title: Regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster [Trx_ATAC]

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

country: Canada

institute: Dalhousie University

summary: We have analyzed regions of accessible chromatin in adult mushroom body neurons of Drosophila melanogaster of a control genetic background using ATAC-seq.

overall_design: Examination of accessible chromatin regions in the adult mushroom body of Drosophila melanogster in a control genetic background using ATAC-seq. Genetic material was extracted from 1/3rd of mushroom body nuclei isolated from pools of 50-60 fly heads in two biological replicates.

middle: G

first: Jamie

last: Kramer


title: The XCL1-XCR1 axis supports intestinal tissue residency and anti-tumor immunity

status: Public on Jan 07 2025

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 Gilman Drive

department: Molecular Biology

country: USA

institute: University of California, San Diego

summary: Tissue-resident memory T cells (TRM) provide frontline protection against pathogens and emerging malignancies. Tumor-infiltrating lymphocytes (TIL) with TRM features are associated with improved clinical outcomes. However, the cellular interactions that program TRM differentiation and function are not well understood. Using murine genetic models and targeted spatial transcriptomics, we found that the CD8+ T cell-derived chemokine XCL1 is critical for TRM formation and conventional DC1 (cDC1) support the positioning of intestinal CD8+ T cells during acute viral infection. In tumors, enforced Xcl1 expression by antigen-specific CD8+ T cells promoted intratumoral cDC1 accumulation and T cell persistence, leading to improved overall survival. Notably, analysis of human TIL and TRM revealed conserved expression of XCL1 and XCL2. Thus, we have shown that the XCL1-XCR1 axis plays a non-cell autonomous role in guiding intestinal CD8+ TRM spatial differentiation and tumor control.

overall_design: Spatial transcriptomics (Xenium) 8 days after infection with LCMV and adoptive transfer of P14 CD8 T cells into XCR1-DTR treated mice.

first: Amir

last: Ferry

first: Alexander

last: Monell


title: Loss of the Aryl Hydrocarbon Receptor (AhR) Promotes Cancer Cells Resistance to BRAFV600E Targeted Therapies. [CRISPR]

status: Public on Jan 12 2025

city: Los Angeles

first: youssef

last: errami

address: 650 Charles E Young Dr S

department: MIMG

institute: University of California Los Angeles

summary: Predicting a patient’s response to chemotherapies and identifying additional molecular targets to improve treatment efficacy are major objectives in cancer research. BRAFV600E inhibitors targeting the MAP kinase pathway showed promising initial clinical results in thyroid cancers (TCs) for metastatic or recurrent tumors refractory to radioiodine treatments. BRAFV600E-targeted therapies have also been approved by the FDA for the treatment of some unresectable or metastatic BRAFV600E+ solid tumors. Still, for most patients, the response to BRAFV600E blocking therapy is transient due to cell proliferation reactivation through escape pathways. We performed a genome-wide CRISPR screen to reveal targets in TCs that facilitate resistance or sensitize thyroid cancer cells to inhibitors of the MAP kinase pathway. Among the genes that consistently altered MAPK inhibitor treatment response, we identified the Aryl hydrocarbon Receptor (AhR) and its molecular partner, the AhR nuclear translocator (ARNT). The AHR-ARNT heteroduplex is an environmental sensor that integrates extracellular, endogenous, and metabolic signals to equilibrate cell activity. Inactivation of AhR or ARNT increased TC cells' resistance to targeted therapies. Our study revealed that AhR-deficient cancer cells expressed elevated activity in genes linked to the TGFβ-mediated SMAD2/3 pathway after drug treatment. Our results suggest that SMAD2/3 competes to bind ARNT and that the loss of AhR gives cancer cells a potent escape pathway to targeted therapies, counteracting MAPK inhibition with SMAD activation to sustain cancer cell proliferation.

overall_design: RNAseq of 8505c-EV cells and 8505c-AhR-KO cells at day zero or after four days treatement with the drug combination 10M Dabrafenib + 10nM Trametinib.

first: Youssef

last: Errami


title: Single cell transcriptomic changes in the THY-Tau22 mouse model of Alzheimer's disease at 17 months of age

status: Public on Jan 06 2025

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

type: Expression profiling by high throughput sequencing

summary: Alzheimer's disease (AD) displays sex-specific differences in prevalence and progression, but the underlying molecular mechanisms remain unclear. To investigate sex-dependent molecular changes associated with tau pathology at a late disease stage, we performed single-cell RNA sequencing on cortical tissue from 17-month-old THY-Tau22 mice and wildtype littermates of both sexes. The analysis revealed extensive sex-specific and sex-dimorphic transcriptomic alterations across multiple cell types, with particularly pronounced changes in microglia and oligodendrocytes. Key pathways affected in a sex-dependent manner included RNA processing and splicing, stress response pathways, neurotransmitter signaling, and protein degradation pathways. Network analysis identified the genes Clu, Mbp, Fos and Junb as potential regulatory hubs. Multiple genes with established implications in AD, including the long non-coding RNA gene MALAT1, showed concordant sex-specific changes when compared with both earlier time points and human AD data. This study provides a comprehensive characterization of sex-dependent transcriptomic changes in late-stage tau pathology, revealing new insights into the interplay between AD-like pathology and biological sex.

