title: High-resolution CRISPR/Cas9 screens identify PAK2 as a suppressor of macrophage proliferation and macropinocytosis.

status: Public on May 01 2024

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

institute: South Dakota State University

summary: Macrophages play critical roles in immune function and are implicated as etiological agents in disease states such as cardiovascular disease and cancer. However, there is limited understanding of macrophage fitness molecular regulators, including survival, proliferation, and adhesion. This work identifies positive and negative regulators of macrophage fitness by harnessing the power of CRISPR/Cas9 whole genome screening technology. Here, we identified loss-of-function gene disruptions that caused mutant bone marrow-derived macrophages (BMDM) to decrease in culture abundance as supporters of macrophage fitness. Similarly, we identified genes that limit or suppress macrophage fitness by identifying those gene disruptions that caused BMDM to increase in abundance in cell culture. To do this, we analyzed the difference in frequency of sgRNA between the purified plasmid library used for lentiviral transfection versus the amplified sgRNA inserts from the DNA of BMDM following a 14-day post-viral transduction culture. With this approach, we identified gene disruptions to canonical essential genes, including previously described macrophage-specific essential genes such as Csf1r, as well as novel genes required for macrophage growth and survival. In addition, we also identified gene disruptions that increased macrophage abundance in culture, including canonical tumor suppressors such as p53 (Trp53) and cell cycle regulators (Cdkn1a/2a). Interestingly, targeting p21-activated kinase-2 (Pak2) led to those mutants becoming more productive, suggesting a novel role for Pak2 in suppressing macrophage fitness. Using targeted knockouts of PAK2, we show that PAK2 protein depletion affects NF2/Merlin-mediated downregulation of cyclin-d1. Further, this work indicates that PAK2 suppresses macropinocytic uptake in macrophages by modulating actin dynamics impacting pro-mitogenic signaling pathways downstream of macropinocytosis. Overall, this work shows how multiple pathways impact macrophage fitness and highlights the central role of PAK2 in macrophage fitness and macropinocytosis.

overall_design: Transgenic mice with a Rosa26-Cas9 knock-in on a C57BL/6J background were received from Jackson Laboratories (Stock No. 026179, Bar Harbor, ME). Mice were euthanized using CO2 inhalation and cervical dislocation, femurs were dissected from the mice, and bone marrow was harvested (Swanson, 1989) by flushing Dulbecco’s phosphate buffer saline (DPBS) without calcium or magnesium (GE Healthcare Life Sciences, Pittsburgh, PA) through the bone using a needle and syringe. Cells were plated in culture media containing 20% HI-FBS and 30% L-cell supernatant in high glucose DMEM in non-tissue culture-treated sterile dishes and incubated at 37°C with 5% CO2. Additional culture media was added to the cells on day two post-isolation. Following cell adherence to the dish, on day 4, the medium was removed entirely, and fresh BMM was added to the culture. On day five cells were treated with 10 mM Cyclosporin A for 20 minutes before adding lentivirus with Brie library to the cells. Multiplicity of infection (MOI) ~ 0.3-0.1. Library coverage was around 100-200-fold representation of each sgRNA. Transduced cells were antibiotic-selected two days after transduction with 5mg/mL puromycin. Cells were cultured for at least 14 days for protein depletion (post-culture). Genomic DNA was extracted from post-culture cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher). The sgRNA inserts from genomic DNA (Post-culture) and library plasmid DNA (Input) were PCR amplified by a single-step PCR protocol (Broad Institute). Barcoded primers with staggered sequences are used for next-generation sequencing (NGS). Sequencing of 75 base reads was conducted on Illumina Nextseq 500. Following quality control analysis using FASTQC, reads were mapped to the sgRNA library to identify genes, and read frequency tables were generated using Model-based Analysis of Genome-wide CRISPR-Cas9 Knockouts (MAGeCK), version 0.5.9 (Li et al., 2014a).

first: Kevin

middle: N

last: Wanniarachchi

first: Astha

last: Neupane

first: Bidhi

last: Kasu

first: Bijaya

last: Pradhan

first: Jason

middle: G

last: Kerkvliet

first: Xijin

last: Ge

first: Adam

middle: D

last: Hoppe


title: An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus [snRNA-seq]

status: Public on Apr 27 2024

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

country: USA

institute: Lieber Institute for Brain Development

type: Expression profiling by high throughput sequencing

summary: The hippocampus contains many unique cell types, which serve the structure’s specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and probe their expression in the SRT data. Using this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.

overall_design:
We obtained tissue blocks of postmortem human brain containing anterior hippocampus from 10 neurotypical adult brain donors. We used the 10x Genomics Visium and 3’ Single Cell Gene Expression platforms to generate paired spatial transcriptomics and single-nucleus RNA-seq data of the human hippocampus. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for two of the 10 donors.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Erik

last: Nelson

first: Madhavi

last: Tippani

first: Anthony

last: Ramnauth

first: Heena

middle: R

last: Divecha

first: Ryan

middle: A

last: Miller

first: Nicholas

middle: J

last: Eagles

first: Elizabeth

last: Pattie

first: Sang

middle: H

last: Kwon

first: Svitlana

middle: V

last: Bach

first: Uma

middle: M

last: Kaipa

first: Jianing

last: Yao

first: Joel

middle: E

last: Kleinman

first: Leonardo

last: Collado-Torres

first: Shizhong

last: Han

first: Kristen

last: Maynard

first: Thomas

last: Hyde

first: Stephanie

middle: C

last: Page

last: Hicks


title: PML restrains p53 activity and cellular senescence in clear cell renal cell carcinoma

status: Public on Apr 23 2024

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

summary: Clear cell renal cell carcinoma (ccRCC), the major subtype of RCC, is frequently diagnosed at late/metastatic stage with 13% 5-year disease-free survival. Functional inactivation of the wild type p53 protein is implicated in ccRCC therapy resistance, but the detailed mechanisms of p53 malfunction are still poorly characterized. Thus, a better understanding of mechanisms of disease progression and therapy resistance is required. Here, we report a novel ccRCC dependence on the promyelocytic leukemia PML protein. We show that PML is overexpressed in ccRCC and that PML depletion inhibits cell proliferation and relieves pathologic features of anaplastic disease in vivo. Mechanistically, PML loss unleashed p53-dependent cellular senescence thus depicting a novel regulatory axis to limit p53 activity and senescence in ccRCC. Treatment with the FDA-approved PML inhibitor arsenic trioxide induced PML degradation and p53 accumulation, and inhibited ccRCC expansion in vitro and in vivo. Therefore, by defining non-oncogene addiction to the PML gene, our work uncovers a novel ccRCC vulnerability and lays the foundation for repurposing an available pharmacological intervention to restore p53 function and chemosensitivity.

overall_design:
RNA-sequencing (RNA-seq) in control and PML silenced RCC4 cells.

UPDATE
[Jul-20-2026] The title, genotype, and treatment fields for GSM7880001 and GSM7880002 were swapped in the original submission and have been corrected.

first: Matilde

last: Simoni

first: Chiara

last: Menegazzi

first: Cristina

last: Fracassi

first: Claudia

last: Biffi

first: Francesca

last: Genova

first: Nazario

middle: P

last: Tenace

first: Roberta

last: Lucianò

first: Andrea

last: Raimondi

first: Carlo

last: Tacchetti

first: James

last: Brugarolas

first: Davide

last: Mazza


title: Monocyte RNA after exposure to platelets

status: Public on Apr 12 2024

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: The effects of platelet expsoure on RNA expression in platelet naïve monocytes

overall_design: Monocytes were incubated overnight with platelets, washed and LPS stimulated

first: Craig

last: Morrell

first: Chen

last: Li


title: Histone modifications of Monocytes in the context of thrombocytopenia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We sought to define changes in open and closed chromatin in monocytes isolated from control and thrombocytopenic mice

overall_design: Mice were made thrombocytopenic or not, and monocytes isolated for ATAC-seq


title: A disease similarity approach identifies short-lived Niemann-Pick type C disease mice with accelerated brain aging as a novel mouse model for Alzheimer’s disease and aging research

status: Public on May 07 2024

city: Richmond

first: Vikas

last: Gujjala

state: Virginia

address: 1000 W Cary Street

department: Biology

institute: Virginia Commonwealth University

summary: Since its first description in 1906 by Dr. Alois Alzheimer, Alzheimer’s disease (AD) has been the most common type of dementia. Initially thought to be caused by age-associated accumulation of plaques, in recent years, research has increasingly associated AD with lysosomal storage and metabolic disorders, and the explanation of its pathogenesis has shifted from amyloid and tau accumulation to oxidative stress and impaired lipid and glucose metabolism aggravated by hypoxic conditions. However, the underlying mechanisms linking those cellular processes and conditions to disease progression have yet to be defined. Here, we applied a disease similarity approach to identify unknown molecular targets of AD by using transcriptomic data from congenital diseases known to increase AD risk, namely Down Syndrome, Niemann Pick Disease Type C (NPC), and Mucopolysaccharidoses I. We uncovered common pathways, hub genes, and miRNAs across in vitro and in vivo models of these diseases as potential molecular targets for neuroprotection and amelioration of AD pathology, many of which have never been associated with AD. We then investigated common molecular alterations in brain samples from an NPC disease mouse model by juxtaposing them with brain samples of both human and mouse models of AD. Detailed phenotypic and molecular analyses revealed the NPCmut mouse as a novel, short-lived in vivo model of AD characterized by accelerated brain aging, concluding that the NPCmut mouse model can serve as a potential short-lived in vivo model for AD research and for understanding molecular factors affecting brain aging. This research represents the first comprehensive approach to congenital disease association with neurodegeneration and a new perspective on AD research while highlighting shortcomings and lack of correlation in diverse in vitro models. Considering the lack of an AD mouse model that recapitulates the physiological hallmarks of brain aging, the characterization of a short-lived NPC mouse model will further accelerate the research in these fields and offer a unique model for understanding the molecular mechanisms of AD from a perspective of accelerated brain aging.

