title: miR-765 induces angiogenesis by inhibiting dipeptidyl peptidase 4 and increasing fibroblast growth factor 2

status: Public on May 08 2024

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Given that extracellular vesicles (EVs) secreted from stem cells contain angiogenic microRNAs (miRNAs), these EVs show equivalent angiogenic therapeutic effect to cell transplantation. This study aimed to identify the angiogenic miRNAs from several miRNAs involved in EVs secreted from stem cells. In human dental pulp stem cells (hDPSCs) under hypoxic culture, vascular endothelial growth factor (VEGF) involved in EVs increased. We hypothesized that angiogenic miRNAs increase in EVs that are secreted from hDPSCs under hypoxic culture compared with those under normoxic culture. In the first screening, the expression levels of miRNAs involved in EVs that were secreted from hDPSCs cultured under hypoxic and normoxic conditions were analyzed using miRNA array. In the second screening, 12 miRNAs were individually involved in EVs, and the growth of human aortic endothelial cells was assayed. In the third screening, miRNA-encapsulated EVs were injected in BALB/c mouse hindlimb ischemia model, followed by angiogenesis evaluation by blood flow analysis. Results showed that miR-765 is an angiogenic miRNA, targeting the 3′ untranslated region of dipeptidyl peptidase 4 (DPP4) and upregulating fibroblast growth factor 2 (FGF2) in vitro and in vivo. In conclusion, as an angiogenesis mechanism, miR-765 increased FGF2 expression levels by inhibiting DPP4.

overall_design: To  compare the expression levels of miRNAs in EVs isolated from the conditioned medium under normoxic conditions and hypoxic conditions and then analyzed the expression levels of miRNAs encapsulated in EVs by array analysis. Human dental pulp stem cells (hDPSCs) (2 × 105 cells/10 mL) were seeded into 10 cm dish  in KBM ADSC-4 (#16030044; Kohjin Bio Co., Ltd.) and cultured 10 dishes of each for 7 days under normoxic and hypoxic conditions. The conditioned medium was concentrated using Amicon Ultra-15(#UFC901024, Merck Millipore Ltd.). Using the total exosome isolation reagent (from cell culture media)(#4478359, ThermoFisherScientific), we made pellets from the concentrated liquid of the conditioned medium. Next, microRNAs were isolated from the pellets by using the miRNeasy Mini Kit (#217004, Qiagen). The miRNA expression levels were analyzed using 3D-Gene® miRNA oligochips (Toray Industries, Inc.)

first: Koji

last: Ueno

first: Ryo

last: Suzuki

first: Hiroshi

last: Kurazumi

first: Takahiro

last: Mizoguchi

first: Toshiki

last: Tanaka

first: Kimikazu

last: Hamano


title: Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling

status: Public on Jun 01 2024

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

country: USA

institute: Oregon Health and Science Univ

type: Expression profiling by high throughput sequencing

summary: During nervous system development, pioneer neurons are the first to extend their axons into target tissues, creating a scaffold for follower neurons. Despite years of study, whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line (pLL) sensory neurons during axon growth using single-cell RNA sequencing (scRNA-seq) revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state, whereas “pioneer” is a later developmental state. The scRNA-seq data revealed active retinoic acid (RA) signaling in followers, but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret, which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development.

overall_design: Fourteen-hour old, eighteen-hour old, twenty-two hour old, forty-eight hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.

first: Benjamin

middle: M

last: Woodruff

first: Lauren

middle: N

last: Miller

first: Lindsey

last: Royer

first: Nicholas

middle: L

last: Calistri

first: Laura

last: Heiser

middle: V

first: Jacqueline

middle: R

last: McVay


title: Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [scRNA-seq]

status: Public on May 06 2024

city: Toronto

first: Carolina

last: Nor

state: Ontario

address: 686 Bay St

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

summary: In this study, we examine the effect of radiation on the transcriptional profile of medulloblastoma tumor cells and its microenvironment that could potentially be leading to metastatic dissemination.

overall_design: Cerebellar tumors from SmoA1 mice treated with radiation (1Gy) were collected at 5h and 24h after treatment and compared to sham-radiated controls by single cell RNA sequencing

first: Michael

middle: D

last: Taylor


title: Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [bulkRNA-seq]

overall_design: Cerebellar tumors from SmoA1 and Ptc het mice treated with radiation (1Gy) or sham radiation were collected at 5h after treatment and compared to normal cerebellum from C57BL/6 mice treated with radiation (1Gy) or sham-radiated controls by bulk cell RNA sequencing


title: DOT1L controls NK cell maturation and lineage integrity [RNA-seq D0 & D2]

status: Public on Apr 30 2024

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

summary: Epigenetic modifiers are promising targets to improve therapies in patients with cancer. Targeting the methyltransferase DOT1L with small molecule inhibitors has shown promising effects on the control of cancerous cells. However, these small molecules are given systemically and may have a profound impact on non-cancerous cells, such as the cells of the immune system. In the innate immune system, natural killer (NK) cells are a critical subset of cells with important roles in controlling transformed cells and tumour inflammation. Previous studies have shown that NK cells can convert into ILC1-like cells in a TGFβ-rich tumour microenvironment (TME). Additionally, cancer patients with acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL) have increased frequencies of ILC1 cells in peripheral blood mononuclear cells (PBMCs), which show reduced production of proinflammatory cytokines and decreased granzyme B production. In this study, we identify DOT1L as a critical regulator of NK cell activation and lineage integrity. We generated NKp46-conditional DOT1L knockout mice (DOT1L.Ncr1) and observed increased frequencies of ILC1-like cells (CD49b+ CD49a+, CD62L-) and reduced frequencies of NK cells (CD49b+ CD49a-, CD62L+) in these mice. While the absence of DOT1L increases the sensitivity to TGFβ, the increased expression of CD49a is highly intrinsic and only partially dependent on TGFβ signalling. Functionally, the increased presence of ILC1-like cells in the tumour microenvironment of DOT1L.Ncr1 mice leads to decreased tumour control. Our assessment of the transcriptional program reveals alternative uses of transcription factors, such as the AP-1 family or SMAD2/3, to maintain NK cell activation and lineage integrity. Our findings provide evidence for a previously unknown role of DOT1L in NK cell biology, and demonstrate the importance of maintaining NK cell lineage integrity for effective tumour control. These findings have significant implications for the development of improved therapies for cancer or other NK cell-lineage dependent malignancies.

overall_design: Splenic NK cells of either WT or DOT1L.Ncr1 mice at steady-state (d0) or 2 days after infection with MCMV (d2) were sorted for NK1.1+ CD3/TCRβ- Ly49H+ cells prior to isolation of RNA


title: Transcriptome profiling of oxidase knockout mice response to gingival inflammation using RNA-seq

status: Public on Apr 23 2024

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Genetic defects in neutrophil function or trafficking are highly associated with oral inflammation and periodontitis. The leukocyte NADPH oxidase enzymes complex is a multi-subunit enzyme that has been described to play important immunomodulatory roles in limiting the inflammatory responses of neutrophils and macrophages. Here, we determined the impact of loss of NADPH oxidase dependent reactive oxygen species (ROS) generation in gingival inflammatory responses using a model of ligature induced murine periodontitis.

overall_design: Total RNA was isolated from inflamed gingival tissues (tissue surrounding the second maxillary ligated molar) as well as gingival tissues of naïve mice. 3 age and sex matched mice were used per group.  Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit along with TruSeq RNA CD Index Plate from Illumina. Sequencing runs were performed on the Illumina NextSeq 500 using the NextSeq 500/550 75 cycle High Output Kit v2.5.

first: Juhi

last: Bagaitkar

middle: C


title: Deciphering bat influenza H18N11 infection dynamics in Jamaican fruit bats on a single cell level

city: Fort Collins

first: Tony

last: Schountz

address: 3185 Rampart Rd

institute: Colorado State University

summary: Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected Jamaican fruit bats with the bat-derived influenza A virus H18N11. Using comparative single-cell RNA sequencing, we generated a single-cell atlas of the Jamaican fruit bat intestine and mesentery, the target organs of infection. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was prominent in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this virus. Our study provides insight into the virus-host relationship and thus serves as a fundamental resource for further characterization of bat immunology.

