title: Glucose-driven histone lactylation promotes the immunosuppressive activity of monocyte-derived macrophages in brain tumors [RNA-seq]

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Macrophages are critical components of the immunosuppressive microenvironment that restrict anti-cancer immunity in glioblastoma (GBM). However, how GBM shapes the regulatory function of macrophages remains elusive. Here, we report that monocyte-derived macrophages (MDM), but not yolk-sac derived microglia (MG), exhibited potent immunosuppressive activity, which was mediated by a population of glycolytic GLUT1+MDM, in an IL10-dependent manner. GBM-derived factors reprogrammed MDM towards glycolytic cells with enhanced avidity for glucose, which was mostly used to generate lactate. In turn, intracellular lactate caused lactylation of histone lysine residues that promoted MDM immunosuppressive activity via regulation of Il10 expression. GBM-primed activation of PERK supported glucose metabolism and regulated GLUT1 expression through ATF4 in MDM. PERK-deletion in MDM abrogated histone lactylation and suppressive activity, thereby promoting polyfunctional T cell-infiltration of tumors. In combination with immunotherapy, PERK-deletion blocked GBM progression. Our study demonstrates that glucose-driven histone lactylation controls MDM immunosuppressive function; all in a PERK-dependent manner.

overall_design: To dissect the mechanism responsible for the immunosuppression activity of macrophage, RNA-seq comparing transcriptomic profile of MG (F4/80+CD11b+CD45loLY6Clo/-LY6G-CD49dlo/-) versus BMDM (F4/80+CD11b+CD45+LY6Clo/-LY6G-CD49dhigh) was performed. MG and BMDM were FACS-sorted from isogenic GL261 brain tumors established orthotopically in the mouse brain.

first: Filippo

last: Veglia

first: Xiaoqing

last: Yu


title: Transcriptome analysis of Escherichia coli TO114 under salt stress

status: Public on May 06 2024

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

country: Japan

institute: Meijo University

type: Expression profiling by high throughput sequencing

summary: Here, we treated Escherichia coli strain TO114 expressing a halotolerant cyanobacterium Halothece sp. PCC7418-derived NhaC Na+/H+ antiporter (H2569) with salt stress (0.4 M NaCl) and performed RNA sequencing analysis.

overall_design: E. coli cells were subjected to salt stress. Then, total RNA was extracted and analyzed by RNA-seq analysis.

first: Rungaroon

last: Waditee-Sirisattha


title: IL-1β inhibition partially negates the beneficial effects of diet-induced lipid lowering

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

country: USA

institute: University of Virginia

summary: Thromboembolic events secondary to rupture or erosion of advanced atherosclerotic lesions are the leading cause of death in the world. The most common and effective means to reduce these major adverse cardiovascular events (MACE), including myocardial infarction (MI) and stroke, is aggressive lipid lowering via a combination of drugs and dietary modifications. However, little is known regarding the effects of reducing dietary lipids on the composition and stability of advanced atherosclerotic lesions, the mechanisms that regulate these processes, and what therapeutic approaches might augment the benefits of lipid lowering.

overall_design: scRNA-seq of atherosclerotic plaques of Apoe-/- mouse (with or without specific SMC with Ab or IgG against Il1b)

first: Santosh

last: Karnewar

first: Vaishnavi

first: Rebecca

last: Deaton

first: Laura

middle: S

last: Shankman

first: Ernest

middle: D

last: Benavente

first: Corey

middle: M

last: Williams

first: Xenia

last: Bradley

first: Gabriel

middle: F

last: Alencar

first: Gamze

middle: B

last: Bulut

first: Sara

last: Kirmani

first: Richard

middle: A

last: Baylis

first: Eli

middle: R

last: Zunder

first: Hester

last: den Ruijter

first: Gerard

last: Pasterkamp


title: Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Schizophrenia affects approximately 1% of the world population. Genetics, epigenetics, and environmental factors are known to play a role in this psychiatric disorder. While there is a high concordance in monozygotic twins, about half of twin pairs are discordant for schizophrenia. To address the question of how and when concordance in monozygotic twins occur, we have obtained fibroblasts from two pairs of schizophrenia discordant twins (one sibling with schizophrenia while the second one is unaffected by schizophrenia) and three pairs of healthy twins (both of the siblings are healthy). We have prepared iPSC models for these 3 groups of patients with schizophrenia, unaffected co-twins, and the healthy twins. When the study started the co-twins were considered healthy and unaffected but both the co-twins were later diagnosed with a depressive disorder. The reprogrammed iPSCs were differentiated into hippocampal neurons to measure the neurophysiological abnormalities in the patients. We found that the neurons derived from the schizophrenia patients were less arborized, were hypoexcitable with immature spike features, and exhibited a significant reduction in synaptic activity with dysregulation in synapse-related genes. Interestingly, the neurons derived from the co-twin siblings who did not have schizophrenia formed another distinct group that was different from the neurons in the group of the affected twin siblings but also different from the neurons in the group of the control twins. Importantly, their synaptic activity was not affected. Our measurements that were obtained from schizophrenia patients and their monozygotic twin and compared also to control healthy twins point to hippocampal synaptic deficits as a central mechanism in schizophrenia

overall_design: iPSCs were derived from fibroblasts from monozygotic twins discordant for schizophrenia and a control group of healthy twins were differentiated into neural progenitor cells (NPCs), 2 months, and 4 months in vitro neurons.

first: Shanni

last: Stern

first: Lei

last: Zhang

first: Meiyan

last: Wang

first: Fed

middle: H

last: Gage


title: Glucose-driven histone lactylation promotes the immunosuppressive activity of monocyte-derived macrophages in glioblastoma

first: jiqiang

last: yao

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To assess the impact of metabolsim on gene expression and consequently on cell function, ATAC-seq analysis  of MG (F4/80+CD11b+CD45loLY6Clo/-LY6G-CD49dlo/-) versus BMDM (F4/80+CD11b+CD45+LY6Clo/-LY6G-CD49dhigh) was performed. MG and BMDM were FACS-sorted from isogenic SB28 brain tumors established orthotopically in the mouse brain.

first: Filippo

last: Veglia

first: Xiaoqing


title: Egr1 is a master regulator of regenerative senescence and cardiac repair

city: Rehovot

first: Lingling

address: Yavne Street 68, 68

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Senescence plays a key role in various physiological and pathological processes. We reported that injury-induced transient senescence correlates with heart regeneration, yet the multi-omics profile and molecular underpinnings of regenerative senescence remain obscure. Using proteomics and single-cell RNA-sequencing, here we report the regenerative senescence multi-omic signature in the adult mouse heart and establish its role in neonatal heart regeneration and Agrin-mediated cardiac repair in adult mice. We identified early growth response protein 1 (Egr1) as a regulator of regenerative senescence in both models. In the neonatal heart, Egr1 facilitates angiogenesis and cardiomyocyte proliferation. In adult hearts, Agrin-induced senescence and repair require Egr1, activated by the integrin/FAK-ERK/Akt1 axis in cardiac fibroblasts. We also identified cathepsins as injury-induced senescence-associated secretory phenotype (SASP) components that promote ECM degradation and potentially assist in reducing fibrosis. Altogether, we uncovered the molecular signature and functional benefits of regenerative senescence during heart regeneration, with Egr1 orchestrating the process.

overall_design: Single-cell RNA sequencing (scRNA-seq) was conducted on Egr1 wildtype and knockout mice treated with PBS or Agrin following myocardial infarction. Single cell isolation was prepared through gentleMACS dissociation, debris removal, red blood cell (RBC) lysis, followed by enrichment for macrophages and endothelial cells using CD45 and CD31 microbeads. 75% of single cells were collected from CD45 and CD31-depleted cells, and 25% of single cells were obtained from CD45 and CD31-enriched cells for sequencing.

first: Jacob

last: Elkahal

first: Tianzhen

first: Racheli

last: Rimmer

first: Alexander

last: Genzelinakh

first: Elad

last: Bassat

first: Jingkui

first: Dahlia

last: Perez

first: Daria

last: Lendengolts

first: Roni

last: Winkler

first: Hanna

last: Bueno-levy

first: Kfir

last: Umansky

first: Avraham

last: Shakked

first: Shoval

last: Miyara

first: Avital

last: Sarusi-Portuguez

first: David

last: Morgenstern

first: Yishai

last: Levin

first: Yoseph

last: Addadi

first: Baoguo

last: Li

first: Varda

last: Rotter

first: Valery

last: Krizhanovsky

first: Elly

last: Tanaka

first: Rachel

last: Sarig

first: Eldad

last: Tzahor


title: A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT&RUN 22]

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

summary: During development neural stem cells (NSCs) in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Shh signaling promotes cortical RGCs to switch lineage to generate cortical oligodendrocytes and OB interneurons. During this lineage switch, cortical RGCs generate intermediate progenitor cells (IPCs) that express Ascl1, Egfr and Olig2, genes critically regulating gliogenesis. The timing of increased Ascl1 expression and the appearance of Egfr+ and Olig2+ cortical progenitors is concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Further, the transcriptional regulation of Olig2 and Egfr has not been explored. Here we show that in cortical progenitor cells, multiple genetic programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple distal enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.

overall_design: ChIp-seq using Gli3 antibodies and wild-type cortical tissue, CUT&RUN using antibodies for H3K4me3, H3K27me3,and H3K27ac and cortical tissues from wild-type, Smo cko, and Smo M2 micce, ATAC-seq for wild-type cortical cells and cortical cells after in utero electroporation of pCAG-ShhN plasmids.

