b treats metastatic breast cancer by targeting stem cell-like properties

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

summary: Despite advances in breast cancer screening and treatment, prognosis for metastatic disease remains dismal at 30% five-year survival. This is due, in large, to the failure of current therapeutics to target properties unique to metastatic cells. One of the drivers of metastasis is miR-10b, a small noncoding RNA implicated in cancer cell invasion, migration, viability, and proliferation. We have developed a nanodrug termed MN-anti-miR10b that delivers anti-miR10b antisense oligomers to cancer cells. In mouse models of metastatic triple-negative breast cancer, MN-anti-miR10b has been shown to prevent onset of metastasis and eliminate existing metastasis in combination with chemotherapy even after treatment has been stopped. Recent studies have implicated miR-10b in conferring stem cell-like properties onto cancer cells, such as chemoresistance. In this study, we show transcriptional evidence that inhibition of miR-10b with MN-anti-miR10b activates developmental processes in cancer cells and that stem-like cancer cells have increased miR-10b expression. We then demonstrate that treatment of breast cancer cells with MN-anti-miR10b reduces their stemness confirming that these properties make metastatic cells susceptible to the nanodrug actions. Collectively, these findings indicate that inhibition of miR-10b functions to impair breast cancer cell stemness, positioning MN-anti-miR10b as an effective treatment option for stem-like breast cancer subtypes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To identify therapeutic mechanisms of mir-10b inhibition, MDA-MB-231 and 4T1 breast cancer cells were treated with MN-anti-miR10b (anti-miR-10b nanodrug), magnetic nanoparticle (MN; vehicle), or left them untreated for 48 hours. We then performed differential gene expression analysis of data from RNA-seq analysis and functional enrichment analyses on significantly upregulated and downregulated genes.

first: Alan

last: Halim

first: Nasreen

last: Al-Qadi

first: Elizabeth

last: Kenyon

first: Sujan

middle: K

last: Mondal

first: Zdravka

last: Medarova

first: Anna

last: Moore


title: LMNA-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells

city: Irvine

first: Michael

middle: V.

last: Zaragoza

state: CA

address: 2042 Hewitt Hall

department: Pediatrics and Biological Chemistry

institute: UC Irvine School of Medicine

summary: LMNA-Related DCM involves cardiomyocyte dysfunction resulting in heart failure or sudden death. It is caused by LMNA mutations encoding Lamin A/C defects involved in nuclear integrity and gene expression. To investigate possible mechanisms, we used iPSC derived from a LMNA c.357-2A>G Patient and her unaffected sister. We differentiated iPSC and conducted scRNA-seq for 4 Patient and 8 Control samples across seven time points from Day 0 to 30. Using a comprehensive bioinformatics workflow, we identified 110,521 high-quality cells and complex heterogeneity: ten main cell types, possible subtypes, and lineage bifurcation for Cardiac Progenitors to Cardiomyocytes and Epicardium-Derived Cells (EPDC). By comparative analyses, we found differentially expressed genes (DEG) and enrichment supporting pathway dysregulation for ZNF genes and RNA polymerase II transcription in Pluripotent cells; BMP4 and TGF Beta/BMP signaling, sarcomere genes and cardiogenesis, CDH2 and EMT in Cardiomyocytes; LMNA and epigenetic regulation and DDIT4 and mTORC1 signaling in EPDC. In addition, top DEG included XIST, six imprinted genes, and gene sets in metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our evidence supports disruption of epigenomic developmental programs in LMNA-Related DCM and also demonstrates current challenges of LMNA disease modeling using Patient-derived iPSC.

overall_design: scRNA-seq for 12 cell samples (4 Patient and 8 Control) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30 during iPSC differentiation to cardiomyocytes.

middle: V

first: Thuy-Anh

last: Bui

first: Halida

last: Widyastuti

first: Mehrsa

last: Mehrabi

first: Zixuan

last: Cang

first: Yutong

last: Sha

last: Grosberg

first: Qing

last: Nie


title: MicroRNA-34c from follicular fluid-derived extracellular vesicles is a modulator of embryo quality