overall_design:
To identify novel biomarkers and treatment strategies against AD in the context of congenital disorders with increased AD-risk, we performed commonality analysis on AD and selected congenital disorders (DS, NPC, MPS I) human samples and mice samples from APP/PS1 mice and NPC1KO (NPC model) mice
We compared frontal cortex transcriptomic data from our NPC1KO mice to both APP/PS1 AD mouse frontal cortex transcriptomic data and human AD frontal cortex data

first: Alaattin

last: Kaya


title: An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus [spatial-visium]

first: Keri

last: Martinowich

first: Erik

last: Nelson

first: Madhavi

last: Tippani

first: Anthony

last: Ramnauth

first: Heena

last: Divecha

first: Ryan

last: Miller

first: Nicholas

last: Eagles

first: Elizabeth

last: Pattie

first: Sang

last: Kwon

first: Svitlana

last: Bach

first: Uma

last: Kaipa

first: Jianing

last: Yao

first: Joel

last: Kleinman

first: Leonardo

last: Collado-Torres

first: Shizhong

last: Han

first: Kristen

last: Maynard

first: Thomas

last: Hyde

first: Stephanie

last: Page

last: Hicks


title: RNA expression in Monocytes from thrombocytopenic mice

first: Tyler

last: Stahl

summary: We sought to define changes in gene expression in monocytes in the context of thrombocytopenia

overall_design: Mice were made thrombocytopenic or not and monocytes isolated from the blood for RNA-seq

first: Craig

last: Morrell

first: Chen

last: Li


title: ATACseq for Young and Old mouse liver

status: Public on Apr 17 2024

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Our goal was to identify how aging affects chromatin accessability in the mouse liver.

overall_design: C57BL/6 mice were euthanized using CO2 and cervical dislocation.  Whole liver was excised and maintained on ice cold DMEM and nuclei were isolated while tissue was fresh. Tagmentation was conducted for 30 minutes at 37 degrees Celsius followed by DNA isolation and library preperation.

first: Aaron

last: Havas

first: Neil

last: Robertson

first: Brandon

last: Sos

first: Kun

last: Zhang


title: Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

status: Public on Mar 21 2024

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

summary: Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factors expressed during early OE patterning. Among these are two Pax3/7 duplicates that we named Pax37A and Pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 is playing a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica Pax37A and Pax37B in the development of the OE, using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals that we compared with scRNA-seq data from C. intestinalis. We revealed that Pax37B but not Pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supports that these cells have a neuroepithelial-like transcriptional signature. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features such as “glue” secreting collocytes of ascidians. Their development seems to be controlled by a fragmented GRN that also operates in ascidian epidermal neurons.

overall_design: To reveal downstream genes that are regulated by Pax37b, we compared the transcriptomes of Pax37b-/- individuals to wild-type transcriptomes

first: David

last: Lagman

first: Anthony

last: Leon

first: Cieminska

last: Nadia

first: Wei

last: Deng

first: Marios

last: Chatzigeorgiou

first: Daniel

last: Chourrout


title: A developmental shift in glucocorticoid receptor expression preserves glucocorticoid sensitivity in the adult suprachiasmatic nucleus.

status: Public on Apr 10 2024

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

country: Germany

institute: UKSH

summary:
The circadian system synchronizes physiology, improving the adaptation to daily environmental changes. In mammals, the master pacemaker, in the suprachiasmatic nuclei (SCN) of the hypothalamus, coordinates “wake” functions by inducing the circadian release of glucocorticoids (GCs). GCs entrain the clocks of a wide variety of tissues through GC receptor (GR) activation, however, the influence of GCs on the SCN is unclear and seems to depend on the maturity of the circuit. During the perinatal period, the mouse SCN express GR and respond directly to GCs while the adult SCN express low GR and have been traditionally considered resistant to GCs. To understand the change of sensitivity to GCs we followed the developmental trajectory of the mouse SCN, and found that while GR is expressed in all SCN cells early in life it remains expressed mainly in astrocytes in the adult. Using a model of prenatal
exposure to GCs we found that offspring from treated mothers, adapt slower to shifted light-dark cycle and shows reduced expression of GR in SCN astrocytes. The adult SCN astrocytes can indeed sense and respond to GCs with rapid astrocytic Ca2+ events that propagate across neighboring cells, an effect that is prevented by the specific inhibition of astrocyte-astrocyte communication. Our findings provide a conceptual advance on how the mouse clock develops and on the influence that GCs have on the SCN. This might be relevant to understand how circadian synchrony is restored in conditions of temporal misalignment, such as jet lag.

overall_design: We have assessed the mRNA expression profile of the developing mouse SCN at single-cell resolution at three key developmental time points (gestational day (GD) 17.5, postnatal day (PND) 2, PND10) and at PND30 when the SCN circuit is fully mature. At GD17.5 a substantial increase in the synchrony of clock genes’ oscillations in SCN cells has been observed concurrent to the neurogenic-gliogenic switch. At PND02 neurons are differentiated and the first peak of astrocytes’ proliferation happens. At PND10 the maturation of the RHT and the innervation of the ventral SCN is complete and the eyes open, light entrainment would promote the final development of the circuit. At PND30, the SCN circuit architecture has reached the maturity of the adult nuclei.

last: Haendler

first: Varun

last: Sreenivasan

first: Violetta

last: Pilorz

first: Celina

last: Martinez-Perez

first: Iratxe

last: Elorduy

first: Tomas

last: Casas

first: Marianne

last: Lehmann

first: Jon

last: Olano Bringas

first: Laura

last: Escobar Castañondo

first: Nora

last: Bengoa-Vergniory

first: Federico

last: Soria

first: Henrik

last: Oster

first: Malte

last: Spielmann

first: Mariana

last: Astiz


title: RNAseq for Young Old mouse liver hepatocytes with and without high fat diet

first: Peter

last: Adams

summary: Our Goal was to determine how hepatocytes of young and old mice differentially respond to 9-weeks of high fat diet vs normal chow.

overall_design: Upon receipt mice were rested for at least 2-weeks prior to initiation of experiment in which mice were maintained on either High fat diet (58y1, TestDiet) or  normal CHOW (Teklad global 18% protein) for 9-weeks prior to euthanasia and hepatocyte isolation.

first: Aaron

last: Havas

first: Xue

last: Lei


title: Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations [MethylationEPIC]

status: Public on Mar 11 2024

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

country: South Korea

institute: KRIBB

type: Methylation profiling by genome tiling array

summary: Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. We then excluded 40 patients with EA and 7 patients with NENA microsatellite instability. Genome analysis revealed that TP53 (25%), KRAS (22%), ROS1 fusion (14%), and SETD2 (11%) were the most frequently mutated  genes  in  NENA  patients.  Proteogenomic  impact  analysis revealed that STK11 and ERBB2 somatic mutations had broader effects on cancer-associated genes in NENA. Through DNA copy-number alteration analysis, we identified 22 prognostic proteins, inﬂuencing transcriptomic and proteomic changes. Gene set enrichment analysis revealed that the estrogen signaling emerged as the key pathway activated in NENA. A lot of proteogenomic evidence supported the increased estrogen signaling, such as copy-number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was suggested as a potential drug for targeting activated estrogen signaling in NENA, and was experimentally validated in vitro using cell line model. In this study, we enhanced our understanding of the etiology of NENA NSLA through the proteogenomic landscape, based on which we proposed saracatinib as an effective drug

overall_design: The Infinium MethylationEPIC BeadChip (Illumina) was employed for methylation array experiments following the manufacturer’s instructions. Briefly, 500 ng of gDNA from lung tissues was treated with 20 µL of sodium bisulfite solution using an EZ DNA Methylation-Gold µKit (Zymo Research). Bisulfite-converted DNA (4 µL) was amplified using the Infinium Methylation Assay Kit (Illumina). The amplified DNA was hybridized to the Infinium MethylationEPIC BeadChip and scanned using an Illumina iSCAN system. CpG methylation values were calculated as average-values using Minfi (v3.11), with the following equation: average = M/(M + U + 100), where M and U are the methylated and unmethylated signal intensities, respectively. Measurements with a p-value <0.05 were considered significant above the background. Additionally, redundant probes, including multi-hit probes and SNPs, which could affect the analysis results, were filtered using the ChAMP package filter function.