first: Xiaoyi

middle: G

last: Liang

first: Kendy

last: Hoang

first: Yue

last: Zhang

first: Sol

last: Katzman


title: Six1 regulates mouse lower incisor development by coordinating Dlx1/2/5 [scRNA-seq]

city: Shanghai

first: Songyuan

last: Luo

state: --None--

address: 639 Zhi-Zao-Ju Road

country: China

institute: Shanghai Ninth People’s Hospital

summary: Tooth development is a complex process orchestrated by intricate gene regulatory networks, involving both odontogenic epithelium and ectomesenchyme. Six1, a pivotal transcription factor (TF), is involved in the development of the lower incisor. However, its precise role during incisor development and the molecular mechanisms underpinning its regulatory functions remain poorly understood. This study employs Six1 deletion mouse models to elucidate the critical regulatory role of Six1 in governing dental mesenchyme development. By performing single-cell RNA sequencing (scRNA-seq), we constructed a comprehensive transcriptome atlas of tooth germ development from the bud to bell stage. Our analyses suggest that the dental follicle (DF) and the dental papilla (DP) are differentiated from dental ectomesenchyme (DEM), and identify the key transcription factors (TFs) underlying these distinct states. Notably, we show that Dlx1, Dlx2, and Dlx5 (Dlx1/2/5) may function as the key TFs that promote the formation of DP. We further show that the deletion of Six1 perturbs dental mesenchyme development by impeding the transitions from DEM to DP states. Importantly, SIX1 directly binds to the promoters of Dlx1/2/5 to promote their co-expression, which subsequently leads to widespread epigenetic and transcriptional remodeling. In summary, our findings unveil Six1's indispensable role in incisor development, offering key insights into transcription factor-driven regulatory networks that govern dental mesenchyme cell fate transitions during tooth development.

overall_design: Single-cell transcriptomes were obtained from the digestion of the incisor germs at E14.5, E15.5, and E16.5.

first: Shuai

last: Wang

first: Zhixu

last: Liu

first: Qian

last: Bian

first: Xudong


title: A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT&RUN]


title: Six1 regulates mouse lower incisor development by coordinating Dlx1/2/5 [CUT&Tag]

overall_design: H3K27ac CUT&Tag assay for E15.5 Six1+/+ and Six1-/- mouse incisor dental germ cells;  SIX1 CUT&Tag assay for E12.5 wide-type  mouse incisor dental germ cells


title: Characterization of neutrophil extracellular trap-associated RNA, a novel DAMP acting in concert with the antimicrobial peptide LL37 as intentional but self-limiting drivers of inflammation

city: Tübingen

first: Marissa

last: Dubbelaar

address: Auf der Morgenstelle 15

department: Peptide-based Immunotherapy

country: Germany

institute: University and University Hospital Tübingen

summary: Neutrophil extracellular traps (NETs) are a key antimicrobial feature of cellular innate immunity mediated by polymorphonuclear neutrophils (PMNs). NETs trap and kill microbes but have also been linked to inflammation in atherosclerosis, arthritis, or psoriasis by unknown mechanisms. We here report that NET-associated RNA (naRNA, which was RNA-sequenced from human primary neutrophil NETs here) stimulated further NET formation in naïve PMNs via a unique TLR8-NLRP3-caspase-1-gasdermin D-dependent inflammasome pathway. Keratinocytes also responded to naRNA with expression of psoriasis-related genes (e.g. IL17, IL36) via atypical NOD2-RIPK signaling. In vivo naRNA drove skin inflammation, which was drastically ameliorated by genetic ablation of RNA sensing. The naRNA-LL37 ‘composite DAMP’ was pre-stored in resting neutrophil granules, defining sterile NETs as intentionally inflammatory webs that amplify neutrophil activation. However, the activity of the naRNA-LL37 DAMP was transient and hence supposedly self-limiting under physiological conditions. Only upon dysregulated NET release like psoriasis, TLR-NLRP3-mediated naRNA sensing may represent both potential cause of disease and new intervention target.

overall_design: Briefly, NETs were prepared by 600 nM PMA treatment for 4 h at 37°C and 5% CO2, or cells were left untreated during the incubation as the mock control.

first: Francesca

last: Bork

first: Alexander

middle: N

last: Weber


title: A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [ATAC-seq]


title: Necroptosis enhances “Don’t eat me” signal and induces macrophage extracellular traps to promote pancreatic cancer liver metastasis

city: Fuzhou

first: Chengyu

last: Liao

state: Fujain

address: 134, east road

department: Shengli Clinical Medical College

institute: Fujian Medical University

summary: We delved into the consequences of METs formation. We treated wild-type PANC-1 with METs-containing CM and performed RNA-seq.

overall_design: Wild-type PANC-1 cells treated by co-cultured CM derived from Panc1-oe-Vector with macrophage and  co-cultured CM derived from Panc1-oe-MLKL with macrophage for 72h.

first: Fengping

last: Kang

first: Zuwei

first: Shi


title: Unraveling CD4+ T Cell Diversity in Abdominal Aortic Aneurysms

city: Wuhan

first: Wangling

last: Hu

state: Hubei

address: 湖北省武汉市江汉区万松园横路圣淘沙大厦B栋2410

institute: Wuhan union hospital

summary: We conducted single-cell RNA sequencing (scRNA-seq) on CD4+ T cells of the aneurysmal aorta and the corresponding splenic cells, in order to unveil the diversity of CD4+ T Cell in Abdominal Aortic Aneurysms.

overall_design: The mouse model of abdominal aortic aneurysm was established, and the spleen was sampled 14 days later to prepare a single cell suspension. CD4+ T cells were sorted by flow cytometry and subsequently analyzed using scRNA-seq.

first: Luna

last: Zhai

first: Jingyong

last: Li

first: Dan

first: Ni

last: Xia

first: Tingting

last: Tang

first: Shaofang

last: Nie

first: Min

first: Jiao

last: Jiao

first: Bingjie

last: Lv

first: Fen

last: Yang

first: Yuzhi

last: Lu

first: Lingfeng

last: Zha

first: Xiajun

first: Shuang

last: Wen

first: Desheng

first: Li

first: Weimin

first: Xiang

last: Cheng


title: Multimodal measurement of the transcriptome and proteome in single cells using nanoSPLITS

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

summary: We report the development of a method (nanoSPLITS) capable of performing global proteome and transcriptome measurements from the same single-cell.

overall_design: scRNAseq data of single human pancreatic islets in parallel with scProteomic analysis.

first: Meng

last: Markillie

first: Hugh

last: Mitchell

first: Kristin

last: Engbrecht

first: William

last: Chrisler

first: Ying

last: Zhu


title: Effects of csr-1 knockdown on gene expression and mRNA splicing

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

summary: The Integrator is an evolutionarily conserved protein complex that functions to process the 3’ maturation of small nuclear RNA molecules that are an essential part of the spliceosome. We performed a genome-wide RNAi screen in the C. elegans system and identified csr-1 as an essential gene required for this process. Knockdown of csr-1 activates an snRNA misprocessing reporter and causes aberrant 3’ cleavage of several endogenous snRNA transcripts. Using whole-transcriptome RNA sequencing, we evaluated the effects of csr-1 knockdown via RNAi relative to empty vector control and found that knockdown of csr-1 causes aberrant expression of various snRNA transcripts along with significant changes to alterantive splicing of ~400 transcripts. Overall, this experiment identified the role of csr-1 as a novel regulator of snRNA processing and profiled its impact on gene expression and alternatively splicing at the transcriptome level.

overall_design: Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq with Alternative splicing data analyzed by rMATS.

first: Brandon

last: Waddell


title: A proteome-wide screen identifies the calcium binding proteins, S100A8/S100A9, as clinically relevant therapeutic targets in aortic dissection: a translational study [scRNA-seq]

city: Hefei

first: Hui

last: Jiang

state: AnHui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

summary: S100A8 and S100A9 (aliases MRP8 and MRP14) are highly expressed in neutrophils and monocytes and are classified as damage-associated molecular pattern (DAMP) molecules or alarm molecules. However, the role of S100A8/A9 in aortic dissection has not been reported. In the present study, by employing an unbiased proteomics approach and RNA sequencing analysis , we found that the protein expression of calcium binding proteins S100A8/A9 were upregulated in the aorta and serum of TAAAD patients and also in a mouse model.

overall_design: We performed a single-cell RNA sequencing analysis of  aorta samples from mice AD model. AD model was established as follows: three-week-old male mice were conventionally fed normal chow and given BAPN (A3134, Sigma-Aldrich, St. Louis, Missouri, USA) in drinking water (1 g/kg/d)) for 4 consecutive weeks, and Paquinimod (ABR 25757, T7310, Targetmol, Shanghai, China) (10 mg/kg/d) was given via intragastric administration until experimental termination.

first: Suowen

last: Xu

first: Jianjun

last: Ge


title: Occupancy profiling of HAND2, MEIS2 and TCF4 by CUT&Tag from Neuroblastoma cells

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: HAND2, MEIS2 and TCF4 are master transcription factors (TFs) in neuroblastoma and create an interconnected core regulatory circuitry (CRC) by directly occupying each other's and their own super-enhancers (SEs), which leads to high levels of each TF expression inside the CRC. Additionally, CRC TFs cooperatively co-occupy the same SE components, which promotes the expression of genes involved in cell identity and cell-type-specific activities. Super-enhancer-mediated CRC enriched at key oncogenes in neuroblastoma. In the present study, CUT&Tag (Cleavage Under Targets and Tagmentation) analysis was performed to explore the target of HAND2, MEIS2 and TCF4 in NB cells.

overall_design: CUT&Tag using antibody against HAND2, MEIS2 and TCF4 in SK-N-BE(2) cells.

first: Ran

last: Zhuo

first: Jian

last: Pan


title: Single cell transcriptomic data of 12 samples collected from twins with Multicentric Castleman Disease and an unaffected sibling

city: Singapore

first: Jing Quan

last: Lim

address: 30 Hospital Boulevard

department: CMR

country: Singapore

institute: National Cancer Centre Singapore

summary: Idiopathic Multicentric Castleman Disease (iMCD) is a rare IL-6-driven hematological disorder characterized by systemic lymphadenopathy, elevated immunoglobulin levels, and prominent plasmacytosis in the bone marrow and lymph nodes. Here, we present an unusual occurrence of iMCD in identical twins. Using single cell sequencing, we identified nodal endothelial cells and fibroblastic reticular cells as the source of IL-6 signals. An “inflammatory” peripheral monocytosis enriched for the expression of S100A family genes was evident in both twins, as well as a group of monocytes expressing cytotoxic gene signatures in the affected twin with milder clinical manifestations.

overall_design: Single-cell RNA-seq (scRNAseq) libraries were prepared from tissue samples from Twin-CS (lymph node and bone marrow), as well as from peripheral blood mononuclear cells (PBMC) from the affected twins and unaffected sister. Tissues were dissociated into single cells using the Tumour Dissociation Kit, human (Miltenyi Biotec, Bergisch Gladbach, Germany) as per manufacturer’s protocol. To better examine the lymph nodal cells from Twin-CS, two additional independent libraries were generated and combined for downstream analysis.

first: Jason

middle: Y

last: CHAN


title: Soybean MKK2 establishes intricate signaling pathways to regulate soybean response to cyst nematode infection.