overall_design: The study investigated transcriptomic changes in the THY-Tau22 mouse model, which expresses human 4-repeat tau with G272V and P301S mutations under control of the neuronal Thy1.2 promoter. Single-cell paired-end RNA sequencing analysis was conducted on cortical tissue from mice at 17 months of age, representing a late disease stage. The experimental design included four groups with balanced sex distribution: male THY-Tau22 transgenic mice (n=4), male wildtype littermates (n=4), female THY-Tau22 transgenic mice (n=5), and female wildtype littermates (n=3). This late-stage analysis builds upon and complements previously published data from the same model at 7 months of age (GSE245035), enabling longitudinal assessment of disease progression and sex-dependent molecular changes.

first: Muhammad

last: Ali

first: Pierre

last: Garcia

first: Laetitia

middle: P

last: Lunkes

first: Alessia

last: Sciortino

first: Melanie

last: Thomas

first: Tony

last: Heurtaux

first: Kamil

last: Grzyb

first: Rashi

last: Halder

first: Alex

last: Skupin

first: Luc

last: Buée

first: David

last: Blum

first: Manuel

last: Buttini


title: Loss of the Aryl Hydrocarbon Receptor (AhR) Promotes Cancer Cells Resistance to BRAFV600E Targeted Therapies. [RNA-Seq]


title: Single-cell transcriptional profiling and gene regulatory network modeling in Tg2576 mice reveal gender-dependent molecular features preceding Alzheimer-like pathologies

status: Public on Jan 02 2025

summary: To identify disease-related molecular processes that occur before the onset of detectable neuropathology in Alzheimer's disease (AD), we performed a comprehensive single-cell analysis of disease-related molecular sex differences in transcriptomic data from the neocortex of 24-week-old Tg2576 mice and wild-type littermate controls. Cell type-specific changes were investigated at the level of individual genes, pathways and gene regulatory networks. The analyses revealed significant cell-type-specific gene expression changes in individual genes, pathways and sub-networks, including sex-specific and sex-dimorphic changes in both upstream transcription factors and their downstream targets, before the onset of overt disease. The study opens a window into the molecular events that may determine sex-specific susceptibility to Alzheimer's disease and uncovers tractable target candidates for potential sex-specific precision medicine for AD.

overall_design: The study used the Tg2576 transgenic mouse model of Alzheimer's disease, which overexpresses human APP with the Swedish mutation. Single-cell RNA-seq was performed on neocortical samples from 24-week-old Tg2576 mice and wildtype littermate controls using the DropSeq approach. The experimental conditions compared were: Tg2576 transgenic males, Wildtype control males, Tg2576 transgenic females, and Wildtype control females (9 mice per genotype/gender, using barcoded pooled replicates with four sample pools, one for each condition and gender).

first: Oihane

last: Uriarte Huarte

first: Beatriz

last: Pardo Rodriguez


title: ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq)

status: Public on Jan 26 2025

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

summary: Maternal pancreatic Beta-cell state is adapted to accommodate gestation metabolism. Defects in this process may cause gestational diabetes mellitus (GDM), with risk factors including a high-calorie diet during pregnancy. However, the regulatory mechanism of maternal Beta-cell adaptation is largely unknown. Using single-cell transcriptome combining genetic analyses, we discovered a precise process of Beta-cell adaptation in mice which is associated with progression of metabolic stress-related Beta-cell dysfunction, increased 40393969acetyl-CoA biosynthesis, and gene element-specific histone acetylation. STAT3 recruits p300 to promote histone acetylation levels of pregnancy-associated genes, and Acetyl-CoA Synthetase 2 (ACSS2) enhances this process. High-fat feeding causes hyperacetylation of chromatin that is specifically opened during pregnancy, which results in overexpression of genes that impair Beta-cell functions and, consequently, hyperglycemia. However, these impairments can be rescued by Beta-cell-specific deletion of Acss2. Therefore, our study reveals a precise adaptation process in Beta-cells at the single-cell level during pregnancy and a specific epigenetic pathway that regulates this process. We also explain the epigenetic regulatory mechanism by which a high-fat diet can lead to GDM and identify ACSS2 as a potential molecular target for controlling the progression of GDM.

overall_design: scRNA-seq of mouse pancreatic islets during gestation and puerperium days.