title: Myeloid PDLIM2 repression as a common causal mechanism of lung disease pathogenesis and susceptibility to infection

status: Public on Feb 29 2024

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

summary: Selective deletion of PDLIM2 in myeloid cells rendered mice more vulnerable to lung injury and mortality after LPS intratracheal instillation, which was associated with the exacerbated activation of pro-inflammation signaling pathways and the more diminished activation of anti-inflammation signaling pathways in the lung, and particularly, in lung macrophages and neutrophils.

overall_design: The experiments started with WT and Pdlim2 myeloid KO (mKO) mice of similar age. Each group was further divided into PBS and LPS-treated ones where treatment was administered through intratracheal injection. Lungs from these 4 groups of mice were dissected 48hr post treatment and were then dissociated into single cell suspension. scRNAseq was done with the combination of 10x genomics single cell 5’ kit and customized sample multiplexing using TotalSeq CD45 tag antibody.

first: Feng

first: Xujie

last: Liu

first: Fan

last: Sun

first: Yadong

last: Xiao

first: Zhaoxia

last: Qu


title: Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations [RNA-seq]

overall_design: Expression profiling by high throughput sequencing


title: Trypanosoma cruzi conserved proteome microarray

status: Public on Feb 28 2024

city: New Orleans

first: Eric

last: Dumonteil

state: LA

address: 1440 Canal st.

department: Tropical Medicine

institute: Tulane University

summary: Antibody recognition of Trypanosoma cruzi conserved proteins was assessed by evaluating pools of patient IgG samples on microarrays of 400,000 peptides covering these proteins as 15-mers with an overlap of 13 amino acids.

overall_design: Trypanosoma cruzi conserved proteome

first: Alicia

last: Majeau

first: Claudia

last: Herrera


title: Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm.

status: Public on Feb 20 2024

city: Wuhan

first: Xiaodan

last: Yan

state: Hubei Province

address: Donghu Road, No. 115, Wuchang District,

department: Medical Research Institute

country: China

institute: Wuhan University

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
Refer to individual Series

** The submitter states that the study's data have undergone significant changes and are no longer accurately reflected in SuperSeries GSE239505 [Feb 20, 2024]. The correct data are in SuperSeries GSE260458. **


title: Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals

status: Public on Feb 14 2024

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

overall_design: Refer to individual Series


title: Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals [RNA-seq]

summary: Lactate is present at a high level in the microenvironment of mammalian preimplantation embryos in vivo and in vitro. However, its role in preimplantation development is unclear. Here, we report that lactate is highly enriched in the nuclei of early embryos when major zygotic genome activation (ZGA) occurs in humans and mice. The inhibition of its production and uptake results in developmental arrest at the 2-cell stage, major ZGA failure, and loss of lactate-derived H3K18lac, and the abnormal phenotypes could be recapitulated by overexpression of H3K18R mutation and rescued by addition of Lac-CoA. By profiling the landscape of H3K18lac in human and mouse preimplantation embryos, we show that H3K18lac is enriched on the promoter regions of most major ZGA genes and corelates with their expressions. Taken together, we demonstrate the important role for lactate in major ZGA via H3K18lac, showing a conserved metabolic mechanism underlies preimplantation development of mammalian embryos.

overall_design: RNA-seq libraries were prepared as described previously. Briefly, 5 embryos were used per group, and three replicates were performed for each group. Embryos were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Phusion Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher). Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were sequenced using the NovaSeq 6000 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

first: Jingyu

last: Li

first: Weibo

last: Hou

first: Qi

last: Zhao

first: Wei

last: Han

first: Jianzhong

last: Su

first: Shaorong

first: Guoning

last: Huang

first: Qingran

last: Kong


title: Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals [CUT&TAG]

overall_design: CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech). Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C. For single-cell CUT&Tag of human embryos, CUT&Tag was performed in well of a microplate. After tagmentation, single human embryos were transferred to 200µl tubes containing 5% Proteinase K. After embryos lysis, PCR buffer and adaptors were directly added to tubes, normal PCR cycle was performed. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (Vazyme Biotech). Libraries were sequenced on the Illumina NovaSeq 6000 platform according to the manufacturer’s instructions.

last: Gao


title: Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm [scRNA-seq]

summary: Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. Remarkably, our findings elucidated that PdeI upregulates cellular levels of c-di-GMP, which acts as an antitoxin to modulate the toxicity of toxin protein HipH. HipH localizes on nucleoid and functions as a potent DNase, inducing cells into a viable but non-culturable state. Conversely, c-di-GMP interacts with HipH, reducing its genotoxic effects and enabling cells to enter a persister state, resulting in drug tolerance. Importantly, by targeting this toxin-antitoxin system, we repressed drug tolerance in Uropathogenic Escherichia coli infections, offering promising therapeutic strategies against chronic and relapsing infections.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
we performed a new single-cell library construction method for three species of bacteria: Escherichia coli MG1655, Pseudomonas aeruginosa PAO1, Staphylococcus aureus 25923 and verified the effect of different treatments during library construction on library data. Then we analysed two E.coli single-cell sequencing datas, because we found that by cluster analysis we can find biofilm's marker gene

** The submitter states that the study's data have undergone significant changes and are no longer accurately reflected in SuperSeries GSE239505 [Feb 20, 2024]. The correct data are in SuperSeries GSE260458. **


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling [Human]

status: Public on Feb 02 2024

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: In order to study the effects and mechanisms of PD inhalation drug delivery, models of LPS-induced murine holistic pneumonia, isolated macrophage inflammation, and epithelial cell co-culture are utilized. For the evaluation of efficacy, pathology and molecular assays have been utilized. Mechanisms of action and targets were screened and validated by molecular means using transcriptome sequencing. Efficacy and mechanism of action were ultimately validated using human BALF cell models. Also studied were pharmacokinetic parameters of inhaled PD.

overall_design: Human monocytic THP-1 and A549 were obtained from the Shanghai Institute of Cell Biology (Shanghai, China). THP-1 cells were cultured in RPMI 1640 (GIBCO, Grand Island, NY) containing 10% FBS (GIBCO, Grand Island, NY) in 5% CO2 at 37 °C. Before further treatment, THP-1 cells (1×106 cells/mL) were inoculated into 6-well plates and treated with 500 nM PMA for 4 h to induce macrophage differentiation. Next, cells were washed 3 times with phosphate-buffered saline (PBS) and incubated for 24 h to exclude PMA interference. THP-1 cells treatment was divided into 3 groups: a control group with no treatment, a model group with LPS at 1 μg/mL, a PD group with 1 μg/mL of LPS and 10 μM of PD.


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Multiome-seq]

status: Public on Jan 11 2024

city: Brookline

first: Ramesh

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed simultaneous gene expression profiling and chromatin analysis at single cell level using data obtained from Multiome-seq at various  time points.

overall_design:
Multiome-seq at various  time points
Please note that processed data generated from both RNA and ATAC is linked to the corresponding  *Multiome-seq, RNA sample records.
barhash.csv.gz
filteredinbarcodes.csv.gz

first: Pratik

last: Singh


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [scRNA-seq]

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed gene expression profiling analysis at single cell level using data obtained from single cell RNA-seq of at various  time points.