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

summary: To investigate the effect of overepxression of wild-type and kinase deactivated GmMKK2 on soybean trangenic hairy root gene expression

overall_design: Transcriptional profiles of WT-GmMKK2, KD-GmMKK2, and Williams 82 under Heterodera glycines HG Type 0 infected and noninfected with three replicates per treatment

first: Tracy

last: Hawk


title: Spatial transcriptomic data of a lymph node from an individual with Multicentric Castleman Disease

overall_design: To spatially resolve the transcriptome of the lymph node from Twin-CS, we applied Spatial Enhanced Resolution Omics-Sequencing (Stereo-seq), involving the use of DNA nanoball (DNB)-patterned arrays and in situ RNA capture. Stereo-seq provides a large field of view spatial transcriptomics at cellular resolution. The lymph node tissue was embedded with pre-chilled Tissue-Tek optimum cutting temperature (OCT) compound (Sakura, 4583) and snap-frozen in liquid nitrogen until the OCT was completely solid, before long term storage at -80°C. The tissue was cryosectioned at a thickness of 10 μm and then placed in a pre-chilled Stereo-seq capture chip, and libraries were prepared following the standard manufacturer's protocol as previously described (MiRXES, Singapore).

first: Jason Yongsheng

last: Chan


title: Multicentric Castleman Disease

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

overall_design: Refer to individual Series


title: Identification of endophenotypes supporting outcome prediction in hemodialysis patients based on mechanistic markers of statin treatment

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: Differentially expressed genes and molecular pathways were identified after statin treatment in kidney cells and assessed in plasma samples of the AURORA cohort.

overall_design: The impact of statin treatment on various kidney cells was evaluated to identify enriched molecular pathways after gene set enrichment analysis. Selected biomarkers were assessed in plasma samples.

first: Paul

last: Perco

first: Gert

last: Mayer


title: Dnmt3a1 regulates memory formation via the downstram target Nrp1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Epigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation whether individual Dnmts play unique or redundant functions in long-term memory formation is not well established. Furthermore, the downstream processes controlled by the Dnmts during the consolidation of memory are not investigated. In this study, we investigated the requirement for Dnmt3a1, the predominant Dnmt in the adult brain, in hippocampal long-term memory formation. Furthermore, we identified an activity-regulated Dnmt3a1-dependent genomic program. Our data showed that Dnmt3a1, similarly to its isoform Dnmt3a2, plays a critical role in memory formation. Furthermore, we uncovered Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 during the formation of memory. Intriguingly, we found that Nrp1 expression is selectively regulated and a specific downstream effector of Dnmt3a1, but not Dnmt3a2. Taken together, our study uncovered a Dnmt3a isoform specific mechanism in memory formation and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in primary hippocampal cultures treated with bicuculline and in Dnmt3a1 knock down conditions (shDnmt3a1).

first: Ana

last: Oliveira


title: Searching for new molecules involved in Anopheles mosquitoes’ response to Plasmodium infection

city: Towada

first: Asako

last: Haraguchi

state: Aomori

department: School of Veterinary Medicine

institute: Kitasato University

summary: Plasmodium parasites within mosquitoes are exposed to various physiological processes, such as blood meal digestion activity, the gonotrophic cycle, and host responses preventing the entry of parasites into the midgut wall. However, when in vitro-cultured ookinetes are injected into the hemocoel of mosquitoes, Plasmodium parasites are not affected by the vertebrate host’s blood contents and do not pass through the midgut epithelial cells. This infection method might aid in identifying mosquito-derived factors affecting Plasmodium development within mosquitoes. This study investigated novel mosquito-derived molecules related to parasite development in Anopheles mosquitoes. We injected in vitro-cultured Plasmodium berghei (ANKA strain) ookinetes into female and male Anopheles stephensi (STE2 strain) mosquitoes and found that the oocyst number was significantly higher in males than in females, suggesting that male mosquitoes better support the development of parasites. Next, RNA-seq analysis was performed on the injected female and male mosquitoes to identify genes exhibiting changes in expression. Five genes with different expression patterns between sexes and greatest expression changes were identified as being potentially associated with Plasmodium infection. Two of the five genes also showed expression changes with infection by blood-feeding, indicating that these genes could affect the development of Plasmodium parasites in mosquitoes.

overall_design: Male and female mosquitoes were analyzed 24 h & 72 h post injection with P. berghei ookinetes or with ookinete medium (negative control).

first: Makoto

last: Takano

first: Kanta

last: Fujiwara

first: Jun

last: Hakozaki

first: Kazuhiko

last: Nakayama

first: Sakure

last: Nakamura

first: Yasunaga

last: Yoshikawa

first: Shinya

last: Fukumoto

first: Kodai

last: Kusakisako

first: Hiromi

last: Ikadai


title: Emergence of CCL18- and IFI27-expressing macrophages in aging lungs, and potential roles for alveolar type 2 cell AGTR2 and macrophage BSG and CTSL expression in COVID-19

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Aging lungs are associated with several lung diseases, including chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and pneumonia. This latter age-associated complication has been particularly prominent in the recent COVID-19 pandemic. We have analyzed carefully selected normal lung samples from human subjects at different ages simultaneously using hashtag-labeled samples and single cell RNA-sequencing technology. We identify prominent changes in macrophage populations in lungs from older individuals, including an emerging populations of macrophages expressing IFI27 and other interferon-regulated genes. We also see increased gene expression of CCL18 and other chemokines in FABP4+/alveolar and SPP1+/interstitial macrophages. All three macrophage populations highly express BSG/CD147a putative SARS-CoV-2 receptor and CSTL, a gene associated with SARS-CoV-2 activation. ACE2, the SARS-CoV-2 receptor, and TMPSS2, a SARS-CoV2 protease activator, are both expressed highly on AT2 cells with increased expression on AT2 cells from older lungs. AGTR2, a recently proposed alternative receptor for SARS-CoV-2 was highly selectively and markedly upregulated by AT2 cells from aging lungs.  Thus, our data show increased lung expression of  ACE2, AGTR2 and TMPRSS2 by AT2 cells with aging. In addition, our data indicate a distinct molecular pathway for lung SARS-CoV-2 infection of lung macrophages. Macrophages may contribute to increased  COVID-19 severity in older patients by specific macrophage populations poised to contribute to the cytokine storm, in particular through enhanced interferon responses and interleukin-6 production.

overall_design: Normal healthy donor lungs were, at the time of procurement, mechanically and enzymatically dissociated to generate single cell suspensions which were cryogenically stored in liquid nitrogen.  Histology was assessed and ten samples procured from individuals of varying ages (19 years old to 78 years old) were selected to be multiplexed together for single cell RNA-sequencing using BioLegend TotalSeq-C cell hashing antibodies and 10X Genomics' Feature Barcoding technology for the 5 Prime Immune Profiling chemistry.

first: Minxue

last: Jia

first: John

last: Sembrat

first: Jordan

last: Bullock

first: Melissa

last: Bulik

first: Humberto

middle: T

last: Bittar

middle: L

last: Mora

first: Panayiotis

middle: V

last: Benos

first: Mauricio

last: Rojas

first: Robert

last: Lafyatis


title: Potent anti-tumor immunity and reversal of CD8 T cell exhaustion by spatially and functionally targeting Treg cells in the tumor microenvironment

status: Public on May 05 2024

city: Columbus

first: Yuzhou

last: Chang

state: OH

address: 5769 Privilege drive, Hilliard

institute: ohio state univeristy

summary: Regulatory T cells (Tregs) are a key mediator of resistance to cancer immunotherapy, including anti-PD-(L)1 immune checkpoint blockade (ICB). Tregs perpetually infiltrate tumors and hamper effective anti-tumor immunity. The mechanisms driving Treg infiltration into the tumor microenvironment (TME) and the consequence on CD8+ T cell exhaustion remains elusive. Herein, we report that heat shock protein gp96 (GRP94) is indispensable for Treg infiltration into the tumor, primarily through gp96’s roles in chaperoning integrins. Among various gp96-dependent integrins, we found that only LFA-1 (αL integrin) but not integrin αV, CD103 (αE) or β7 was required for Treg homing into the tumors. Loss of Treg infiltration into the TME by genetically deleting gp96/LFA-1 potently induces rejection of multiple ICB-resistant murine cancer models in a CD8+ T cell dependent manner without loss of self-tolerance. Moreover, gp96 deletion impeded Treg activation primarily by suppressing IL-2/phosphorylated STAT5 (pSTAT5) signaling pathway, which also contributes to tumor regression. Notably, by a mechanism in part through competing for IL-2 in the TME, intra-tumoral Tregs prevent activation of CD8+ tumor-infiltrating lymphocytes (TILs), drive TOX induction and induce bona fide CD8+ T cell exhaustion. By contrast, Treg ablation leads to a striking CD8+ T cell activation without TOX induction, demonstrating clear uncoupling of the two processes. Our study reveals that the gp96/LFA-1 axis plays a fundamental role in Treg biology and intratumoral CD8+ T cell exhaustion. We suggest that, Treg-specific targeting of gp96/LFA-1 represents a novel strategy for cancer immunotherapy without inflicting autoinflammatory conditions.

overall_design: 1×106 of splenic GFP+ Tregs were purified from WT (n=4) and KO mice (n=4) via FACS isolation. RNA was extracted using RNeasy Micro Kit (Qiagen) following its standard protocol and RNA degradation and contamination was monitored on 1% agarose gels. For RNA sequencing, libraries were prepared using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. All samples were prepared at the same time and sequenced on the same lane. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data in FASTQ format were processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.

first: Lei

last: Zhou


title: Lung single cell RNA sequencing of hepatic Bmal1 and Hif1adeficient mice

city: Houston

first: Rachel

last: Van Drunen

state: TX

address: Pressler

institute: MD Anderson University of Texas Health Science Center Houston

summary: Previous bulk-RNA sequencing suggested changes in gene expression of BHLKO lungs versus AlbCRE lungs. Here we carried out scRNAseq on lungs collected from BHLKO (3M) and ALbCre (control) (3M) in order to identify gene expression changes at a cell specific level.