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

institute: Ghent University

summary: Oocyte competence is progressively acquired during follicle growth, with large follicles containing more often competent oocytes than small follicles. A competent oocyte is able to mature in vitro, be fertilized, and develop to the blastocyst stage. Extracellular vesicles (EVs) and their cargo micro RNAs (miRNAs) are critical in mediating intercellular communication inside the follicle and facilitating oocyte maturation. Whether follicular EVs are also involved in the acquisition of oocyte competence in the growing follicle remains unclear. Here, we have been using an individual culture system to distinguish follicular fluid and their corresponding bovine oocytes as competent or noncompetent. We used a qEV single-column method to isolate EVs from follicular fluid. RNA sequencing revealed 16 differentially expressed (DE) miRNAs in EVs from follicular fluid derived from either competent or noncompetent oocytes . Among the up-regulated miRNAs, we selected bta-miR-34c to further validate its effect on oocyte competence during in vitro maturation using mimics and inhibitors. By supplementing miR-34c mimics to the oocyte maturation medium, we could significantly improve blastocyst quality, as evidenced by higher cell numbers, while supplementation of miR-34c inhibitors produced the opposite effect. Taken together, the up-regulation of miR-34c in EVs derived from follicular fluid from competent oocytes is indicative of its regulatory role, and, when added during in vitro maturation of unselected oocytes, is able to increase total cell number and inner cell mass of resulting embryos, thus contributing to the development of healthy offspring

overall_design: Ovarian follicles (2-4 mm) from slaughterhouse-derived bovine ovaries were used to collect oocytes. Bovine oocytes were distributed in five different categories according to the in vitro maturation protocol used: control, microRNA-34c mimic supplementation, microRNA-34c inhibitor, negative control mimic supplementation, and negative control inhibitor supplementation. After 22 hours of in vitro maturation, oocytes were fertilized, and the resulting zygotes were put in in vitro embryo culture. After 8 days post-insemination, 10 embryos/group were pooled for transcriptome profile analysis. We performed 5 replicates of microRNA-34c mimic, 4 replicates of Control, 3 replicates of microRNA-34c inhibitor, negative control mimic and negative control inhibitor.

first: Camilla

last: Benedetti

first: Krishna

last: Pavani

first: Filip

last: Van Nieuwerburgh

first: Koen

last: Deserranno

first: Katrien

last: Smits

first: Nima

last: Azari-Dolatabad

first: Osvaldo

last: Bogado Pascottini

first: Luc

last: Peelman

first: Yuan

last: Fan

first: An

last: Hendrix

first: Guan

last: XueFeng

first: Joachim

last: Hamacher

first: Rani

last: Six

first: Annekatrien

last: Boel

first: Ann

last: Van Soom


title: Constitutively activating MEK1 mutations drive treatment refractory histiocytic neoplasms but confer response to ERK inhibition

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Histiocytic neoplasms are clonal disorders of the monocyte/macrophage lineage defined by mutations activating MAP kinase signaling, including BRAFV600E mutations in ~50% of patients, which confer robust responses to BRAF inhibition. More recently, the MEK inhibitor cobimetinib was FDA-approved for BRAFV600-wild-type histiocytosis patients. Here following genomic analysis of 500 pediatric and adult patients with diverse histiocytoses, the most common alteration following BRAFV600E was MEK1E102_I103 in-frame deletion. MEK1E102_I103del and related RAF-independent MEK mutants were associated with an aggressive multi-system clinical phenotype with worse progression-free survival with MEK inhibition as compared to patients with other classes of MEK1/2 mutations. Given that cancer-associated MEK1/2 mutations have not been modeled in vivo and the clinical importance of MEK1 mutations in histiocytoses, we generated MEK1E102_I103del conditional knock-in mice. Using three distinct hematopoietic Cre drivers, these mice developed a 100% penetrant, lethal disorder by 6 weeks of age with expansion of classical and non-classical monocytes, macrophages, and Cd11b+ conventional dendritic cells which infiltrated hematopoietic organs, liver, and skin. MEK1-mutant mice were sensitive to single-agent treatment with the oral ERK inhibitor ulixertinib. We consequently treated five MEK1E102_I103del-mutant patients with ulixertinib on prospective IRB-approved Single Patient Use Expanded Access protocols, four of whom had disease refractory to MEK inhibition. Four of five patients experienced objective clinical and/or radiological responses to ulixertinib. These data reveal the impact of oncogenic MEK kinase mutations in vivo, identify patients with likelihood of resistance to MEK inhibition, and nominate ERK inhibition as a therapeutic approach to overcome resistance to MEK inhibition in histiocytoses.