title: Extracellular Vesicle and Particle miRNAs in Human Milk

status: Public on Jan 30 2024

city: Lebanon

first: Caitlin

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: EVP miRNAs levels were measured in the supernatant fraction of 54 human milk samples collected approximately 6 weeks postpartum from individuals in New Hampshire using the NanoString nCounter Human v3 miRNA expression panel

overall_design: 54 human milk samples


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling [Mouse]

summary: Background: There are no highly effective medications for treating pneumonia. Ginseng and its derivatives have anti-inflammatory properties, but their unstable physicochemical and metabolic properties prevent them from being used to treat pneumonia. The aforementioned issues may be resolved by inhalation, but the precise mechanism of action must be investigated.  Methods: In order to study the effects and mechanisms of PD inhalation drug delivery, models of LPS-induced murine holistic pneumonia, isolated macrophage inflammation, and epithelial cell co-culture are utilized. For the evaluation of efficacy, pathology and molecular assays have been utilized. Mechanisms of action and targets were screened and validated by molecular means using transcriptome sequencing. Efficacy and mechanism of action were ultimately validated using human BALF cell models. Also studied were pharmacokinetic parameters of inhaled PD.  Results: Inhalation of PD dose-dependently reduced LPS-induced lung inflammation in mice, including inflammatory cell infiltration, lung histopathology, and inflammatory factor expression. Oral PD had the same anti-inflammatory effect as inhalation, but inhalation was more effective at the same dose. It could be a result of its increased bioavailability and improved pharmacokinetic parameters. Using transcriptome analysis and validation of macrophage and epithelial cell experiments, we discovered that PD may inhibit TNFA/TFNAR and IL7/IL7R signaling to inhibit macrophage inflammatory factor-induced epithelial cell apoptosis and promote value-added initiation. Human alveolar lavage cell experimentation confirmed this result.  Conclusion: PD inhalation alleviates lung inflammation and pathology by inhibiting TNFA/TFNAR and IL7/IL7R signaling. PD may be a novel drug for the clinical treatment of lung inflammation.

overall_design: Animals were randomly divided into 3 groups (n = 6 in each group): control (sterile saline [0.9% NaCl]), model (LPS 50 μg/mouse), E (LPS+PD (10 mg/mL, inhalation [ih.])).  For the inhaled group, mice were put into an inhalation box connect with a aerosol device (PARIBOY SX, Germany) .


title: Systematic mapping of TF-mediated cell fate changes by a pooled inductioncoupled with scRNA-seq and multi-omics approaches

status: Public on Feb 05 2024

city: AUSTIN

first: Qingqing

last: Guo

state: TX

address: 2506 Speedway

institute: The University of Texas at Austin

summary: Transcriptional regulation controls various cellular functions via the interactionsbetween cell-type-specific transcription factors (TFs) and their chromosomaltargets. While multiple TFs capable of converting cell fates from one to anotherhave been reported, only a few systematic studies aiming to understand thefate conversion potential of numerous individual TFs have been reported. Here,we propose an iTF-seq method (pooled induction of individual TFs followed bysingle-cell RNA sequencing) to identify potent TFs capable of converting cellfates and elucidate their lineage specification potential at a single-cell level.Enabling metabolic biotinylation of TFs during the process, the method allowssubsequent multi-omics approaches to understand underlying actionmechanisms of TFs during cell fate changes. Our pilot iTF-seq of 80 TFs inmouse embryonic stem (ES) cells has identified multiple previously known andunknown TFs triggering transcriptome changes within one day of TF induction.Subsequent tests revealed that Gcm1 and Otx2 function as activators andpioneer factors, while they resulted in distinct cell fates and gene expressionprograms upon induction.

overall_design: BioChIP-seq was performed on Gcm1 and Otx2 SBFB cells after 24h of Dox induction with uninduced control cells as well as Nanog FB mESCs. ATAC-seq was performed on Gcm1 and Otx2 SBFB cells after 24h of Dox induction with uninduced control cells.

first: Jonghwan

last: Kim


title: ZNF200 interacts with DDX17 in the RBP-J promoter region to regulate the transcriptional activity of RBP-J.[ATAC-Seq]

status: Public on Feb 26 2026

city: hefei

first: xiaozheng

last: wei

address: tanghelu

institute: Anhui Medical University

summary: We knocked down ZNF200 and DDX17 in the H520 and A549 cell lines, respectively. Using ATAC-seq, we examined changes in chromatin accessibility.

overall_design:
Knock down ZNF200 and DDX17 in H520 and A549 cell lines, perform ATAC-seq, and compare with the control group.

UPDATE
[Jul-16-2026] The Sample titles and processed data files were updated to remove "H3K4me3".

first: Weixiao

last: Zheng

first: Qian

last: Dai

first: Yanke

last: Zhang


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [ChIP-seq]

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then analysed active histone marks using data obtained from H3K27ac ChIP-seq at various  time points.


title: Phosphorylation of SF3B1 by CDK11 1 orchestrates spliceosome activation via SNIP1 dependent RES complex recruitment

status: Public on Feb 24 2026

city: Pamplona

first: Igor

last: Ruiz de los Mozos

state: Nyp

address: C. del Sadar s/n

department: Department of Personalized Medicine

country: Spain

institute: NASERTIC

summary: Splicing Factor 3b Subunit 1 (SF3B1), a core component of the spliceosome, undergoes dynamic phosphorylation and dephosphorylation during the splicing cycle to regulate pre-mRNA splicing. Twenty-eight threonine/proline repeats are phosphorylated by CDK11 during spliceosome activation and remain phosphorylated in the catalytically active spliceosomes. The function of phosphorylated SF3B1 (P-SF3B1), and the identity of spliceosomes stalled by CDK11 inhibition remain unclear. Using quantitative proteomics of chromatin-associated spliceosomes, we identify a previously uncharacterized intermediate complex BOTS964, arrested by CDK11 inhibitor OTS964, that incorporates the nineteen-related (NTR) but not nineteen (NTC) complex. iCLIP-seq revealed that P-SF3B1 engages with the U6 snRNA internal stem-loop (ISL), suggesting a potential role in stabilizing the RNA catalytic core. We further demonstrate that P-SF3B1 is recognized by forkhead-associated (FHA) domain of SNIP1, which promotes recruitment of retention and splicing (RES) complex during spliceosome activation. Acute SNIP1 depletion disrupts RES incorporation, causes widespread splicing defects, and promotes hyperphosphorylation of SF3B1 by CDK11. Mutations in SNIP1 FHA domain, including the neurodevelopmental disorder associated E366G variant, impair P-SF3B1 binding, pre-mRNA splicing, and cell viability. Together, these findings uncover the phosphorylation-dependent CDK11/P-SF3B1/SNIP1 signaling axis that is critical for pre-mRNA splicing and cellular proliferation and provide a mechanistic insight into its dysregulation in disease.

overall_design: Examination of RNA-seq in the presence or absence of SNIP1 protein on HCT116 dTAG SNIP1 cells.

first: Pavla

last: Gajduskova

last: Ruiz de Los Mozos

first: Milan

last: Hluchy

first: Antonina

last: Myskova

first: Katerina

last: Zabrady

first: Peter

last: Manik

first: Neda

last: Dragisic

last: Hanakova

first: David

last: Potesil

first: Sara

last: Bologna

first: Jiri

last: Novacek

first: Caroline

last: Friedel

first: Konstantinos

last: Tripsianes

first: Zbynek

last: Zdrahal

first: Dalibor

last: Blazek


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Cut&Run]

first: Ramesh

last: Shivdasani

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then analyzed ASCL1 and NEUROD1 binding using data obtained from CUT&RUN of at 96h.

overall_design: CUT&RUN of at 96h.

first: Pratik

last: Singh


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling

first: Yicheng

last: Xie

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [bulk RNA-seq]

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 independent human lines at various  time points.


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [bulk ATAC-seq]

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed chromatin analysis using data obtained from ATAC-seq of 2 independent human lines at various  time points.


title: Periostin Upregulated in Cancer-Associated Fibroblasts upon Direct Contact with Cancer Cells Promotes Esophageal Squamous Cell Carcinoma Progression by Enhancing the Migration of Cancer Cells and Stromal Cells

status: Public on Jan 08 2024

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
Cancer-associated fibroblasts (CAFs) in the tumor microenvironment are involved in the progression of esophageal squamous cell carcinoma (ESCC). We generated CAF-like cells by direct co-culture of human bone marrow-derived mesenchymal stem cells (MSCs), one of the origins of CAFs, with ESCC cell lines and found that periostin is highly expressed in CAF-like cells. Periostin activated Akt and Erk signaling pathways in ESCC cells, enhancing survival and migration via integrin β4, one of the receptors for periostin. Periostin also enhanced migration of MSCs and macrophages and caused macrophages to acquire tumor-associated macrophage (TAM)-like properties.
High periostin expression in cancer stroma was associated with several clinicopathological factors and expressions of CAF markers and numbers of infiltrating TAMs. Moreover, ESCC patients with high periostin expression exhibited significantly poor postoperative outcomes. Thus, periostin secreted from CAFs enhanced the migration of ESCC cells, MSCs, and macrophages and contributed to developing the tumor microenvironment. These results indicate that periostin may be a novel therapeutic target for ESCC.

