title: Decreased chondrocyte features of articular cartilage during short-term repeated overloading: a synovium-cartilage interaction via inhibin subunit beta A

city: Tokyo

first: Yusuke

last: Arino

address: 7-3-1 Hongo, Bunkyo-ku

institute: University of Tokyo

summary: The primary goal of this study is to investigate the ultrashort-term responses and molecular mechanisms in both the synovium and cartilage under conditions of excessive mechanical loading, a major contributing factor in the pathogenesis of osteoarthritis (OA). While cartilage degeneration is a hallmark of OA, the involvement of the synovium in disease progression and pain, particularly in relation to synovitis, has been increasingly recognized. Despite this, the immediate molecular changes in both tissues following mechanical stress, and the interactions between them, remain unclear. To address these gaps, we developed a mouse model that simulates excessive mechanical loading through treadmill exercise combined with weight attachment. We investigated the ultrashort-term gene expression changes in the synovium and cartilage at 1, 4, and 24 hours post-exercise using RNA sequencing (RNA-seq). Additionally, we examined the effects of repeated overloading by analyzing tissue samples from mice subjected to four consecutive days of overloading. This approach allowed us to capture both the acute and repeated stress responses in these tissues. Through transcriptomic analysis, we aimed to identify key molecular mediators driving both the rapid transcriptional changes in each tissue and the synovium-cartilage interaction.

overall_design: To investigate the effect of excessive mechanical loading, we established a new mice model which undego treadmill exercise combined with weight attachment. We harvested synovium and cartilage at 5 different points(control included) , and performed gene expression profiling analysis of RNA-seq.

first: Taku

last: Saito


title: Low-inflammatory lipid nanoparticle-based mRNA vaccine elicits protective immunity against H5N1 high-pathogenicity avian influenza virus with reduced adverse reactions (using dendritic cell of lymph node)

status: Public on Mar 05 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary: Messenger RNA vaccines based on lipid nanoparticles (mRNA-LNPs) are promising vaccine modalities. However, mRNA-LNP vaccines frequently cause adverse reactions such as swelling and fever in humans, partly due to the inflammatory nature of LNP. Modification of the ionizable lipids used in LNP is one approach to avoid these adverse reactions. Herein, we report the development of mRNA-LNP vaccines with better protective immunity and reduced adverse reactions using LNP, including SS-cleavable and pH-activated lipid-like materials with oleic acid (ssPalmO) as an ionizable lipid (LNPssPalmO). We used mRNA expressing H5N1 subtype high-pathogenicity avian influenza virus-derived hemagglutinin or neuraminidase to generate mRNA-LNP vaccines against H5N1 influenza. Compared with conventional LNP, mRNA-LNPssPalmO induced comparable antigen-specific antibodies and better IFN--producing Th1 responses in mice. Both mRNA-LNPssPalmO and conventional mRNA-LNP conferred strong protection against homologous H5N1 virus challenge. In addition, mRNA-LNPssPalmO showed better cross-protection against heterologous H5N1 virus challenge compared to conventional mRNA-LNPs. Furthermore, we observed that mRNA-LNPssPalmO induced less inflammatory responses (e.g., inflammatory cytokine production and vascular hyperpermeability) and fewer adverse reactions (e.g., weight loss and fever) compared with conventional mRNA-LNP. These results suggest that mRNA-LNPssPalmO would be a safe alternative to conventional vaccines to overcome mRNA-LNP vaccine hesitancy.

overall_design:
To thoroughly evaluate inflammatory response induced by LNPssPalmO, we analyzed the gene expression profile from an RNA-seq data obtained from the draining lymph nodes of mice subjected to control and experimental treatments (three treatments in total).
Comparative gene expression profiles from draining lymph node of mice vaccinated with PBS, LNPssPalmO, or LNPSM-102.
Samples from mice treated with PBS served as reference samples.

first: Atsushi

last: Kawai

first: Taro

last: Shimizu

first: Hiroki

last: Tanaka

first: Shintaro

last: Shichinohe

first: Jessica

last: Anindita

first: Mika

last: Hirose

first: Eigo

last: Kawahara

first: Kota

last: Senpuku

first: Le

last: Thi Quynh Mai

first: Ryo

last: Suzuki

first: Takuto

last: Nogimori

first: Takuya

last: Yamamoto

first: Toshiro

last: Hirai

first: Takayuki

last: Kato

first: Tokiko

last: Watanabe

first: Hidetaka

last: Akita

first: Yasuo

last: Yoshioka


title: Identification of TERT Delta 2-4 knockdown effect by Long read RNA seq.

city: Ann Arbor

first: Andrew

last: Ludlow

state: Education

address: 830 N University Ave

country: USA

institute: University of Michigan

summary: All cancer cells must adopt a telomere maintenance mechanism to achieve replicative immortality. Most human cancer cells utilize the enzyme telomerase to maintain telomeres. Alternative splicing of TERT regulates the amount and function of telomerase, however many alternative splicing isoforms of TERT have unknown functions. Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin- induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls. Overall, our data indicate that TERT produces many isoforms that influence the function TERT and the abundance and activity of telomerase.

overall_design: Calu-6 cells, which are non-small cell lung cancer (NSCLC) cells, treated with siRNA targeting TERT Delta 2-4 had RNA extracted, mRNA purified, cDNA made and RNA-Seq libraries generated. The libraries were then sequenced on an Oxford Nanopore MinIonMk1c

middle: T


title: Discovery of TERT isoforms by Long read RNA seq

overall_design: Human induced pluripotent cells, and three human lung cancer cell lines had RNA extracted, cDNA made and TERT specific amplicon libraries generated. The libraries were then sequenced on an Oxford Nanopore MinIonMk1c


title: Direct effects of prolonged TNF-α and IL-6 exposure on neural activity in human iPSC-derived neuron-astrocyte co-cultures

city: Livermore

first: Aimy

last: Sebastian

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: In a concentration-response study, we have employed a human-relevant brain microphysiological system (bMPS), containing human-iPSC derived glutamatergic and GABAergic neurons co-cultured with primary human astrocytes, to monitor and detect the changes in the electrical activity of engineered human iPSC-derived neural networks to increasing concentrations of tumor necrosis factor alpha (TNF). Transcriptomic analysis was conducted at day 7 of exposure to evaluate gene expression changes that could have contributed to how neurons communicated following TNF exposure.

overall_design: human iPSC-derived glutamatergic and GABAergic neurons co-cultured with primary human astrocytes were co-cultured on a 6-well multi-electrode array. Co-cultures were allowed to mature for up to 25 DIV before exposed to one of 3 concentrations  of TNF (25 pg/mL,  10 ng/mL, and 100 ng/mL) for 7 days, after which RNA was isolated and sequnced to determine TNF exposure induced transcriptional changes.

first: Doris

last: Lam

first: Noah

last: Goshi

first: Heather

last: Enright


title: Low-inflammatory lipid nanoparticle-based mRNA vaccine elicits protective immunity against H5N1 high-pathogenicity avian influenza virus with reduced adverse reactions (using whole lymph node)

first: Daisuke

last: Motooka

first: Atsushi

last: Kawai

first: Taro

last: Shimizu

first: Hiroki

last: Tanaka

first: Shintaro

last: Shichinohe

first: Jessica

last: Anindita

first: Mika

last: Hirose


title: Dickkopf-1 promotes tumor progression of gefitinib- resistant non-small cell lung cancer through cancer cell-fibroblast interactions

city: Seoul

first: Keon Wook

last: Kang

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: seoul national university

summary: Cancer cell-secreted proteins play a critical role in tumor progression and chemoresistance by influencing intercellular interactions within the tumor microenvironment. Investigating the intratumoral functions of these secretory proteins may provide insights into understanding and treating chemoresistant cancers. This study aims to identify potential anticancer target(s) in gefitinib-resistant non-small cell lung cancer (NSCLC), with a focus on secretory proteins and their effects on intercellular interactions. Here, we clarified that DKK1 mediates interactions between cancer cells and fibroblasts in gefitinib-resistant lung cancer, contributing to tumor progression.

overall_design: Examination of RNA expression in MRC-5 treated with supernatant of HCC827-LV-con or HCC827-DKK1 OE.


title: Transcriptional Responses of in vitro Blood-Brain Barrier Models to Shear Stress

city: Morgantown

first: Moriah

last: Katt

state: WV

address: 1306 Evansdale Dr

institute: West Virginia University

summary: Endothelial cells throughout the body sense blood flow, eliciting transcriptional and phenotypic responses. Brain endothelium, known as the blood-brain barrier (BBB), possesses unique barrier and transport properties which are in part regulated by blood flow. We utilized next generation sequencing to analyze the transcriptome of primary cultured rat brain microvascular endothelial cells (BMECs) as well as three human induced pluripotent stem cell-derived models. We compared the transcriptional responses of these cells to either low (~0.5 dyne/cm2) or high (12 dyne/cm2) shear stresses, and subsequent analysis identified genes and pathways that were influenced by shear including key BBB-associated genes (SLC2A1, LSR, PLVAP) and canonical endothelial shear stress response transcription factors (KLF2, KLF4). In addition, our analysis suggests that shear alone is insufficient to rescue de-differentiation caused by in vitro primary BMEC culture. Overall, these datasets and analyses provide new insights into the role of shear on BBB models that will aid in model selection and guide further model development.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Stem cell derived and rat brain vasculature endothelial cells were exposed to shear stress at either 12 dyne/cm2 or 0.1 dyne/cm2 for 72 hours and mRNA was collected and sequenced

first: Foreman

last: Koji


title: TRAIL-/- male and female mice irradiated with 20 Gy and treated with TLY012 to suppress radiaiton induced pneumonitis

city: Providence

first: Wafik

middle: S

last: El-Deiry

state: Rhode Island

address: 70 Ship Street

department: Pathology and Laboratory Medicine

institute: Brown University

summary: Cancer therapy is often limited by toxicity from pneumonitis. This often-lethal side effect is known to be impacted by innate immunity, and in particular the pathways regulated by the TRAIL death receptor DR5. We investigated whether DR5 agonists could rescue mice from the lethal effects of radiation. We found that two different agonists, parenteral PEGylated trimeric-TRAIL (TLY012) and oral TRAIL-Inducing Compound #10 (TIC10/ONC201), could achieve this goal. Both compounds could completely protect mice from lethality by reducing pneumonitis, alveolar-wall thickness, and oxygen desaturation.  Protection extended to the late effects of radiation including less fibrosis at 22-weeks in TLY012-rescued survivors versus un-rescued surviving irradiated-mice. Wild-type orthotopic breast tumor-bearing mice receiving 20-Gy thoracic radiation were protected from pneumonitis with disappearance of tumors. At the molecular level, this protection appeared to be due to the inhibition of CCl22, a macrophage-derived chemokine previously associated with radiation pneumonitis and pulmonary fibrosis. The discovery that short-term treatment with TRAIL pathway agonists effectively rescues animals from high doses of radiation exposure has important translational implications.