overall_design: Jamaican fruit bats were infected with 5x10^5 TCID50 25 µL of either WT H18N11 (n=6) or the NS1-deficient variant delNS1 (n=6). At 3 and 9 dpi 3 animals each were euthanized and the mesentery and intestine of each bat was processed for scRNA-seq. Four uninfected control bats were included.

first: Geoffroy

last: Andrieux

first: Melanie

last: Boerries

first: Kevin

last: Ciminski

first: Susanne

last: Kessler


title: DOT1L controls NK cell activation and lineage integrity [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K79me2 in NK cells.


title: DOT1L controls NK cell maturation and lineage integrity

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

overall_design: Refer to individual Series


title: Deterioration of multi-level 3D genome organization during breast cancer progression [third-party re-analysis]

status: Public on Aug 06 2024

city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.

relation:
Reanalysis of: GSM2258716
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Reanalysis of: GSM2949413
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Reanalysis of: GSM2949415
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Reanalysis of: GSM4158376
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Reanalysis of: GSM5504443
Reanalysis of: GSM5504444
Reanalysis of: GSM5504445

overall_design:
We reanalyzed publicly available ChIP-seq datasets (CTCF, H2AZ, H3K9ac, H3K9me3, H3K27ac, H3K4me3, H3K27me3, H3K79me2, gH2AX, p53) for MCF10A, MCF10AT1 and MCF10Ca1a to compare chromatin states with our subcompartment annotation (GSE246947) (note that not all experiments included dataset for MCF10AT1 and MCF10Ca1a).

The re-analyzed samples are from GSE85158, GSE93757, GSE98551, GSE100234, GSE109721, GSE134297, GSE140252, and GSE181524 Series records.
The sample titles and their GEO, SRA, biosample accessions are provided in the 're-analyzed_sample_accns.txt' and the processed data file associated with each sample is listed in the  'sample_to_processed-data-file.txt'

**Re-analysis data processing step:
nf-core/chipseq v2.0.0
Samples were processed using nf-core/chipseq after collapsing replicates.
hg38 and Gencode v43 were used as reference genome assemby and gene annotation, respectively.
The effective genome size for MACS2 provided to the pipelien through the –macs_gsize option was computed using unique-kmers.py from khmer v2.1.1.
Peaks for transcription factors were called in narrow peak mode, while the rest of the peaks were called in broad peak mode.

**processed data files format and content:
BigWig files contain ChIP coverage scaled to 1 million mapped reads. Files containing coverage for background (control) are suffixed with “_input”.
Files in narrowPeak and broadPeak format contain the peaks called with MACS2.

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Philippe

last: Collas

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [scRNA-seq]

status: Public on Apr 12 2024

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary:
Atherosclerotic plaques are complex tissues composed of a heterogeneous mixture of cells. However, our understanding of the comprehensive transcriptional and phenotypical landscape of the cells within these lesions is limited.
To characterize the landscape of human carotid atherosclerosis in greater detail, we combined cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to classify all cell types within lesions (n=21; 13 symptomatic) to achieve a comprehensive multimodal understanding of the cellular identities of atherosclerosis and their association with clinical pathophysiology.
We identified 25 cell populations, each with a unique multi-omic signature, including macrophages, T cells, NK cells, mast cells, B cells, plasma cells, neutrophils, dendritic cells, endothelial cells, fibroblasts, and smooth muscle cells (SMCs). Among the macrophages, we identified 2 proinflammatory subsets enriched in IL1B or C1Q expression, 2 TREM2 positive foam cells (one expressing inflammatory genes), and subpopulations with a proliferative gene signature and SMC-specific gene signature with fibrotic pathways upregulated. Further characterization revealed various subsets of SMCs and fibroblasts, including SMC-derived foam cells. These foamy SMCs were localized in the deep intima of coronary atherosclerotic lesions. Utilizing CITE-seq data, we developed a flow cytometry panel, using cell surface proteins CD29, CD142, and CD90, to isolate SMC-derived cells from lesions. Lastly, we observed reduced proportions of efferocytotic macrophages, classically activated endothelial cells, and contractile and modulated SMC-derived cells, while inflammatory SMCs were enriched in plaques of clinically symptomatic vs asymptomatic patients.
Our multimodal atlas of cell populations within atherosclerosis provides novel insights into the diversity, phenotype, location, isolation, and clinical relevance of the unique cellular composition of human carotid atherosclerosis. These findings facilitate both the mapping of cardiovascular disease susceptibility loci to specific cell types as well as the identification of novel molecular and cellular therapeutic targets for the treatment of the disease.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on carotid athersclerotic plaques from 12 subjects (6 symptomatic).

first: Alexander

last: Bashore


title: Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

status: Public on Mar 26 2024

city: Moscow

first: Ilya

middle: Andreevich

last: Pletenev

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skoltech

summary: Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit distinct structure in neurons, which corroborates with increased cohesin levels in neurons and therefore might be attributed to elevated neuronal loop extrusion activity.

overall_design:
Hi-C experiments on NeuN+ and NeuN- cells isolated from human post-mortem brain samples (BA22p)

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

middle: A

first: Maria

last: Bazarevich

first: Diana

last: Zagirova

first: Anna

last: Kononkova

last: Cherkasov

first: Olga

middle: I

last: Efimova

first: Eugenia

last: Tiukacheva

first: Kirill

last: Morozov

first: Dmitriy

last: Komkov

last: Tvorogova

first: Vera

middle: E

last: Golimbet

first: Nikolay

last: Kondratyev

first: Sergey

last: Razin

first: Philipp

last: Khaitovich

last: Ulianov

first: Ekaterina

last: Khrameeva


title: Unlocking the power of transcriptomic biomarkers in qualitative and quantitative genotoxicity assessment of chemicals II

status: Public on Mar 27 2024

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: There is a need to move from binary hazard assessment to more quantitative assessment of genotoxicity to better inform human health risk assessment and understand the relevance of positive in vitro genotoxicity findings. New approach methodologies (NAMs), including transcriptomic biomarkers combined with high-throughput technologies, enable the testing of a broad concentration range, which allows quantitative assessment of in vitro results. Initial work with the transcriptomic GENOMARK and TGx-DDI biomarkers demonstrate their potential use for hazard identification and chemical prioritization; however, no study has evaluated the concordance and complementarity of GENOMARK and TGx-DDI. The overall aim of this study is to examine if a combined approach of integrating both transcriptomic biomarkers for genotoxicity in human relevant HepaRGTM cells increases the certainty in hazard calls and potency rankings of chemicals. A sub-aim is to investigate whether GENOMARK is applicable to the TempO-Seq® high-throughput sequencing technology, to collect concentration-response data to rapidly perform hazard classification and potency ranking.  Therefore, HepaRGTM cells were exposed to 10 chemicals (i.e. eight known in vivo genotoxicants and two in vivo non-genotoxicants) in increasing concentrations over 72h. TempO-Seq® was used to obtain concentration-response data for both biomarkers. Benchmark concentration (BMC) modelling of chemicals that were classified positive was conducted to obtain BMCs and transcriptomic points of departure (tPODs) for potency ranking. The results confirm that GENOMARK is applicable to TempO-Seq® since it achieved 100% predictive accuracy. In addition, a high concordance was observed in the hazard classifications and potency rankings between both biomarkers. Overall, our findings show that in vitro transcriptomic data can be used to rapidly and effectively identify genotoxic hazards while simultaneously providing additional insights on potency that is more informative in a modern hazard assessment paradigm. The results of this case study support the high value of integrating these NAMs in a weight of evidence evaluation of genotoxicity using the important human-liver cell line.

overall_design: A total of 71 samples were sequenced using a whole human transcriptome panel for this toxicogenomics study on a qualitative and quantitative genotoxicity assessment of chemicals, including technical controls (reference RNA; and cells with no treatment). The solvent controls were comprised of 0.5% DMSO in medium. 5 concentrations of each chemical were tested in triplicate, meaning in three different batches of HepaRGTM cells.