overall_design: To induce the CAF-like cells, MSCs and TE cells were seeded in the same dish. Direct co-culture was performed for 4 days in DMEM high-glucose (Wako) with 10% FBS and 1% antibiotic-antimycotic. MSCs and TE cells were seeded and cultured similarly without co-culture as controls. Cell suspensions were mixed with CD326 (EpCAM) microbeads (#130-061-101; Miltenyi Biotec) and incubated at 4°C for 30 minutes. Prepared cell suspensions were separated from EpCAM-positive and -negative cells using the autoMACS Pro Separator. Mono-cultured TE cells and mono-cultured MSCs were collected using autoMACS Pro Separator as well as cells after direct co-culture. We performed cDNA microarray analysis between mono-cultured MSCs and CAF9 (MSC co-cultured with TE-9 cells) cells.

first: S

last: Miyako

first: Y

last: Koma


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation

status: Public on Jan 10 2024

summary: Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.

overall_design: Enteroendocrine differentiation was induced by transient (48h) NEUROG3 activation in 2D human ISCs. This triggered full and efficient EEC differentiation over a period of 6-8 days during which we examined step-wise dynamic profile of enhancers and genes at bulk and single-cell resolution. We identify the binding pattern of crucial intermediate factors ASCL1 and NEUROD1 using CUT&RUN and CRISPR-edited specific transcription factors to determine their role in differentiation program.


title: Distinct roles for COMPASS core subunits Set1, Trx, and Trr in the epigenetic regulation of Drosophila heart development

status: Public on Jan 03 2024

city: Baltimore

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: This study investigated the role Complex of Proteins Associated with Set1 (COMPASS) in heart development. These are evolutionarily highly conserved multiprotein complexes required for H3K4 methylation. In Drosophila, their core subunits are Set1, Trx, and Trr. We studied flies deficient for either of these three subunits their hearts. These flies showed high lethality at eclosion (emergence of adult flies from their pupal case) and significantly shortened lifespans for the adults that did emerge. Furthermore, their hearts showed reduced H3K4 monomethylation (H3K4me1) and dimethylation (H3K4me2), and significantly altered gene expression patterns. The data revealed that each of the COMPASS core subunits (Set1, Trx, and Trr) control methylation of different sets of genes with distinct temporal activity: Set1 throughout, whereas Trr was active early and Trx at later stages of heart development. We found that many metabolic pathways were active early in development and throughout, while muscle and heart differentiation processes were methylated during later stages of development. Taken together, the findings demonstrate the importance of COMPASS complexes during heart development, therewith supporting their implication in congenital heart diseases.

overall_design:
To investigate the gene expression patterns regulated by Set1, Trx, and Trr. We employed the Drosophila UAS-Gal4 system combined with RNAi knockdown. We used twist (twi)-Gal4 to tissue knockdown Set1, trx, or trr specifically in the Drosophila heart.
We then performed gene expression profiling analysis using data obtained from RNA-Seq of three different samples for each genotype.
Comparative gene expression profiling analysis of RNA-Seq data for wildtype and its knock-down (RNAi) derivatives (Set1, trx, and trr).

first: Junyi

last: Zhu

first: Zhe

last: Han


title: Association of HBsAg levels with differential gene expression in NK, CD8 T, and memory B cells in treated patients with chronic HBV

status: Public on Jan 01 2024

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

summary: Hepatitis B surface antigen (HBsAg) secretion may impact the immune response in chronic hepatitis B virus (HBV) infection. Therapeutic approaches to suppress HBsAg production are being investigated. Our study aims to examine the immunomodulatory effects of high and low levels of circulating HBsAg by analyzing single-cell RNA sequencing data (scRNAseq) from blood and liver fine-needle aspirates (FNA). This will help to better understand anti-HBV immunity.

overall_design: An optimized 10X Genomics scRNAseq-workflow was applied to blood and FNA samples from 18 patients undergoing tenofovir or entecavir treatment (NUC) for chronic HBV infection. They were categorized based on their HBsAg levels: high (920- 12447 IU/mL) or low (1-100 IU/mL). Cluster frequencies, differential gene expression, and phenotypes were analyzed.

first: Zgjim

last: Osmani


title: CELLULAR SENESCENCE CONTRIBUTES TO THE PROGRESSION OF HYPEROXIC BRONCHOPULMONARY DYSPLASIA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Oxidative stress (OS), inflammation, and endoplasmic reticulum (ER) stress sequentially occur in the rat model of hyperoxia (HOX) induced bronchopulmonary dysplasia (BPD), and they all increase DNA damage. Tumor suppressors increase after DNA damage, followed by apoptosis or cellular senescence when the damage becomes irreparable. Although cellular senescence contributes to wound healing, its persistence will inhibit growth potential. Therefore, we hypothesized that the persistence of cellular senescence plays a role in BPD progression. We detected evidence of increased cellular senescence in rat and human BPD lungs. Foxo4-p53 binding was increased in BPD rat lungs, and inhibition of this binding attenuated BPD severity, indicating that such binding contributes to BPD's cellular senescence. Treatment with tauroursodeoxycholic acid (TUDCA) decreases ER stress. N-Acetyl-lysyltyrosylcysteine-amide (KYC) reduced toxic oxidant production by myeloperoxidase (MPO) and subsequent OS and inflammation. Both agents effectively decreased cellular senescence. Concomitantly, alveolar complexity and the number of type 2 alveolar cells increased, indicating that MPO-mediated OS and ER stress preceded cellular senescence in BPD rat pup lungs. These data suggest that cellular senescence plays an essential role in BPD progression. Reducing MPO toxic oxidant production, ER stress, and attenuating cellular senescence are potential therapeutic strategies for halting BPD progression.
Using multiomic data to investigate the role of cellular senescence in the development of BPD in rat model.

overall_design: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. According to the study design, two or four pregnant rats were used for each experiment. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). An oxygen sensor continuously monitored oxygen concentrations (Reming Bioinstruments Co., Redfield, NY). Pups were then recovered in room air between P11-P21. Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity. Lungs obtained at P21 from both NOX and HOX groups were used for transcriptomic studies using Affymetrix chips, histology, and immunoblots.

first: Xigang

last: Jing

first: Shuang

last: Jia

first: Maggie

last: Teng

first: Billy

middle: W

last: Day

first: Adeleye

last: Afolayan

first: Jason

last: Jarzembowski

first: Kirkwood

last: Pritchard

first: Stephen

last: Naylor

first: G

last: Konduri

first: Ru-Jeng


title: Systems-based identification of the Hippo pathway for promoting fibrotic mesenchymal differentiation in systemic sclerosis

status: Public on Dec 06 2023

first: Feiyang

last: Ma

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

department: Molecular Biology Institute

institute: UCLA

summary: Systemic sclerosis (SSc) is a devastating autoimmune disease characterized by excessive production and accumulation of extracellular matrix, leading to fibrosis of skin and other internal organs. However, the main cellular participants in SSc skin fibrosis remain incompletely understood. Here using differentiation trajectories at a single cell level, we demonstrate a dual source of extracellular matrix deposition in SSc skin from both myofibroblasts and endothelial-to-mesenchymal-transitioning cells (EndoMT).  We further define a central role of Hippo pathway effectors in differentiation and homeostasis of myofibroblast and EndoMT, respectively, and show that myofibroblasts and EndoMTs act as central communication hubs that drive key pro-fibrotic signaling pathways in SSc. Together, our data help characterize myofibroblast differentiation and EndoMT phenotypes in SSc skin, and hint that modulation of the Hippo pathway may contribute in reversing the pro-fibrotic phenotypes in myofibroblasts and EndoMTs.

overall_design: Single cell RNA sequencing and spatial sequencing on human scleroderma skin tissues

first: Johann

last: Gudjonsson


title: Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction [RNAseq_Fetal]

status: Public on Nov 26 2023

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

institute: POSTECH

summary: Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. The OSKM-induced forced dedifferentiation showed similar molecular features of intestinal regeneration, including a transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing gene signatures of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following damage. In contrast to normal intestinal regeneration involving Ptgs2 induction, the OSKM promotes autonomous production of prostaglandin E2 via epithelial Ptgs1 expression. These results indicate prostaglandin synthesis is a common mechanism for intestinal regeneration, but involves a different enzyme when partial reprogramming is applied to the intestinal epithelium.

overall_design: We used intestinal organoids from adult and fetal mice.

first: Jumee

first: Seung-Yeon

last: Lee

first: Hwa-Ryeon

first: Bon-Kyoung

last: Koo

first: Jong

middle: K

first: Hyuk-Jin

last: Cha


title: MDA5 guards against infection by surveying cellular RNA homeostasis

status: Public on Nov 28 2023

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

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

overall_design: Refer to individual Series


title: Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

status: Public on Dec 01 2023

city: Durham

first: Amy

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

summary: The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. To better understand the roles of TrmB and TbsP, we conducted expression profiling in ∆trmB, ∆tbsP, ∆trmB∆tbsP in response to glucose availability. TrmB and TbsP jointly regulate the transcription of gapII, fbp, and ppsA.