overall_design: Sorted live cells were harvested from frozen/thawn bone marrow and spleen samples from Mx1-cre-Map2k1-E102_I103del mutant (n=3) and control mice (n=3) mice for 3' scRNA sequencing.

first: Eli

last: Diamond

first: Jean-François

last: Emile

first: Julien

last: Haroche

first: Anne

middle: S

last: Reiner

first: Dana

last: Bossert

first: Michael

last: Singer

first: Alexander

last: Lewis

first: Salima

last: Benbarche

first: Nina

last: Fox

first: Cynthia

last: Castro

first: Steven

last: Tittley

first: Matthew

last: Witkowski

first: Neal

last: Rosen

first: Omar

last: Abdel-Wahab

first: Benjamin

last: Durham


title: On the role of glucocorticoid signaling in the differentiation of virus-specific CD8+ T cell memory

city: Mohali

first: Sharvan

last: Sehrawat

state: Punjab

address: SAS Nagar

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research

summary: We show that signaling through the glucocorticoid receptor, NR3C1, regulates CD8+ T cell memory differentiation. An analysis of single cell RNASeq (scRNASeq) dataset of virus-specific CD8+ T cells revealed lower NR3C1 activity within the cluster exhibiting higher expression of memory CD8+ T cell associated genes. Dexamethasone exposure of antigen-stimulated CD8+ T cells increased the representation of memory precursors within the pool of activated cells both in vitro and in vivo during the acute phase of a resolving infection, thus elevating the pool of persisting memory. RNAseq and biochemical analysis performed on dexamethasone exposed CD8+ T cells revealed a modulation of intrinsic programming resulting in metabolic alteration, lower ROS accumulation and enhanced levels of Bcl2 expression that promoted transition of effectors into memory cells. The phenomenon was evident at a low dose of dexamethasone as higher doses caused mitochondrial toxicity. We, therefore, identify NR3C1 as a modulator of memory CD8+ T cell differentiation and provide a putative strategy for increasing the pool of anti-viral CD8+ T cell memory.

overall_design: C57BL/6 mice were intraperitoneally infected with MHV-68-SIINFEKL and either given sham treatment with the diluent or given 10mg/kg body weight dexamethasone intraperitoneally from 4 to 6 days post infection. The animals were then sacrificed at 8 days post infection and CD8+CD44+ cells were sorted from each group. Samples from 12 mice were pooled into one sample for RNA isolation and sequencing. We then performed pathway enrichment analysis to elucidate the pathways affected within the responding CD8+ T cells upon dexamethaone treatment.

first: Azeez

last: Tehseen


title: Gene expression profiling of brain tissue from neuronopathic Gaucher disease mouse model of PG9VN, PG9V and wild type mice

city: Cincinnati

first: Yi

last: Lin

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital

summary: To understand the intrinsic link between PGRN and Gba D409V mutation dosage in regulating lysosomal function and disease pathogenesis, we generated nGD model of GbaD409V/D409V and loss of PGRN (Grn-/-), termed  PG9V that displayed typical neuronopathic GD (nGD). With decreasing the dose of Gba D409V, i.e., D409V/Null, in Grn KO mice (Grn-/-;GbaD409V/Null, PG9VN) led to much earlier onset and more severe neurodegenerative nGD than PG9V mice. To explore the correlation between the Gba mutation dosage and both neurodegeneration and inflammation, as well as to attain molecular insights into the underlying brain pathology in PG9VN mice, we performed bulk RNA sequencing analysis on 7.5-month-old PG9VN, PG9V and WT brain tissues containing thalamus, hypothalamus and midbrain, the predominant regions displaying the neuroinflammation and neurodegeneration. Gene Ontology (GO) analysis classified similar molecular pathways were altered in both PG9V and PG9VN mice. The heightened dysregulation of these pathways may be a contributing factor to the more severe disease phenotypes observed in PG9VN mice. This dysregulation appears to be controlled by a threshold effect related to Gba dosage.

overall_design: Brain tissues containing thalamus, hypothalamus and midbrain from 7.5-month-old PG9VN, PG9V and wild type mice were analyzed for bulk RNA sequencing. Three biological replicates are available for each genotype group. All together, 9 samples were available and profiled.