first: Cheng-Ran

first: Yu

last: Zhang

first: Shuang

last: He

first: Xi

last: Wang

first: Xin

first: Mao-Yang

first: Xin-Xin

last: Yu


title: The T3SS structural and effector genes of Chlamydia trachomatis are expressed in distinct phenotypic cell forms.

city: Moscow

first: Scott

middle: Stephen

last: Grieshaber

state: ID

address: 875 Perimeter Drive MS 3051

department: Biological Sciences

institute: University of Idaho

summary: Bacteria in the chlamydiales order are obligate intracellular parasites of eukaryotic cells. Within this order, the genus Chlamydia contains the causative agents of a number of clinically important infections of humans. Biovars of C. trachomatis are the causative agents of trachoma, the leading cause of preventable blindness worldwide, as well as sexually transmitted infections with the potential to cause pelvic inflammatory disease and infertility. Irrespective of the resulting disease, all chlamydial species share the same obligate intracellular life cycle and developmental cell forms. They are reliant on an infectious cycle consisting of at least three phenotypically distinct cell forms termed the reticulate body (RB), the intermediate body (IB) and the elementary body (EB). The EB is infectious but does not replicate. The RB replicates in the host cell but is non-infectious, while the IB is an intermediate form that transitions to the EB form. In this study, we ectopically expressed the transcriptional repressor Euo, the two nucleoid-associated proteins HctA and HctB, and the two component sensor kinase CtcB in the RB. Transcriptional analysis using RNA-seq, differential expression clustering and fluorescence in situ hybridization analysis show that the chlamydial developmental cycle is driven by three distinct regulons corresponding to the RB, IB or EB cell forms. Moreover, we show that the genes for the T3SS were cell type restricted, suggesting defined functional roles for the T3SS in specific cell forms.

relation:
Reanalysis of: GSM8173080
Reanalysis of: GSM8173079
Reanalysis of: GSM8173078
Reanalysis of: GSM8173083
Reanalysis of: GSM8173082
Reanalysis of: GSM8173081
Reanalysis of: GSM8173086
Reanalysis of: GSM8173085
Reanalysis of: GSM8173084
Reanalysis of: GSM8173089
Reanalysis of: GSM8173088
Reanalysis of: GSM8173087
Reanalysis of: GSM8173092
Reanalysis of: GSM8173091
Reanalysis of: GSM8173090
Reanalysis of: GSM8173095
Reanalysis of: GSM8173094
Reanalysis of: GSM8173093
Reanalysis of: GSM8173098
Reanalysis of: GSM8173097
Reanalysis of: GSM8173096
Reanalysis of: GSM8173101
Reanalysis of: GSM8173100
Reanalysis of: GSM8173099
Reanalysis of: GSM8173104
Reanalysis of: GSM8173103
Reanalysis of: GSM8173102
Reanalysis of: GSM8173107
Reanalysis of: GSM8173106
Reanalysis of: GSM8173105
Reanalysis of: GSM8499642
Reanalysis of: GSM8499643
Reanalysis of: GSM8499644
Reanalysis of: GSM8499645
Reanalysis of: GSM8499646
Reanalysis of: GSM8499647
Reanalysis of: GSM8499648
Reanalysis of: GSM8499649

overall_design:
RNA-seq analysis of Chlamydia trachomatis timeline infecting HeLA cells and ectopicaly expressing the regulatory proteins, Euo, HctA, CtcB and HctB

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The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Grieshaber

last: Scott

last: Nicole

first: Appa

last: Cody

first: Omsland

last: Anders


title: Transcriptomic signatures of oxytosis/ferroptosis are enriched in Alzheimer’s disease

first: K. Garrett

last: Evensen

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Oxytosis/ferroptosis is a non-apoptotic regulated cell death pathway characterized by glutathione (GSH) depletion with consequent inhibition of the GSH-dependent enzyme GSH peroxidase 4 (Gpx4), activation of lipoxygenases (LOXs), production of reactive oxygen species (ROS) and mitochondrial dysfunction, that culminates in cell death. Most of these changes are observed with aging and exacerbated in Alzheimer’s disease (AD). Furthermore, it has been shown that novel inhibitors of oxytosis/ferroptosis are protective in mouse models of aging and AD. One of the most potent of these inhibitors is the neuroprotective compound CMS121. The goal of the present study was to investigate the occurrence of oxytosis/ferroptosis in the AD brain by examining transcriptomic signatures of oxytosis/ferroptosis in multiple cellular and animal models of AD as well as in human AD brain samples. Our data show that different signatures of oxytosis/ferroptosis are enriched to varying extents in the brains of AD mice and human AD patients. https://doi.org/10.1186/s12915-025-02235-6

overall_design: We carried out a study of the whole transcriptome of mouse HT22 nerve cells in conditions of non-induced and induced oxytosis/ferroptosis in the absence and presence of 1uM CMS121. In cell culture, oxytosis/ferroptosis can be triggered by inhibiting cystine uptake via the cystine/glutamate antiporter system xc- with glutamate which subsequently depletes intracellular GSH. For this study, cells were harvested 6h after exposure to glutamate in the absence and presence of CMS121, prior to any cell death, and the whole RNA was isolated and sequenced.