overall_design: 3 whole lungs from BHLKO and 3 whole lungs from AlbCRE mice were taken at ZT4 and dissocaited into single cell suspenssion. The 6 samples were analyzed with single RNAseq

first: Vaishanvi

last: Dandavate

first: Marina

last: Golik

first: Gad

last: Asher


title: YTHDC1 is essential for cardiac development [RNA-seq]

city: changchun

first: lei

last: shi

address: changchun

institute: jilin university

summary: The goal of this study is to investigate how YTHDC1 regulate cardiac development.

overall_design: mRNA profiles in heart of Ythdc1flox/flox and Ythdc1-HKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).

last: Shi

first: Zhiguo

last: Zhang


title: YTHDC1 is essential for cardiac development [ATAC-seq]

overall_design: To assess chromatin accessibility in the heart casued by cardiac deletion of Ythdc1, ATAC-seq analysis of heart samples in Ythdc1flox/flox and cardiac-specific Ythdc1 knockout (Ythdc1-CKO) mice was performed.


title: The effect of microcurrent-stimulation on mouse macrophages

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

summary: Microcurrent-stimulation often uses wound healing, its effect on macrophages cells is unknown. This study analysed the mechanism of action of MCS, focusing on the circadian clock mechanism and phagocytic capacity of macrophages.

overall_design: Differences in gene expression in macrophages at zeitgeber  time (ZT) 2 or 14, with and without microcurrent-stimulation were measured.

first: Naoya

last: Matsunaga

first: Tomohito

last: Tanihara

first: Kaori

last: Yasuda

first: Hiroko

last: Hagiwara

first: Atsushi

last: Doi


title: Diet-induced obesity dysregulates rapid epigenetic response to hypoxia in macrophages (ChIP-Seq)

city: Syracuse

first: Norifumi

last: Urao

state: New York

address: 750 E. Adams St.

department: Pharmacology

institute: SUNY Upstate Medical University

summary: Macrophages play important roles in tissue homeostasis and tissue healing process. The response to hypoxic environment is a trigger to induce key signaling pathways in macrophages. Functions of macrophages are dysregulated in metabolic diseases such as diabetes and obesity resulting in poor tissue healing. Epigenetic status including histone modification in macrophages is regulated by hypoxia. However, whether and how obesity influences histone modification under hypoxia is unknown. Using chromatin immunoprecipitation-sequencing (ChIP-seq), RNA-seq on mouse bone marrow-derived macrophages, we sought to determine whether hypoxia alters histone 3-lysine 4 trimethylation (H3K4me3) and gene expression profile in macrophages and how obesity influences H3K4me3 enrichment on the genome in hypoxia-dependent and -independent manner.

overall_design: Comparative H3K4me3 marked peak analysis of ChIP-seq data for bone marrow-derived macrophages (BMDMs) obtained from C57B6/J mice fed a high-fat diet or a normal-fat diet with or without 1% hypoxia treatment for 1 hour.

first: Kentaro

last: Takahashi


title: Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [RNA-seq]

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Flowering time is a critical trait to determine regional adaptation and yield of crops including soybean. Evening Complex (EC) components soybean LUX1, LUX2, and ELF3a are critical for flowering and adaptation to lower latitudes. However, the mechanisms of EC in regulating flowering time remain largely unclear in soybean. Here, we identified GmJMJ19 and GmJMJ20 gene paralogs encoding JmjC-domain containing proteins, which co-express and interact with GmLUX2. In vitro and in vivo assays demonstrate that GmJMJ19 and GmJMJ20 bind to histone, but lack histone demethylase activity. Notably, simultaneous mutation of GmJMJ19 and GmJMJ20 causes delayed flowering time. Further transcriptomic, CUT&Tag and ChIP-seq analyses show that GmJMJ19/20 and GmLUX2 primarily co-repress transcription of 168 genes, which are not associated with the alternation of examined histone methylation state. Strikingly, we identify that the direct repression of GmSVP by GmJMJ19/20-GmLUX2 module is independent of the classical EC-E1 pathway. Interestingly, haplotype analyses support the idea that GmJMJ19 might undergo selection during soybean expansion to lower latitude. In summary, our findings reveal a mechanistic insight of GmJMJ19/20-GmLUX2 into flowering time control beyond EC complex in plants and also provide resources for improving soybean adaptability through molecular breeding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 17-day-old leaves of Williams 82 and gmjmj1920-2

first: Yapeng

last: Han

first: Yingxiang

last: Wang


title: Transcript Profiles of Microglia/Macrophage Cells at the Borders of Chronic Active and Subpial Gray Matter Lesions in Multiple Sclerosis

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Microglia/macrophages line the border of demyelinated lesions in both cerebral white matter and cortex in multiple sclerosis brains. Microglia/macrophages associated with chronic white-matter lesions are thought to be responsible for slow lesion expansion and disability progression in progressive multiple sclerosis whereas those lining gray matter lesions are less studied. Profiling these microglia/macrophages could help to focus therapies on genes or pathways specific to lesion expansion and disease progression. We compared the morphology and transcript profiles of microglia/macrophages associated with borders of white matter (WM line) and subpial gray matter lesions (GM line) using laser capture microscopy. We performed RNAseq on isolated cells followed by immunocytochemistry to determine distribution of translational products of transcripts increased in WM line. Cells in WM line appear activated with shorter processes and larger cell bodies, whereas those in GM Line appear more homeostatic with smaller cell bodies and multiple thin processes. Transcript profiling revealed 176 genes in WM lines and 111 genes in GM lines as differentially expressed. Transcripts associated with immune activation and iron homeostasis were increased in WM line whereas genes belonging to canonical Wnt signaling pathway were increased in GM line. We propose that mechanisms of demyelination and dynamics of lesion expansion are responsible for differential transcript expression in WM lines and GM lines, and posit that increased expression of Fc epsilon receptor, spleen tyrosine kinase, and Bruton’s tyrosine kinase play a key role in regulating microglia/macrophage function at the border of chronic active white matter lesions.

overall_design: To characterize the transcriptional profiles of microglia at the borders of white matter lesions and subpial cortical lesions , we use laser captured microglia followed by RNA-seq

first: Anthony

last: Chomyk

first: Rikki

last: Kucinski

first: Emilie

last: Christie

first: Kaitlyn

last: Cyncynatus

first: Zachary

last: Gossman

first: Zhihong

last: Chen

first: Brian

last: Richardson

first: Timothy

last: Turner

first: Ranjan

last: Dutta

first: Burce

last: Trapp


title: YTHDC1 is essential for cardiac development

first: lei

last: shi


title: Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [CUT&Tag]

overall_design: Genomic occupancy of H3K4me3, H3K9me2, H3K27me3 and H3K36me3 in soybean leaves at ZT12 in Williams 82 and gmjmj1920-2


title: Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression [RNA-Seq]

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

country: South Korea

institute: Korea national institute of health

summary: Hepatitis C virus (HCV) infection has been successfully managed by anti-viral therapies, however, high prevalence to severe chronic liver disease state including non-alcoholic fatty liver disease (NAFLD) is a problem encountered even after the cure of hepatitis C. Moreover, there is currently no reliable in vitro model capable of investigating host-viral interactions and monitoring the progression of viral hepatitis to chronic liver diseases. Recent organoid technology has been reported for successful infection of HCV, but there is still lack of non-parenchymal cells, which play a crucial role in disease progression. Here, we provided a novel multicellular liver organoid model using co-culture system of macrophages and liver organoids differentiated from the same cell source, human embryonic stem cells. Surprisingly, HCV infection led potent lipid accumulation in liver organoids through regulation of host lipid metabolism, which was further promoted by macrophage co-culture. Lipid enriched condition provided by longterm-treatment with fatty acid accelerated potent HCV amplification and further promotion of inflammation and fibrosis progression. Therefore, our model may be a valuable novel platform recapitulating diverse phenotypes with host-virus intercommunication and inter-cellular interactions and further progressive features of hepatitis C-associated chronic NAFLD progression of patients with HCV.

overall_design: Liver organoids were cultured without or with macrophages, then treated with fatty acid and/or HCV, and the results were analyzed using RNA-seq.

first: Jaeseo

last: Lee

first: Myung

middle: J

last: Son

first: Jung-Hyun


title: Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA [ChIRP-seq]

city: Beijing

first: Yangyang

last: Fan

address: No.5 Yiheyuan Road Haidian District,

institute: Peking University

summary: Arabidopsis noncoding RNA HID1 acts as a positive regulator to promote phyB-mediated seed germination by modulating the biosynthesis of abscisic acid.

overall_design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. For seed germination-related experiments, all plants were grown side-by-side, and the seeds were harvested on the same day. The seeds were dried at room temperature for about 2 months prior to subsequent experiments. Including sterilization and plating, seeds were exposed to white light for 1 hour. For the phyB-off condition, the seeds were exposed to far-red light (5 μmol·m-2·s-1) for 5 min to inactivate phyB. For the phyB-on condition, the seeds were irradiated with red light (20 μmol·m-2·s-1) for 5 min to activate phyB. The seeds were then incubated in the dark for the indicated time, and the germination rates were determined in the dark room.

first: Yuqiu

first: De

first: Xing

middle: W

last: Deng

first: Danmeng

last: Zhu


title: Gene expression profile at single cell level of xenograft tumors

first: Shengzhe

last: Zhang

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the Gene expression upon Crebbp KO.

overall_design: Presc cells with Crebbp WT and KO were injected on the back of nude mice, tumors were collected for scRNA sequencing.


title: Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression

overall_design: Refer to individual Series


title: Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [CHIP-seq]

first: Chenjiang

last: You

overall_design: Genomic occupancy of JMJ20 in soybean leaves at ZT12 in JMJ20-OE transgenic plants

first: Yapeng

last: Han

first: Yingxiang

last: Wang


title: Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA [ChIP-seq]


title: Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean.


title: Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression [scRNA-Seq]

overall_design: Liver organoids were cultured without or with macrophages and analyzed using scRNAseq.

last: Kim


title: Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (scRNA-Seq)

city: Philadelphia

first: Patrick

last: Viatour

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: we report the mRNA expression of single cells at two different time points of HCC development upon inactivation of Rb family. The first time point corresponds to lesions appearing in the portal triad area 9 weeks after Rb family inactivation. The second time point corresponds to macroscopic tumors, typically visible at the 20-25 weeks time point.

overall_design: YFP+ cells collected from each time point (a pool of three mice for early lesions) are processed for 10x sc-Seq analysis


title: Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model


title: Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (Bulk RNA-Seq)

summary: we report the expression profiles of various liver progenitor subpopulations upon inactivation of the Rb family of genes

overall_design: YFP+ cells eventually further fractioned on the basis of Thy1 and Epcam surface marker expression are processed for bulk RNA-Seq expression analysis.