first: Anouck

last: Thienpont

first: Eunnara

last: Cho

first: Andrew

last: Williams

last: J Meier

first: Carole

last: L Yauk

last: Rogiers

first: Tamara

last: Vanhaecke

first: Birgit

last: Mertens


title: Fif3 regulates the development of Penicillium oxalicum fungi and the expression of cellulolytic genes

status: Public on Mar 13 2024

city: Qingdao 266237

first: Ma kexuan

last: Qin yuqi

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

country: China

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT) and Fif3 deletion strain (DFif3) under conditions of 1% bran + 1% microcrystalline cellulose as carbon source. The results of correlation analysis between each sample showed that the gene expression level of DFif3 was significantly different from that of the WT strain. The deletion of DFif3 significantly down-regulates the expression levels of sporulation process genes. And the absence of DFif3 can broadly up-regulate the expression level of cellulase-encoding genes, indicating that DFif3 can cause a decrease in cellulase synthesis by affecting the expression of cellulase-encoding genes.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Fif3 deletion mutant strain in 18h in modified Mendal’s medium with 1% bran + 1% microcrystalline cellulose as carbon sources. Three replicates were included for each samples.

first: Kexuan

last: Ma

first: Yuqi

last: Qin


title: Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival

status: Public on Mar 01 2024

first: Alex

last: Nechiporuk

summary: Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish, this function is mediated by Rohon-Beard somatosensory neurons (RBs). RBs are optically accessible and amenable to experimental manipulation, making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however, the number and molecular make up of these potential RB subtypes have not been well defined. Using a single-cell RNA sequencing (scRNA-seq) approach, we demonstrate that larval RBs in zebrafish fall into three, largely non-overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross-species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A-fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities, including mechanical stimulation and chemical irritants. We leveraged our scRNA-seq data to determine that the fibroblast growth factor (Fgf) pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover, this phenotype can be phenocopied by treatment with an FDA-approved Fgf inhibitor dovitinib, which is used in clinic and causes peripheral neuropathy. Importantly, dovitinib-mediated axon loss can be suppressed by loss of Sarm1, a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug.

overall_design: Thirty-hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.

first: Adam

last: Tuttle

first: Lauren

last: Miller

first: Lindsey

last: Royer

first: Jimmy

middle: J

last: Kelly

first: Nicholas

last: Calistri

first: Laura

last: Heiser


title: Viral reprogramming of host transcription initiation [RNA-seq]

status: Public on Feb 01 2024

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Viruses are master remodelers of the host cell environment in support of infection and virus production. For example, viruses typically regulate cell gene expression through modulating canonical cell promoter activity. Here, we show that Epstein Barr virus (EBV) replication causes “de novo” transcription initiation at 29,674 new transcription start sites throughout the cell genome. De novo transcription initiation is facilitated in part by the unique properties of the viral pre-initiation complex (vPIC) that binds a simple TATT[T/A]AA, TATA box-like sequence and activates transcription with minimal support by additional transcription factors. Other de novo promoters are driven by the viral transcription factors, Zta and Rta and are influenced by directional proximity to existing canonical cell promoters, a configuration that fosters transcription through existing promoters and transcriptional interference. These studies reveal a new way that viruses interact with the host transcriptome and shed light on primal features driving promoter function

overall_design: RNA-Sequencing of B cell lines, Mutu (EBV+), Akata (EBV+), during latency and reactivation conditions and DG75 (EBV-) following Zta/Rta transfection.

first: Nate

last: Ungerleider


title: Schizophrenia risk gene ZNF804A controls ribosome localization and synaptogenesis in developing human neurons

status: Public on Jan 30 2024

city: London

last: Sichlinger

address: 5 Cutcombe Rd

country: United Kingdom

institute: King's College London

summary: ZNF804A was amongst the first genes robustly associated with schizophrenia based on findings from large-scale genomic studies. Previous research has implicated ZNF804A inthe regulation of gene expression and synaptic function, but the role this gene plays inneurodevelopment and in relation to schizophrenia pathogenesis remains unclear. To study the function of this gene during neurodevelopment, we generated isogenichuman induced pluripotent stem cells (hiPSCs) with reduced ZNF804A expression, differentiated them into developing cortical glutamatergic neurons and studied theirtranscriptomic, synaptic and protein signatures. Mutant neurons showed modest changes in gene expression. However, high-content confocal imaging revealed increased excitatory synapse density in mutant neurons. Cell-compartment specific proteomic analysis further revealed that mutant neurons had higher levels of ribosomal andtranslational proteins in their neurites, and high-content imaging confirming increased local protein synthesis efficiency. Overall, these results demonstrate that in human developing cortical glutamatergic neurons, ZNF804A regulates excitatory synapse formation potential via increased local protein translation.

overall_design: This study aimed to investigate the role of the schizophrenia susceptibility gene ZNF804A through transcriptomic analysis in a relevant cellular model. We conducted a comprehensive expression profile of ZNF804A during glutamatergic cell development, identifying immature post-mitotic forebrain neurons as a suitable model. CRISPR/Cas9 genome editing was employed to induce mutations in ZNF804A, and bulk RNAseq was performed to assess transcriptional changes.

first: Lucia

last: Dutan Polit

first: Rodrigo

last: Duarte

first: Timothy

last: Powell

first: Deepak

middle: P

last: Srivastava


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing

status: Public on Jan 17 2024

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

platform_organism:
Mus musculus
synthetic construct


title: Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation

city: Atlanta

first: Anita

middle: H.

last: Corbett

state: Georgia

address: 1510 Clifton Road

department: Biology

institute: Emory University

summary: The RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3-subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.

overall_design: RNA-seq analysis of biological triplicates of budding yeast RNA exosome mutant cells (rrp4-G226D, rrp40-S87A, rrp40-W195R, rrp45-I15P, rrp46-Q86I, rrp46-L127T, rrp46-L191H, rrp6∆) and budding yeast RNA exosome control cells (RRP4, RRP40, RRP45, RRP46, RRP6).

first: Maria

last: Sterrett

first: Lauryn

last: Cureton

last: Cohen

first: Ambro

last: van Hoof

first: Sohail

last: Khoshnevis

first: Milo

middle: B

last: Fasken

middle: H

first: Homa

last: Ghalei


title: Single-cell multimodal profiling of atherosclerosis identifies CD200 as a cell surface lineage marker of vascular smooth muscle cells and their derived cells

first: Chenyi

last: Xue

summary: Vascular smooth muscle cells (VSMCs) play a central role in the development of atherosclerosis due in part to their capability to phenotypically transition into either a protective or harmful state. However, the ability to identify and trace VSMCs and their progeny in vivo is limited due to the lack of well-defined VSMC cell surface markers. Therefore, investigations into VSMC fate must utilize lineage-tracing mouse models, which are time-consuming and challenging to generate and not feasible in humans. Here, we employed CITE-seq to characterize the phenotypic expression of 119 cell surface proteins in mouse atherosclerosis. We found that CD200 is a highly expressed and specific marker of VSMCs, which persists even with phenotypic modulation. We validated our findings using a combination of flow cytometry, qPCR, and immunohistochemistry, all confirming that CD200 can identify and mark VSMCs and their derived cells in early to advanced mouse atherosclerotic lesions. Additionally, we describe a similar expression pattern of CD200 in human coronary and carotid atherosclerosis. Thus, our data support the use of CD200 as a lineage marker for VSMCs and VSMC-derived cells in mouse and human atherosclerosis.

overall_design: Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was used to perform in-depth cell surface phenotyping of all cells within mouse atherosclerotic lesions. Aortas from ROSA26LSL-ZsGreen1/+Myh11-CreERT2 vascular smooth muscle cell lineage traced mice at various times of western diet feeding (0, 8, 16, and 26 weeks) were digested in an enzyme cocktail containing 4U/mL Liberase, 60U/mL Hyaluronidase and 60U/mL DNase in RPMI for 1 hour. Cell suspension was then labeled with the TotalSeq-A Mouse Universal Cocktail (BioLegend: 199901) oligo-conjugated antibodies and subsequently fluorescently activated cell sorted and viable cells were identified as being DRAQ5+ and DAPI-. Cells were then submitted for single cell profiling using the 10x Genomics 3’ v3 protocol. Single cell analysis identified CD200 as a potential cell surface lineage marker for VSMCs and their derived cells. To validate this, we used flow cytometry to isolate CD200+ and CD200- cells and performed qPCR on isolated cells.