first: Xiangli

last: Zhao

first: Chuanju

last: Liu

first: Ying

last: Sun


title: Validation studies and multi-omics analysis of Zhx2 as a candidate quantitative trait gene underlying brain oxycodone metabolite (oxymorphone) levels and behavior

city: Boston

first: Camron

middle: Davis

last: Bryant

state: MA

address: 140 The Fenway, X138

institute: Northeastern Universitty

summary: Sensitivity to the subjective reinforcing properties of opioids has a genetic component and can predict addiction liability of opioid compounds. We previously identified Zhx2 as a candidate gene underlying increased brain concentration of the oxycodone (OXY) metabolite oxymorphone (OMOR) in BALB/cJ (J) versus BALB/cByJ (By) females that could increase OXY state-dependent reward. A large structural intronic variant is associated with a robust reduction of Zhx2 expression in J mice, which we hypothesized enhances OMOR levels and OXY addiction-like behaviors. We tested this hypothesis by  modeling the loss-of-function variant through knocking out the Zhx2 coding exon (E3KO). Integrative transcriptomic and proteomic analysis of E3KO mice identified astrocyte function, cell adhesion, extracellular matrix properties, and endothelial cell functions as pathways influencing brain OXY metabolite concentration and behavior. These results support Zhx2 as a quantitative trait gene underlying brain OMOR concentration that is associated with changes in OXY behavior and implicate potential quantitative trait mechanisms that together inform our overall understanding of Zhx2 in brain function.

overall_design:
To investigate potential mechanisms for how Zhx2 influences OXY metabolism and state-dependent reward learning, we established a CRISPR-mouse line where Zhx2 Exon3 (the only coding exon) has been constitutively knocked out in all tissues in BALB/cByJ mice.
Brains were harvested from drug-naïve CRISPR offspring and the University of Chicago Genomics Facility performed RNA-sequencing on right brain hemisphere for gene expression profilling.
Pathway enrihment anaysis using Gene-Set Enrichment Analysis was performed on transcriptomic data as well as combined transcriptomic and proteomic data of shared genes.

middle: D


title: A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [bulk_ATACseq]

first: Maurilio

last: Sampaolesi

overall_design: Fusion-negative rhabdomyosarcoma (FN-RMS) cell line models were transfected with either lipofectamine or miR-449a + miR-340 for 60 hours, and subsequently bulk ATACseq was performed

first: Enrico

last: Pozzo


title: A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [Human_RNAseq_bulk]

overall_design: Human fusion-negative rhabdomyosarcoma (FN-RMS) cell line RD18 was transfected with either lipofectamine or miR-449a + miR-340 for 60 hours, and subsequently bulk RNAseq was performed


title: Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females [ARC]

city: San Francisco

first: Muriel

middle: Elisabeth

last: Babey

address: 1550 4th Street

department: Department of Medicine, Division of Endocrinology

institute: University of California, San Francisco

summary: During lactation, mothers initiate cycles of bone formation followed by significant bone loss to meet the high calcium (Ca2+) demand by progeny. While estrogen functions typically as an anabolic driver of bone remodeling, this sex steroid is absent in postpartum females. Here, we report that a brain-derived secreted from neurons of the arcuate nucleus (ARC) fills this void and functions as a potent osteogenic factor to promote bone mass in lactating females. We previously reported an extraordinarily sex-specific high bone mass phenotype in female mice that persists with aging and is central in origin after eliminating estrogen receptor alpha signaling in ARCKISS1 neurons. Parabiosis and bone transplant studies established that a humoral factor in mutant females accounts for this unusual skeletal phenotype. High bone mass in mutant females could be traced back to the skeletal stem cell (SSC) level, reflected by their increased frequency and osteochondrogenic potential. Based on ex-vivo, in vivo, and in vitro assays, one protein emerged as the most promising secreted pro-osteogenic factor from the ARC, acting in mice and human SSCs at low concentrations (<nM) independent of age and sex. The role of this brain-derived factor in bone formation was confirmed by in vivo gain and loss of function studies. Unexpectedly, in wild-type females, a transient spike of this protein appears in ARCKISS1 neurons coincident with lactation when bone remodeling and high calcium demand intensify in estrogen-depleted mothers. Our findings establish a potentially new therapeutic anabolic bone hormone that functions in a novel female-specific brain-bone axis to ensure mammalian species survival.