overall_design: Transcripome profiling (RNA-seq) of TrmB and TbsP in the halophilic archaeon Haloferax volcanii in the presence and absense of glucose after 24 hours.

first: Rylee

last: Hackley

first: Preeti

last: Bhanap

first: Mar

last: Martinez Pastor


title: OSKM-induced mouse intestinal organoids [RNAseq_Dox]

summary: Tissue regeneration after injury is thought to involve the dedifferentiation of somatic cells, which is often understood as evidence for natural adaptative reprogramming in vivo. In the intestinal epithelium, acute tissue damage triggers the rapid emergence of injury-responsive cells with fetal-like characteristics, a sign of dedifferentiation. However, there is no direct evidence that tissue regeneration involves a shared molecular mechanism with direct cellular reprogramming. It is also not known whether dedifferentiation shares a single (de)differentiation pathway or consists of multiple parallel routes between adult and fetal states. Here, we induced dedifferentiation of intestinal epithelial cells by forced partial reprogramming in vivo using the “Yamanaka factors” (Oct4, Sox2, Klf4 and c-Myc: OSKM). The induced dedifferentiation showed shared molecular features of intestinal regeneration, with rapid transition from homeostatic intestinal cell types to injury-responsive-like cells sharing a common gene signature of revival stem cells and atrophy-induced villus epithelial cells. When applied to intestinal organoids, induced dedifferentiation allowed the organoids to adopt fetal characteristics ex vivo, suggesting a direct effect on the intestinal epithelium. In vivo, induced dedifferentiation promoted regeneration from acute tissue injury caused by ionizing radiation (IR) via the formation of injury-responsive-like cells. Taken together, in the intestinal epithelium, in vivo reprogramming shares the same molecular pathway as damage-induced tissue regeneration and facilitates the repair process.

overall_design: We used intestinal organoids from doxycycline(Dox)-inducible OSKM-expressing mice. Two different concentration of Dox was treated in the organoids to induce OSKM to different degrees. Two biological replicates were used.


title: Single-Cell RNA Sequencing Unveils Lrg1's Role in Cerebral Ischemia‒Reperfusion Injury by Modulating Various Cells

city: Nanchang

first: Yanni

last: Lv

address: Yongwai street No. 17

institute: The First Affiliated Hospital of Nanchang University

summary: Leucine-rich alpha-2 glycoprotein 1 (Lrg1) appears to be associated with the progression of cerebral ischemia-reperfusion injury, but its exact mechanism remains unknown. Here, we utilized scRNA-seq to compare the microenvironmental changes in the brains of Lrg1 knockout mice and wild-type mice following MCAO/R, in order to elucidate the role of Lrg1 after MCAO/R.

overall_design: The brains of 11 mice were collected, consisting of brains from wild-type mice following sham surgery, Lrg1 knockout mice following sham surgery, Lrg1 knockout mice following MCAO/R and wild-type mice following MCAO/R.

first: Zhaohui

last: Ruan

first: Guosheng

last: Cao

first: Yisong

last: Qian

first: Longsheng

last: Fu

first: Jinfang

last: Hu

first: Tiantian

last: Xu

first: Yaoqi

last: Wu


title: Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction.

status: Public on Nov 24 2023

first: Somi

last: Kim


title: Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction [RNAseq_IR]

overall_design: We used intestinal organoids and irradiated the IR samples.

first: Jumee

first: Seung-Yeon

last: Lee

first: Hwa-Ryeon

first: Bon-Kyoung


title: OSKM-induced epithelial cells of mouse intestine [scRNA-seq]

overall_design: We used Doxycline-inducible OSKM-overexpressing mice to induce OSKM in vivo. Dox was administrated to a mouse to induce OSKM.

last: Koo

first: Jong

first: Hyuk-Jin


title: COMBINATION OF MESENCHYMAL STEM CELLS-DERIVED EXOSOMES AND SILVER NANOPARTICLES: PERSPECTIVES ON WOUND HEALING

city: Hanoi

first: Quang

middle: Minh

last: Dang

address: 458 Minh Khai Street

country: Viet Nam

institute: Vinmec-VinUni Institute of Immunology

summary: Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing.

overall_design:
To investigate the role of umbilical cord mesenchymal stem cells (UC-MSC) and their secretome in the regulation of wound healing, we isolated and cultured mesenchymal stem cells from the umbilical cord, and isolated exosomes secreted by these cells.
We then performed gene expression profiling analysis using RNA-seq of a triplicate of UCMSC-derived exosomes and their corresponding mother cells
Comparative gene expression profiling analysis of RNA-seq data for UC-MSCs and their exosomes.

first: Uyen

middle: T

last: Than

first: Hoai

last: Nguyen

first: Huyen

first: Nhung

last: Hoang

first: Thanh

first: Duc

last: Vu

first: Huong

last: Phi

first: Quynh

last: Luu

first: Hai

middle: X

last: Do

first: Huy

last: Dao

first: Xuan

first: Nam


title: The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

status: Public on Nov 16 2023

first: Amy

last: Schmid

address: 125 Science Dr.

summary: Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that works as the major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.

overall_design:
Using RNA seq, we compared the trancriptome of cells from parental strain versus the troR knockout strain, growing in minimal media containing iron in excess to understand if the TF TroR was involved in those cellular mechanims that determine iron homeostasis.
RNA was checked for quality, and 300-500 micrograms of  total RNA were depleted using RIBOZERO to remove rRNA.Libraries were constructed using ~50 ng of mRNA using the Kapa Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems, Illumina).

first: Mar

last: Martinez Pastor


title: Characterization of the zinc finger µ-protein HVO_0758 from Haloferax volcanii: biological roles, zinc binding, and NMR solution structure

status: Public on Nov 13 2023

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

summary: Transcriptome analysis based on total RNA-seq was performed on different Haloferax volcanii strains including mutants strains iincluding deletion strains for two small proteins. Differential expression analysis showed that a subset of genes were found to be regulated in the absence of the small proteins.

overall_design: 2 replicates of Total RNA-seq from different Haloferax volcanii strains

first: Lydia

last: Hadjeras

first: Jörg

last: Soppa

first: Deniz

last: Üresin

first: Cynthia

last: Sharma

first: Rolf

last: Backofen


title: Transcriptomic profiling of A549 cells in response to Dexamethasone, in the context of GR inhibition based on antagonists as well as a novel GR-PROTAC

status: Public on Nov 12 2023

city: Zürich

first: Katharina

last: Gapp

address: Winterthurerstrasse 190

department: Health Science and Technology

country: Switzerland

institute: Swiss Federal Institue of Technology

summary: Glucocorticoid receptors (GR) are important therapeutic targets due to regulation of stress hormones, glucocorticoids (GCs). GCs are altered in neuropsychiatric diseases, but also in cancers and autoimmunes. GR antagonists show some success in modulating GC levels. Yet, occupancy-driven mode of action of the available inhibitors, prevents full inhibition and requires high doses, causing risks in the long-term. To complement the existing tools, we present a highly potent novel catalytic-driven GR degrader, KH-103. We show highly efficient and rapid GR chemical knockdown at nanomolar concentrations. KH-103 is selective for GR, has almost no transcriptional side-effects, and shows higher efficiency in blocking ligand-induced genomic effects compared to other antagonists. Application in cortical cultures, revealed a GR-dependent GC-induced increase in calcium peak-intervals negatable by KH-103 pretreatment. Finally, an in-vivo proof-of-concept application of KH-103 is presented. KH-103 opens new opportunities for more lucid interpretation of GR-functions without disadvantages of genetic-interventions with clinically translatable potentials.

overall_design: We cultured A495 cells and exposed them to different treatment regimes including dexamethasone (100nM), mifepristone (1uM), CORT113176 (1uM) and  KH-103 (100nM) or a combination there-of with varying exposure time and order. For exact timescales see column "title"/"B", then harvested cells to extract RNA using Quick-RNA Microprep Kit (Zymoresearch, R1051).  RNA samples at 25 ng/ul concentration were processed at  Novogene, UK. Non-directional Poly-A library preparations were performed according to the manufacturer's recommendations (Next® Ultra RNA Library Prep Kit for Illumina®)

first: Mahshid

last: Gazorpak

first: Karina

last: Hugentobler

first: Johannes

last: Bohacek

first: Erick

last: Carreira


title: Single cell insights into development of the bovine placenta

status: Public on Nov 08 2023

city: Pullman

first: Kimberly

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

summary: A central determinant of pregnancy success is proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Although the gross morphology and histology of the bovine placenta has been well studied, the cellular and molecular mechanisms regulating placenta development and trophoblast differentiation and function remain essentially undefined. Here single cell RNA-seq analysis was performed on the day 17 bovine conceptus and chorion of day 24, 30 and 50 conceptuses (n = 3-4 samples per day) using the 10X Genomics platform. Bioinformatic analyses identified cell types and their ontogeny including trophoblast, mesenchyme, and immune cells. Loss of IFNT-expressing trophoblast uninucleate cells (UNC) occurred between days 17 and 30, whereas binucleate cells (BNC), identified based on expression of placental lactogen (CSH2) and pregnancy-associated glycoproteins (PAGs) marker genes, first appeared on day 24. Several different types of UNC were present in day 24, 30 and 50 samples, but only one (day 24) or two types of BNC (days 30 and 50). Cell trajectory analyses provided a conceptual framework for UNC development and BNC differentiation, and upstream transcription factor binding enrichment analyses identified candidate transcription factors governing differentiation and function of the trophoblasts. The digital atlas of cell types in the developing bovine conceptus reported here serves as a resource to discover key genes and biological pathways regulating its development during the critical periods of implantation and placentation.