first: Alexander

last: Bashore


title: Ferroptosis as a senolytic target to clear primary and secondary senescent cells

city: Mountain View

first: Tesfahun

middle: Dessale

last: Admasu

state: CA

address: 110 pioneer way, ste. j

department: ApoptoSens

institute: SENS Research Foundation

summary:
Purpose: Next-generation sequencing (NGS) on senescent primary endothelial cells. The goals of this study was to compare NGS-derived transcriptome profiling (RNA-seq) of DPP4+ primary and secondary senescent endothelial cells isolated from multiple donors.
Methods: Gene expression profile of DPP4+ isolated primary and secondary senescent endothelial cells were generated by deep sequencing, in triplicate, using Illumina Hiseq4000. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Results: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Conclusions: Our study represents the first detailed analysis of primary and secondary senescent cells  transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles of primary and secondary senescence. Our results show that primary and secondary senescent cells have distinct gene expression profile.

overall_design: senescence was induced for 7 days and DPP4+ senescent cells were isolated. Gene expression profiles of DPP4+ primary and secondary senescent endothelial cells were determined.

first: Alexandra

last: Stolzing

first: Amit

last: Sharma


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [ISS, Cartana]

summary: Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.

overall_design: Kidney spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (ISS, Cartana) and 10X Visium

first: Benjamin

last: Humphreys


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [RNA-seq]

status: Public on Jan 10 2024

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF Forkhead box A (FOXA), required for endoderm lineage commitment, coordinates with the PR domain zinc finger 1 (PRDM1) TF to recruit Polycomb repressive complexes, which establish bivalent enhancers and repress alternative lineage programs. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to repress cell differentiation programs in pluripotent stem cells, suggesting this is a common feature of pioneer TFs. We propose that pioneer and PRDM TFs coordinate recruitment of Polycomb complexes to safeguard cell fate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human PSCs, endoderm, mesoderm, and neuroectoderm and their KD derivatives (FOXA-TKD, PRDM1-KD, and OCT4-KD)

first: Satoshi

last: Matsui

first: Marissa

last: Granitto

first: Morgan

last: Buckley

first: Joseph

last: Shiley

first: William

last: Zacharias

first: Christopher

last: Mayhew

first: Makiko

last: Iwafuchi


title: High/low MNase-seq in foregut, Control and FOXA-TKD

summary: Nucleosome occupancy and positioning were examined in foregut stage to compare control and FOXA-TKD using high/low MNase-seq

overall_design: low-MNase-seq for identify accessible/fragile nucleosomes and high-Mnase-seq for identify stable nucleosomes


title: Rigor and Reproducibility of Acoustofluidics of saliva from healthy donors

status: Public on Dec 29 2023

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: This is for Rigor and Reproducibility study to demonstrate the reproducibility of AFS SOP for EV separation, RNA isolation, and RNA analysis by using saliva samples from healthy individuals. Blinded saliva samples have been processed by two independent AFS operators for EV separation and subjected to miRNA-seq analysis. EV-associated miRNA seqeunces were used as a monitoring tool for Rigor and Reproducibility of AFS process between operators.

overall_design: Saliva samples from healthy volunteers (5 female and 5 male) were collected based on our research SOP and split into two fractions for AFS analysis by two independent operators. Resulting two AFS fractions (waste and collected) per sample per operator were blinded and sent to UCSD for miRNA-seq analysis. Resulting sequencing data have been analyzed for the statistical evaluation of Rigor and Reproducibility in AFS separation of EV’s. This has been determined by evaluating the statistical difference in miRNA’s existing in EV’s separated from each sample by two independent operators.

first: David

last: Wong

first: Tony

last: Huang

first: Yong

last: Kim

first: Louise

last: Laurent

first: Jianping

last: Xia

first: Abbas

last: Hakim


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate [CUT&Run and ChIP-seq]

overall_design: ChIP-seq or CUT&RUN for transcription factors, PRC components, and histone modifications in human PSCs, definitive endoderm, foregut cells, and their KD derivatives (FOXA-TKD and OCT4-KD) .


title: Transcriptome analysis of gene expression in Lasiodiplodia theobromae

status: Public on Dec 31 2023

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Botryosphaeriaceae is an important fungal family that can colonize a wide range of woody hosts including economically important plants and cause serious diseases worldwide. To uncover the virulence variation in Lasiodiplodia theobromae, we sequenced the transcriptome of Las1 in L. theobromae inoculated with the stems of V.vinifera using dual-RNAseq method. We found a lot of expanded genes were induced after inoculated with grapevine compared with the transcriptome of Las1 that was maintained in PDA under the same condition.

overall_design: The L. theobromae strain Las1 was selected for inoculation tests on detached Vitis vinifera cv. ‘Summer Black’ branches. Briefly, wounds of green grapevine shoots were inoculated with mycelium plugs (5 mm in diameter) cut with a cork borer and then maintained under an alternating dark/light cycle inside a growth chamber with constant humidity and a temperature of 25 °C. All the inoculated grapevine tissues were collected at 24 h post-inoculation, and fungal mycelia collected from PDA at 24 h post-culturing at 25 °C were used for subsequent RNA-seq analyses. Total RNA was extracted and processed following Novogene Company methodologies for preparing Illumina RNA-seq libraries. Paired-end sequencing was performed on an Illumina HiSeq 4000 platform to generate 150-bp paired-end reads. RNA-seq was performed on three independent biological replicates.

first: Jiye

last: Yan


title: Molecular mechanisms underlying the high mortality of hypervirulent Klebsiella pneumoniae and its effective therapy development

status: Public on Dec 26 2023

city: Hong Kong

first: QI

last: XU

address: B2530, Yeung Kin Man Academic Building, City University of Hong Kong, Hong Kong

department: Department of Infectious Disease and Public Health

institute: City University of Hong Kong

summary: High-resolution single-cell RNA-seq reveals the immune landscape of hvKp-infected lungs

overall_design: Lung cells of the C57B/L6 mice were isolated and analyzed using scRNAseq.

first: Qi

first: Xiaoxuan

last: LIU

first: Heng

last: HENG

first: Sheng

last: CHEN


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes

status: Public on Dec 15 2023

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design:
We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability.

This project includes the following series:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193274
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193296
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193299
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193313
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193339
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193372
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193458
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193499
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201248
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201830
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201910
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201933
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202033
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202062
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202125
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202162
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249238
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249336
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249399
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249705

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

middle: M

last: Behrens

first: Eran

last: Mukamel


title: Non-coding RNA analysis in IgM monoclonal gammopathies: an underrecognized role of microRNA and long non-coding RNA differentiating Waldenström macroglobulinemia from IgM-MGUS

status: Public on Dec 08 2023

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Waldenström macroglobulinemia (WM), is a rare non-Hodgkin lymphoma preceded by a clinically asymptomatic benign monoclonal gammopathy of undetermined significance (IgM-MGUS). The factors underlying the malignant progression between these two IgM-monoclonal gammopathies remain poorly understood. The non-coding genome is increasingly recognized as an important driver of disease pathogenesis, and there remains a lack of exploration of the influence of non-coding RNAs within the IgM-monoclonal gammopathy disease spectrum. The present study explores the role of microRNA (miRNA) and long non-coded RNA (lncRNA) in IgM-gammopathies and specifically elucidates potentially regulated protein-coding genes and pathways. A comprehensive analysis of miRNA, lncRNA and protein-coding coding genes was conducted on 28 subjects, 17 patients with WM, 6 patients with IgM-MGUS, and 5 normal controls. Differential expression analysis revealed a number of dysregulated miRNA and lncRNA between IgM-gammopathies compared to normal controls and specifically between IgM-MGUS and WM. Pathway analysis was conducted utilizing differentially expressed mRNA with correlated biological expression of targeting miRNA. Here, a number of pathways were implicated influencing a gamut of cellular functions, including cell signaling, metabolism, replication, and immune regulation in both WM compared to IgM-MGUS and IgM-gammopathies compared to controls. This report is additionally one of the first published analyses of lncRNAs in WM, where we demonstrate a number of lncRNA associated with transcription and apoptosis regulation genes in WM compared to IgM-MGUS. This study highlights the role of non-coding RNA in IgM-gammopathies and the potential to recognize novel targets which may halt or slow the malignant progression between these two diseases.