overall_design: To investigate the comparative gene expression profiling analysis of bulk RNA-seq data for microdissected ARC from control Esr1fl/fl with normal bone mass and Esr1Nkx2-1Cre mutant female mice with high bone mass (27 weeks of age) on chow diet and after HFD challenge (17 weeks)

first: M

first: W

last: Krause

first: J

last: Nikkanen

first: H

last: Ingraham


title: Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females

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

overall_design: Refer to individual Series


title: Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females [liver]

overall_design: To investigate the comparative gene expression profiling analysis of bulk RNA-seq data for liver from control Esr1fl/fl with normal bone mass and Esr1Nkx2-1Cre mutant female mice with high bone mass (27 weeks of age) on chow diet and after HFD challenge (17 weeks).


title: Brain-Derived CCN3 Is An Osteoanabolic Hormone That Sustains Bone in Lactating Females [pituitary gland]

overall_design: To investigate the comparative gene expression profiling analysis of bulk RNA-seq data for pituitary gland from control Esr1fl/fl with normal bone mass and Esr1Nkx2-1Cre mutant female mice with high bone mass (27 weeks of age) on chow diet and after HFD challenge (17 weeks).


title: Lipids impair NK cell anti-tumor immunity and transcription [ATAC-seq]

city: Jinan

first: Deyan

last: Jiao

address: wenhuaxi road

institute: shandong university

summary: NK cell is an important immune cell, we detected the change of chromatin accessibility after OA treatment (0.2mM oleic acid (OA) for 36h. The treatment processed only once.)

overall_design: In order to detect the difference of chromatin accessibility in OA-treated NK cells, we performed RNA-seq analysis for NK cells treated with or without OA for 36h.

first: Xiaohong

last: Liang


title: Lipids impair NK cell anti-tumor immunity and transcription [RNA-seq]

summary: NK cell is an important immune cell, we detected the change of transcription level after OA treatment (0.2mM oleic acid (OA) for 36h. The treatment processed only once.).

overall_design: In order to detect the difference of gene expression in OA-treated NK cells, we performed RNA-seq analysis for NK cells treated with or without OA for 36h.


title: Bypassing the Brain Barriers: Upregulation of Serum miR-495 and miR-543-3p Reflects Thyroid-Mediated Developmental Neurotoxicity in the Rat

city: Research Triangle Park

first: Katherine

last: O'Shaughnessy

state: North Carolina

address: 919 TW Alexander Drive

department: Public Health and Integrated Toxicology Division

institute: US Environmental Protection Ageny

summary:
We investigated if a serum microRNA signatured correlated with the presence of thyroid-mediated developmental neurotoxicity in the rat.
We isolated serum from control (euthyroid) and exposed (hypothyroid) rat pups on PN8. The maternal exposure utilized to induce developmental hypothyroidism was propylthiouracil (PTU). PTU was administered in the drinking water during pregnancy and lactation.

overall_design: Comparative microRNA profiling of miRNA-seq data from euthyroid (control) and hypothyroid (PTU) rat pups collected on postnatal day 8.

first: O'Shaughnessy

last: Katherine


title: Transcriptome profiling of lichen myco- and photobionts of Lobaria pulmobaria during ultraviolet-B exposure

city: Kazan

first: Ilya

last: Leksin

address: 2 Lobachevsky str.

country: Russia

institute: Federal Research Center Kazan Scientific Center of Russian Academy of Sciences

summary: We used raw RNA-Seq data from the lichen Lobaria pulmonaria to analyze changes in gene expression in response to ultraviolet-B (UV-B) treatment. The aim of the present work was to unravel the UV-B-induced defense response in the lichen Lobaria pulmonaria based on physiological traits and transcriptional profiling. Here we analyzed gene expression in mycobionts (Lobaria pulmonaria) and photobionts (Symbiochloris reticulata) after 80 min daily application of UV-B treatment of Lobaria pulmonaria thalli for two weeks. Special attention was paid to the UV-B-induced expression of the genes encoding stress tolerance proteins (heat shock proteins, antioxidants, etc.) and enzymes involved in the biosynthesis of photoprotective metabolites.

overall_design: The thalli of Lobaria pulmonaria from the experimental groups were irradiated with UV-B fluorescent erythema lamps (3 W/m2) for 80 min daily for 14 days. Total RNA was extracted from samples at day 0, 2, 7 and 11. Samples from each irradiation time point were sequenced in two or three biological replicates.