title: Single-cell transcriptome atlas in C57BL/6 mice encodes morphological phenotypes in the aging kidneys

status: Public on May 04 2024

city: guangzhou

first: shanzhi

last: yang

address: 2nd zhongshan road

institute: guangdong provincial people's hospital

summary: Using single-cell transcriptome data, we evaluated how various biological process appear in particular cell types and investigated the potential mechanism of formation of GBM konbs.

overall_design: A total of 10, 895 and 4408 cells were isolated from whole kidney cell suspensions from the young and senescent mice, respectively.


title: Murine GMP- and MDP-derived classical monocytes have distinct functions and fates.

city: Rehovot

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

institute: Weizmann Institute of Science

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


title: Murine GMP- and MDP-derived classical monocytes have distinct functions and fates [dataset 2]

summary: Monocytes are short-lived myeloid immune cells that arise from adult hematopoiesis and circulate for a short time in the blood. They comprise two main subsets, in mice defined as classical Ly6Chigh and non-classical Ly6Clow monocytes (CM, NCM). Recent fate mapping and transcriptomic analyses revealed that CM themselves are heterogeneous. Here, we report surface markers that allow segregation of murine GMP- and MDP-derived CM in the BM and blood. Functional characterization, including fate definition following adoptive cell transfer, established that GMP-Mo and MDP-Mo could equal rise to homeostatic CM progeny, such as NCM in blood and gut macrophages, but differentially seeded selected other tissues. Specifically, GMP-Mo and MDP-Mo gave rise to distinct interstitial lung macrophages, thus linking CM dichotomy to previously reported pulmonary macrophage heterogeneity. Collectively, we provide comprehensive evidence for the existence of two functionally distinct CM subsets in the mouse, which differentially contribute to peripheral tissue macrophage populations in homeostasis and following challenge. Our findings are indicative of impact of monocyte ontogeny on in situ differentiation.

overall_design: Cells were sorted to purity and subjected to bulk RNAseq. These include classical monocytes from BM and blood defined either by fatemappers (DR samples) or defined by surface markers (others). Lung IM were derived from adoptively transferred monocytes or BM chimeras.

first: Sébastien

last: Trzebanski


title: Murine GMP- and MDP-derived classical monocytes have distinct functions and fates [dataset 1]

summary: Monocytes are ephemeral myeloid immune cells that arise from adult hematopoiesis and circulate in the blood. They comprise two main subsets, in mice defined as classical and non-classical monocytes (CM, NCM). Recent fate mapping and transcriptomic analyses revealed that CM themselves are heterogeneous. Here, we report surface markers that allow segregation of murine GMP- and MDP-derived CM, as well as their functional characterization, including fate definition following adoptive cell transfer. GMP-Mo and MDP- Mo gave equal rise to homeostatic CM progeny, such as blood NCM and gut macrophages; the cells however differentially seeded selected other tissues, including the dura mater and lung. Specifically, GMP-Mo and MDP-Mo gave rise to distinct interstitial lung macrophages, linking CM dichotomy to previously reported pulmonary macrophage heterogeneity. Collectively, we provide evidence for the existence of two functionally distinct CM subsets in the mouse, which differentially contribute to peripheral tissue macrophage populations in homeostasis and following challenge.

overall_design: Bone marrow cells were isolated from femur of a 10 week-old C57BL6 female mouse. The cells were stained with antibody panel containing 174 oligo-conjugated antibodies

first: Daliya

last: Kancheva


title: Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (ATAC-Seq)

summary: we report the chromatin conformation profile of various liver progenitor subpopulations upon inactivation of the Rb family of proteins.

overall_design: YFP+ cells fractioned on the basis of Thy1 and Epcam surface expression are isolated by flow cytomtry prior to standard processing for ATAC-Seq.


title: Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA [RNA-seq]


title: Transcriptome sequencing of normal and lens clouded eyes in the Myodes rufocanus (Sundevall, 1846)

city: Changchun

first: Shengnan

state: Jilin

address: Xi'an road No.5333

institute: Jilin University

summary: We selected normal Myodes rufocanus eyes and lens clouded eyes for transcriptome sequencing, and excavated the lens clouded eyes by analyzing and comparing. We investigated the genes and mechanisms involved in congenital cataract.

overall_design: Comparing the difference in gene expression between LE and RE

first: Yulu

last: Geng

first: Xiaoping


title: Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA.

first: Yangyang


title: Transfection of entomopathogenic Metarhizium species with a novel mycovirus confers hypervirulence against two lepidopteran pests

status: Public on May 03 2024

first: Jiashu

last: Guo

address: No. 12, Zhongguancun South Street, Haidian District, Beijing

institute: Chinese Academy Of Agricultural Sciences

summary: Although most known mycoviruses are asymptomatic or reduce the virulence of their host fungi, those that confer hypervirulence to entomopathogenic fungus still need to be explored. Here, we discovered and studied a novel mycovirus in Metarhizium flavoviride, isolated from Laodelphax striatellus. Based on molecular analysis, we tentatively designated the mycovirus as Metarhizium flavoviride partitivirus 1 (MfPV1), a novel species in genus Gammapartitivirus, family Partitiviridae. MfPV1 has two double-stranded (ds) RNAs as its genome, 1,775 and 1,575 bp in size respectively, encapsidated in isometric particles. When we transfected commercial strains of M. anisopliae and M. pingshaense with MfPV1, conidiation was significantly enhanced (t-test; P-value < 0. 01), and the significantly higher mortality rates of the larvae of Plutella xylostella and Spodoptera frugiperda, two important lepidopteran pests were found in virus-transfected strains (ANOVA; P-value < 0.05). Transcriptomic analysis showed that transcript levels of pathogenesis-related genes in MfPV1-infected M. anisopliae were obviously altered, suggesting increased production of metarhizium adhesin-like protein, hydrolyzed protein and destruxin synthetase. Further studies are required to elucidate the mechanism whereby MfPV1 enhances the expression of pathogenesis-related genes and virulence of Metarhizium to lepidopteran pests. This study presents experimental evidence that the transfection of other entomopathogenic fungal species with a mycovirus can confer significant hypervirulence and provides a good example that mycoviruses could be used as synergistic agent to enhance the biocontrol activity of entomopathogenic fungi.

overall_design: To investigate a novel mycovirus induced hypervirulence in the host fungus, we analyzed the RNA-seq data from hyphae of three virus-infected and three virus-free strains of M. anisopliae cultured in cicada slough induced PBD medium.

first: Peipei

last: Wu

first: Wenwen

last: Liu

first: Yan

first: Huaibing

last: Jin

first: Frederic

last: Francis

first: Xifeng


title: Tetrastigma hemsleyanum Polysaccharides Alleviate Imiquimod-Induced Psoriasis-Like Skin Lesions in Mice by Modulating the JAK/STAT3 Signaling Pathway

city: hanzhou

first: Yishan

last: Lv

address: 548 Binwen Road

institute: Zhejiang Chinese Medical University

summary: Crosstalk between keratin-forming cells and aberrant immune cells due to immune imbalance is a key factor in the pathogenesis of psoriasis. Most of the current clinical treatments provide rapid symptomatic relief but bring side effects that should not be ignored. Tetrastigma hemsleyanum polysaccharides (THP) have significant immunomodulatory and anti-inflammatory properties. In this study, we used imiquimod (IMQ)-induced psoriasis mouse model and LPS/IL-6-stimulated HaCaT cell model. The potential and mechanism of action of THP for psoriasis treatment were assessed by Psoriasis Area Severity Index (PASI) score, histopathology, flow cytometry, Western blot, and reverse transcription-polymerase chain reaction. The signs and symptoms of psoriatic mice induced by IMQ were significantly relieved by percutaneous administration of THP, including the improvement of psoriatic skin signs (erythema, folds, scales), pathological changes, decreased PASI score, and decreased spleen index. Results of in vivo and in vitro studies suggest that THP inhibits abnormal cell proliferation and excessive inflammation at skin lesions, balances Th17 immune cells, and blocks the keratinocyte-Th17 cell cycle, thus playing a role in psoriasis treatment by a mechanism that may be related to the regulation of the JAK/STAT3 signaling pathway.

overall_design: After 1 week of adaptation, mice were randomly divided into two experimental groups: (1) Control group (CON); (2) IMQ group (MOD). Except for the negative control group, each mouse received local treatment with 62.5 mg of IMQ on the shaved dorsal skin for 6 consecutive days. At the end of the experiment, mice were intramuscularly injected with 0.02 mg/mL atropine (0.02 mL/10 g), intraperitoneally injected with 6.5 mg/mL zoledronic acid (0.1 mL/10 g), blood was collected via cardiac puncture, and euthanasia was performed by cervical dislocation. A portion of the skin tissue was fixed in 10% formalin, while another portion was rapidly frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Spleen tissue was weighed, with a portion placed in pre-chilled phosphate-buffered saline (PBS) for flow cytometry analysis, and the remaining portion fixed in 10% formalin.

first: Liu

last: Yang

first: Fangmei

last: Zhou

first: Yujian

last: Ye


title: OXPHOS-Arachidonic acid-PPAR signalosome controls brown adipocyte peroxisomal function.

city: Suzhou

first: Xiaoqin

address: NO. 199 Renai Road

institute: Soochow University

summary: Brown adipose tissue plays a crucial role in modulating whole-body energy expenditure through the thermogenic function of its mitochondrial respiratory chain. Pharmacological interventions targeting this function hold significant therapeutic promise. Thus, gaining a comprehensive understanding of the pathophysiological regulation of brown adipose tissue is imperative for future therapeutic applications. In this study, we investigated the metabolic mechanisms underlying the regulation of mature brown adipocyte function by the mitochondrial respiratory chain. Our findings indicate that deficiency in mitochondrial complex I in mature brown adipocytes leads to lipidomic remodeling. This remodeling results in an increase in arachidonic acid content and prostaglandin E2 (PGE2) production, leading to reduced transcriptional activity of peroxisome proliferator-activated receptor gamma (PPARγ) and peroxisome proliferator-activated receptor alpha (PPARα) and alterations in the content of PPAR activator complexes, which consequently result in reduced brown adipocyte thermogenesis and peroxisomal gene expression in mature brown adipocyte. In summary, our study elucidates that the mitochondrial-derived arachidonic acid signal regulates brown adipocyte thermogenesis and peroxisome biogenesis by modulating the PPAR activator complex."