title: Cell proliferation suppressor RBR1 interacts with ARID1 to promote pollen mitosis via stabilizing DUO1 in Arabidopsis

city: Shanghai

first: Lei

last: Li

address: Xinjiangwancheng

institute: Fudan University

summary: In plants, sperm cell formation involves two rounds of pollen mitoses, in which the microspore initiates the first pollen mitosis (PMI) to produce a vegetative cell and a generative cell, then the generative cell continues the second mitosis (PMII) to produce two sperm cells. DUO1, a R2R3 Myb transcription factor, is activated in the generative cell to promote S-G2/M transition during PMII. Loss-of-function of DUO1 caused a complete arrest of PMII. Despite the importance of DUO1, how DUO1 is regulated is largely unexplored. We previously demonstrated that ARID1, an ARID transcription factor, stimulates DUO1 transcription. Here, we show that cell proliferation suppressor RBR1 interacts with ARID1 to stabilize DUO1. While the C-terminus of RBR1 is dispensable for vegetative growth, it plays a crucial role in reproductive development and facilitates interaction with ARID1. Moreover, DUO1 is a short-lived protein, ARID1 promotes the RBR1-DUO1 interaction, and RBR1 stabilizes DUO1 in a proteasome-dependent manner. Thus, RBR1 promotes DUO1-dependent PMII progression via antagonizing its repressive role in the cell cycle factors CDKA;1 and CYCB1;1. Collectively, we uncover that ARID1 and RBR1 act in concert to regulate DUO1 at both the transcriptional and post-transcriptional levels, balancing cell specification and cell division.

overall_design: RNA-seq analysis of mature pollen from Col-0 and rbr1-4, two biological replicates for each genotype were made.

first: Binglian

last: Zheng


title: lncSLERT promotes liver metastasis in colorectal cancer by down-regulating HUNK expression via RBM15-mediated m6A modification

status: Public on Jan 01 2025

city: Zunyi

first: lin

state: 贵州省遵义市新蒲新区

address: 贵州省遵义市新蒲新区学府西路6号

institute: Zunyi Medical University

summary: Metastasis constitutes a hallmark of cancer and serves as the principal cause of cancer-related mortality. Nevertheless, the mechanism of liver metastasis in CRC remains incompletely clarified. This study investigates the long non-coding RNA (lncRNA) SLERT and its critical role in promoting liver metastasis of colorectal cancer (CRC) by downregulating HUNK expression. We found that SLERT was significantly upregulated in CRC tissues, correlating with poorer survival outcomes. Functional assays revealed that silencing SLERT inhibited CRC cell migration and invasion, while its overexpression promoted these metastatic behaviors. Mechanistic analysis showed that SLERT interacts with the RNA-binding protein RBM15, impairing its ability to stabilize HUNK mRNA, leading to decreased HUNK levels and increased metastatic potential. The cytoplasmic localization of SLERT indicates its active role in regulating gene expression within the tumor microenvironment. Collectively, these results suggest that SLERT serves as a potential diagnostic biomarker and therapeutic target, indicating that targeting SLERT or restoring HUNK expression could provide novel strategies to combat liver metastasis in CRC and improve patient prognosis.

overall_design: To investigate the mechanism of SLERT in liver metastasis of imaging rectal cancer, we knocked down SLERT in LoVo cell line and overexpressed SLERT in HCT116

first: liming

last: zhao

last: wang

first: Zhaoxu


title: Antibiotics and Immune Responses study

status: Public on Jan 14 2025

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: Blood collected from infants at week 6 and week 7 of life to profile how the transcriptome is changed following routine early life vaccination. Paired faecal metagenomic data is available for these infants under BioProject PRJNA807448 at the Sequence Read Archive.

overall_design: Total RNA sequenced from healthy infants at week 6 and week 7 of life

first: David

last: Lynn


title: Structural basis of the DEK-nucleosome complex and its functional implications [CUT&Tag]