title: Small (non coding) RNA profiling in water- versus Xcf-inoculated common bean seeds at two developmental stages

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

summary: Transcriptome approach of small RNA was performed at two stages of seed development during early maturation (24DAP) and seed maturity (42DAP) to differentially profile smallRNA accumulation from Xcf-inoculated and water-inoculated seeds.

overall_design: Triplicates of seeds at two developmental stages from water- and Xcf-inoculated plants

first: Armelle

last: Darasse

first: David

last: Lalanne

first: Matthieu

last: Barret

first: Martial

last: Briand


title: Methylome analysis of water- versus Xcf-inoculated common bean seeds at seed maturity stage

type: Methylation profiling by high throughput sequencing

summary: DNA Methylation profiling was performed at seed maturity to compare between seed methylomes from Xcf-inoculated and water-inoculated seeds.

overall_design: Triplicates of mature seeds from water- and Xcf-inoculated plants


title: Lipids impair NK cell anti-tumor immunity and transcription


title: Transcriptomic analysis of water- versus Xcf-inoculated common bean seeds at three developmental stages

summary: transcriptome approach was performed at three stages of seed development during seed filling, seed maturation and seed maturity to compare between seed transcriptomes from Xcf-inoculated and water-inoculated seeds.

overall_design: Triplicates of seeds at three developmental stages from water- and Xcf-inoculated plants


title: Genome-wide CRISPR/Cas9 loss-of-function screen for prostate cancer cell line

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary:
Prostate cancer (PCa) is the most frequently diagnosed malignancy in men worldwide. Epigenetic regulation has been recognized as a main mechanism of cancer evolution. PRMT5 is the major type II protein arginine methyltransferase catalyzing the symmetric dimethylation of arginine in mammalian. PRMT5 is found upregulated in PCa. However, its exact functional contribution to prostate tumorigenesis is unknown. PRMT5 inhibition via pharmacological inhibition (EPZ015666) reduces stemness with paralleled differentiation and arrests cell cycle progression but without causing appreciable apoptosis.To understand the mechanisms of cell tolerance to PRMT5 inhibition and to identify potential pathways that function synergistically with EPZ015666, we performed a genome-wide CRISPR/Cas9 loss-of-function screen in the presence of EPZ015666. Our data unravel that many clinical-grade drugs of known oncogenic pathways can be repurposed to target castration-resistant PCa when used in synergy with EPZ015666 at low doses.
Genome-wide CRISPR/Cas9 loss-of-function screen in the presence of EPZ015666 in DU145

first: Cheng

last: Zou

first: Qinju

last: He


title: Chromatin-occupancy profiling of PRMT5 and METTL3 in prostate cancer cells

summary:
Prostate cancer (PCa) is the most frequently diagnosed malignancy in men worldwide. Epigenetic regulation has been recognized as a main mechanism of cancer evolution. PRMT5 is the major type II protein arginine methyltransferase catalyzing the symmetric dimethylation of arginine, and METTL3 is the enzymatic component of the large N6-adenosine-methyltransferase complex in mammalian responsible for N6-methyladenosine (m6A) modification in diverse RNA species. Both genes are found upregulated in PCa. However, their exact functional contribution to prostate tumorigenesis is unknown. As both proteins can regulate transcription via binding to chromatin, we seek to explore their DNA binding profiles in both AR+ LNCaP and AR- PC3 cells via recently developed CUT&Tag technique. Antibodies we used were Active Motif #61001 for PRMT5 and Abcam #195352 for METTL3. Our data suggests that both proteins regulate PCa cell biology, at least partially, through chromatin-binding and subsequent transcriptional regulation.
CUT&Tag assay for arginine methyltransferase PRMT5 and N6‐adenosine‐methyltransferase METTL3 in LNCaP and PC3 cells

overall_design: Dingxiao, Zhang

first: Yuqing

last: Feng


title: Primary lung fibroblasts respond to IL-33, IL-13, and IL-17a and secrete factors that activate macrophages [JV210]

city: Baltimore

first: Alan

middle: L

last: Scott

address: 615 N Wolfe St

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University

summary:
Primary lung fibroblats were stimulated with cytokines in vitro
Total RNA was isolated and submitted to Novogene for NGS