overall_design: The study included samples from 28 subjects, 17 patients with WM, 6 patients with IgM-MGUS, and 5 normal controls. Bone marrow samples were collected and selection for CD19+ and/or CD138+ B cells was performed. mRNA and miRNA analyses were peformed on the isolated cells.

first: Stephen

last: Ansell

first: Jonas

last: Paludo

first: Karan

last: Chohan


title: Molecular Clusters and Tumor-Immune Drivers of IgM Monoclonal Gammopathies

summary: Purpose: IgM monoclonal gammopathy of undetermined significance (MGUS) and Waldenström macroglobulinemia (WM) represent a disease spectrum with highly varied therapeutic management, ranging from observation to chemoimmunotherapy. The current classification relies solely on clinical features and does not explain the heterogeneity that exists within each of these conditions. Further investigation is warranted to shed light on the biology that may account for the clinical differences.    Experimental design: We used bone marrow (BM) clonal CD19+ and/or CD138+ sorted cells, matched BM supernatant, and peripheral blood serum from 32 patients (7 MGUS, 25 WM) to perform the first multi-omics approach including whole-exome sequencing, RNA sequencing, proteomics, metabolomics, and mass cytometry.    Results: We identified three clusters with distinct pathway activation, immune content, metabolomic, and clinical features. Cluster 1 included only patients with WM and was characterized by transcriptional silencing of genes involved in cell cycle and immune response, enrichment of mitochondrial metabolism, infiltration of senescent T effector memory cells, and aggressive clinical behavior. Genetic/structural alterations of TNFAIP3 were distinct events of this cluster. Cluster 2 comprised both MGUS and WM patients with upregulation of inflammatory response, senescence and glycolysis signatures, increased activated T follicular helper and T regulatory cells, and indolent clinical behavior. Cluster 3 also included both MGUS and WM patients and exhibited intermediate features, including proliferative and inflammatory signaling, as well as glycolysis and mitochondrial metabolism.

first: Patrizia

last: Mondello


title: Microglia care for neurons through tunneling nanotubes

status: Public on Dec 01 2023

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

country: Germany

institute: University Hospital Bonn

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

overall_design: Refer to individual Series


title: Microglia care for neurons through tunneling nanotubes [Dataset 2 Microglia mRNA-seq]

summary: We report the transfer of alpha-s-ynuclein aggregates from neurons to microglia and examined transcriptomic changes following protein extraction. By obtaining RNA samples, we performed differential expression analysis and generated gene ontology enrichment and network analysis.

overall_design: mRNA sequencing of Microglia from mice cocultured in the presence of murine neurons treated with and without aSyn

first: Hannah

last: Scheiblich

first: Frederik

last: Eikens

first: Lena

last: Wischhof

first: Sabine

last: Opitz

first: Kay

last: Jüngling

first: Csaba

last: Cserép

middle: V

first: Tracy

last: Bellande

first: Balázs

last: Pósfai

first: Charlotte

last: Geck

first: Jasper

last: Spitzer

first: Alexandru

last: Odainic

first: Stephanie

last: Schwartz

first: Donato

last: Di Monte

first: Daniele

last: Bano

first: Ádám

last: Dénes

first: Eike

last: Latz

first: Ronald

last: Melki

first: Hans-Christian

last: Pape

first: Michael

middle: T

last: Heneka


title: Expression Data from Brucella abortus strain 2308 and isogenic mavR mutant cells

status: Public on Nov 20 2023

city: Pittsford

first: Paul

last: M Dunman

address: 695 W. Bloomfield Rd

institute: University of Rochester

summary:
MavR is a 160 nucleotide regulatory RNA molecule that is produced during B. abortus strain 2308 growth in nutrient-replete broth.
We used custom-made Affymetrix B. abortus strain 2308 derived GeneChips to compare the gene expression properties of wild type and isogenic mavR mutant cells.

overall_design: B. abortus strain 2308 or mavR mutant cells were grown to late exponential growth phase in brucella broth , total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of abcR1 and abcR2 RNA species.

last: Dunman

first: Clayton

last: Caswell


title: Identify proinsulin regulators using CRISPR screen and mouse genetics

status: Public on Nov 15 2023

city: Cleveland

first: Sisi

last: Lai

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identify proinsulin regulators using CRISPR screen and mouse genetics [RNA-Seq]

summary: Proinsulin is the precursor of insulin in pancreatic beta cells. Altered proinsulin and proinsulin to insulin ratio mark beta cell dysfunction, predictuing disease progression into type 1 and type 2 diabetes. Of essential role for beta cell function, knowledge about proinsulin production and its role in disease are currently very limited. Using genome wide CRISPR screen, we identified 84 proinsulin regulators including classical protein convertases Pcsk1 and Cpe, and novel factors like Pdia6. Among the list 29 proinsulin regulators were trajectory genes involved in disease progression in obesity and type 2 diabetes in humans. In vivo mouse genetics study revealed unique genetic architecture and quantitative trait loci (QTLs) modulating plasma proinsulin levels. Integrative analyzing and mapping of the QTL signals directly pinpointed to proinsulin regulators identified from the CRISPR screen, which in return greatly improved resolution of the mouse genetic study. 4 out of 5 overlapped genes can be individually validated. Knocking down the leading hits Pdia6 leads to decreased proinsulin content and remarkable loss of proinsulin granules in beta cells. Consequently, proinsulin secretion was greatly decreased. Mechanistically, protein translation rate was greatly impaired after knocking down Pdia6. Our study demonstrated the power of combining in vitro functional genomics with in vivo mouse genetics study to identify proinsulin regulatory network in pancreatic beta cells.

overall_design: RNA-seq of MIN6 and EndoC-bH3 cells in the context of non-targeting control and shRNA (MIN6) or siRNA (EndoC-bH3) mediated Pdia6 knocking down.

first: Weng

last: Chen

first: Shanshan

last: Zhang

first: Peidong

last: Gao

first: Yan

last: Li


title: Corticostriatal cocaine-seeking ensembles are defined by differing gene expression from sucrose-seeking ensembles using a within-subject dual self-administration and seeking mouse model

status: Public on Nov 08 2023

city: Fort Collins

first: Ana-Clara

last: Bobadilla

state: Colorado

address: 1350 Centre Ave

department: Biomedical Sciences

institute: Colorado State University

summary: Recurrent cocaine seeking is a hallmark of cocaine use disorder. To develop therapeutic targets, it is critical to understand the neurobiological changes specific to cocaine-seeking in context with the seeking of non-drug rewards, e.g., sucrose. The nucleus accumbens and medial prefrontal cortex are known regions associated with cocaine- and sucrose-seeking ensembles, i.e., a sparse population of co-activated neurons linked with behavior. Within ensembles, transcriptomic alterations in the NAc and mPFC underlie the learning and recall of cocaine- and sucrose-seeking behavior. However, the transcriptomics exclusively driving cocaine seeking independent from sucrose seeking have not yet been defined using a within-subject approach. Using Ai14:cFos-TRAP2 transgenic mice in a dual cocaine and sucrose self-administration model, we fluorescently sorted and characterized the transcriptomes defining cocaine-seeking in reference to the sucrose-seeking ensemble, overlapping ensemble in between cocaine and sucrose-seeking, and the non-ensemble population. Our data suggests there are robust transcriptomic changes linked with cocaine-seeking that differ from sucrose-seeking ensembles and the non-ensemble population which could guide future studies aimed to detangle cocaine-seeking behavior without altering non-drug reward seeking.

overall_design: The 48 RNA-sequencing fastq sample files are labeled in the sequential order: sex (male = M; female = F), region (nucleus accumbens = N; medial prefrontal cortex = P), replicate (replicate 1 = 1; replicate 2 = 2; replicate 3 = 3), and cell population type (cocaine-seeking ensemble = C; sucrose-seeking ensemble = S; overlapping ensemble = O; non-ensemble = NonEns). Supplemental files for each sample are unnormalized and unfiltered transcript count output from Salmon.