overall_design: Nuclei were isolated and libraries prepared following the 10X Genomics platform protocols

first: Eleanore

last: O'Neil

first: M Sofia

last: Ortega

first: Amanda

last: Patterson

first: Andrew

last: Kelleher

first: Wesley

last: Warren

first: Thomas

last: Spencer


title: Deletion of Slc9a1 in Cx3cr1+ cells stimulated microglial subcluster CREB1-BDNF signaling and oligodendrocyte crosstalk

status: Public on Nov 06 2023

city: Pittsburgh

first: Shanshan

last: Song

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

summary: Microglial Na/H exchanger-1 (NHE1) protein, encoded by Slc9a1, plays a role in white matter demyelination of ischemic stroke brains. In this study, we conducted single cell RNA-seq transcriptome analysis of corpus collosum and external capsule from wild-type (WT) and conditional Slc9a1 knockout (cKO) mice at 3 days post-stroke to study microglia-oligodendrocyte interactions.

overall_design:
White matter tissues were dissected from the WT or Nhe1 cKO brains at 3 days post-tMCAO

Grant ID: 933134 (Career Development Award)
Grant title: Modulating microglia-oligodendrocyte interactions for white matter repair
Funding source: American Heart Association
Grantee: Shanshan Song

first: Chaim

last: Sneiderman

first: Gary

last: Kohanbash

first: Dandan

last: Sun


title: Short C-terminal Musashi-1 proteins regulate pluripotency states in embryonic stem cells

status: Public on Nov 05 2023

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

summary: To understand the function of MSI1 in pluripotent stem cells, RNA-seq assays were performed on mouse embryonic stem cells R1, MSI1 knockout cell line R1-C5, human embryonic stem cells H9, RRM knockout cell line H9-C8, MSI1 full-length overexpression cell line H9-MSI1OE, MSI1C variant overexpression cell line H9-MSI1 (138-362) OE , H9-MSI1(272-362)OE. RNA bound by MSI1 in R1 and H9, and MSI1C variants MSI1 (138-362), MSI1(272-362) were detected using RIP-seq.

overall_design: RNA-seq for mESC cell line R1 (R1-WT and MSI1-KO cell line R1-C5 ), hESC cell line H9 (H9-WT, MSI1 RRM KO cell line H9-C8, MSI1 overexpression cell H9-MSI1FL and MSI1-C variant  overexpression cell H9-MSI1V138 and H9-MSI1V272). RIP-seq for MSI1 binding RNA in R1 and H9 by using anti-MSI1 antibody for RIP. RIP-seq for MSI1-C variants binding RNA in H9 by using anti-Flag antibody for RIP.

first: Youwei

last: Chen


title: FOXC2 and WT1 regulate transcriptional reprogramming during the podocyte response to injury

status: Public on Nov 01 2023

city: Boston

first: Jordan

last: Kreidberg

state: MA

address: 99 Brookline Ave

institute: BIDMC Research North

summary: In the context of human disease, the mechanisms whereby transcription factors reprogram gene expression in reparative responses to injury are not well understood. We have studied the mechanisms of transcriptional reprogramming in disease using murine kidney podocytes as a model for tissue injury. Podocytes are a crucial component of glomeruli, the filtration units of each nephron. Podocyte injury is the initial event in many processes that lead to End Stage Kidney Disease. FOXC2 is a transcription factor known to regulate gene expression in podocytes. FOXC2 and WT1 are both required for podocyte differentiation. Using murine models and human kidney organoids, we investigated FOXC2-mediated transcriptional reprogramming during the course of podocyte injury. Correlating FOXC2 and WT1 ChIP-seq analyses demonstrated that they co-bind many genes expressed in podocytes. Reprogramming the transcriptome involved highly dynamic changes in the binding of FOXC2 and WT1 to target genes during a reparative injury response.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FOXC2

first: Sandrine

last: Ettou

first: Anya

last: Greenberg

first: Liang

first: Dongwon

last: Lee


title: Eosinophils promote lung emphysema via CTSL

status: Public on Oct 17 2023

summary: Patients with chronic obstructive pulmonary disease (COPD) having higher blood eosinophil levels exhibit worse lung function and more severe emphysema, implying the potential role of eosinophils in emphysema development. However, the specific mechanism underlying eosinophil-mediated emphysema development is not fully elucidated. In this study, single-cell RNA sequencing was used to identify eosinophil subgroups in mouse models of asthma and emphysema and analyze their functions. Analysis of the accumulated eosinophils revealed differential transcriptomes between the mouse lungs of elastase-induced emphysema and ovalbumin-induced asthma., Eosinophil depletion alleviated elastase-induced emphysema. Notably, eosinophil-derived cathepsin L (CTSL) degraded the extracellular matrix (ECM), causing emphysema in the pulmonary tissue. Eosinophils were positively correlated with serum CTSL levels, which were increased in patients with emphysema than in those without emphysema. Collectively, these results suggest that CTSL expression in eosinophils plays an important role in ECM degradation and remodeling and is related to emphysema in patients with COPD. Therefore, eosinophil-derived CTSL may serve as a potential therapeutic target for patients with emphysema.

overall_design: 13 sample from lung tissue

first: Xia

last: Xu


title: Gene expression profile at single cell level of newborn and adult mouse dorsal skin organoids

status: Public on Sep 13 2023

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

summary: The formation of tissue patterns is critical for organ functions in development and regeneration. To advance the use of organoids for organ regeneration, we learn principles that govern the skin organoids to regenerate hairs. We show the formation of epidermal-dermal coupled cysts function as competent morphogenetic units (CMU) which harbor the ability of skin organoids to regenerate. ScRNA-sequencing shows the emergence of cell types and new cell interactions during CMU formation. In newborn skin organoids, epidermal cells undergo apical-basal polarization via the IFNr-PKR-PKC signaling module. Dermal-Tgfb regulates Gsk3 to establish basement membranes between the epidermal cyst and dermal cells. Meanwhile, VEGF signaling mediates dermal cell attachment to the cyst. Adult cells cannot form organoids but can be induced to generate CMUs and regenerate hairs by adding IFNr or VEGF. We compare the similar principles and different paths used to establish morphogenetic competency in developing skin, wound-induced hair neogenesis, and organoids.

overall_design: Cells were derived from the dorsal skin of neonatal mice within 24 hours of birth. The skin was floated in 0.25% trypsin solution at 4°C to separate into the dermis and epidermis. Epidermal cells were cut with scissors, pipetted, and filtered through a 70um cell strainer followed by centrifugation. The dermis was digested in 0.35% collagenase for 20 minutes, then filtered through a 70um cell strainer followed by centrifugation. The dissociated epidermal cells and dermal cells were mixed at a ratio of 1:9 and were dropped onto the upper chamber of a transwell culture insert, and the lower chamber was filled with 700ul DMEM/F12 (Corning) culture medium containing 10% FBS (Gibco). For adult cell culture, the growth factors were added from D0 to D4, followed by adding MMP14 recombinant protein from D4 to D7. PKC inhibitors were added throughout the cultivation period. The cells were cultured in a 5% CO2 at 37°C incubator, with the culture medium being changed every other day.

first: Mingxing

last: Lei

first: Cheng-Ming

last: Chuong


title: Transcriptome Alteration Between Young and Senile Human Bone MSC

status: Public on Sep 20 2023

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: In order to uncover mechanisms of hBMSC senescence, we performed high-throughput RNA-seq using young and senile human bone MSC (hBMSC).

overall_design: We used three independent samples in each groups. And the young hBMSC was set as control group.