overall_design: Comparative gene expression profiling analysis of RNA-seq data friom primary lung fibroblasts treated with cytokines

first: Jarrett

last: Venezia

first: Naina

last: Gour

first: Jeffrey

last: Loube

first: Wayne

last: Mitzner


title: Primary lung fibroblasts respond to IL-33, IL-13, and IL-17a and secrete factors that activate macrophages [JV214]

summary:
Primary alveolar macrophages were stimulated with cytokines in vitro
Total RNA was isolated and submitted to Novogene for NGS

overall_design: Comparative gene expression profiling analysis of RNA-seq data from macrophages treated with cytokines


title: Integrative genome-wide DNA methylome and transcriptome data reveals key genes involved in the dysregulation of adipose-stem cells linked to Crohn’s disease [Array]

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

type: Methylation profiling by genome tiling array

summary: Creeping fat, also known as mesenteric fat, which is connected to the inflamed segments of the intestine and is a hallmark of Crohn's disease (CD), appears to be correlated with disease activity. Adipose-stem cells isolated from the creeping fat of CD subjects were found to be dysfunctional (exhibiting a high inflammatory profile, high invasive and phagocytic capacities, and worse immunosuppressive properties), and this dysfunction persisted in hASCs taken from CD subjects who were in remission of the disease. We hypothesized that the abnormal behavior of adipose stem cells is caused by the accumulation of epigenetic modifications due to the inflammatory environment underlying active CD. DNA methylation and transcriptomics were performed in adipose-derived stem cells (ASCs) isolated from visceral adipose tissue biopsies of active and inactive CD patients and non-IBD patients. An integrative analysis of both omics was performed to obtain the best gene candidates.

overall_design: Genomic DNA extracted from human adipocyte stem cells (hASCs) derived 18 Crohn’s disease (CD) patients samples and 7 healthy individual samples were analyzed with Human Methylation EPIC Infinium assay beadarrays to profile 850,000 sites in the human genome. CD samples were derived from different tissues and disease states: 6 creeping fat samples from active Crohn’s disease (CF_aCD), 7 mesenteric samples from active Crohn’s disease (hMES_aCD), and 5 mesenteric samples from inactive Crohn’s disease (hMES_iCD).

first: Diandra

last: Monfort-Ferré

first: Albert

last: Boronat-Toscano

first: Jose-Francisco

last: Sánchez-Herrero

first: Aleidis

last: Caro

first: Margarita

last: Menacho

first: Maria-José

last: Mañas

first: Beatriz

last: Espina

first: Raquel

last: Pluvinet

first: Lidia

last: Cabrinety

first: Carme

last: Abadia

first: Marc

last: Marti

first: Carolina

last: Serena


title: Parkinson Disease Frontal Cortex ncRNA Profiling

city: Barcelona

first: Eulalia

address: Passeig de la Vall d’Hebron, 171

department: Institute of Neurosciences

institute: University of Barcelona

summary: We aimed to profile the expression of the entire population of annotated lncRNAs (GENCODE 15) in the Frontal Cortex (FC) of Parkinson diseased (PD) individuals compared to age-matched controls.

overall_design: The microarray used contained two probes for each lncRNA, targeting 22001 lncRNA transcripts, in addition to probes targeting 17535 randomly selected protein-coding transcripts. Samples obtained from post-mortem FC of 18 symptomatic PD patients (Braak stage 4-5) and 18 control individuals without neuropathological lesions or neurological signs.

first: Joan

last: Pallares


title: Primary lung fibroblasts respond to IL-33, IL-13, and IL-17a and secrete factors that activate macrophages

first: Alan

last: Scott


title: Expression profile of CircRNA in Type2 diabetes mellitus patients with retinopathy

status: Public on Sep 02 2024

city: Beijing

first: Bingyan

last: Wang

address: 49 North Garden Rd

department: General surgery

institute: Peking University Third Hospital

summary: Diabetic retinopathy (DR) is one of the common chronic complications of diabetes. Circular RNA (circRNA) plays a vital role in the pathological process of diabetic retinopathy (DR), this study aims to explore the differences in circRNA expression profiles and functions between DR and non-DR patients.Serum from diabetes mellitus (DM) patients with DR (n=5) and without DR (n=5) were extracted for circRNA microarray analysis using Arraystar Human circRNA expression profile (v2.0). Another 5 DR and 5 non-DR patients were included for quantitative reverse transcription polymerase chain reaction (RT-qPCR) validation. Enriched signaling pathways were analyzed by GO and KEGG analysis. circRNA–miRNA networks were constructed by bioinformatics analysis.