overall_design: all mice were irradiated with a single whole-thorax x-ray irradiation dose of 20 Gy and then treated with control or TLY012 up until sacrifice at two weeks post irradiation

first: Jillian

last: Strandberg


title: Analysis of rabbiteye blueberry metabolomes and transcriptomes reveals mechanisms underlying potassium-induced anthocyanin production

city: GuiYang

first: Zeyang

last: Song

state: GuiZhou

address: West Campus: Jiaxiu South Road, Huaxi District.

country: China

institute: Guizhou University

summary: Environmental factors play an important role in anthocyanin biosynthesis, and potassium, an essential nutrient for blueberry growth, can act as an enzyme activator. However, few reports exist on the transcriptional and anthocyanin metabolic changes in blueberries regulated by potassium. In this study, blueberries treated with potassium at different stages were compared for changes in enzyme activity, transcription, and metabolism related to anthocyanin synthesis. The results showed that potassium treatment significantly enhanced the activities of key enzymes F3H, F3'5'H, and UFGT in the anthocyanin synthesis pathway of blueberry fruit. Metabolomic results indicated that the contents of malvidin, petunidin, and delphinidin were higher with potassium fertilization, and potassium treatment promoted the early color change of blueberry fruit. The transcriptome analysis identified 102 glucose metabolism-related genes and 12 differential potassium transport genes potentially involved in potassium-regulated anthocyanin synthesis and accumulation. It was found that thirteen genes relate to anthocyanin synthesis. UFGT, F3H, CHI, HCT, C12RT1, DFR, and F3'5'H were all closely associated with potassium-controlled flavonoid and anthocyanin metabolite synthesis. It provides valuable insights into the molecular mechanisms that regulate the synthesis of anthocyanins in blueberries.

overall_design: Analytically pure potassium sulfate was dissolved in water, and 10g of potassium fertilizer was applied to each plant at the flowering stage (KH) and young fruit stage (YG), respectively. The same amount of water was applied for the CK treatment.

first: Ting

last: Yan

first: Zejun


title: Gene expression profile at single cell level of BM MNCs from CCUS patients and healthy donors

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: To evaluate whether wild-type cells from CCUS patients are transcriptionally dysfunctional, we performed long-read single-cell RNA sequencing analyses of heathy donor  and CCUS bone marrow (BM) mononuclear cells.

overall_design: BM MNCs were isolated by Fluorescence-activated cell sorting and analyzed using scRNAseq.

first: Juan

middle: J

last: Rodriguez-Sevilla

first: Simona

last: Colla


title: CCL3-Mediated Inflammatory Reprogramming of the Hepatocellular Carcinoma Microenvironment Enhances Macrophage Antigen Presentation and Adaptive Immune Response (scRNA-Seq)

city: changsha

first: Muqi

last: Liu

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

summary: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality worldwide, largely due to its complex and immunosuppressive tumor immune microenvironment (TIME), which significantly impairs the efficacy of conventional therapies and immune checkpoint blockade (ICB). This study investigates the role of C-C motif chemokine ligand 3 (CCL3) in modulating the HCC TIME, focusing on its impact on immune cell recruitment, macrophage-mediated antigen presentation, and the overall antitumor immune response. We analyzed CCL3 expression in human HCC samples and examined its correlation with inflammatory gene signatures and immune cell infiltration. Using high-dimensional single-cell RNA sequencing (scRNA-seq), multiparameter flow cytometry, and multiplex immunofluorescence, we elucidated how CCL3 influences macrophage functionality and T cell activation. In preclinical HCC models and ex vivo tumor fragment assays, we explored the mechanisms by which CCL3 affects macrophage function and its broader implications for antitumor immunity. Our findings reveal that CCL3 effectively recruits immune cells to the HCC TIME, promotes the formation of tertiary lymphoid structures, and enhances macrophage-mediated antigen phagocytosis and presentation, leading to improved T cell effector functions and cytotoxic activity. This research underscores the critical role of CCL3 in reshaping the HCC TIME to enhance antitumor immunity and suggests that targeting CCL3 could be a promising strategy to improve the efficacy of immunotherapy in liver cancer.

overall_design: In situ liver cancer mouse models were constructed using C57BL/6J mouse and Hepa1-6 mouse liver cancer cell lines, and the effects of chemokine CCL3 on the immune microenvironment of liver cancer were observed by tail vein injection of rAAV8-Ccl3 and its control rAAV8-NC.

first: Xiaoqian

first: Wei

last: Wang


title: IGF2BP3 Regulates Expression and Alternative Splicing of Genes associated with the Progression of Gastric Cancer in AGS cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

summary: Gastric cancer has become the fifth largest malignant tumor in the world, with a mortality rate ranking fourth. IGF2BP3, as a multifunctional RNA binding protein, is involved in regulating alternative splicing and m6A modification. Research has shown that IGF2BP3 plays a carcinogenic role in the development of gastric tumors. However, there is currently relatively little research on the impact of IGF2BP3 as an RNA binding protein (RBP) on alternative splicing in gastric cancer cells. The specific function of IGF2BP3 as an RBP and its molecular mechanisms involved in the development and progression of gastric cancer are still unclear. The aim of this study is to explore the mechanism by which IGF2BP3 affects gene expression and alternative splicing by binding to mRNA, and thus plays a role in the development of gastric cancer cells. We overexpressed IGF2BP3 in gastric cancer cells (AGS) and obtained transcriptome data (RNA seq) on the effects of IGF2BP3 using high-throughput transcriptome sequencing. We then analyzed potential targets in AGS cells where transcription and alternative splicing levels are regulated by IGF2BP3, and explored the molecular mechanisms by which IGF2BP3 affects gene expression and alternative splicing in AGS cells.

overall_design: By overexpressing IGF2BP3  in  AGS cell, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the down stream targets of IGF2BP3 , including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs).

first: Xiangyue

last: Zeng


title: Gene expression profile at single cell level of BM MNCs and NK/T cells from CCUS patients and healthy donors

summary: To evaluate whether a dysfunctional immune phenotype could contribute to the maintenance of CCUS HSPCs, we performed single-cell RNA sequencing analyses of heathy donor  and CCUS bone marrow (BM) mononuclear cells and dissected the intercellular crosstalk between each BM population

overall_design: BM MNCs and NK/T cells were isolated by Fluorescence-activated cell sorting and analyzed using scRNAseq.


title: Targeting the mitotic kinase NEK2 improves the efficacy of CDK4/6 inhibitors

city: Cleveland

first: Jessica

middle: Rose

last: Bobbitt

state: Ohio

address: 9620 Carnegie Ave N Bldg

department: Pathology

institute: Case Western Reserve University

summary: Selective inhibitors that target cyclin dependent kinases 4 and 6 (CDK4/6i) are FDA approved for treatment of a subset of breast cancers and are being evaluated in numerous clinical trials for other cancers. Despite this advance, a subset of tumors are intrinsically resistant to these drugs and acquired resistance is nearly inevitable. Recent mechanistic evidence suggests that in addition to stalling the cell cycle, the anti-tumor effects of CDK4/6i involve the induction of chromosomal instability (CIN). Here, we exploit this mechanism by combining CDK4/6i with other instability-promoting agents to induce maladaptive CIN and irreversible cell fates. Specifically, dual targeting of CDK4/6 and the mitotic kinase NEK2 in vitro drives the accumulation of CIN that induces catastrophic mitoses, cell cycle exit, and cell death. Dual targeting also induces CIN in vivo and significantly decreases mouse tumor volume to a greater extent than either drug alone, without inducing toxicity. Importantly, we provide evidence that breast cancer cells are selectively dependent on NEK2, but non-transformed cells are not, in contrast with other mitotic kinases that are commonly essential in all cell types. These findings implicate NEK2 as a potential therapeutic target for breast cancer that could circumvent the dose-limiting toxicities that are commonly observed when blocking other mitotic kinases. Moreover, these data suggest that NEK2 inhibitors could be used to sensitize tumors to FDA-approved CDK4/6i for the treatment of breast cancers, improving their efficacy and providing a foundation for expanding the patient population that could benefit from CDK4/6i.

overall_design: To assess the efficacy of combined NEK2 and CDK4/6 inhibition, we utilized patient derive xenograft mouse tumor models. After tumors formed, we treated them with vehicle, NEK2 inhibtor, CDK4/6 inhibitor, or the combination. After the last day of treatment (day 21), we harvested tumors from the mice, extracted RNA, and sent it for RNA-sequencing.

middle: R

first: Leslie

last: Cuellar-Vite

first: Kristen

last: Weber-Bonk

first: Marlee

last: Yancey

first: Parth

last: Majmudar

first: Ruth

middle: A

last: Keri


title: Deciphering Motor Dysfunction and Microglial Activation in mThy1-α-Synuclein Mice: A Comprehensive Study of Behavioral, Gene Experssion, and Methylation Changes

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Deciphering Motor Dysfunction and Microglial Activation in mThy1-α-Synuclein Mice: A Comprehensive Study of Behavioral, Gene Experssion, and Methylation Changes [RNA-Seq]

summary: BACKGROUND: Synucleinopathy disorders are characterized by aggregates of α-synuclein (α-syn), which engage microglia to elicit a neuroinflammatory response. However, the influence α-syn has on DNA methylation and gene expression patterns for other genes has not been thoroughly explored. Our objective is to determine gene expression and methylation changes in microglia induced by aggregate α-syn. METHODS: Transgenic mThy1-Asyn mice overexpressing human α-syn are a model of synucleinopathy. Microglia from 7 and 10-month-old mice were used to isolate nucleic acids for methylated DNA and RNA-sequencing. α-Syn-induced changes in gene expression and genomic methylation were determined and examined for pathway and functional enrichment. RESULTS: Microglial DNA isolated from our 7-month cohort had 6,712 differentially methylated regions (DMR), while RNA levels demonstrated a change in 1,141 differentially expressed genes (DEGs) between mThy1-Asyn mice and wild-type littermate controls. The 7-month DEGs and DMRs were highly associated with neuroinflammation likely via TLR pathways. We observed 8,531 DMRs and 1,686 DEGs in 10-month mThy1-Asyn mice. These genes were often predicted by Ingenuity Pathway Analysis to demonstrate inhibition of previously activated inflammatory pathways at 7 months. CONCLUSION: We observed significant α-syn-induced methylation and gene expression changes in microglia. Our data suggest that α-syn overexpression initiates microglial activation leading to neuroinflammation and cellular metabolic stresses, which is associated with disease progression.