first: Litif

middle: G

last: Carl

first: Flom

last: Levi

first: Sandum

middle: L

last: Kathryn

first: Hodgins

last: Skylar

first: Vaccaro

last: Lucio

first: Stitzel

last: Jerry

first: Ungerleider

last: Nathan

first: Mannino

last: Maria Constanza

first: Gigley

last: Jason

first: Schoborg

last: Todd

first: Bobadilla

last: Ana-Clara


title: Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Poly(ADP-ribose) polymerases (PARP1 and PARP2) contribute to DNA base excision repair (BER) and DNA demethylation and has been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.

overall_design: Single-strand break sequencing of 2i-cultivated murine embryonic stem cells (+/- TDG), treated with PARP-inhibitor Talazoparib

first: Jianming

last: Xu

first: Simon

middle: D

last: Schwarz

first: Primo

last: Schär


title: Gene expression profile at single cell level of nucleus pulposus cells (NPCs) from the nucleus pulposus (NP) tissue in the mild degenerative intervertebral discs (MDD) and server degenerative intervertebral discs(SDD).

status: Public on Oct 30 2023

city: Guangzhou

first: Jianru

last: Wang

state: Guangdong

address: No. 58, Zhongshan road II, Guangzhou 510080, People’s Republic of China

institute: Sun Yat-sen University First Affiliated Hospital

summary: It has been shown that the divergence of NPCs plays an important role in the progression of intervertebral disc degeneration (IVDD). We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of NPCs in the IVDD.

overall_design: NP tissue of the different degenerative grade of  IVDs  were isolated in patient IVDs  and analyzed using scRNAseq.


title: DPEP INHIBITS CANCER CELL GROWTH AND SURVIVAL VIA SHARED AND CONTEXT-DEPENDENT TRANSCRIPTOME PERTURBATIONS

status: Public on Oct 10 2023

city: NEW YORK

first: LLOYD

middle: A.

last: GREENE

state: NEW YORK

address: 650 W. 168TH STREET

department: PATHOLOGY AND CELL BIOLOGY

institute: COLUMBIA UNIVERSITY

summary: Dpep is a cell-penetrating peptide targeting transcription factors ATF5, CEBPB and CEBPD that selectively promotes apoptotic death of multiple tumor cell types in vitro and in vivo.  To better understand its mechanism of action, we compared transcriptomes of 6 cancer cell lines of varying origins before and after Dpep exposure. This revealed a context-dependent pattern of regulated genes that was unique to each line, but that exhibited a number of shared elements with other lines. This included upregulation of pro-apoptotic genes and tumor suppressors as well as enrichment of genes associated with responses to hypoxia and interferons.  Downregulated transcripts included oncogenes and dependency genes and enriched genes associated with different phases of the cell cycle as well as with DNA repair.  In each case, such changes have the potential to lie upstream of apoptotic cell death. We also detected regulation of unique as well as shared sets of transcription factors in each line, suggesting that Dpep may initiate a cascade of transcriptional responses that culminate in cancer cell death. Such death thus appears to reflect context-dependent, yet shared disruption of multiple cellular pathways as well as of individual survival-relevant genes.

overall_design: To illuminate the potential mechanisms by which Dpep promotes death of a wide range of tumor cell types, we carried out PLATE-seq (a technology that permits high throughput transcriptomic analysis on multiple samples) on 6 diverse human tumor cell lines: HCT116 (colorectal carcinoma), MDA-MB-231 (triple -negative breast cancer), MCF7 (breast cancer), T98G (glioblastoma) A375 (BRAF mutated melanoma), and A549 (non-small-cell lung cancer). In each case, the cells were treated with or without 20 µM Dpep for 48 hrs prior to analysis. This Dpep concentration is near the IC50 for each line and under these treatment conditions, appreciable cell death only becomes apparent by about 72 hrs, with little at 48 hrs.  Six replicate cultures were assessed for each condition.

first: Lloyd

last: Greene

first: Qing

last: Zhou


title: SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans

status: Public on Oct 04 2023

city: Lyon

first: Cecile

last: Bedet

address: 46 allée d'Italie

department: Bilogie

country: France

institute: ENS de Lyon


title: SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans [sin-3(tm1276)]

summary: The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However,  little is know on its complexity of interactions and functions in developmental processes. Here we show that loss of SIN-3, the single SIN3 homologue in Caenorhabditis elegans, results in maternal effect sterility associated with deregulation of the germline transcriptome, including derepression of X-linked genes. Using proteomics analysis we identify at least two SIN3 complexes containing distinct HDACs and differentially contributing to fertility. Single cell smFISH reveals that loss of sin-3 stochastically derepresses X linked genes in individual germ cells. We further identify acetylation marks whose abundance depends on SIN3. Together, this work provides a powerful paradigm for the in vivo study of SIN3 and associated proteins.

overall_design: Gene expression profiling of germlines from young adults sin-3(tm1276) mutant and wild-type (wt) worms (used as control)

first: Marion

last: Herbette

first: Francesca

last: Palladino

first: Valerie

last: Robert


title: Cerebrospinal fluid immune cells appear similar across neuropathic and non-neuropathic pain conditions.

status: Public on Oct 03 2023

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

summary: Microglia have been implicated in the pathophysiology of neuropathic pain. Here, we sought to investigate whether cerebrospinal fluid (CSF) might be used as a proxy-measure of microglial activation in human participants. For this, we preformed fluorescent-activated cell sorting (FACS) of CSF immune cell populations derived from individuals who experienced pain with neuropathic features. We sorted CD4+, CD8+ T cells and monocytes and analyzed their transcriptome using RNA sequencing. We also performed Cellular Indexing of Transcriptomes and Epitopes (CITE)-seq to characterize the expression of all CSF immune cells in a patient with postherpetic neuralgia and in a patient with neuropathic pain after failed back surgery.   Immune cell numbers and phenotypes were not obviously different between individuals regardless of the etiology of their pain. This was true when examining our own dataset, as well as when comparing it to previously published single-cell RNA sequencing data of human CSF. In all instances, CSF monocytes showed expression of myeloid cell markers commonly associated with microglia (P2RY12, TMEM119 and OLFML3), which will make it difficult to ascertain the origin of CSF proteins: do they derive directly from circulating CSF monocytes or could some originate in spinal cord microglia in the parenchyma? We conclude that it will not be straightforward to use CSF as a biomarker for microglial function in humans.

overall_design: Human CSF immune cell populations were sorted via FACS and either processed using bulk RNA sequencing of sorted populations or at single cell level using CITE-seq.


title: MoTrPAC: Endurance Exercise Training Study In 6 Months Old Rats

status: Public on Sep 30 2023

city: Stanford

first: Euan

last: Ashley

address: 870 Quarry Road

institute: Stanford University

summary:
MoTrPAC endurance exercise training study targets young adult (6-month-old) rats. Specifically, male and female Fischer 344 rats (n = 12) were subjected to progressive treadmill endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last exercise bout. Sex-matched sedentary, untrained rats were used as controls.
This study contributes to MoTrPAC's broader mission, which is to identify molecular changes occurring due to exercise. The ultimate goal is to understand how physical activity can improve and sustain health across various ages and fitness levels.
The program is supported by the NIH Common Fund. For additional information, visit the MoTrPAC Data Hub at https://motrpac-data.org/.

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE242354
SuperSeries of: GSE242355
SuperSeries of: GSE242357

overall_design: 6-month-old young adult rats (Fischer 344) were subjected to progressive endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last training bout. Sex-matched sedentary, untrained rats were used as controls. Whole blood, plasma, and 19 solid tissues were analyzed using genomics, proteomics, metabolomics, and protein immunoassay technologies, with most assays performed in a subset of these tissues. Depending on the assay, between 3 and 6 replicates per sex per time point were analyzed.


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [ATAC-seq]

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.

overall_design:
Regular exercise promotes whole-body health and prevents disease, yet the underlying molecular mechanisms throughout a whole organism are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, and immunome in whole blood, plasma, and 18 solid tissues in Rattus norvegicus over 8 weeks of endurance exercise training. The resulting data compendium encompasses 9466 assays across 19 tissues, 25 molecular platforms, and 4 training time points in young adult male and female rats.