overall_design: To investigate the impact of  the NADH dehydrogenase complex inhibition on gene expression in mature brown adipocytes, cells were treated overnight with either 100 nM Rotenone or DMSO as a control. Subsequently, gene expression profiling was conducted using RNA-seq data obtained from three independent replicates.

first: Jingjing

first: Wen

last: Lu

first: Dongyue

last: Yan

first: Junyan

first: Xiong

last: Su


title: Yield and diversity of human distal lung epithelial cells isolated by different sorting strategies

city: Nashville

first: Jonathan

last: Kropski

department: Medicine

institute: Vanderbilt University Medical Center

summary: Single-cell RNA-sequencing of lhuman lung epithelial cells from 3 donors sorted using CD66 or Lysotracker.

overall_design: Single cell suspensions were generated from cryopreserved minced tissue from 3 lung explants and CD66-/Lysotracke+ or CD66+/Lysotracker- epithelial cells were sorted by FACS, pooled, and underwent 10X scRNA-seq.

first: Kropski

last: Jonathan A.

first: McCall

last: A Scott

first: Blackwell

last: Timothy S.


title: Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [ATAC-Seq]

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

summary: Using ATAC-seq analysis from GNPs to MBSHH we discovered a massive modification in chromatin accessibility during MBSHH formation. Next, using integrative bioinformatics, we identified genes of the nuclear factor I (NFI) family that function as oncogenes on the MBSHH epigenome. We demonstrate not only that these genes are essential in the early stages of murine MBSHHs tumorigenesis, but also that their genetic silencing inhibits tumor growth in murine and human MBSHHs in vitro and in vivo. Finally, we discovered that NFIA/B are post-translationally modified by an activating methylation in MBSHH, making it possibility to target this pathway. Further studies revealed that pharmacological inhibition of this methylated NFIA/B hindered tumor proliferation, demonstrating the requirement of NFIA/B for tumor progression. Collectively our data shed light on the mechanism underlying the epigenome during the formation of the most malignant pediatric brain tumor and emphasizes the importance of deciphering cancer-specific epigenome for identification of new therapeutic avenues.

overall_design: Chromatin accessiblity of tumorigenesis process of medulloblastomas using mouse GEMM model; knockdown experiment of a medulloblastoma mouse cell line with siRNA (control siRNA and siNfia and siNfib)

first: Ryo

last: Shiraishi

first: Gabriele

last: Cancila

first: Reo

last: Maruyama

first: Olivier

last: Ayrault

first: Daisuke

last: Kawauchi


title: A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex

city: Santa Cruz

first: Bin

last: Chen

state: CA

address: 1156 High St.

institute: University of California Santa Cruz


title: Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [CUT&Tag]

overall_design: Nfia and Nfib binding sites of tumorigenesis process of medulloblastomas using mouse GEMM model and a cell line.


title: Cancer-Specific Epigenome Identifies Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression


title: Osteosarcoma uses host-derived growth factors to drive ERK phosphorylation and MCL1 expression to survive in the metastatic environment

city: Columbus

first: Matthew

last: Cannon

address: 700 Childrens Drive

department: Center for Childhood Cancer

institute: Nationwide Childrens Hospital

summary: Purpose: For patients with osteosarcoma, disease-related mortality most often results from lung metastasis—a phenomenon shared with many solid tumors. While established metastatic lesions behave aggressively, very few of the tumor cells that reach the lung will survive. By identifying mechanisms that facilitate survival of disseminated tumor cells, we can develop therapeutic strategies that prevent and treat metastasis. Methods: We analyzed scRNAseq data from murine metastasis-bearing lungs to interrogate changes in both host and tumor cells during colonization. We used these data to elucidate pathways that become activated in cells that survive dissemination and identify candidate host-derived signals that drive activation. We validated these findings through live cell reporter systems, immunocytochemistry, and fluorescent immunohistochemistry. We then validated the functional relevance of key candidates using pharmacologic inhibition in models of metastatic osteosarcoma. Results: Expression patterns suggest that the MAPK pathway is significantly elevated in early and (to a lesser degree) established metastases. MAPK activity correlates with expression of anti-apoptotic genes, especially MCL1. Niche cells produce growth factors that increase ERK phosphorylation and MCL1 expression in tumor cells. Both early and established metastases are vulnerable to MCL1 inhibition, but not MEK inhibition in vivo. Combining MCL1 inhibition with chemotherapy both prevented colonization and eliminated established metastases in murine models of osteosarcoma. Conclusion: Niche-derived growth factors drive MAPK activity and MCL1 expression in osteosarcoma, promoting metastatic colonization. Although later metastases produce less MCL1, they remain dependent on it. MCL1 is a promising target for clinical trials in both human and canine patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To study transcriptional changes during metastasis of osteosarcoma, we collected samples from OS17 PDX models at timepoints from primary tumor through 49 days post metastasis. We also include normal lung as a control.

first: Camille

last: McAloney

first: Rawan

last: Makkawi

first: Yogesh

last: Budhathoki

first: Emily

last: Franz

first: Amy

last: Gross

first: Maren

last: Cam

first: Tatyana

last: Vetter

first: Alexander

last: Davies

first: Ryan

last: Roberts


title: (1) Effect of KLHL6 loss on the transcriptome in DLBCL upon NOTCH ligand stimulation. (2) Effect of KLHL6 and NOTCH2 loss on the transcriptome in DLBCL. (3) Effect of DLBCL-associated NOTCH2 mutants on the transcriptome in DLBCL.

first: Luca

last: Busino

address: 421 Curie Blvd, 705 BRB II/III

department: Cancer Biology

institute: Luca Busino

summary: (1) Assessment of the transcriptional changes regulated by KLHL6 upon NOTCH ligand stimulation. Bulk RNA-seq in KLHL6 WT or KO U2932 cells was performed upon incubation with stromal OP9 cells stably expressing NOTCH ligand DLL1. (2) Assessment of the transcriptional changes regulated by the KLHL6-NOTCH2 axis in a xenotransplant model of DLBCL. Bulk RNA-seq was performed in in KLHL6+/+NOTCH2+/+(WT), KLHL6-/-NOTCH2+/+(K6-KO), KLHL6+/+NOTCH2-/-(N2-KO), KLHL6-/-NOTCH2-/-(DKO) U2932 cells xenotranplanted in NSG mice trated with CHOP. (3) Assessment of the transcriptional changes regulated by the DLBCL-associated NOTCH2 mutants. Bulk RNA-seq was  performed inU2932 cells stably expressing NOTCH2(WT), NOTCH2(S2156A), NOTCH2(R2400*) or NOTCH2(Q2140*).

overall_design: (1) Comparative gene expression profiling analysis of RNA-seq data for KLHL6 WT or KO U2932 cells that were incubated with stromal OP9 cells stably expressing NOTCH ligand DLL1. (2) Comparative gene expression profiling analysis of RNA-seq data for KLHL6+/+NOTCH2+/+(WT), KLHL6-/-NOTCH2+/+(K6-KO), KLHL6+/+NOTCH2-/-(N2-KO), KLHL6-/-NOTCH2-/-(DKO) U2932 cells. (3) Comparative gene expression profiling analysis of RNA-seq data for U2932 cells stably expressing NOTCH2(WT), NOTCH2(S2156A), NOTCH2(R2400*) or NOTCH2(Q2140*).

last: Zhou

first: Qinglan

last: Li


title: Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Essential Transcriptional Factors during Medulloblastoma Tumorigenesis [[CUT&Tag 2]

first: Kohei

last: Kumegawa

overall_design: H3K27Ac of tumorigenesis process of medulloblastomas using mouse GEMM model and a cell line.

first: Ryo

last: Shiraishi

first: Gabriele

last: Cancila

last: Maruyama


title: Anti-CX3CL1 (fractalkine) monoclonal antibody attenuates lung and skin fibrosis in sclerodermatous graft-versus-host disease mouse model

city: Tsukuba

first: Yoshimasa

last: Sakamoto

state: Ibaraki

address: 5-1-3 Tokodai

institute: Eisai Co Ltd.

summary: To assess the preclinical utility and functional mechanism of intraperitoneal anti-CX3CL1 mAb therapy in the skin and lung fibrosis, sclerodermatous chronic graft-versus-host disease (Scl-cGVHD) model mice were analyzed by RNA-sequencing assays.

overall_design: Gene expression profiling analysis of RNA-seq data for skin, harvested from 3 syngenic mice dosed with control IgG, 5 syngenic mice dosed with anti-CX3CL1 mAb, 3 GVHD mice dosed with control IgG, 3 GVHD mice dosed with anti-CX3CL1 mAb (0.5 mg/head), and 5 GVHD mice dosed with anti-CX3CL1 mAb (1 mg/head).

first: Hasegawa

last: Takumi

first: Utsunomiya

last: Akira

first: Chino

last: Takenao

first: Matsushita

last: Takashi

first: Obara

first: Ishi

last: Naoto

first: Ogasawara

last: Hideaki

first: Ikeda

last: Wataru

first: Imai

last: Toshio

first: Oyama

last: Noritaka

last: Minoru


title: Employment of exosome-mimetic nanovesicles as a plasma adjuvant for cancer targeting through Golgi stress-associated ferroptosis

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

institute: Kangwon National University

summary: Plasma oncology is a promising therapeutic method that employs ionized gas to selectively target cancer cells. However, despite its efficacy in directly exposing external cancer cells to plasma, a stable delivery method through the circulatory system to internal cancer cells has yet to be developed. In this study, we revealed that bioinspired exosome-mimetic nanovesicles (EMs) can serve as a plasma adjuvant to enhance the anti-cancer effect. EM treatment increased the half-life of plasma reactive species such as nitrogen oxide in solution, thereby increasing the cytotoxicity towards cancer cells. Our syngeneic mice model experiment demonstrated that EM-treated plasma (EM-Plasma) inhibited in vivo cancer growth more efficiently than conventional plasma administration. Furthermore, we uncovered a molecular mechanism through which EM-Plasma selectively induces cancer cell death, namely, Golgi stress-associated ferroptosis. Our study provides a promising approach for the clinical application of plasma oncology in cancer treatment.

overall_design: Transcriptomic profiles of B16 melanoma cells with or without EM-Plasma treatment.