overall_design: We performed transcriptomic and methylomic analysis of murince brain homogenate subjected to IBA1 selection for microglia from mice overexpressing full-length human wild-type α-syn under the murine Thy-1 promoter on the X chromosome. Transcriptomic and methylomic profiles were analyzed for biological meaning using Gene ontology and Ingenuity Pathway Analysis on differentially expressed genes (DEGs) and genes annotated to differentially methylated regions (DMRs). HEM samples are mice overexpressing human alpha-synuclein while WT mice are controls. The corresponding background of these mice is the B6D2F1/J mice (stock# 100006) from The Jackson Laboratory (Bar Harbor, ME). There are five 10-month-old HEM mice and five 10 month wild-type controls. There are six 7-month HEM mice and four 7-month wild-type controls.

first: James

middle: E

last: Porter

first: Brett

last: McGregor


title: ZAR1/2-regulated Histone Modifications are Required for Zygotic Activation and Age-associated Oocyte Quality Maintenance

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The developmental competence and epigenetic progression of oocytes gradually become dysregulated with increasing maternal age. However, the mechanisms underlying age-related epigenetic regulation in oocytes remain poorly understood. Zygote arrest proteins 1 and 2 (ZAR1/2) are two maternal factors with redundant roles in maintaining oocyte quality. Here, we found that Zar1/2-deleted oocytes exhibited reduced levels of multiple histone modifications and of the corresponding histone modifiers, along with over-condensed chromatin, leading to disordered histone modification, compromised zygotic genome activation and deficient embryo development following fertilisation. Cytoplasmic ZAR1/2 participated in intranuclear epigenetic maturation by binding to the transcripts that encoding histone modifiers in oocytes, and regulating their stability and translational activity. Moreover, oocytes from older mice exhibited similar histone-modification deficiency to Zar1/2-deleted oocytes. In contrast, forced ZAR1/2 expression in aged mouse oocytes partially restored histone modifications. ZAR1/2 mRNA and protein levels were lower in oocytes from older mice and in those from older women, suggesting ZAR1/2 as regulators of aging-associated epigenetic disorganizations. This study presents a new nucleo-ooplasmic interaction mechanism that is vital for oocyte epigenetic maturation and declining of developmental potentials with female aging. Further, it provides the potential gene targets for diagnosis and clinical intervention in age-associated deficiency in oocyte and embryo development.

overall_design: The growing oocytes (GO) were harvested from 12-day-old WT and Zar1/2 knockout female mice, GV stage oocytes were harvested from 4-week-old WT and Zar1/2 knockout female mice 32-48h after PMSG and the late 1-cell embryos were harvest from 4-week-old WT and Zar1/2 knockout female mice by IVF. All the oocytes/embryos were washed by 0.2% BSA containing PBS for 3 times, then fresh 30 oocytes/embryos per sample were used for the ATAC-seq library construction following the protocol of the High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina®) (Novoprotein, cat#N248).

first: Yan

last: Rong

first: Yuke

last: Wu

first: Yunwen

first: Hengyu


title: Uncovering two neutrophil-committed progenitors that immediately precede the promyelocytes during human neutropoiesis

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

summary: Technological advances have greatly improved our knowledge of myelopoiesis, for instance with the discovery of granulocyte-monocyte-DC progenitors (GMDPs), monocyte-DC progenitors (MDPs), common dendritic progenitors (CDPs) and common monocyte progenitors (cMoPs) based on sophisticated flow cytometry approaches. Concomitantly, little progress has been made to characterize the very early phases of human neutropoiesis, despite the recently reported eNePs, PM w/o eNePs, ProNeus, preNeus, all of them being, however, CD66b+neutrophil progenitors. More recently, we identified four SSCloLin-CD66b-CD45dimCD34+/CD34dim/-CD64dimCD115-cells as the earliest precursors specifically committed to the neutrophil lineage present in human bone marrow (BM), which we called neutrophil-committed progenitors (NCPs), namely from NCP1s to NCP4s.  In this study, we report the isolation and characterization of two new SSChiCD66b-CD64dimCD115-NCPs that, by phenotypic, flow cytometric SSC, transcriptomic, maturation and immunohistochemistry properties/features, stand after NCP4s but precede the CD66b+Promyelocytes (PMs) during the neutropoiesis cascade. These cells, similarly to SSCloCD45RA+NCP2s/NCP3s and SSCloCD45RA-NCP1s/NCP4s, exhibit phenotypic differences in CD45RA expression levels and, therefore, were named as SSChiCD45RA+NCP5s and SSChiCD45RA-NCP6s. In addition, NCP5s result more immature than NCP6s, as determined by both their cell differentiation and proliferative potential, and by their transcriptomic and phenotypical features. Finally, by examining whether NCPs and all other CD66b+neutrophil precursors are altered in representative hematological malignancies, we found that, in patients with chronic-phase chronic myeloid leukemia (CP-CML), but not with systemic mastocytosis (SM), there is an increased frequency of NCP4s and all downstream neutrophil progenitors, particularly, the CD45RA-cells, like NCP6s, suggesting their involvement in CML pathogenesis. Altogether, our data advance our knowledge of human neutropoiesis.

overall_design:
Examination of the gene expression profiles of neutrophil-committed progenitors (NCPs), promyelocytes (PMs), myelocytes (MYs) metamyelocytes (MMs), band cells (BCs) and segmented neutrophils (SNs) from Bone Marrow of healthy donors, isolated by cell sorting by using a Becton Dickinson FACS Aria Fusion (BD Biosciences)
Neutrophil progenitors were sorted and lysed for RNA extraction. Then  bulk RNA-seq  were performed and compared to samples in published study GSE175880: GSM5772727,GSM5772728,GSM5772729,GSM5772730,GSM5772731,GSM5772732,GSM5772733,GSM5772734,GSM5772735,GSM5772736,GSM5772737,GSM5772738,GSM5772739,GSM5772740,GSM5772741,GSM5772742,GSM5772743,GSM5772744,GSM5772747,GSM5772748,GSM5772749,GSM5772751,GSM5772752,GSM5772753,GSM5772756,GSM5772757,GSM5772758

first: Nicola

last: Tamassia

first: Marco

last: Cassatella


title: ITIH5-mediated fibroblast/macrophage crosstalk exacerbates cardiac remodelling after myocardial infarction

first: Yirong

state: 浙江省

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital

summary: Background: Myocardial infarction (MI) and subsequent ischaemic cardiomyopathy (ICM) are the primary causes of heart failure. Inter-α trypsin inhibitor heavy chain 5 (ITIH5) is an ECM protein and has been identified as a myocardial marker of ICM. However, its diagnostic value in patients with ICM and its function and molecular mechanism in regulating cardiac repair and remodelling after MI remain unknown.  Methods: Three microarray datasets including 117 ICM and 152 non-failing (NF) myocardial tissue samples were merged and analysed. Peripheral blood and clinical information were collected from 53 patients with ICM and 40 NF controls. The effects of ITIH5 on cellular interactions and cardiac remodelling was studied using ITIH5 RNAi adeno-associated virus and mouse MI model in vivo and in fibroblast–macrophage co-culture model in vitro. Results: ITIH5 was upregulated in the myocardial tissue and peripheral blood of patients with ICM and could be an independent risk factor for ICM. Experiments in mice suggested that ITIH5 promotes cardiac fibrotic remodelling at all phases after MI. Downregulation of ITIH5 increased the risk of death within 7 d after MI but inhibited ventricular remodelling and improved cardiac function on the long-term. ITIH5 promotes the primary cardiac fibroblasts (CFs) proliferation, migration, and improves survival rather than activiation. Morover, ITIH5 directly promotes macrophage tissue infiltration, maturation, and profibrotic phenotype transformation, thereby promoting fibrotic remodelling. By using fibroblast–macrophage co-culture model, we demonstrated ITIH5 enhanced the fibroblast/macrophage crosstalk manifest as macrophage profibrotic phenotype transformation and CFs activation, mainly by enhancing the hyaluronan stability, the ability of ITIH5 to bind macrophage CD44 receptors and the downstream activation of the signal transduction and activator of transcription 3 pathway in macrophages.  Conclusions: ITIH5 could be used as a diagnostic marker for ICM. Moreover, ITIH5 expression was upregulated after MI, which accelerated ECM-fibroblast-macrophage interaction, thereby promoting macrophage profibrotic phenotype transformation, CFs activation, and cardiac fibrotic remodelling.

overall_design: ITIH5 may indirectly regulate post MI fibrosis by immune regulation . We  conduct mRNA sequencing  on the mice infraction myocardium in widetype and ITIH5 knockdown mouse at 7 days after MI.

first: Yizhou

last: Xu


title: The MR1/MAIT cell axis reduces dystrophic neurite development in Alzheimer’s disease

city: Indianapolis

first: Season

last: Johnson

state: Indiana

address: 950 W Walnut ST, R2 359 Research II

department: Microbiology and Immunology

institute: IU School of Medicine

summary: Plaques are a hallmark feature of Alzheimer’s disease (AD). We found that the loss of mucosal-associated invariant T (MAIT) cells and its antigen-presenting molecule MR1 caused a delay in plaque pathology development in AD mouse models. However, it remains unknown how this axis is impacting dystrophic neurites. Brain tissue from 5XFAD mice and those that are MR1-deficient (MR1 KO), were analyzed for dystrophic neurites, amyloid plaques, and synapses via immunofluorescence, RNA sequencing, ELISA, and Western blot. In 8-month-old 5XFAD/MR1 KO mice, there was reduced expression of LAMP1, Ubiquitin, and n-terminal APP in the hippocampus as compared to 5XFAD mice (p < 0.05). 5XFAD/MR1 KO mice also had less insoluble Aβ40 (p < 0.001) and higher levels of PSD95 (p < 0.01) in the hippocampus. Our data contribute additional mechanistic insight into the detrimental role of the MR1/MAIT cell axis in AD pathology development.

overall_design: Hippocampal samples from 8 month old 5XFAD and 5XFAD/MR1 KO mice, with a male and female mouse pooled together for 1 sample

last: Wyatt-Johnson

first: Jun

last: Wan

first: Sheng

last: Liu

first: Randy

last: Brutkiewicz


title: Regulation of adipocyte de-differentiation and subsequent re-differentiation

city: Beijing

first: Meng

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: We show the presence of de-differentiated fat (DFAT) cells in subcutaneous and visceral adipose depots under different dietary intervention conditions, whose transcriptomes resemble adipocytes with high differentiation potential and late-stage adipose stem and progenitor cells (ASPC). These data uncover the potential of adipocytes to undergo de-differentiation under regular physiological conditions and shed light on its role in life style change-induced weight loss and regain.