Contributor: Molecular Transducers of Physical Activity Consortium (MoTrPAC)


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [RRBS]


title: MoTrPAC- Endurance Exercise Training Study In 6 Months Old Rats [RNA-seq]

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old month) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.


title: Maternal obesity disrupts epigenetic reprogramming via peroxisomal-dependent phospholipid-methyl uncoupling during zygotic genome activation

status: Public on Sep 07 2023

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

summary: Maternal obesity is known to cause systemic lipid dysregulation, yet its effect on lipid reprogramming during the maternal-to-zygotic transition (MZT) remains unknown. Here we show that obesity disrupts very-long-chain fatty acid (VLCFAs) storage in oocytes and downregulates PEX13, impairing peroxisomal protein import in 2-cell embryos. Normally, peroxisomal β-oxidation converts oocyte-stored VLCFAs into medium- and long-chain fatty acids, which fuel triglyceride synthesis and drive phosphatidylethanolamine (PE) methylation to phosphatidylcholine (PC). This metabolic flux consumes methyl donors to facilitate H3K4me3 erasure and zygotic genome activation (ZGA). In obese mice, VLCFA deficiency and PEX13 dysfunction lead to metabolic-epigenetic uncoupling, depleting lipid droplets and sustaining H3K4me3, thereby suppressing ZGA and blastocyst development. Importantly, supplying long-chain fatty acids or overexpressing PEMT restores the phospholipid-methyl cycle, rescuing epigenetic reprogramming and development. Our findings establish peroxisomal β-oxidation as a metabolic-epigenetic nexus essential for MZT and reveal a phospholipid-methyl coupling mechanism underlying obesity-associated embry development, offering novel therapeutic entry points to improve fertility in metabolic disorders.

overall_design: GV oocyte, MII oocyte, Zygote, 2-cell embryo from normal diet mice. GV oocyte, MII oocyte, 2-cell embryo from high-fat diet mice. Control embryos and siAcox1 embryos at 2-cell embryos were performed RNA sequencing.

first: Xiao-Guohui

last: Zhang

first: Xie

last: Feng

first: Yu-Wei

first: Shi-Ming

last: Luo

first: Qing-Yuan

last: Sun

first: Xiang-Hong

last: Ou


status: Public on Sep 25 2023

overall_design: control embryo compared with siAcox1-2-cell embryo of H3K4me3 modification by CUT&Tag

first: Linli

first: Guohui

last: Zhangxiao

first: Shiming

first: Qingyuan

first: Xianghong


title: RNAseq of CD4 T cells from female Rheumatoid arthritis patients [NeumRA_CD4]

status: Public on Sep 06 2023

city: Gothenburg

first: Maria

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 60 female RA patients activated with aCD3 for 2 hours. Patients were collected crossectionally from the Rheumatology clinic during 2019-2020. Age md 64, range 23-76 years, Disease duration md 10, range 1-45 years.

overall_design: 60 women with  rheumatoid arthritis, CD4 cells  from human PBMC isolated by positive selection on Dynabeads (cat.11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich)  for 2h

first: Karin

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Nina

last: Oparina

first: Eric

last: Malmhäll-Bah


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [mRNA_APAP]

status: Public on Sep 01 2023

city: Hangzhou

first: CHAO

last: CHEN

state: Zhejiang

address: The First Affiliated Hospital, College of Medicine, Zhejiang University, NO.79 Qingchun Road, Hangzhou, Zhejiang 310003, China

institute: zhejiang university

summary: Acute liver failure is a serious clinical manifestation resulting from sudden liver injury, which can be triggered by various factors. One of the most frequent causes of acute liver failure is excessive ingestion of acetaminophen (APAP), which is known to damage hepatocytes directly by reducing glutathione levels in cells, ultimately leading to hepatocyte death.PGE2 can play a dual role in inflammation, either promoting or inhibiting the inflammatory response, depending on the cell type, local concentration, receptor type, and tissue microenvironment. Early studies have shown that PGE2 significantly alleviated acute liver failure induced by galactosamine/lipopolysaccharide, APAP, and carbon tetrachloride. However, the precise mechanism by which PGE2 alleviates APAP-induced acute liver failure remains unclear. The aim of this study is to investigate the mechanisms underlying the protective effects of PGE2 against APAP-induced hepatocyte injury.

overall_design: RNA-seq was conducted on total RNA isolated from livers of AILI mice treated with 500 mg/kg APAP or dmPGE2 300μg/kg for 6 h; n = 3 per group.

first: Chao

last: Chen

first: Xinyu

last: Gu

first: Qingfei

last: Chu

first: Jun

last: Guan

first: Haihong

last: Zhu


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [circRNA_APAP]


title: Single-Cell Transcriptomic Profiling of Heart Reveals ANGPTL4 Linking Fibroblasts and Angiogenesis inHeart Failure with Preserved Ejection Fraction

city: Chongqing

first: Wujian

last: Liu

state: Chongqing

address: No. 83 Xinqiao Main Street, Shapingba District

institute: Xinqiao Hospital of Army Medical University


title: Single-Cell Transcriptomic Profiling of Heart Reveals ANGPTL4 Linking Fibroblasts and Angiogenesis inHeart Failure with Preserved Ejection Fraction [scRNA-seq]

summary: Heart failure with preserved ejection fraction (HFpEF) is a complex, heterogeneous disease involving multiple cellular lineages and mechanisms. Here, we aimed to characterize the cellular heterogeneity and potential mechanisms of HFpEF at single-cell resolution.

overall_design:
Eight-week-old male C57BL/6N mice were randomly divided into two groups: an HFpEF group administered with a high-fat diet and N-nitro-L-arginine methyl ester (L-NAME, 0.5 g/L in drinking water) and a control group fed on normal diet and water. Both groups were exposed to a 12-h light/dark cycle daily. After 5 weeks, cardiac ultrasound was conducted to assess the mice's ejection fraction and diastolic function. Then, mice were euthanized by excess inhalation of CO2, followed by the isolation of the hearts and the removal of atrial tissue. Three and five ventricular samples for single-cell sequencing and bulk RNA-seq. respectively, were then obtained from each group.
IMPORTANT: Please note that there was an inconsistency when referring to the control group, i.e., control group vs. CON. To avoid confusion, I have used “control group” consistently throughout the manuscript.

first: Guoxing

last: Li

first: Huilin

last: Zhao

first: Junjin

first: Zhe

last: Cheng

first: Yuhong

last: Qin

first: Gang

first: Yongzheng

last: Guo


title: Liver Transcriptomics from Male and Female HET3 Mice on Control, Low Amino Acid and Low Isoleucine Diets when started in Young and Middle Aged Mice

status: Public on Nov 07 2023

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

summary: Mice were put on either a control, low amino acid or low isoleucine diet at 9 weeks of age or 6 months of age and their liver transcriptomic expression was measured after 14 weeks and 18 months respectively on diet after an overnight fast. This was to discover the impact of sex, protein and isoleucine level on the metabolism of the liver.

overall_design: To compare the metabolic effect of total amino acid and just isoleucine restriction in hetergeneous mice on different sexes and ages, 9-week-old or 6-month-old mice were placed on either a Control, Low Amino Acid or Low Isoleucine diets for 13 weeks. All mice were maintained at a temperature of approximately 22°C. Mice were euthanized by cervical dislocation and livers were harvested and snap frozen in liquid nitrogen following overnight (16-hr) fasting.


title: Adrenomedullin promotes the migration of interneurons in a human forebrain assembloid model for hypoxic interneuronopathy of prematurity.