first: Bum-Ho

last: Bin

first: Byeong-Mun

last: Kwak

first: Hyojin

last: Heo

first: Sofia

last: Brito

first: Byungsun

last: Cha


title: NOTCH2 mutants

first: Luca

last: Busino

overall_design: Refer to individual Series


title: Cynomolgus macaques: Young vs Elder

city: Fukuoka

first: Takahiro

last: Tomiyama

state: Fukuoka

address: 3-1-1 Maidashi. Higashi-ku

department: Surgery and Science

institute: Kyushu University

summary: Transcriptional profiling of cynomolgus macaques liver tissue comparing control young macaques with elder macaques. Goal was to determine the liver genetic change with aging of macaques.

overall_design: Two-condition experiment, Young vs. elder cells. Biological replicates: 7 young replicates, 6 elder replicates.

first: Tomoharu

last: Yoshizumi

first: Takuya

last: Yamamoto


title: MCF7 cells with LIFR knockdown

first: Rachelle

last: Johnson

address: 2215B Garland Ave

summary: MCF7 cells were infected with lentiviral particles containing LIFR-targeted shRNAs then chemically selected to create a stable pooled population of shLIFR MCF7 cells. The goal of the study was to determine the downstream targets of LIFR in human MCF7 breast cancer cells.

overall_design: There are three biological replicates of the control MCF7 cells expressing non-silencing control shRNAs, and three biological replicates of the MCF7 cells expressing LIFR shRNAs. Each biological replicate was collected from independent experiments and all cells were grown in standard 2D tissue culture plates.


title: Effect of DLBCL-associated NOTCH2 mutants on genomic RBP-J localization and H3K27 acetylation

summary: Assessment of the genome-wide effect of DLBCL-asscociated NOTCH2 mutants in DLBCL on RBPJ and H3K27acetylation. DLBCL cell lines U2932 cells stably expressing HA-tagged NOTCH2(WT), NOTCH2(R2400*) or NOTCH2(Q2140*) were subjected to  chromatin immnunoprecipitation DNA-sequencing (ChIP-seq) for RBP-J and H3K27ac.

overall_design: ChIP-seq analysis or RBP-J and H3K27ac in U2932 cells stably expressing HA-tagged NOTCH2(WT), NOTCH2(R2400*) or NOTCH2(Q2140*)

last: Zhou

first: Yiman

last: Liu

first: Qinglan

last: Li

first: Liling

last: Wan


title: RNAseq and Small-RNAseq dataset to comprehensively study the miRNA expression profiling of drug-resistant melanoma patients and cell lines

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

type: Non-coding RNA profiling by high throughput sequencing

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


title: Transcriptomic profile of melanoma clinical samples treated with BRAF and MEK- inhibitors

summary: To analyse the RNA expression differences between melanoma tumour samples treated with BRAF and MEK-inhibitors at different time points

overall_design: Total RNA was extracted from tumour biopsies of treated with BRAF- and MEK-inhibitors at different time points

first: R

first: P

last: Carotenuto


title: SmallRNAome profile of melanoma cell lines A375 and A375-BIR (BIR-BRAF INHIBITOR RESISTANT) during dabrafenib treatment

summary: To analyse smallRNA expression differences between A375 and A375-BIR during the treatment with dabrafenib (DAB)

overall_design: Total RNA was extracted from n=3  A375, A375-BIR treated with DAB 200nM for 48h and vehicle control (DMSO, 0.1%)


title: Exploring the mechanisms of high-altitude adaptation in yak based on single-cell transcriptome atlas.

city: Chengdu

first: Daoliang

last: Lan

state: Sichuan

address: #16, South Section, 1st Ring Road

institute: Southwest Minzu University

summary: This study explores how yaks, an ideal animal model for studying plateau adaptability, adapt to high-altitude environments. The lung is a representative organ of the yak’s adaptation to high-altitude environments. The F1 hybrids of yak and cattle, known as dzho, also exhibit adaptability to plateau conditions. This study constructed a single-cell transcriptome atlas of the lungs in yak, dzho and cattle, containing 51 subtypes. We initially found that the differential subtypes among yak, dzho and cattle were mainly concentrated in T&NK cells and fibroblasts. Most of them belonged to new cell subtypes. Subsequently, we speculated that NKG7 and CD4 played a central regulatory role in T&NK cells, contributing to T cell activation and affecting the adaptive immune response of yaks. In fibroblasts, MYL9 and IGF2 are believed to play key regulatory roles, participating in maintaining cellular energy metabolism balance. These results provide an important scientific basis for systematically analysing the molecular regulatory mechanisms of yak adaptation to high-altitude hypoxia.

sample_organism:
Bos taurus
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Construction of single cell transcriptional profiles in lungs of yak, dzho, and cattle (n=3) using scRNA-seq.


title: Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos II

summary: In order to identify the effects of the absence of SEDL on Medaka transcriptome, we performed RNAseq experiments  Transcriptome analysis of the liver of mice trated with CD95 activating antibody, compared with liver of mice trated with saline.

overall_design: Total RNA was extracted from n=3 SEDL Knock Out stage 40 embryos (named "KNOCKOUT") and n=3 Control stage 40 embryos (named "Ctrl")

first: F

last: Zappa


title: Single cell RNA-sequencing analysis of astrocyte-to-neuron conversion in 5xFAD mouse hippocampus

status: Public on May 02 2024

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

summary: Collectively, our findings demonstrate that NeuroD1 significantly alters the transcriptomic landscape of astrocytes, suggesting a role for NeuroD1 in neuronal fate reprogramming.

overall_design: 5xFAD mouse Hippocampi were injected with AAV9 and extracted from control and NeuroD1 treated mice at 3 weeks post injection (n = 3 mice per group). Hippocampi were dissociated, and single-cell suspensions were prepared and isolated using a microfluidic chip, followed by scRNA-seq processing.

first: Liang

last: Xu

first: Yu

last: Xie

first: Gong

last: Chen


title: A scalable, low cost, multi-omic interrogation and sample hashing workflow for single-cell analysis using the Seq-Well S3 platform

city: Somerville

first: Daniela

middle: Dolores

last: Russo

state: Massachusetts

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

summary: Clinical samples promise unparalleled insights into the cellular mechanisms that underlie pathological conditions and therapeutic responses. However, they often can be precious, with few cells available for single-cell analysis, necessitating effort to maximize the amount of information that can be garnered from each. Here, we introduce a low material input, cost-effective protocol for conducting multi-omic analyses and sample hashing on single-cell suspensions using the Seq-Well S3 platform. Our protocol, designed to be both accessible and affordable, leverages readily available reagents and standard laboratory equipment, significantly lowering barriers to entry for researchers in low- and middle-income countries. The method detailed herein offers a streamlined and efficient workflow for: (1) precise staining of single-cell suspensions with antibody-oligo conjugates for accurate cell surface protein identification and effective sample multiplexing; (2) reliable generation of Seq-Well S3 sequencing libraries; (3) optional generation of bulk-RNA sequencing libraries through an optimized SMART-seq2 protocol; and, (4) robust computational pipelines for in-depth multi-omic data analysis. This protocol works with fragile and limited cell inputs (here, outlined for 15,000 cells per 200 µL - a fraction of the input required by most commercial methods). It also offers significant cost and time savings, with the entire process from cell isolation to sequencing taking only 3-6 days, plus an additional 1-2 days for data processing. In sum, this generally applicable pipeline empowers researchers around the globe to apply single-cell multiomics to advance their own research agendas.

overall_design: Peripheral blood mononuclear cells (PBMCs) from three donors were multiplexed onto two Seq-Well arrays. Seq-Well S3 and CITE-Seq were performed in unison to demonstrate the utility of a multi-omic protocol combining single-cell RNA sequencing with protein expression analysis to enhance the identification and characterization of various cell types, particularly immune cells. Additionally, bulk RNA-seq was performed using Smart-seq2 to develop SNP profiles for each patient to perform downstream genetic demultiplexing.

first: Sarah

last: Quinn

first: Olha

last: Kolod

first: Michael

last: Elovitz

first: Douglas

last: Lauffenburger

first: Pardis

last: Sabeti

first: Boris

last: Juelg

first: Andrea

last: Edlow

first: Sergio

last: Triana

first: Alex

middle: K

last: Shalek

first: Brittany

last: Goods


title: Transcriptome profile of wildtype and SEDL knockdown Medaka embryos and Human ARPE-19 cells

first: Rossella

last: De Cegli

sample_organism:
Oryzias latipes
Homo sapiens

platform_organism:
Oryzias latipes
Homo sapiens


city: Wuhan

first: Mingliang Wei

last: Mingliang Wei

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from Methionine- and choline-deficient diet (MCD) and regular chow diet mice.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from MCD and regular chow diet mice.
MCD group: MCD-1, MCD-2, MCD-3.  Regular chow diet group: NC-1, NC-2, NC-3.

first: Chuanfei

last: Zeng

first: Huan

last: Li

first: Mingliang

last: Wei

first: Linxin

last: Yu

first: Ziqi

last: Mu

first: Ziyin

last: Huang

first: Yujia

last: Ke

first: Min

first: Ming-Kai

first: Lian-Yun

first: Yong

last: Xiao


title: Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos

summary: Transcriptomic profile of Stage 40 Oryzias latipes (Medaka) embryos wild type and KO for SEDL

first: R

first: A

middle: M

last: Guarino


title: RNAseq Transcriptomic Analysis of IMhu-M Cells

city: Barakaldo

first: Koen

last: Vandenbroeck

state: Bizkaia

address: Plaza Cruces, s/n

department: Biochemistry and Molecular Biology

country: Spain

institute: Basque Country University / IIS Biobizkaia

summary: Identification of differential gene expression genes in ANRD55 transfected verus not transfected microglia cell line

overall_design: To investigate the expression levels of transfected IMHu-M cell line with ANKRD55 two biological replicates were analyzed for each of 2 conditions (transfected and not transfected)


title: Mouse single positive thymocyte bulk RNA-seq from Kmt2d knockout and control littermates.

city: Cincinnati

first: Sarah

last: Potter

address: 240 Albert Sabin Way, S6.540, MLC 7028

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: To evaluate the hypothesis that dysregulated thymocyte development contributes to immune deficiencies in individuals with KS1. We generated bulk murine CD4+ or CD8+ single positive thymocyte RNA-seq data from cells which lack the histone methyltransferase, Kmt2d SET domain (exons 50/51), with a conditional Cre-recombinase driven by Lck-CreMar (T cell specific) or Vav1-iCre (hematopoietic). Expression profiling by high throughput sequencing.