overall_design: DFAT cells and the major cell types in the white adipose tissue were collected under different dietary conditions and sent for sequencing, not only in vivo but also in vitro.

last: Li

first: Carlos

middle: F

last: Ibáñez


title: CUT-TAG for AML cell line

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results in AML cell line.

overall_design: CUT-TAG for IRF1 and ETV6

first: Jian

last: Pan

first: Shaoyan

last: Hu

first: Fenli

last: Zhang


title: Deciphering Motor Dysfunction and Microglial Activation in mThy1-α-Synuclein Mice: A Comprehensive Study of Behavioral, Gene Experssion, and Methylation Changes [Enzymatic Methyl-Seq]

first: Junguk

last: Hur

first: James

last: Porter

first: Brett

last: McGregor


title: Generation of phenotypically stable and functionally mature human bone marrow MSCs derived Schwann cells via the induction of human iPSCs-derived sensory neurons

city: Shenzhen

first: haohui

last: Lin

state: Guangdong

address: 1066 Xueyuan avenue

department: Medical School

institute: Shenzhen university

summary: Phenotypically unstable Schwann cell-like cells (SCLCs), derived from mesenchymal stem cells (MSCs) require intercellular contact-mediated cues for Schwann cell (SCs)-fate commitment. Although rat dorsal root ganglion (DRG) neurons provide contact-mediated signals for the conversion of SCLCs into fate-committed SCs, the use of animal cells is clinically unacceptable. To overcome this problem, we previously acquired human induced pluripotent stem cell-derived sensory neurons (hiPSC-dSNs) as surrogates of rat DRG neurons that committed rat bone marrow SCLC to the SC fate. Therefore, in this study, we explored whether hiPSC-dSNs could mimic rat DRG neurons effects to obtain fate-committed SCs from hBMSC-derived SCLC. The derived cells exhibited bi-/tri-polar morphology of SCs and maintained the expression of the SC markers S100, p75NTR, p0, GFAP, and Sox10, even after withdrawing the glia-inducing factors or hiPSC-dSNs cues. Electronic microscopy and RNA-seq analysis further provided evidence that human BMSC-dSCs were similar to the original human SCs in terms of their function and a variety of characteristics. Furthermore, these cells formed myelin basic protein-positive segments and secreted neurotrophic factors to facilitate the neurite outgrowth of Neuro2A, demonstrating that they were functionally mature. Our results provide a promising approach through which stable and fully developed hBMSC-dSCs can be used for transplantation and myelin sheath regeneration following traumatic nerve injuries.

overall_design: To further confirm the schwann cell-lineage identity of hBMSC-dSCs, we performed RNA-seq to compare the gene expression profiles of hBMSCs, human SCs and hBMSC-dSCs.

first: Yu

first: Haohui

first: Manhon

last: Chung

first: Yi

last: Yang

first: Li

first: Xiaohua

first: Sa

last: Cai


title: RNA-seq for MV4-11 cell line in either the absence or presence of IRF1

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for MV4-11 cell line in either the absence or presence of IRF1.

overall_design: 2 MV4-11 samples with no treatment and 2 MV4-11 samples with IRF1 knockdown


title: Selective activation of FZD2 and FZD7 reveals non-redundant function during mesoderm differentiation

city: Toronto

first: Rony

last: Chidiac

state: Ontario

address: 160 College St

department: CCBR

country: Canada

institute: University of Toronto

summary: Wnt-ßcatenin signalling controls stem cell self-renewal and cell fate decisions and therefore its precise control could influence differentiation protocols efficiency and cell therapy efforts. During gastrulation, Wnt-ßcatenin signalling dictates lineage bifurcation choices leading from pluripotency to distinct primitive streak patterning, ultimately resulting in various mesendoderm cell types. However, the nature of the Wnt receptors involved in this process and how their signaling dynamics impact mesoderm specification remain elusive. Here, we used selective Frizzled and LRP5/6 antibody-based agonists (FLAgs) to investigate the function and activation kinetics of Frizzled receptor complexes during directed mesoderm differentiation of hPSCs. We found that FZD2 and FZD7 are expressed at the surface of hPSCs and that their activation triggers ßcatenin signaling with different kinetics thereby influencing  mesoderm patterning choices. Using bulk and single-cell RNA sequencing, we showed that FZD7 activation promotes lineage commitment towards both paraxial and lateral mesoderm whereas FZD2 engagement preferentially induces paraxial mesoderm. Mechanistically, our results demonstrate that although the short-term response following FZD2 and FZD7 activation is similar, ßcatenin signaling kinetics differs. FZD2 activation results in a sustained Wnt activation profile that drives hPSCs differentiation to paraxial mesoderm while blocking lateral mesoderm. In contrast, FZD7 activation kinetics consists of a similar initial activation followed by dampening of the response to a low level of ßcatenin signaling that is permissive for lateral mesoderm induction in addition to paraxial mesoderm specification. Our results suggest that the function of FZD2 and FZD7 during mesoderm specification is non-redundant and that their selective activation to temporally modulate Wnt-ßcatenin signaling can be leveraged for precise directed differentiation outcomes.

overall_design: Bulk RNA-Seq was performed in hESC treated with either F2L6.13 or F7L6.13 for 4 days. These conditions were compared to the standard differentiation protocols used to derive paraxial or lateral mesoderm adapted from Loh K. et al. Cell 2016 in which CHIR99021 was used to activate Wnt signaling. 3 replicates of each condition was done and compared to the control H1 hESC.

first: Andy

first: Stephane

last: Angers


title: Hepatic lipid metabolism is altered in Ubiad1+/- mice of both sexes

city: Oslo

first: Frode

middle: Amador

last: Norheim

address: Sognsvannsveien 9

department: Faculty of Medicine

country: Norway

institute: University of Oslo

summary: UbiA prenyltransferase domain containing 1 (Ubiad1) has the potential to affect cholesterol and phospholipid levels in the cornea. We previously identified Ubiad1 as a candidate gene for regulating subcutaneous fat pad weight in a mouse genome-wide association study. Here we evaluated the relationship between Ubiad1 and obesity-related traits in cohorts of humans and mice, and in Ubiad1+/- mice fed a high-fat diet. In both humans and mice, adipose tissue Ubiad1 mRNA expression correlated negatively with adiposity and positively with mitochondria-related genes. To determine the role of Ubiad1 in obesity, we disrupted the Ubiad1 gene in mice. Deletion of Ubiad1 was embryonically lethal in C57BL/6N mice, preventing analysis of adult Ubiad1-/- mice. Thus, male and female Ubiad1+/+ and Ubiad1+/- mice were fed high-fat diet for 10 weeks, with no difference in weight gain and adipose tissue organ weights observed between the genotypes. Analysis of liver mRNA expression revealed that Ubiad1 heterozygosis (Ubiad1+/-) altered several pathways involved in lipid metabolism. Detailed lipid quantification with HPLC-qTOF/MS showed increased levels of hepatic ceramides in female Ubiad1+/- mice, while phosphatidylglycerols, phosohatidylinositol and lysophosphatidylethanolamines were reduced in male Ubiad1+/- mice. Our findings reveal sex-specific effects of Ubiad1 expression on hepatic lipid metabolism.

overall_design: Total RNA was obtained from Ubiad1+/+  male, Ubiad1+/- male, Ubiad1+/+  female, and Ubiad1+/- female under high-fat diet intervention.

first: Ryoko

last: Higa

last: Amador Norheim


title: Intestinal Bacteroides drives glioma progression by regulating CD8+ T cell tumor infiltration

city: Saint Louis

first: David

middle: H.

last: Gutmann

state: MO

address: 1 Childrens Place Suit 2130

institute: Washington University in St. Louis

summary: Changes in the gut microbiome can have profound effects on the nervous system through modulation of T cell and microglia function. Since our prior studies demonstrated that T cells and microglia positively regulate low-grade glioma growth through the establishment of T cell-microglia immune circuit, we sought to explore the impact of changes in the gut microbiota on tumor biology. For these studies, genetically engineered Neurofibromatosis type 1 (NF1) optic glioma (Nf1-OPG) mice were raised in a germ-free environment or treated with antibiotics to deplete gut bacteria. First, we demonstrated that Nf1-OPG mice raised in a germ-free (gnotobiotic) environment or treated with specific antibiotics lacked optic gliomas and had improved OPG-induced retinal pathology (increased retinal nerve fiber layer thickness). Second antibiotic-treated Nf1-OPG mice gavaged with fecal microbiota from Nf1-OPG mice raised in a standard barrier facility restored optic glioma growth. Third, we showed that both germ-free and antibiotic-treated Nf1-OPG mice exhibited reduced intra-tumoral CD8+ T cell content resulting from decreased microglia chemokine production. Collectively, these findings establish a mechanistic relationship between the gut microbiota and brain tumor growth relevant to potential therapeutic interventions for pediatric low-grade gliomas.

overall_design: All experiments were performed under active Animal Studies Committee protocols at Washington University School of Medicine(Washington University in St Louis Institutional Animal Care and Use Committee).Mice harboring a neomycin cassette insertion in exon 31 (Nf1+/-) with GFAP-Cre-mediated. Nf1 loss in neuroglial progenitors (Nf1flox/neo; GFAP-Cre, Nf1-OPG mice) (Bajenaru et al., 2003). Mice were either treated with Vancomycin or PBS from 6-12 weeks of age and optic nerves were harvested for single cell seq.