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The nuclear factor Dek is notably enriched within chromatin; nevertheless, the precise binding mechanism of Dek to the nucleosome remains elusive. In this study, we employ cryo-electron microscopy (cryo-EM) to elucidate the high-resolution structure of the Dek-Nucleosome Core Particle (NCP) complex. We identify specific domains responsible for DEK interaction with the histone octamer and DNA within the nucleosome. The veracity of these binding domains is confirmed through a series of meticulous biochemical experiments. Subsequently, cellular experiments reveal that Dek lacking nucleosome-binding capacity exhibits a deficiency in chromatin interaction. Remarkably, this impairment induces a shift towards the primitive endoderm fate in mouse embryonic stem cells, underscoring the pivotal role of Dek in determining cell fate through its nucleosomal interactions.

overall_design: Wild-type DEK and various key domain mutations were overexpressed in DEK-knockout cells. CUT&Tag for histone modifications and Suz12 was employed to assess the impact of mutations on the epigenetic states.

first: Yunfan

last: Shen

first: Yanhong

last: Liu

first: Hongda

last: Huang

first: Kai

last: Yuan


title: Suppression of inflammaging prolongs hematopoietic healthspan  [dataset 2]

status: Public on Jan 03 2025

city: New York

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: The impact of recombinant Thbs1 (rThbs1) on HSC activity is unknown. In this experiment, RNA Seq analysis was performed on BM HSCs derived from young (4 month-old) control mice that were cultured ex vivo for 11 days in the presence or absence of rThbs1 (500 ng/mL). Additionally, RNA Seq analysis of HSCs cultured with rThbs1 in the presence of its neutralizing antibody (Clone A4.1) or its isotype control was performed to identify the pathways that are altered in HSCs upon exposure to rThbs1.

overall_design: Comparative gene expression profiling analysis of BM HSCs cultured in the presence of recombinant Thbs1 and its neutralizing antibody.

first: Pradeep

last: Ramalingam

first: Michael

last: Poulos

first: Jason

last: Butler


title: The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X]

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

summary: To comprehensively define the cellular heterogeneity of glioblastoma (GBM), the GBM CARE (Cellular Analysis of Resistance and Evolution) consortium set out to profile 121 GBMs with extensive clinical annotation, by single-nucleus RNA-sequencing and bulk tumor DNA sequencing. The resulting dataset enabled us to characterize GBM heterogeneity at three levels. First, GBMs are classified by their cellular composition, encompassing malignant, immune, neuronal and glial cell types. Second, within each cell type, and particularly among the malignant cells, we describe the diversity of cellular states and their pathway-based functional activities. Third, after controlling for the frequencies of cellular states, we find that the remaining variation between GBMs highlights three baseline gene expression programs which we labeled Neuronal, Glial, and Extracellular Matrix. These three layers of heterogeneity are inter-related and partially associated with specific genetic aberrations, thereby defining three stereotypic ecosystems in GBM. This work provides an unparalleled view of the multi-layered transcriptional architecture of GBM.

overall_design:
Nuclei from frozen tumor tissue were isolated. The nuclear suspensions were inspected by microscope, counted using a hemocytometer, and used for 10x Genomics workflow.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Avishay

last: Spitzer

first: Kevin

middle: C

last: Johnson

first: Luciano

last: Garofano

first: Anna

last: Lasorella

first: Roel

last: Verhaak

first: Antonio

last: Iavarone

first: Itay

last: Tirosh

first: Mario

middle: L

last: Suvà


title: Nuclear IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming [RNA-seq]

city: zhengzhou

first: li

last: mengjia

address: Science Road 100, Zhengzhou, Henan, 450001, P.R.

institute: zhengzhou university

summary: Although, IDH1 has been recognized to play critical roles in the regulation of dynamic chromatin states, the mechanism remained largely unknown. Here, using the human erythropoiesis system, we presented an innovative perspective of metabolism independent role of nuclear IDH1. We discovered that IDH1 acted as a nuclear located chromatin-binding protein. Knockdown of IDH1 induced chromatin reorganization and subsequently aroused aberrant biological events germination on erythroid precursors in a metabolism independent manner. IDH1 knockdown induced genome-wide coordinate changes in the distribution and intensity of multiple histone marks, among which H3K79me3 was identified to be the decisive factor in chromatin state reprogramming. Integrating ChIP-seq, ATAC-seq and RNA-seq recognized SIRT1 to be the key gene affected by IDH1 deficiency. Taken together, these findings provided a novel insight for further clarifying the fundamental biological function of IDH1 which had substantial implications for an in-depth understanding of the pathogenesis of diseases with IDH1 dysfunction and accordingly the development of therapeutic strategies.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at D15 cultured of erythroid cells.Comparative gene expression profiling analysis of RNA-seq data  and its KD derivatives (Luciferase-shRNA，IDH1-shRNA).

first: Mengjia

last: Li

first: Lixiang

last: Chen


title: The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [smart-seq2]

overall_design:
Nuclei from frozen tumor tissue were isolated. The nuclear suspensions were inspected by microscope, counted using a hemocytometer, and used for Smart-seq2 workflow.
The file All_cells_metadata.xlsx includes information for all individual nuclei analyzed in this study.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<


title: Suppression of inflammaging prolongs hematopoietic healthspan.