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

summary: We developed a model for hypoxic injury of migrating human cortical interneurons using forebrain organoids and forebrain assembloids derived from hiPSCs.

overall_design: Human subpallial organoids at day 46 in culture were exposed to hypoxia (<1% oxygen) for 12 and 24 hours. Some samples were exposed for 24 hours and  subsequently reoxygenated for 72 hours. Samples were immediately collected and snap frozen for processing.

first: Anca

last: Pasca

first: Jeremy

middle: A


title: The  application of epiphenotyping approaches to DNA methylation array studies of the human placenta

status: Public on Aug 08 2023

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary:
204 placentas from three cohorts were processed for DNAme arrays in Vancouver, Canada. The three cohorts consisted of: (i) V-NORM, a normative population of term pregnancies recruited at BC Women’s Hospital (BCWH) in Vancouver, Canada (n=35), as part of a study on Epigenetics in Pregnancy Complications (EPIC); ii) V-SSRI, a population of pregnant individuals recruited in Vancouver, Canada in the 20th week of gestation (n=64), with/without clinical depression, and with/without the use of selective serotonin reuptake inhibitors (SSRIs); and (iii) QF-2011, a population of term pregnancies that were exposed to sudden-onset stress during gestation due to catastrophic flooding in the Australian state of Queensland in early January 2011 (n=105).
DNA samples from all three cohorts were run on Illumina Infinium MethylationEPIC arrays in Vancouver, BC, Canada. Processing included DNA purification after extraction using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA), bisulfite conversion using the EZ DNAme Kit (Zymo Research, Orange, CA, USA), and hybridization to and processing of the Illumina Infinium MethylationEPIC BeadChip arrays according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Samples from the three cohorts were randomized and run in 3 array batches across 44 eight-sample chips as illustrated in Supp Figure 5. In the case of the V-SSRI and QF-2011 cohorts, sample exposure groups (SSRI exposed/non-exposed and objective flood stress high/low) and infant sex were carefully distributed across array chips (1-44) and rows (1-8) to minimize potential batch effects.    DNAme data from raw IDAT files were read into R v4.2.2(54) and annotated with the Illumina Infinium MethylationEPIC v1.0 B4 Manifest. Several data quality control checks were undertaken using the R packages minfi(55,56), wateRmelon(57,58), and ewastools(59). First, each sample was assessed at 17 Illumina control probes to evaluate bisulfite conversion efficiency and array run quality; all samples passed the manufacturer-recommended thresholds at the control probes. Next, average total (methylated + unmethylated) fluorescence intensity was assessed between samples, and between array batches. All samples had similar total fluorescence, though samples run on the EPIC array in Batch 3 had slightly higher average intensities than those in Batch 1 and 2. Sample sex was assessed with the ewastools package(59), using the mean total fluorescence intensity (methylated + unmethylated) of the X and Y chromosome probes, normalized to the per-sample mean autosomal total fluorescence intensity, and was confirmed to match the clinically-reported sex of the infant in all cases. Sample genetic identity was assessed using the 59 SNP (‘rs’) probes on the EPIC array with the call_genotypes() and enumerate_sample_donors() functions (ewastools)(59). Finally, DNAme beta value density plots of all samples were visually assessed to determine overall similarity of the beta value distributions between samples, with no outliers identified.

overall_design: 204 placentas and 19 technical replicates were analyzed with the Illumina Infinium Methylation EPIC array. These samples came from 3 distinct collection cohorts but were processed for arrays at a single facility in Vancouver, Canada. The tools included in the PlaNET R package (https://www.bioconductor.org/packages/release/bioc/html/planet.html) were used to estimate epiphenotype variables of ancestry, gestational age, and cell type composition in these samples, and these estimates were evaluated for relationships with each other, and with technical and biological variables associated with these cohorts.

first: Almas

last: Khan

first: Amy

last: Inkster

first: Maria

middle: S

last: Penaherrera

first: Suzanne

last: King

first: Sue

last: Kildea

first: Cathy

last: Vaillancourt

first: Tim

middle: F

last: Oberlander

first: Ursula

last: Brain

first: Ella

middle: O

last: Beraldo

first: Alexander

last: Beristain

first: Vicky

last: Clifton

first: Giulia

last: Del Gobbo

first: Wan

last: Lam

first: Gerlinde

last: Metz

first: Jane

last: Ng

first: David

last: Olson

first: E

last: Price

first: Johanna

last: Schuetz

first: Victor

last: Yuan

first: Elodie

last: Portales Casamar


title: Analysis of micro-RNA expression profiles in human islets and islet-derived exosomes during cytokine mediated β cell stress and death

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: Biomarkers capable of monitoring β cell stress during the evolution of type 1 diabetes (T1D) are currently lacking. MicroRNAs (miRNAs) are a class of small non-coding RNAs ~22 nucleotides in length that modulate gene expression by binding to the 3’untranslated region of target mRNAs.  Given their stability in biological fluids and enrichment in cell-derived EVs, we hypothesized that miRNAs from human islet and islet-derived EVs could identify β-cell stress/death and be leveraged in T1D biomarker strategies. To test this, human islets were obtained from 10 cadaveric donors (5 male/5 female) and treated with or without cytokines (IL-1β and IFN-γ) for 24 hrs, as an ex vivo model of T1D. Small RNA sequencing was performed and  identified 1110 and 890 miRNAs in total and 20 and 14 differentially expressed (DE) miRNAs (fold change≥1.5 and p<0.05) from islets and EVs, respectively. These findings were validated in an independent set of cytokine-treated islets and islet-derived EVs (7M and 5F donors). Interestingly, miRNA expression pattern was strikingly different between male and female donors at baseline and under cytokine stress with < 10% overlap among the DE miRNAs. miR-155-5p and miR-146a-5p were the only two miRNAs that were upregulated in cytokine-treated islets and EVs in both the sexes. Functional enrichment analysis of DE miRNAs identified pathways such as insulin signaling, ER stress and apoptosis. Taken together, these data suggest that miRNA expression patterns change dynamically in both human islets and islet-derived EVs in response to pro-inflammatory cytokine stress. EV miRNAs were largely distinct from those in the islet fraction, suggesting that miRNAs are selectively packaged into EVs in response to extrinsic cues. Finally, these data highlight the importance of considering sex as a biological variable when defining T1D biomarkers.

overall_design: Identification of differentially expressed miRNAs from human islets and islet-derived exosomes treated with/without proinflammatory cytokines (IL-1B + IFN-g)

first: Farooq

last: Syed

first: Preethi

last: Krishnan


title: Surprising mechanisms and regulatory roles of yeast transcription factors [RNA-seq]

status: Public on Aug 01 2023

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: DNA sequence-specific transcription factors (TFs) modulate transcription and chromatin architecture, acting from regulatory sites in enhancers and promoters of eukaryotic genes. How multiple TFs cooperate to regulate individual genes is still unclear. Most yeast TFs are thought to regulate transcription via binding to Upstream Activating Sequences, situated within a few hundred base pairs upstream of the regulated gene1. While this model has been validated for individual TFs and specific genes, it has not been tested in a systematic way. We integrated information on the binding and expression targets for the near-complete set of yeast TFs. Here we show that, contrary to expectations, there are few TFs with dedicated activator or repressor functions with most TFs having a dual role. While nearly all protein coding genes are regulated by one or more TFs, our analysis revealed limited overlap between TF binding and gene regulation. Rapid depletion of many TFs also revealed numerous regulatory targets distant from detectable TF binding sites, suggesting unexpected regulatory mechanisms. Our study provides a comprehensive survey of TF functions, offering insights into interactions between the set of TFs expressed in a single cell type and how they contribute to the complex program of gene regulation.

overall_design: Newly synthesized RNAs were labeled with 4TU, purified and analyzed with RNA-seq. Depletion of TFs was achieved through targeted degradation (auxin-degron system). Control and treatment sample files are labeled DMSO and 3IAA (3-indole acetic acid), respectively. All experiments were done in three replicates (A,B,C).

first: Linda

last: Warfiled

first: Rafal

last: Donczew

first: Steven

last: Hahn


title: Surprising mechanisms and regulatory roles of yeast transcription factors

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

overall_design: Refer to individual Series


title: Surprising mechanisms and regulatory roles of yeast transcription factors [ChIP-seq]

overall_design: Standard ChIP-seq approach including crosslinking, chromatin extraction, DNA fragmentation and immunoprecipitation. All experiments were done in triplicates.


title: Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

overall_design: ChEC-seq method was used to map genome-wide binidng of transcription factors. Experiments were done in two, three (A,B,C) replicates