first: Jit

last: Chatterjee

first: Xuanhe

last: Qi

first: Rui

last: Mu

first: Xuanwei

last: Li

first: Talia

last: Eligator

first: Megan

last: Ouyang

first: Stephanie

middle: L

last: Bozeman

first: Rachel

last: Rodgers

first: Somya

last: Aggarwal

first: Danielle

last: Campbell

first: Lawrence

last: Schriefer

last: Baldridge

middle: H


title: HDAC inhibitors induce transcriptional activation of Hippo pathway signaling and is associated with improved outcomes in Hormone Receptor positive breast cancer

city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming Chiao-Tung University

summary: Breast cancer has constantly been the leading causes of death in women, and hormone receptor (HR) positive, HER2 negative is the majority subtype. Treatment modalities for HR (+) metastatic breast cancer (mBC) includes endocrine therapy (tamoxifen, fulvestrant, aromatase inhibitors) in addition to targeted therapies (CDK4/6 inhibitors, PI3K/AKT/mTOR inhibitors, histone deacetylase (HDAC) inhibitors, and others. The hippo pathway LATS1/2-YAP/TAZ-TEAD signaling cascade is a fundamentally important pathway that governs multiple essential biological functions in cell biology and cancer biology. YAP/TAZ are often viewed as pro-tumorogenic, however, recent studies support a role of YAP as a tumor suppressor in HR (+) breast cancer due to its inhibition of estrogen signaling. Few studies have investigated the link between HDAC inhibitors and the Hippo pathway. In our study, we demonstrate that HDAC inhibitors induce transcriptional downregulation of YAP expression, while conversely activating a TEAD mediated transcriptional program with upregulation of many Hippo pathway canonical genes. We further identified 4 genes (CCDC80, GADD45A, F3, TGFB2) that were upregulated by HDAC inhibitors and associated with significantly improved survival in a HR (+) breast cancer cohort. We also correlate in patients samples from a clinical cohort of HR (+) metastatic breast cancer that upregulation of Hippo downstream genes are correlated with improved outcomes. Our study provide a novel mechanistic explanation for the clinical benefit of HDAC inhibitors, while providing further experimental support that Hippo-TEAD transcriptional activation profile is associated with better outcomes in HR (+) breast cancer.

overall_design: human breast cancer cell lines MCF-7 and T47D treated with romidepsin 50nM for 24 hours

first: Ting-I

last: Lin

first: Yi-Ru

last: Tseng

first: Chih-Yi

first: Yi-Hsin

last: Ni

first: Wei-Ting

last: Chung

first: Chun-Yu

last: Liu

first: Yi-Fang

last: Tsai

first: Chi-Cheng

last: Huang

first: Ling-Ming

first: Ta-Chung

last: Chao


title: DMS-MaPseq chemical probing of pri-miRNA and human mRNA segments

city: Boston

first: Silvi

last: Rouskin

state: MA

address: 77 avenue louis pasteur

institute: Harvard Medical School

summary: Understanding macromolecular structures, such as proteins and nucleic acids, is critical for discerning their functions and biological roles. Advanced techniques like crystallography, NMR, and CryoEM have facilitated the determination of over 180,000 protein structures, all cataloged in the Protein Data Bank (PDB). This comprehensive repository has been pivotal in developing deep learning algorithms for predicting protein structures directly from sequences. In contrast, RNA structure prediction has lagged, primarily due to a scarcity of RNA structural data. Here, we present the secondary structures of 1098 pre-miRNAs and 1456 human mRNA regions determined through chemical probing. We develop a novel deep learning architecture, inspired from the Evoformer model of Alphafold and traditional architectures for secondary structure prediction. This new model, called eFold, was trained on our newly created database and over 100,000 secondary structures across multiple sources. We benchmark eFold on a set of challenging RNA structures and show that both our new architecture and dataset contributes to increasing the prediction performance, and outperforming similar end-to-end methods.This result reveals that merely expanding the database size is inadequate; rather, incorporating a greater diversity and complexity of structures is crucial for enhancing performance.

overall_design: DMS MaP seq method in vitro. 1.5% DMS

first: Fede

last: Fuchs

first: Dragui

last: Salazar


title: TR4 and BCL11A Repress gamma-globin Transcription via Independent Mechanisms

city: Ann Arbor

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

department: DCMB

institute: University of Michigan

summary: Nuclear receptor TR4 was previously shown to bind to the -117 position of the gamma-globin gene promoters in vitro, which overlaps with the BCL11A binding site recently described. The role of TR4 in human gamma-globin gene repression has not been extensively characterized in vivo, and the relationship between TR4 and BCL11A binding to the gamma-globin promoters remained elusive. We showed in vitro that TR4 and BCL11A competitively bind to overlapping but distinct consensus sequences which both include the -117 position of the gamma-globin promoter. We show here that TR4 represses gamma-globin transcription and HbF accumulation in a BCL11A-independent manner. We characterized the chromatin occupancy of TR4 within the beta-globin locus in comparison to BCL11A and found that both bind to the hypersensitive sites avidly but only BCL11A binds to the gamma-globin promoters at significant levels, suggesting that BCL11A is the predominant repressor acting through the -117 gamma-globin promoter sequence in vivo. These data resolve an important discrepancy in the literature, and thus helps to clarify possible approaches to treatments for sickle cell disease or beta-thalassaemia.

overall_design: To elucidate how TR4 might repress γ-globin transcription, we performed TR4 CNR in HUDEP-2 cells and compared its binding to BCL11A. HUDEP-2 clones were generated by genome editing bearing either of 2 modifications: TR4 C-terminally tagged with 3FLAG+3MYC epitopes (cell line T) and BCL11A tagged with 3HA+3MYC epitopes (cell line B). In addition, a third clone was created bearing both BCL11A::3HA3MYC and TR4::3FLAG3MYC modifications (cell line TB). These epitope-tagged clones not only improved the recovery of the epitopes, but also facilitated comparison of TR4 and BCL11A chromatin occupancy by immune-precipitation of the common MYC epitope using CUT&RUN.

first: Wang

last: Yu

first: Myers

last: Greggory

first: Yu

last: Lei

first: Deng

last: Kaiwen

first: James

middle: D

last: Engel


title: Prolonged water limitation in B. napus restricts growth but maintains photosynthesis through genotype specific time-of-day changes in transcriptomes and sulfur-related metabolomes

city: St. Paul

first: kathleen

last: Greenham

state: MN

address: 1445 Gortner Avenue

institute: University of Minnesota

summary: Water availability is a major determinant of crop production and rising temperatures from climate change is leading to more extreme droughts. To maximize the impact of irrigation on crop yields, we need to develop varieties that are more tolerant to water limited conditions. We aimed to determine how diverse crop types of the allopolyploid Brassica napus, a species that contains the economically important canola oilseed crop, respond to prolonged water limitation. We exposed plants to an 80% reduction in water and assessed growth and color on a high throughput phenotyping system over four weeks and ended the experiment with tissue collection for a time course transcriptomic study. We found an overall reduction in growth across cultivars but to various degrees. The transcriptome analysis did not reveal strong indicators of abiotic stress suggesting that the cultivars had adjusted to the water limited conditions. However, we found significant genotype-specific changes in time-of-day regulation of photosynthesis, carbohydrate metabolism, and sulfur metabolism. Interestingly, there was extensive variation in which paralogs responded to water limitation across crop types that could be due to rearrangements of regulatory regions in these allopolyploid lines. Follow up experiments on select cultivars confirmed that plants maintained photosynthetic health during the prolonged water limitation while slowing growth. In two cultivars examined, we found significant time-of-day changes in levels of glucosinolates, sulfur and nitrogen rich specialized metabolites, consistent with the transcriptomic responses. These results suggest that these lines are adjusting their sulfur and nitrogen stores under water limited conditions through distinct time-of-day regulation.

overall_design: We subjected 16 Brassica napus cultivars to an 80% reduction in available water for four to five weeks and collected leaf tissue for RNAsequencing at the end of the experiment at ZT (Zeitgeiber; hours after lights on) 1, 7, 13 and 19.

first: Angela

last: Ricono

first: Ella

last: Ludwig

first: Anna

last: Casto

first: Stevan

last: Zorich

first: Joshua

last: Sumner

first: Kevin

last: Bird

first: Patrick

middle: P

last: Edger

first: Adrian

last: Hegeman

first: Malia

last: Gehan

first: Kathleen


title: Circulating KLRG1+ memory T cells retain the flexibility to become tissue-resident

city: SAINT PAUL

first: Sara

last: Hamilton Hart

state: Minnesota

address: 1898 Eustis St.

summary: KLRG1+ CD8 T cells persist for months after clearance of acute infections and maintain high levels of effector molecules, contributing protective immunity against systemic pathogens. Upon secondary infection, these long-lived effector cells (LLECs) are incapable of forming other circulating KLRG1− memory subsets such as central and effector memory T cells. Thus, KLRG1+ memory T cells are frequently referred to as a terminally differentiated population that is relatively short lived. Here, we show that following viral infection of mice, effector cells derived from LLEC rapidly enter nonlymphoid tissues and reduce pathogen burden, but are largely dependent on receiving antigen cues from vascular endothelial cells. Single-cell RNA sequencing revealed that secondary memory cells in nonlymphoid tissues arising from either KLRG1+ or KLRG1− memory precursors developed a similar transcriptional signature. Thus, although LLEC cannot differentiate into other circulating memory populations, they still retain the flexibility to enter tissues and establish residency.

overall_design:
Secondary P14 memory cells from C57Bl/6 mice infected with LCMV-Armstrong were isolated by Fluorescence activated cell sorting (FACS) from different tissue sites (spleen, lymph nodes, small intestine and kidney. Cells were stained with TotalSeq-A antibodies and hashtagged before pooling for library construction and sequencing.
Please note that as de-multiplexed files are unavailable for each sample, each sample record represents mixed-sample (of LLEC, TCM, TEM from spleen, lymph nodes, small intestine and kidney; 12 samples).
Each of processed data file (the GEX text file, HTO text file, ADT text file and the SeuratObject_metadata text file) have  information on all 12 samples, as detailed in the readme.txt.

first: Mathew

last: Huggins

first: Erin

last: Lucas

last: Hart

first: Christine

last: H O'Connor


title: Maternal obesity disrupts histone modifications mediated by Ezh2 and Ampk interactions and induces cell fate defects during embryonic cortical neurogenesis. [RNA-seq]

city: Al Ain

first: Suraiya

last: Ansari

address: Tawam

country: United Arab Emirates

institute: United Arab Emirates University

summary: In this study, we have used a rat model of maternal obesity induced by high fat diet (HFD) prior to and during gestation to investigate the cellular and molecular repercussions of maternal obesity on embryonic cortical neurogenesis. Maternal obesity is noted to substantially disrupt neurogenesis, leading not only to imbalances in cell proliferation vs neuronal differentiation ratios but also prompting a shift towards astrogliogenesis. Differentially expressed genes (DEGs) revealed disruptions in key developmental signaling pathways and reduced Akt phosphorylation particularly notable at the E14.5. These changes were associated with epigenetic alterations, mainly the differential expression and phosphorylation of Ezh2 and subsequent changes in global histone modifications. ChIP-seq revealed reduced H3K27me3 at genes upregulated due to maternal obesity which could have resulted from reduced expression and increased phosphorylation of Ezh2 at Thr311. Interestingly Ezh2 also showed increased O-GlcNAcylation in HFD embryos along with increased association with Ampk-Thr172 in accordance with previous studies showing that Ezh2-Thr311p is catalyzed by Ampk. These results led to propose an epigenetic gene regulatory mechanism mediated by Ampk and Ezh2 interactions resulting in reduced H3K27me3 and de-repression of key developmental genes which could have led to cell fate defects observed in the developing embryo brain cortex due to maternal obesity.