first: David

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

overall_design: Refer to individual Series


title: Nuclear IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at D15 cultured of erythroid cells.Comparative gene expression profiling analysis of RNA-seq data  and its KD derivatives (Luciferase-shRNA, IDH1-shRNA).


title: Transcriptomic data of  Aeromonas hydrophila 201416 isolated from Scatophagus argus under different salinity exposures

status: Public on Dec 31 2024

city: guangdong

first: yuan

last: sun

state: shenzhen

address: Zhiyuan Building, Canghai Campus, 3688 Nanhai Avenue, Nanshan District, Shenzhen City

institute: shenzhen universuty

summary: Analysis of Ah201416 cells harvested after being cultured in an LB medium with different salinity levels (0, 10, and 20 g/L of NaCl concentration) for 18 h.The results provided insights into the molecular basis of the enhanced virulence of Ah201416 in response to salinity elevation.

overall_design: The Ah201416 cells were harvested after being cultured in the medium containing 0, 10, and 20 g/L NaCl for 18 h.

first: Yuan

last: Sun

first: Maoliang

last: Su

first: Lingyun

last: Hao

first: Jianbing

last: Liang


title: SIRT4 controls acetyl-CoA synthesis to promote stemness and invasiveness of hepatocellular carcinoma through deacetylating MCCC2 [RNA-seq]

first: Tianjiao

address: Balizhuang Street

institute: Peking University Cancer Hospital and Institute

summary: The mitochondria sirtuin 4 (SIRT4) is well-known as a tumor suppressor by controlling several metabolic pathways, although it is highly expressed in certain cancers including hepatocellular carcinoma (HCC). Here, we reported that SIRT4 was highly expressed in a subset of the voltage-gated calcium channel α2δ1 subunit-positive HCC tumor-initiating cells (TIC), and was upregulated by α2δ1-mediated calcium signaling. Furthermore, SIRT4 is functionally sufficient and indispensable to promote TIC properties and invasiveness of HCC cells by directly deacetylating the leucine catabolism pathway enzyme－3-methylcrotonyl-CoA carboxylase 2 (MCCC2) at K269, leading to the formation of a stable MCCC1/MCCC2 complex with robust MCCC enzymatic activity to produce increased levels of acetyl-CoA, which subsequently resulted in increased levels of H3K27 acetylation and stem cell-like properties at tested doses≤2 µM. Interestingly, the expression of SIRT4 in HCC tissues was predictive of poor prognosis of the patients. These findings identify SIRT4 as an oncogene to promote stemness and invasiveness by controlling the production of acetyl-CoA, linking α2δ1-mediated calcium signaling to SIRT4-mediated epigenetic regulation of the stem cell-like properties which hold significant potential for the development of innovative therapeutic strategies targeting HCC TICs.

overall_design: RNA-seq were compared between Huh-7 cells expressing MCCC2 K269R and MCCC2 K269Q


title: SIRT4 controls acetyl-CoA synthesis to promote stemness and invasiveness of hepatocellular carcinoma through deacetylating MCCC2

overall_design: CHIP-seq were compared between Huh-7 cells expressing MCCC2 K269R and MCCC2 K269Q


title: mRNA-Sequencing data of herpes simplex virus type 1 (HSV1)-infected primary mouse microglia

city: Seoul

first: Soo-Jin

last: Oh

address: Guro-go

country: South Korea

institute: Korea University

summary: We report mRNA-Sequencing analysis of primary mouse microglia infected with HSV1 and/or treated with ALT001, which is mitophagy inducing drug

overall_design: Investigation of the differential expression patterns of mRNAs in response to mock- or HSV1-infected primary microglia followed by Veh- or ALT001 treatment

first: Ok Sarah

last: Shin

first: Jeanho

last: Yun


title: Somatic epimutations enable native single-cell clonal tracking on hematopoietic cell state landscapes across the murine and human lifespan

city: Barcelona

first: Michael

last: Scherer

address: C/ Dr. Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

type: Methylation profiling by high throughput sequencing

summary: Current approaches to track stem cell clones through differentiation require genetic engineering or rely on sparse somatic DNA variants. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a method for transgene-free lineage tracing based on microfluidic, targeted single-cell DNA methylation analysis. Applied to mouse and human hematopoiesis, we captured hundreds of clonal differentiation trajectories across tens of individuals and almost 400,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation while at the same time providing cell state resolution similar to transcriptomic data. Applied to unperturbed hematopoiesis in murine ageing, we demonstrate that myeloid bias and low output of old HSCs are restricted to a small number of expanded developmental clones, while many functionally young-like clones persist in old age. In human ageing, we demonstrate that clones carrying CHIP mutations are part of a spectrum of age-related expansions of low-output clones. EPI-clone is compatible with the multiplexed readout of surface protein, somatic variants and RNA from the same single cell. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.