overall_design: 1) RNA-sequencing from 3 biological replicates of paired single positive (SP) thymocytes from Cre-recombinase (Lck-CreMar-driven: CD4+ and CD8+ SP thymocytes; or Vav1-iCre-driven: CD8+ SP thymocytes) Kmt2d knockout single positive thymocytes and corresponding Cre-negative control littermate. 2) Re-analysis of 7 Lck-Cre; Dot1l control and knockout CD8+ thymocyte RNA-Seq samples (GSE138910; GSM4121514-GSM4121516, GSM4121521-GSM4121524) and Kmt2d control and knockout peripheral naive CD4+ T cells RNA-seq (GSE69162; GSM1694174-GSM1694177) and ChIP-Seq (GSE69162; GSM1694154, GSM1694155) samples.


title: A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [ChIP-seq]

first: Bin

last: Chen

department: MCD Biology

summary: During development neural stem cells (NSCs) in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Shh signaling promotes cortical RGCs to switch lineage to generate cortical oligodendrocytes and OB interneurons. During this lineage switch, cortical RGCs generate intermediate progenitor cells (IPCs) that express Ascl1, Egfr and Olig2, genes critically regulating gliogenesis. The timing of increased Ascl1 expression and the appearance of Egfr+ and Olig2+ cortical progenitors is concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Further, the transcriptional regulation of Olig2 and Egfr has not been explored. Here we show that in cortical progenitor cells, multiple genetic programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple distal enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.

overall_design: ChIp-seq using Gli3 antibodies and wild-type cortical tissue, CUT&RUN using antibodies for H3K4me3, H3K27me3,and H3K27ac and cortical tissues from wild-type, Smo cko, and Smo M2 micce, ATAC-seq for wild-type cortical cells and cortical cells after in utero electroporation of pCAG-ShhN plasmids.

first: Xiaoyi

last: Liang

first: Kendy

last: Hoang

first: Yue

last: Zhang

first: Sol

last: Katzman


title: Cytoadhesion of Plasmodium falciparum-infected red blood cells changes the expression of cytokine-, histone- and antiviral protein-encoding genes in brain endothelial cells

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

institute: Bernhard Nocht Institute for Tropical Medicine

summary: Introduction Malaria remains a significant global health problem, particularly due to the human malaria parasite Plasmodium falciparum, which is responsible for most fatal infections. Infected red blood cells (iRBCs) evade spleen clearance by adhering to endothelial cells (ECs), triggering capillary blockage, inflammatory cytokine release, endothelial dysfunction, and altered vascular permeability, prompting an endothelial transcriptional response. Methods The iRBCIT4var04/HBEC-5i model, where iRBCs present IT4var04 (VAR2CSA) on their surface was employed to analyse the effects of iRBC binding on ECs. We used this model to investigate how cytoadhesion of iRBCs to ECs influences their expression profile depending on the temperature (37°C vs 40°C). Results Binding of non-infected RBCs (niRBCs) and fever alone significantly changes expression of hundreds of genes in ECs. Comparing the expression profile of HBEC-5i cultured either in the presence of iRBCs or in the presence of niRBCs, genes encoding proteins assigned to the GO terms immune response, nucleosome assembly, NF-kappa B signaling, angiogenesis, and antiviral immune response/interferon-alpha/beta signaling pathway were significantly up-regulated. If the cultivation temperature is increased from 37°C to 40°C, which simulates fever, a further significant increase in expression can be observed for most regulated genes, especially for genes coding for cytokines and proteins involved in angiogenesis. Conclusion The presence of iRBCs leads to the stimulation of ECs, activating several immunological signaling pathways and affecting antiviral (-parasitic) mechanisms and angiogenesis. Furthermore, to our knowledge, the induction of the interferon-alpha/beta signaling pathway in ECs in response to iRBCs has been described for the first time.

overall_design: The iRBCIT4var04/HBEC-5i model, where Plasmodium falciparum infected red blood cells (iRBC) present IT4var04 (VAR2CSA) on their surface was employed to analyse the effects of iRBC binding on endothelial cells (ECs). We used this model to investigate how cytoadhesion of iRBCs to ECs influences their expression profile depending on the temperature (37°C vs 40°C).

first: Michael

last: Bartels

first: Hanifeh

last: Torabi

first: Maria del Pilar Tauler

last: Martinez

first: Nahla

last: Metwally

first: Thomas

last: Roeder

last: Gutsmann

first: Iris

last: Bruchhaus


title: Bidirection activation of stem-like programs in metastatic cancer and alveolar type II cells within the niche [ATAC-seq]

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

summary: A key step for metastatic outgrowth involves the generation of a deeply altered microenvironment (niche) that supports the malignant behavior of cancer cells. However, it is unclear whether a fundamental program driving the generation of this de novo cellular environment can be identified. Here, by focusing on breast cancer metastasis to the lung, we describe a cancer-dependent chromatin remodeling and activation of developmental programs in alveolar type II (AT2) cells. We have identified a relationship linking high metastatic competency in the lung with the induction of a multilineage state in AT2 cells in the niche. In turn, this cancer-induced reprogramming of AT2 cells promoted stem-like features in the cancer cells. In conclusion, we propose the concept of “reflected stemness” during metastatic niche initiation, whereby metastatic cells reprogram the local tissue into a stem-like state that enhance intrinsic cancer-initiating potential, creating a positive feedback loop where tumorigenic programs may be amplified.

overall_design: To investigate the chromatin remodeling that happens in AT2 cells from two different metastatic tumor models. Syngeneic BALB/c mice (6- to 8-week-old) were intravenously injected with 0.8 x 106 labeling-4T1 or labeling-CT26 tumor cells and lungs were collected 7 days after tail vein injection. Three biological independent samples were generated for each condition (4T1; AT2 distal and AT2 niche / CT26; AT2 distal and AT2 niche) and each sample was prepared by pooling 5 lungs.

first: F

last: Rodrigues

first: I

first: M

last: Llorian


title: Transcriptome analysis reveals the gene expression profile in 17,18-EEQ treated HUVECs

city: Tianjin

first: Ting

last: Zhou

address: Qixiangtai road 22

institute: Tianjin medical university

summary: Our research aimed to understand the gene expression profile in human umbilicial vein endothelial cells treated with 17,18-EEQ, then find the sepcific mechanism and signaling pathway in response to 17,18-EEQ stimulation.

overall_design: In this study, primary HUVECs were pretreated with 1 μM 17,18-EEQ for 24 h. The control group and 17,18-EEQ-treated group were collected for RNA sequencing.

first: Ding

last: Ai


title: Single cell sequencing data of zebrafish spinal cord injury

city: 南通

first: xing

middle: yi

last: song

state: 江苏

address: 江苏省南通市启秀路19号

department: 神经再生

institute: 南通大学

summary: After spinal cord injury in adult zebrafish, the spinal cord was taken out for single-cell data sequencing

overall_design: The spinal cord of adult zebrafish was taken for single cell sequencing

first: Lingyan

last: Xing

first: Jiaqi

last: Wang

first: Gang

last: Chen


title: Critical Role of Runx Transcription Factors in Maintaining Epididymal Epithelial Differentiation

city: Turku

first: Petra

last: Sipilä

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

overall_design: Refer to individual Series


title: Critical Role of Runx Transcription Factors in Maintaining Epididymal Epithelial Differentiation [RNA-seq II]

summary: To study the role of RUNX transcription factors in the epididymal epithelial cells we deleted Runt domains of Runx1 and Runx2 from mouse epididymal cell line mE-Cap18 using CRISPR-Cas9 technique.

overall_design: RNA-seq was performed from 3D organoids from Control and Runx-deletion cell lines.

first: Mervi

last: Toriseva

first: Jesse

last: Mattson

first: Asta

last: Laiho


title: Low input RNA-seq of HSCs.

first: chen

last: minqi

address: No.74, 2nd Zhongshan Road

institute: Sun Yat-sen University

summary: Both mHSCs and nHSCs had activated differentiation genes upon LM challenge; however, mHSCs more robustly increased cell cycle and T lymphocyte-differentiation genes but reduced myeloid-, erythrocyte- and B cell-differentiation genes compared to nHSCs upon LM challenge

overall_design: Low input RNA-seq on HSCs

first: Meng

last: Zhao

first: Xue

last: Han

first: Minqi


title: ATAC-seq of HSCs.

overall_design: ATAC-seq on HSCs


title: FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

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


title: FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk [ncRNA-Seq]

summary: The transcription factor FOG2 (ZFPM2) is upregulated in human heart failure and increased FOG2 expression causes heart failure in mice.  We found that FOG2 directly intersects a gene regulatory network driven by the atrial-enriched TF TBX5 and required for atrial cardiomyocyte rhythm control gene expression

overall_design: Transcriptomic and epigenomic analyses of FOG2-TBX5I dependent-networks in cardiac  rhythm

first: Carlos

last: Perez-Cervantes

first: Rangarajan

middle: D

last: Nadadur

first: Michael

last: Broman


title: Biological Aging of Human Skeletal Muscle

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

summary: The age-related loss of skeletal muscle mass and function (sarcopenia) is one of the most dramatic changes affecting the human body. A clear understanding of the mechanisms involved is thus of paramount importance in ensuring quality of life in the old age. Most previous studies of sarcopenia in human investigated chronological aging, as they relied on comparisons between young and old subjects. Notably, no previous study has taken into consideration inter-individual differences (biological aging) in prevalence of sarcopenia. To obtain an integrative view of muscle biological aging our project uses a single biopsy from 72 well-phenotyped 80 years healthy subjects with different muscle loss/gain (PROOF cohort), to provide an extended characterization of the muscle tissue, including microstructural and omic analyses.

overall_design: To obtain an integrative view of biological aging, the research program 4 components encompassing: metabolomic, cellular, transcriptomic and proteomic parameters. We  assess biological aging in both men and women by comparing groups with either decreased, increased or stable appendicular lean mass (ALM).

last: Béchet

first: Marine

last: Gueugneau

first: Léonard

last: Féasson

first: Frédéric

last: Roche


title: FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk [ChIP-Seq]

first: Pingzhu

last: Zhou

first: William

last: Pu