overall_design: Healthy female and male Wistar Rats were fed on the normal chow and the ‘High Fat Diet (HFD) group fed on the commercially available high fat diet produced by Research Diets Inc. (60% calories by fat, 20% calories by protein, and 20% calories by carbohydrate; Product No.: D14292). Normal Weight and obese female rats were crossed with healthy males and were sacrificed on embryonic days, E14.5, E16.4 and E18.5. Pups’ brains were removed and dissected out for further processing.

first: S


title: Targeting long non-coding RNA H19 in Subchondral Bone Osteocytes Alleviates Cartilage Degradation in Osteoarthritis

city: Hong Kong

first: Rongliang

last: WANG

address: PRINCE OF WALES HOSPITAL, DEPT OF Orthopaedics and Traumatology, RM 1003 LKS MEDICAL SCIENCE BLDG

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
Introduction: Emerging evidence suggests long non-coding RNA (lncRNA) H19 is associated with osteoarthritis (OA) pathology. However, how H19 contributes to OA has not been reported. This study aims to investigate the biological function of H19 in OA subchondral bone remodeling and OA progression.
Methods: Clinical joint samples and OA animal models induced by medial meniscus destabilization (DMM) surgery were used to verify the causal relationship between osteocyte H19 and OA subchondral bone and cartilage changes. MLO-Y4 osteocyte cells subjected to fluid shear stress were used to verify the mechanism underlying H19-mediated mechano-response. Finally, the antisense oligonucleotide (ASO) against H19 was delivered to mice knee joints by magnetic metal-organic framework (MMOF) nanoparticles in order to develop a site-specific delivery method for targeting osteocyte H19 for OA treatment.
Results: Both clinical OA subchondral bone and wildtype mice with DMM-induced OA exhibit aberrant higher subchondral bone mass with more H19 expressing osteocytes. On the contrary, osteocyte-specific deletion of H19 mice is less vulnerable to DMM-induced OA phenotype. In MLO-Y4 cells, H19-mediated osteocyte mechano-response through PI3K/AKT/GSK3 signals activation by EZH2-induced H3K27me3 regulation on PP2A inhibition. Targeted inhibition of H19 (using ASO-loaded MMOF) substantially alleviates subchondral bone remodeling and OA phenotype.
Discussion: In summary, our results provide new evidence that the elevated H19 expression in osteocytes may contribute to aberrant subchondral bone remodeling and OA progression. H19 appears to be required for the osteocyte response to mechanical stimulation, and targeting H19 represents a new promising approach for OA treatment.

overall_design:
To investigate the role of H19 in the regulation of osteocyte mechanotransduction, we establish MLO-Y4 cell lines in which target gene could be knocked down by ASO and throughout FSS
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells
Comparative gene expression profiling analysis of RNA-seq data for ASO-treated and control MLO-Y4 cells

last: Wang


title: Protein folding dependence on Selenoprotein M contributes to steady cartilage extracellular matrix repressing ferroptosis specifically access to PERK/ATF4/CHAC1 axis

city: Xi'an

first: Yitong

last: Zhao

state: Shaanxi

address: West Yanta Street No.76

department: Department of Biochemistry and Molecular Biology

institute: Xi'an Jiaotong University School of Basic Medical Sciences

summary: Oateoarthritis (OA) commonly attends persistent inflammatory injury, extensive cartilage structural destruction and severe extracellular matrix (ECM) degradation. This study provides an overview of decreasing endoplasmic reticulum (ER)-resident selenoprotein M (SELM) probed into OA cartilage. Overexpression of SELM in chondrocytes positively promoted the synthesis of ECM. RNA-Seq results represented the mobilization of genes touched on various parts of degenerative diseases, inflammation and ferroptosis after SELM knockdown, which also negatively regulated cellular response to misfolded proteins and led to the activation of ER stress mediated by the PERK/P-EIF2A/ATF4 pathway in chondrocytes. Protein docking results captured that SELM was overwhelmingly likely to be involved in protein disulfide bond formation and modification processes by interacting with PDI, GRP94, CNX and CRT, resting on its thioredoxin domain. Decreased SELM also deepened GSH/GSSG homeostasis imbalance through the ATF4/CHAC1 axis and sparking ferroptosis. In vitro supplementation of SELM was buffering the effects of IL-1β on tattered cartilage explants. Furthermore, SELM also powered up the maintenance of favorable proliferative and homeostatic phenotypes among to an inhibitory effect on the hypertrophic phenotype in chondrocytes. These results make conclusive proof to unravel the involvement of SELM in ER stress induced cartilage damage and depict the distinctive function of SELM in protein folding, which renews directions for molecular therapeutic of degenerative diseases.

overall_design: Primary chondrocytes derived from three different patients’ smooth cartilage sites were divided into two groups and subjected to treatment with Selenoprotein M-specifically siRNA or adenovirus for a duration of 24 hours. Following stimulation, the total RNA was extracted and transferred for transcriptome sequencing by Sangong Biotech (Shanghai, China).

first: Ying

last: Zheng

first: Han

last: Li

first: Ru


title: Maternal obesity disrupts histone modifications mediated by Ezh2 and Ampk interactions and induces cell fate defects during embryonic cortical neurogenesis.

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

overall_design: Refer to individual Series


title: CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to DON treatment. we performed CUT&Tag sequencing in murine PDAC cells.  sgPaxip1 cells were treated in Cont group or DON group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

overall_design: For library preparation, murine PDAC cell lines with Cont, DON were first established. CUT&Tag and DNA library were prepared according to manufacturer’s instructions.

first: Xuqing

last: Shen

first: Jing

last: Xue


title: RNA sequencing (RNA-seq) of LAIR-1 overexpression in SKOV-3 ovarian cancer cell lines

city: Yantai

first: Huachang

last: zhang

state: Shandong

address: 346 Guanhai Road, Laishan District

institute: Binzou medical university

summary: Leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1), is widely expressed by solid tumor cells and functions as a tumor suppressor. Our previous studies have found that LAIR-1 is expressed in ovarian cancer tumor tissues and in a variety of epithelial ovarian cancer cell lines and that LAIR-1 could inhibit ovarian cancer cell growth by suppressing the PI3K-AKT-mTOR pathway. The aim of the present study was to obtain a comprehensive understanding of the molecular mechanism of LAIR-1 in regulating the biological behavior of ovarian cancer cells. The approach taken was to perform RNA-seq sequencing on SKOV3 cells overexpressing LAIR-1, and to conduct further validation by combinatorial integration of bioinformatics analyses to assess the genetic alterations and using biological experimental findings.

overall_design: There are two groups cells used for this expression profile comparison : NC (negative control) and OE(LAIR-1–overexpression) . Total RNA was extracted with Trizol, 1 μg of total RNA was hybridized to the probe and digested with RNase H followed by DNase I. RNA was purified using VAHTS RNA purification beads, 18.5 μL Frag/Prime Buffer (1x) was added, mixed by pipetting, and allowed to stand for 2 minutes at room temperature. After standing on a magnetic stand for 5 minutes to allow the solution to clear, 16 μL of supernatant was gently aspirated into a new nuclease-free centrifuge tube, and the samples were fragmented using a PCR instrument and sequenced using an Illumina sequencer.


title: siRNA knockdown screening of possible NF-kB p65 interactors influencing IL-1-NF-kB gene expression

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: The transcription factor NF-κB p65 plays a key role in innate and adaptive immunity. It functions as a master regulator of the inflammatory response by inducing the expression of pro-inflammatory genes including secreted cytokines (IL6), chemokines (IL8, CXCL2), and multiple regulatory intracellular proteins (NFKBIA). NF-κB is activated by the so-called canonical, noncanonical and atypical signalling  pathways. In the canonical pathway, activation of the Interleukin-1 receptor complex triggers degradation of the cytosolic p65 inhibitor IBα followed by nuclear translocation of p65 where it is directed by unknown pathways to the enhancers and promoters of pro-inflammatory genes. Despite its pleiotropic functions in adaptive and innate immunity or stress reactions, the entire repertoire of p65 interacting factors that contribute to its general or stimulus-specific functions within the nucleus or other cell compartments is still elusive.   We identified the p65 interactomes in intact cells by BioID pulldowns under inflammatory condition (+IL-α). Extensive bioinformatics analysis of the proximity labeling data sets revealed several hundred high confidence interactors including multiple novel factors that have not been reported in the literature. We investigated which of our 38 high-confidence interactors have an impact on IL-1 NF-kB gene expression by siRNA screening. We found 5 interesting hits in the context of inflammation which will be further assessed by microarray analysis.

overall_design: 22 groups with 2-4 biological replicates in a 2-factorial design. Factors are as follows: (i) siRNA treatment: siLuci = luciferase control, untrans = untransfected control, si{{symbol} = siRNA against gene {symbol}; (ii) IL1A: yes = addition of 1 µg/ml IL-1a for 1h, no = no IL-1a added.

first: J

first: M

last: Kracht

last: Juli


title: Maternal obesity disrupts histone modifications mediated by Ezh2 and Ampk interactions and induces cell fate defects during embryonic cortical neurogenesis. [ChIP-Seq]


title: Transcriptome comparison of primary and immortalized endothelial cells of the human choroid plexus under consideration of the Wnt signaling pathway

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Endothelial cells act as important regulators of vascular permeability and angiogenesis, and supply surrounding tissues with required nutrients. They exist in a highly distinct heterogeneity, ensuring optimal adaptation to the different needs of these tissues. The vessels of the human choroid plexus (CP), a cellular convolute located in the brain ventricles whose epithelial cells mainly contribute to the formation of the blood-cerebrospinal fluid (CSF) barrier (BCSFB), have fenestrated endothelial cells. By ectopic expression of human telomerase reverse transcriptase (hTERT) in primary human CP endothelial cells (HCPEnC) we recently generated immortalized HCPEnC (iHCPEnC). To determine the similarity of iHCPEnC to the primary cells in more detail, we compared primary cells of the sixth passage (HCPEnC p6) with a lower (p20) and a higher passage (p50) of iHCPEnC by transcriptome analysis via massive analysis of cDNA ends (MACE). A very high concordance of HCPEnC and iHCPEnC was observed, as only small proportions of the transcripts examined were significantly altered, supporting the suitability of iHCPEnC as an in vitro model of the CP endothelium. Differentially expressed genes (DEG) were identified and assigned to potentially affected biological processes by gene set enrichment analysis (GSEA). Several of the identified DEG were endothelium-relevant, including representatives of the Wnt signaling pathway. Although various components of the Wnt signaling pathway were detected in HCPEnC as well as iHCPEnC, activation of Wnt signaling was only marginal, supporting down-regulation of β-catenin (CTNNB) signaling in CP endothelial cells. Our results support the suitability of iHCPEnC for use in in vitro models of BCSFB investigations.