overall_design: Single-cell DNA methylation data was generated using scTAM-seq providing single-CpG, single-cell resolution. Data is provided as a count matrix showing the number of sequencing read per amplicon (CpG) in each of the single cells.

first: Indranil

last: Singh

first: Martina

last: Braun

first: Chelsea

last: Szu-Tu

first: Alejo

last: Rodriguez-Fraticelli

first: Lars

last: Velten


title: Genome-wide synthetic lethal screen identifies SRM as a target that enhances erdafitinib efficacy in FGFR-mutant bladder cancer

city: wuhan

first: 砚超

last: 余

state: 湖北

address: xinhua street

institute: huazhong university of science and technology

summary: Mutations of the fibroblast growth factor receptor (FGFR) family members are frequently observed in metastatic bladder cancer. The development of erdafitinib, a pan-FGFR inhibitor, provides a significant therapeutic advance in bladder cancer, but resistance still limits its efficacy. In this study, we perform an unbiased whole-genome CRISPR-Cas9 synthetic lethal screen on FGFR-mutant bladder cancer cell lines treated with erdafitinib-targeted therapy and identify SRM as a critical contributor to erdafitinib resistance. In polyamine metabolism, SRM catalyzes the production of spermidine, which subsequently promotes the hypusination of eukaryotic translation factor 5A (eIF5A). Moreover, we demonstrate that hypusinated eIF5A (eIF5AHyp) facilitates the efficient translation of HMGA2, which in turn promotes EGFR expression. Notably, pharmacologic inhibition of SRM using MCHA enhances the efficacy of erdafitinib both in vitro and in vivo. Together, these results offer evidence of the synthetic lethality between SRM inhibition and erdafitinib, suggesting that combination treatment is a promising therapeutic strategy to overcome erdafitinib resistance for FGFR-mutant bladder cancer.

overall_design: We perform crispr screen on MGH-U3 and SW780 cells to explore essential genes mediating erdafitinib resistance.


title: Suppressor of cytokine signaling 2 is induced in Huntington’s Disease and involved in autophagy

city: Suwon

first: Kyoung

last: Cho

state: Gyeonggi-do (41)

address: 154-2 Gwanggyosanro, Youngtong-gu

department: Life Science

institute: Kyonggi University

summary: Suppressor of cytokine signaling (SOCS) proteins are primarily feedback inhibitors of cytokine signaling. The two conserved domains of SOCS proteins have distinct functions. Src homology 2 (SH2) domain inhibits cytokine receptor, while SOCS box acts as an E3 ubiquitin ligase. SOCS2, a cytokine signaling suppressor, has been primarily implicated in regulating inflammatory conditions in neuronal diseases. However, SOCS proteins have been suggested to play diverse roles in healthy and diseased nervous system including neurodegenerative disorders. In this study, SOCS2 was found to be upregulated in Huntington’s disease and was substantially induced in extended polyglutamine (polyQ)-expressing striatal cells. The induced level was augmented under aging conditions. In extended polyQ-expressing cells, downregulated SOCS2 improved autophagic dysfunction rather than altered inflammatory conditions. Overall, we suggest that SOCS2 involves in regulating autophagy by functioning as an E3 ligase in extended polyQ conditions, and consequently regulates cell damage and cell death type.

overall_design: To examine gene expression changes in subregions of the brain (striatum and cortex) according to age (before and after the onset of disease symptoms) in Huntington's disease mice, total mRNA was isolated from tissues of striatal and cortical subregions of the brain of HD mice (R6/2) and WT mice (normal R6/2 littermate) of the same age, and RNA-seq was performed.  Gene expression profiling analysis of RAN-seq data from each mouse brain tissue.

first: KyoungJoo


title: Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

institute: Centenary Institute

summary: Metazoans employ chromodomain helicase DNA-binding (CHD) enzymes to reposition nucleosomal DNA for transcription and replication. The CHD family consists of nine distinct members (CHD1-9) that possess highly conserved chromo and ATPase domains. These domains are flanked by poorly characterised N- and C-termini, which are enriched with intrinsically disordered regions (IDRs) and short aggregation-prone regions (APRs). The contribution of IDRs and APRs to CHD function has remained elusive. In this study we used affinity purification followed by mass spectrometry analysis (AP-MS) to define the protein-protein interaction (PPI) networks within the N- and C-termini of each CHD family member. The results illustrate a comprehensive map of CHD1-9-specific binding proteins that include dozens of novel interactions with transcription regulators and epigenetic factors. Using AlphaFold Multimer we examined the structural predictions of high confidence PPIs from our AP-MS screens and identified APR regions with alpha helical structures that contribute to PPIs. We further investigated a highly conserved APR within the C-terminus of the CHD4 protein and demonstrate that it contributes to the interaction of CHD4 with the nucleosome remodelling and deacetylase (NuRD) and CHD, ADNP, HP1 (ChAHP) complexes. Peptides mimicking this APR effectively disrupt CHD4 binding to both NuRD and ChAHP complexes, consequently triggering the transcriptional activation or repression of hundreds of target genes. Our results emphasise the crucial role that the N- and C-termini of CHD chromatin remodelers play in establishing protein-protein interaction (PPI) networks, which drive unique transcriptional programs.