overall_design: This study aims to explore the differences in circRNA expression profiles and functions between DR and non-DR patients.

first: Huixian

last: Yan

first: Wencheng

last: An


title: Investigating Subpopulation Dynamics in Clonal CHO-K1 Cells with Single-Cell RNA Sequencing

first: Luke

last: Morina

state: MD

address: 3400 N Charles St; CLARK HALL Rm118a

summary: CHO cells have primarily been studied in bulk, assuming that these bulk samples are identical because of genetic clonality across the sample. In this study, we performed single-cell RNA sequencing on two clonal CHO-K1 cell populations with different stability phenotypes over a 90 day culture period.

overall_design:
Two Chinese Hamster Ovary were cultured for 30 population doublings in different culture conditions, with samples gathered before the first and final passages. Banked samples were sequenced with scRNA sequencing.
---------------------------------------------
Authors state "due to company restrictions (our sample source) they do not want us to deposit the raw FASTQ (Level 1) but will allow the counts matrix to be deposited".

first: Haoyu

last: Cao

first: Siqi

last: Chen

first: Swetha

last: Kumar

first: Kevin

last: McFarland

first: Natalia

middle: I

last: Majewska

first: Michael

middle: J

last: Betenbaugh

first: Winston

last: Timp


title: LINC01007 Overexpression Transcriptomic analysis

summary: We analyzed the transcriptome of SH-SY5Y cells overexpressing LINC01007 through CRISPRa.

overall_design: We compared 4 biological replicates of SH-SY5Y cells expressing a sgRNA construct targeting the lncRNA LINC01007 to 4 biological replicates of the same cell line expressing a sgRNA construct targeting GFP, which is not present on the human genome, and to 4 biological replicates not expressing any sgRNA. construct.


title: Parkinson Disease Frontal Cortex Transcriptomic analysis

summary: We analyzed the transcriptome of the Frontal Cortex (FC) of Parkinson diseased (PD) individuals compared to age-matched controls.

overall_design: Samples obtained from post-mortem FC of 8 symptomatic PD patients (Braak stage 4-5) and 7 control individuals without neuropathological lesions or neurological signs.


title: Transcriptome reprogramming of Nannochloropsis oceanica in response to CO2 fluctuated environment

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

summary: To be consistent with ChIP-seq data in this study, transcription regulation of CCM was reaccessed. In this experiment, about 800M clean reads were obtained for each sample. Obtained clean reads in each sample were over 84%, which were then mapped to the N. oceanica IMET1 reference genome. Differential expression analysis between low CO2-treated (LC) and control (high CO2; 5% CO2; HC) samples was performed by edgeR. The result showed that 217 genes (including 158 up-regulated and 59 down-regulated) displayed differential regulation at least two-fold change (P<0.05).

overall_design: mRNA profiles of Nannochloropsis oceanica under high (5% CO2) and low (0.04%) CO2

last: Wei


title: A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis [P25]

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

summary: Male infertility can be caused by chromosomal abnormalities, mutations, and epigenetic defects. Epigenetic modifiers pre-program hundreds of spermatogenic genes in spermatogonial stem cells (SSCs) for expression later in spermatids, but it remains mostly unclear whether and how those genes are involved in fertility. Here, we report that Wfdc15a, a WFDC family protease inhibitor pre-programmed by KMT2B, is essential for spermatogenesis. We found that Wfdc15a is a non-canonical bivalent gene carrying both H3K4me3 and facultative H3K9me3 in SSCs but is later activated along with the loss of H3K9me3 and acquisition of H3K27ac during meiosis. We show that WFDC15A deficiency causes defective spermiogenesis at the beginning of spermatid elongation. Notably, depletion of WFDC15A causes substantial disturbance of the testicular protease-antiprotease network and leads to an orchitis-like inflammatory response associated with TNFa expression in round spermatids. Together, our results reveal a unique epigenetic program regulating innate immunity crucial for fertility.

overall_design: To investigate the function of Wfdc15a for spermatogenesis, we performed RNA-seq using whole testis from P25 Wfdc15a mice.

first: Kazuyuki

last: Ohbo