overall_design: The vasculature of the human choroid plexus is built by human choroid plexus endothelial cells (HCPEnC). To determine whether immortalized HCPEnC (iHCPEnC) exhibit stable gene expression across advanced passages, two different passages were analyzed by MACE. A lower passage of primary HCPEnC (p6; "HCPEnC p6") as well as a low passage of immortalized iHCPEnC (p20; "iHCPEnC p20") and a higher passage of iHCPEnC (p50; "iHCPEnC p50") were examined. Three biological replicates of the primary cells and of each of the two different passages of iHCPEnC were included in the analysis.

first: Lea

last: Denzer

first: Walter

last: Muranyi

first: Rosanna

last: Herold

first: Carolin

last: Stump-Guthier

first: Hiroshi

last: Ishikawa

first: Horst

last: Schroten

first: Christian

last: Schwerk

first: Stefan

last: Weichert


title: MicroRNA profiling identifies miR-2355-5p as a key modulator in Renal Cell Carcinoma tumor growth

city: Moncton

first: Eric

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

institute: Vitalité Health Network

summary: Inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene is one of the first truncal event in  clear cell Renal Cell Carcinoma (ccRCC) tumorigenesis. Accumulation of the Hypoxia Induced Factors (HIFα)  acquired from VHL loss can promote ccRCC tumorigenesis through regulating microRNAs (miRNA)  expression. Here, we performed a miRNA profiling and used high throughput analysis to identify a panel  of VHL dependent miRNAs in ccRCC. Validation of these miRNAs uncovered overexpression of miR-2355-5p  in ccRCC cell models, and primary tumors. Moreover, we showed a significant increase of circulating  miR-2355-5p in plasma from patients with ccRCC. Mechanistically, miR-2355-5p overexpression was confirmed  to be HIF-2α-dependent. Indeed, targeting miR-2355-5p with the CRISPR/cas9 system did not only negatively  disturbed ccRCC cell’s ability to stimulate angiogenesis, but also decreased cell proliferation and drastically  reduced tumor growth in mice xenograft models. Finally, miR-2355-5p pulldown assay identified five tumor  suppressor genes, ACO1, BTG2, CMTM4, SLIT2, and WDFY2, as potential targets. All five genes were significantly  downregulated in ccRCC tumors and mice xenograft tumors. Results from this research demonstrate the oncogenic  ability of miR-2355-5p and shed light on the possible route in which the miRNA controls angiogenesis and tumor  growth in VHL-deficient ccRCC

overall_design: To identify RNA targets of both miR-2355-5p and miR-1271-5p in ccRCC tumors, we performed a miRNA Pulldown assay in 786-0 cells. Biotinylated synthetic miRNA duplexes were transfected into 786-0 cells for 48h in triplicates. Biotinylated miRNA and bind RNA were retrieved and analyzed through sequencing platform. Enrich RNA transcripts were labeled as potential miRNA targets.

first: Patric

last: Page

first: Sandra

last: Turcotte

first: Tamiko

last: Nishimura

first: Yasser

last: Riazalhosseini


title: Effect of iron exposure on the gene expression profile of human brain vascular pericytes.

city: Erlangen

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

summary:
We hypothesize blood breakdown products present after hemorrhage to be inducers of brain edema via the ferroptosis-induced cell death of pericytes leading to comprimised blood-brain-barrier.
RNAseq was applied to investigate the intracellular response of  pericytes to iron exposure from cerebral hemorrhage.

overall_design: Differential gene expression analysis of RNA-seq data for pericytes treated with Ammonium iron (II) sulfate hexahydrate (AE2S) or iron (III) chorid (FeCl3) compared with medium only.

first: Stefanie

last: Balk

first: Maximilian

last: Sprügel

first: Franziska

last: Panier

first: Arif

middle: B

last: Ekici

first: Hagen

last: Huttner


title: Dietary tyramine promotes colon cancer risk and development via increased DNA damage and enhanced inflammation [ApcMin/+]

city: London

first: Maria

last: Glymenaki

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: High consumption of dietary red or processed meat and fat are linked to increased risk of colorectal cancer (CRC). A number of potential mechanisms have been reported, such as the presence of dietary carcinogenic compounds, and elevated gut microbial degradation of proteins and glycoproteins. Tyramine is a commonly found biogenic amine in processed food and can also be produced by the gut microbiota from the dietary amino acid tyrosine. The role of tyramine in intestinal mucosal health and CRC tumorigenesis has not been well studied. Therefore, we used the human colorectal HCT116 cell line and the ApcMin/+ mouse model to investigate the role of tyramine in CRC.

overall_design: ApcMin/+ and WT mice at 6 weeks of age were oral gavaged daily with sterile-filtered tyramine solution at 3.2 mM and pH=7.01 (Sigma-Aldrich) or water for 7 weeks. We culminated the experiment at 13 weeks of age of mice, which represents an early stage of disease based on the previous survival analysis in ApcMin/+ mice that showed a drop in survival after 18-20 weeks of age (Curio et al., 2022).

first: Jia

middle: V

last: Li


title: Gene expression profile at single cell level of immune cells from STING-NP treated 4T1 BALB/c tumors

city: Chicago

first: Tony

last: Pan

address: 5801 S Ellis Ave

institute: University of Chicago

summary: scRNA-seq was performed on immune cells isolated from 4T1 BALB/c tumors to investigate their response to various treatments.

overall_design: Cells from tumor suspension were washed and labeled with anti-CD45 antibodies (to label immune cells) and Total-seq anti-mouse Hashtag antibodies (for multiplexing) and sorted prior to scRNA-seq


title: Dietary tyramine promotes colon cancer risk and development via increased DNA damage and enhanced Inflammation [HCT116]

summary: High dietary consumption of red or processed meat is associated with increased risk of colorectal cancer (CRC), likely through the presence of dietary carcinogens. Tyramine is a biogenic amine commonly found in processed food and can be produced by the gut bacteria from tyrosine. However, the role of tyramine in intestinal mucosal health has not been studied. Therefore, we used the human colonic HCT116 cell line to investigate the role of tyramine in modulating CRC risk and development

overall_design: We treated HCT116 cells with two concentrations of tyramine, 1.2 and 1.6mM, for 24hrs to understand the molecular mechanisms involved. Gene expression profiling analysis was performed using RNA-seq.


title: Dietary tyramine promotes colon cancer risk and development via increased DNA damage and enhanced Inflammation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Hi-C  of  motor neurons under simulated microgravity (SMG) and normal gravity (NG)

city: 武汉市

first: yang

last: fei

address: 狮子山街道

institute: 无

summary: We differentiated motor neuron progenitor cells through small molecule combination and put them under microgravity and normal gravity respectively, and then performed gene expression profiling analysis using data obtained from RNA-seq of cells from 2 different group.

overall_design: HiC

first: Danxia

last: Huang

first: Fei

last: Yang


title: Genome-wide deciphering the translation ratio of hESCs under OCT4 siRNA treatment and hypoxia by RNC-seq

city: Hangzhou

first: Yingjie

last: Wang

state: Zhejiang

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

institute: Zhejiang University

summary: We set out experiment to systematically decipher the translation ratio of hESCs under OCT4 siRNA treatment and hypoxia by RNC-seq.

overall_design: RNA-seq and RNC-seq were carried out on hESCs samples under OCT4 siRNA treatment and hypoxia.

first: Bo

last: Kang


title: Single-cell RNA sequencing of inguinal and gonadal adipose stromal vascular fractions from wild-type C57BL/6J mice

city: changsha

first: Hui

last: Xie

state: hunan

address: #87 Xiangya Road

department: Orthopedics

institute: Central South University

summary: Endothelial cells (ECs) have been reported to be a source of adipose tissue-derived stromal cells (ADSCs), and ADSCs expressing endothelial markers have been suggested to originate from ECs. To further investigate the lineage relationship between ECs and ADSCs in postnatal mice, we performed single-cell RNA sequencing (scRNA-seq) on ECs and ADSCs isolated from inguinal and gonadal white adipose tissues (IWATs and GWATs) of 12-week-old wild-type C57BL/6J mice, and analyzed the expression of endothelial markers in ADSCs.

overall_design: We profiled ECs and ADSCs from mouse IWATs and GWATs using scRNA-seq. Overall, IWATs and GWATs of 12-week-old wild-type mice were collected and digested with a mixture of collagenase, dispase and DNase. Subsequently, the stromal vascular fractions of the samples were subjected to lineage positive cell depletion by fluorescence-activated cell sorting (FACS). Cells positive for B220, Ter119, Gr-1, CD11b, CD3e, CD45, CD71, CD3, CD19 were depleted. Finally, we analyzed ADSCs expressing endothelial markers Pecam1, Cdh5, Tek, and Emcn in the scRNA-seq analysis, and validated these findings with EC lineage tracing models, flow cytometry, and immunostaining analyses.


title: Evaluation of the effect of morphine and maternal immune activation on pigs

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

summary: Female and male pigs were studied. Half of the pigs were exposed to immune activation from virally-infected mothers, and half were not exposed. At 17 days of age half the pigs were injected with morphine for 4 days and the remainder with saline.

overall_design: RNA samples were obtained at 21 days of age. The prefrontal cortex samples were subjected to paired-end RNA sequencing.


title: The Gut-larynx Axis and its Contribution to Laryngeal Immunity

status: Public on Mar 04 2025

city: Madison

first: Yixuan

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

summary: The larynx is essential for swallowing, breathing, coughing, and voice production, supported by its unique microbial and immunological environment. Our previous research highlighted the role of resident laryngeal microbiota in shaping local immune responses. With growing interest in the gut-lung axis—the bidirectional communication between gut and respiratory immunity—the potential influence of gut microbiota on laryngeal immunity warrants exploration. We hypothesized that a gut-larynx axis may exist, where both resident laryngeal and gut microbiota contribute to immune modulation in the larynx. To investigate this, we treated conventionally raised, wild-type C57BL/6J mice with an oral antibiotic regimen known to disrupt gut microbiota, comparing them to untreated controls. Following treatment, the gut microbiota was significantly disrupted, while the laryngeal microbiota remained largely unchanged. However, antibiotic-treated mice exhibited marked changes in epithelial and immune cell proportions, as well as fibroblasts. Differential gene expression across cell types highlighted pathways related to epithelial barrier integrity, immune signaling, and bacterial response. Additionally, gut dysbiosis affected gene regulatory networks, with the activity of regulons Etv4(+), Irf3(+), Hltf(+), Mga(+), and Nfil3(+) showing significant changes. Notably, cell-cell communication was also altered, especially in immune-epithelial interactions, with integrin-mediated signaling emerging as a key ligand-receptor pathway in these intercellular communications. These findings suggest that gut and laryngeal microbiota may work synergistically to modulate immune responses in the larynx, underscoring the importance of considering gut-larynx interactions in studies of respiratory immunity.