first: Feifei

last: Li


title: Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk and Endometrial Function

status: Public on Sep 12 2023

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

institute: University of Queensland

summary: Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Biological and genetic effects on DNA methylation (DNAm) can influence gene regulation and contribute to complex disease. Herein, we characterize variation in endometrial DNAm and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genome-wide genotype data and methylation at 759,345 DNAm sites in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles and DNAm networks, associated with endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

overall_design: Bisulphite converted DNA from the 984 endometrial samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip

first: Linda

last: Giudice


title: AHR-TFAP2A regulates epidermal differentiation in response to environmental cues [RNA-seq]

status: Public on Sep 08 2023

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

institute: Radboud University

summary: The Aryl Hydrocarbon Receptor (AHR) is an environmental sensor and an indispensable regulator of epithelial homeostasis. To investigate AHR-mediated gene regulation, we performed a comprehensive transcriptomic and epigenomic analysis using human primary epidermal keratinocytes. Our results showed that AHR activation led to the induction of canonical transcription factors involved in epidermal differentiation as an early response, i.e. Transcription Factor AP-2α (TFAP2A), while epidermal differentiation-related genes, such as filaggrin and keratins, were activated as late responsive genes. The identified AHR-TFAP2A axis and its role in keratinocyte terminal differentiation was confirmed through AHR and TFAP2A knockout using CRISPR/Cas9. Our findings demonstrate that AHR regulates epidermal differentiation through the transient activation of specific transcription factors, such as TFAP2A, in response to environmental cues. The herein identified AHR-TFAP2A axis provides a promising target for the treatment of diseases related to skin barrier dysfunction.

overall_design: To characterize the gene expression pattern upon AHR activation in keratinocytes, we performed RNA-seq on either TCDD or CT treated keratinocytes. In addition, to identify AHR-responsive enhancers, we performed ChIP-seq of AHR and H3K27ac that marks active enhancers in the genome of keratinocytes after TCDD treatment for 30 and 90 minutes. With integrated analyses of  RNA-seq, AHR, and H3K27ac ChIP-seq data, we identified that TFAP2A is a direct AHR target and is an important transcription factor involved in epidermal differentiation. To further test our hypothesis that AHR controls epidermal differentiation via TFAP2A expression, we knocked down TFAP2A in monolayer primary keratinocyte cultures and performed RNA-seq analysis.

first: Jieqiong

last: Qu

first: Jos

last: Smits

first: Felicitas

last: Pardow

first: Noa

last: van den Brink

first: Huiqing

first: Ellen

last: van den Bogaard


title: Single-cell dissection of the multicellular ecosystem and molecular feature sunderlying microvascular invasion in hepatocellular carcinoma

city: Wenzhou

first: Meng

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

summary: Microvascular invasion (MVI) is a significant pathological feature of hepatocellular carcinoma (HCC) associated with poor outcomes, early recurrence, and intrahepatic metastasis in post-surgical resection and transplant patients. However, the tumor microenvironment (TME) and transcriptional programs underlying MVI remain poorly understood. In this study, we conducted single-cell RNA sequencing of 46,789 individual cells from 10 samples of MVI+ (MVI present) and MVI- (MVI absent) HCC patients, providing a comprehensive single-cell atlas of MVI. Single-cell dissection of the multicellular ecosystem revealed the emergence or expansion of cycling T cells, LAMP3+ dendritic cells, TREM2+ macrophages, myofibroblasts, and tumor-promoting arterial i endothelial cells within the MVI+ TME. MVI+ malignant cells are characterized by high proliferation rates and the ability to evade immune detection through the upregulation of non-classical MHC class I molecules. In contrast, MVI-malignant cells exhibit an inflammatory milieu.  Furthermore, we identified the CCL16/CCR1 interaction between TREM2+ macrophages and malignant cells as a contributing factor in MVI formation and tumor progression. Notably, we identified a unique multicellular module that plays the dominant role in shaping the immunosuppressive microenvironment of MVI and correlates with poor prognosis. In summary, these findings enhance our understanding of the underlying cellular and molecular mechanisms driving MVI and provide valuable insights for improving clinical diagnosis and developing more effective treatment strategies.

overall_design: Ten independent surgical resected specimens were collected from five HCC patients (3 MVI present patients and 2 MVI absent patients), including 5 HCC tissues and 5 adjacent non-tumor tissues for single-cell RNA sequencing . Inclusion criteria for patients comprised the absence of apparent metastases, a singular tumor of dimensions between 3 and 5 cm, and no prior therapeutic intervention.

first: Ke

first: Zhaoyang

last: Lu

first: Yifeng

last: Cui


title: Gene expression in nucleus accumbens tissue of Foxp2 heterozygous mice (S321X/+) and wild-type littermates (WT) following single cocaine or saline injection

status: Public on Aug 31 2023

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

country: France

institute: INSERM U839

summary:
Foxp2 heterozygous mice and wildtype mice were injected with cocaine or saline, 1h post-injection nucleus acumbens RNA was extracted and analysed
We have tested a potential role for the transcription factor Foxp2 in dopamine signaling and reward associated synaptic plasticity and behavior. We found that Foxp2 is acutely downregulated in reward associated circuits in the nucleus accumbens following a single injection of cocaine. In Foxp2 heterozygous mutant mice, loss of transcriptional suppression by Foxp2 causes an increased constitutive expression of dopamine signaling related genes which corresponds with impairments in synaptic plasticity and reward associated behaviors.

overall_design: Nucleus accumbens tissue was extracted 1 hour after injection (i.p.)  of either saline or cocaine (15mg/kg). mRNA microarrays (Illumina MouseWG-6 v2) were used to analyzed gene expression in biological replicates (6 for WT cocain, 6 for WT saline, 5 for HET (S321X/+) saline, 6 for HET (S321X/+) cocain).

first: Cedric

last: Mombereau

first: Tanay

last: Ghosh


title: Investigating the role of Bax/Bak as a driver of inflammation in aging

status: Public on Aug 16 2023

city: La Jolla

first: Peter

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Senescent cells drive age-related tissue dysfunction partially via the induction of a chronic senescence-associated secretory phenotype (SASP). Mitochondria are major regulators of the SASP; however, the underlying mechanisms have not been elucidated. Mitochondria are often essential for apoptosis, a cell fate distinct from cellular senescence. During apoptosis, widespread mitochondrial outer membrane permeabilization (MOMP) commits a cell to die. Here, we find that MOMP occurring in a subset of mitochondria is a feature of cellular senescence. This process, called minority MOMP (miMOMP), depends on the formation of BAX and BAK macropores leading to the release of mitochondrial DNA (mtDNA) into the cytosol, which in turn activates the cGAS-STING pathway, a major regulator of the SASP. Importantly, we found that inhibition of MOMP in vivo decreases inflammatory markers and improves healthspan in aged mice. Our results reveal, unexpectedly, that apoptosis and senescence are regulated by similar mitochondrial-dependent mechanisms, and that sub-lethal mitochondrial apoptotic stress is a major driver of the SASP. We also provide proof-of-concept that inhibition of miMOMP-induced inflammation may be a new therapeutic avenue to improve healthspan.

overall_design:
Aged mice (20 months old) were treated with the Bax inhibitor, BAI1, three times a week for three months. The drug was delivered by IP injections.

(April 13, 2024) Update:  The old processed files were aggregated matrix using Cellranger aggr by combining two samples together. To make it more clear and easy to access, the processed data were updated with the matrix for each sample separately.

first: Stella

last: Victorelli

first: Nicholas

last: Pirius

first: Joao

last: Passos

first: Xue

last: Lei


title: Sub-lethal apoptotic stress enables mtDNA release during senescence and drives the SASP

summary: Senescent cells drive age-related tissue dysfunction partially via the induction of a chronic senescence-associated secretory phenotype (SASP). Mitochondria are major regulators of the SASP; however, the underlying mechanisms have not been elucidated. Mitochondria also control apoptosis, a cell fate generally perceived as distinct from cellular senescence, which is apoptosis resistant. Here, we show that mitochondrial outer membrane permeability (MOMP) occurring in a small subset of mitochondria is a feature of cellular senescence. This process, called minority MOMP (miMOMP), depends on the formation of BAX and BAK macropores and results in release of mitochondrial DNA (mtDNA) into the cytosol, which in turn activates the cGAS/STING pathway, a major regulator of the SASP. Importantly, we found that inhibition of MOMP in vivo decreases inflammatory markers and improves healthspan parameters in aged mice. Our results propose the novel concept that apoptosis and senescence are regulated by similar mitochondrial-dependent mechanisms, and that sub-lethal mitochondrial apoptotic stress is a major driver of the SASP. We also provide proof-of-concept that inhibition of miMOMP may be a new therapeutic avenue to improve healthspan.

overall_design: mRNA profiles of senescent fibroblasts upon mitochondria clearance and following the re-introduction of mitochondrial DNA. We also examined the effects of Bax and Bak knockout on mRNA profile of proliferating and senescent fibroblasts.

first: Helene

last: Martini

first: Maria

middle: G

last: Vizioli


title: AHR-TFAP2A regulates epidermal differentiation in response to environmental cues

first: Jo Huiqing

last: Zhou

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

overall_design: Refer to individual Series