overall_design: We have two experimental conditions: antibiotics treated mice and untreated control mice. Each moue group has 6 biological replicates (3 males, 3 femles). Each biological replicate was a pool of three male/female mosue larynges.

first: Ran

last: An

first: Elliot

first: John

last: Binns

first: Federico

last: Rey

first: Christina

last: Kendziorski

first: Susan

last: Thibeault


title: The first application of biological pretreatment in Chinese spirits, utilizing cellulose-degrading probiotics from Jiangshui to improve the quality of Highland Barely Liquor

city: Lanzhou

first: Zemin

state: Gansu

address: Lanzhou university

institute: Lanzhou university

summary: Highland barley liquor is a distilled spirit made from highland barley on the Tibetan Plateau, but its alcohol yield is limited by the high fiber content of the raw material. In the field of biomass resources, functional microorganisms are commonly used in pretreatment to degrade cellulose and other substances, improving fermentation output. In this study, we isolated the cellulose-degrading probiotic Lactobacillus delbrueckii GR-8 (CMCase 6.21 U/mL) from the traditional vegetable-based fermented food "Jiangshui" and applied biological pretreatment to the fermentation of highland barley liquor. During pretreatment, probiotics enhanced cellulase and amylase activities in the fermented grains, resulting in a 25% reduction in cellulose content and a 112% increase in free reducing sugar content. The pretreatment significantly altered the microbial community structure, enhancing microbial diversity. After distillation, alcohol yield increased by 3.5%, and total acid and ester contents rose by 25% and 23%, respectively. Pyrazine compounds increased by 1290%, while higher alcohols like nonanol, phenylethanol, and hexanol decreased. The treated liquor caused less harm to mice, who showed improved memory, motor skills, and lower oxidative liver damage. This study demonstrates that biological pretreatment enhances both fermentation and the quality of Chinese spirits.

sample_organism:
fermentation metagenome
mouse metagenome

overall_design: Probiotics Lactobacillus delbrueckii were used for pretreatment before highland barely liquor fermentation, and fermented grain samples were collected on the first day of fermentation, the third and seventh days of pretreatment, and the 1st, 4th, 13th, and 26th days of formal fermentation, and the bacterial and fungal communities were determined by the method of measuring the bacterial V3V4 region, and the fungi were determined by measuring the ITS sequence. In addition, the mice were given fermented and distilled barley liquor by gavage, and the bacterial flora structure of the cecal contents was determined after three days of feeding.

first: Xiangkai


title: Comprehensive Molecular Profiling of Combined Hepatocellular Carcinoma and Cholangiocarcinoma reveals Distinct Notch Signaling Subgroups with Prognostic Significance

city: Suwon-si

first: chanmo

last: yang

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu, Song Jae-gwan 207-5

department: Department of Pathology

institute: Ajou University School of Medicine

summary: Combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CCC) exhibits distinct Notch signaling activation patterns, with elevated Notch1 and downstream target expression compared to HCC and CCC. Stratification into three subgroups based on Notch1 and Hes5 expression revealed that Notch-responsive tumors (high Notch1 and Hes5) demonstrated aggressive biological behavior, poor prognosis, and molecular profiles resembling CCC. These findings underscore the heterogeneity of cHCC-CCC and suggest that Notch1 and Hes5 serve as potential biomarkers for risk stratification and therapeutic targeting, particularly for Notch pathway and immune checkpoint inhibitors.

overall_design: This study involved the molecular profiling of combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CCC), hepatocellular carcinoma (HCC), and cholangiocarcinoma (CCC). RNA sequencing and immunohistochemical staining were performed to assess Notch signaling activation. Samples were categorized into three subgroups based on Notch1 and Hes5 expression levels.

first: Chan Mo

first: Jaehong

last: Lim

first: Myung-Giun

last: Noh

first: Taebum

last: Lee

first: Sangjoon

last: Choi

first: Ara

last: Ko

first: Young-Bae

last: Kim

first: Dakeun

first: Seokhwi


title: Revealing Novel Roles of TLR4 In Macrophage Immunity and Macrophage-Pulmonary Vascular/Lymphatic Endothelial Cell Interactions in Sepsis

city: Pittsburgh

first: Jie

last: Fan

address: 200 Lothrop Street

department: Department of Surgery

institute: University of Pittsburgh School of Medicine

summary: In sepsis, acute lung injury (ALI) is a severe complication and a leading cause of death, involving complex mechanisms that include cellular and molecular interactions between immune and lung parenchymal cells. In recent decades, the role of Toll-like receptor 4 (TLR4) in mediating infection-induced inflammation has been extensively studied. However, how TLR4 facilitates interactions between innate immune cells and lung parenchymal cells in sepsis remains to be fully understood. This study aims to explore the role of TLR4 in regulating macrophage immunity and metabolism in greater depth. It also seeks to reveal how changes in these processes affect the interaction between macrophages and both pulmonary endothelial cells (ECs) and lymphatic endothelial cells (LECs). Using TLR4 knockout mice and the combined approaches of single-cell RNA sequencing and experimental validation, we demonstrate that in sepsis, TLR4-deficient macrophages upregulate Abca1, enhance cholesterol efflux, and reduce glycolysis, promoting M2 polarization and attenuating inflammation. These metabolic and phenotypic shifts significantly affect their interactions with pulmonary ECs and LECs. Mechanistically, we uncovered that TLR4 operates through multiple pathways in endothelial dysfunction: macrophage TLR4 mediates inflammatory damage to ECs/LECs, while endothelial TLR4 both directly sensitizes cells to lipopolysaccharide-induced injury and determines their susceptibility to macrophage-derived inflammatory signals. These findings reveal the complex role of TLR4 in orchestrating both immune-mediated and direct endothelial responses during sepsis-induced ALI, supporting that targeting TLR4 on multiple cell populations may present an effective therapeutic strategy.

overall_design: These cells were isolated from the lungs of Tlr4-/- mice at 24 hours post-CLP and sham procedures.

first: Yu

last: Fu

first: Ting

last: Gong

first: Patricia A

last: Loughran

first: Yuehua

last: Li

first: Timothy R

last: Billiar

first: Youtan

last: Liu

first: Zongmei

last: Wen


title: Small RNA Sequencing in Polytrauma Patients: High vs. Low Troponin T Levels

city: Frankfurt

first: Jiaoyan

last: Han

address: Theodor-Stern Kai 7

department: Department of Trauma Surgery and Orthopedics

institute: Goethe University Frankfurt, University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, small RNA sequencing was performed on plasma samples from 10 polytraumatized patients (Injury Severity Score, ISS ≥ 16), who were stratified into two groups based on their initial Troponin T (TnT) levels at the emergency room. The high TnT group (n = 5) included patients with TnT concentrations > 50 pg/mL, while the low TnT group (n = 5) included those with TnT concentrations < 12 pg/mL. The aim of this dataset is to identify differentially expressed miRNAs associated with elevated TnT levels, a marker of cardiac injury in trauma patients. Differential expression analysis revealed several candidate miRNAs that may serve as potential biomarkers for cardiac dysfunction. This dataset highlights the diagnostic potential of miRNAs in post-trauma cardiac injury.

overall_design: Small RNA sequencing profiling of plasma samples from polytraumatized patients stratified into high- and low-Troponin T groups to identify miRNAs associated with cardiac injury.

first: Liudmila

last: Leppik

first: Birte

last: Weber


title: Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation.

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: RNA-Sequencing of onion bulbs exposed to managed stress

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: The goal of this study was to compare differentially expressed transcripts in onion bulbs induced in response to managed stress under field conditions using transcriptome profiling (RNA-seq). The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)  and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (variety Matahari) in response to nitrogen stress under optimal water identified 3092 and 2204 Differentially Expressed Genes (DEGs) unique genes under optimal nitrogen vs low nitrogen. while under sub-optimal nitrogen, 2770 and 2198 unique genes were identified under optimal nitrogen vs low nitrogen respectively.

overall_design: Methods: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs exposed to managed stresses (nitrogen and water) at the time of harvest. The samples collected from field were used for RNA extractions. For the nitrogen stress set of samples exposed to optimal water and nitrogen (HW_HN1, HW_HN2, HW_HN3) were compared to samples collected from optimal water and sub-optimal nitrogen (HW_LN4,HW_LN5,HW_LN6). Likewise, samples collected from sub-optimal water under optimal nitrogen (LW_HN7, LW_HN8,LW_HN9) were compared to sub-optimal nitrogen (LW_LN10, LW_LN11,LW_LN123). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount


title: Hepatic stellate cells regulate liver fatty acid utilization via plasmalemma vesicle-associated protein [snRNA-seq]

city: Odense M

first: Daniel

last: Hansen

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: The liver is essential for normal fatty acid utilization during fasting. Circulating fatty acids are taken up by hepatocytes and esterified as triacylglycerols for either oxidative metabolization and ketogenesis or export. Whereas the regulation of fatty acid oxidation in hepatocytes is well understood, the uptake and retention of non-esterified fatty acids by hepatocytes is not. Here, we show that murine hepatic stellate cells (HSCs) and their abundantly expressed plasmalemma vesicle-associated protein (PLVAP) control hepatic substrate preference for fasting energy metabolism. HSC-specific ablation of PLVAP in mice elevated hepatic insulin signaling and improved glucose tolerance. Fasted HSC PLVAP knockout mice showed suppressed hepatic fatty acid esterification to di- and triacylglycerols shifting fasting metabolism from fatty acid oxidation to reliance on carbohydrates. By super-resolution microscopy we localized HSC PLVAP to caveolae residing along the sinusoidal lumen supporting a role for HSCs and PLVAP-diaphragmed caveolae in normal fasting metabolism of the liver.

overall_design: 10x Genomics single-nucleus RNA-sequencing of fasted littermate control and HSC-Plvap knockout mice

first: Kim

last: Ravnskjaer


title: Genome-wide loop structure analysis in HGC27 gastric cancer cell.

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

institute: Chiba University

summary: We analysed loop structure between gene promoters and enhancers in HGC27 cell using H3K27ac HiChIP.

overall_design: Hi-C experiments in HGC27 gastric cancer cell.

first: Atsushi

last: Okabe

last: Kaneda