overall_design: G1E-ER4 cells were cultured to a density of 2.5 × 105 in 12-well plates. CHD4-APR (-YWLLAGII-Tat) and CTRL (AAAAAAA-Tat) peptides were added to the culture media each at 10 μM concentration. After 2 h cells were treated with 100 μM of Tamoxifen for another 28 h and cells were collected for RNA extraction. Cell pellets were lysed in 1 mL of TRIzol™ Reagent (Invitrogen).

first: Yue

last: Feng

first: Cynthia

last: Metierre

first: Chirag

last: Parsania

first: Mehdi

last: Sharifi Tabar


title: Remodeling of gene expression during C. elegans hibernation. [RNA-Seq]

city: Oslo

first: Eivind

last: Valen

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: In the wild, many animals respond to cold temperatures by entering hibernation. In the clinic, controlled cooling is used widely in transplantation and emergency medicine. Yet, the molecular mechanisms the cells use in response to cold remain largely unexplored. One aspect of cold adaptation is a global downregulation of protein synthesis. Here, we performed total RNA sequencing combined with ribosome profiling to assess specific mRNA levels and their translational status during Caenorhabditis elegans hibernation.

overall_design: Total RNA sequencing and ribosome profiling analysis was performed on synchronzied wild-type animals that were grown at different temperatures. For the 20°C condition, animals were grown from the L1 stage to 1-day-old adults at 20°C before collection. For the 10°C condition, animals were grown from the L1 stage to 1-day-old adults at 20°C, after which they were grown for 2 hours at 10°C before collection. For the 4°C 1, 3, or 5 days conditions, animals were grown from the L1 stage to 1-day-old adults at 20°C, after which they were grown for 2 hours at 10°C followed by 1, 3, or 5 days at 4°C before collection.

first: Melanie

last: Engelfriet

first: Yanwu

last: Guo

first: Andreas

last: Arnold

first: Rafal

last: Ciosk


title: Modeling Hereditary Diffuse Leukoencephalopathy with Axonal Spheroids using microglia-sufficient brain organoids

first: Wei Jie

last: Wong

address: Chong Qing Nan Road 280

institute: shanghai jiaotong univeristy

summary: Hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) is a rare, fatal, adult-onset neurodegenerative disease that is most often caused by mutations affecting the Colony Stimulating factor-1 Receptor (CSF-1R). To understand how CSF-1R-mutation affects human microglia – the specialized brain-resident macrophages of the central nervous system – and the downstream consequences for neuronal cells, we used a macrophage and forebrain organoid co-culture system based on induced pluripotent stem cells generated from two patients with HDLS, with CSF-1R gene-corrected isogenic organoids as controls. Macrophages derived from iPSC (iMacs) of patients exhibited a metabolic shift towards the glycolytic pathway and reduced CSF-1 sensitivity, which was associated with higher levels of IL-1β production and an activated inflammatory phenotype. Single-cell RNA sequencing revealed that iMacs adopt a reactive state that leads to impaired regulation of neuronal cell populations in organoid cultures, thereby identifying microglial dysregulation and specifically IL-1β production as key contributors to the degenerative neuro-environment in HDLS.

overall_design: To better understand how diseased or non-diseased macrophages affect the developing brain, we co-cultured iMacs and forebrain organoids generated from donor-derived iPSCs (HD1 and HD2). Isogenic control counterparts were also derived. We then performed gene expression profiling analysis using data obtained from the bulk RNA-seq of iMacs before and after co-culture, as well as neurons and NPCs populations from forebrain organoid.

first: WeiJie

first: Ziyi

last: Li

first: Florent

last: Ginhoux


title: Remodeling of gene expression during C. elegans hibernation. [Ribo-Seq]


title: Nigral dopaminergic sirtuin 3 inhibits aging-related locomotor decline

city: Daegu

first: Jun-Yeong

last: Lee

address: Daehak-ro 80, Buk-gu

department: School of Life Sciences

institute: Kyungpook National University

summary: Aging reduces locomotor capacity. Although a decrease in the activity of the nigrostriatal dopamine (DA) system is one of key mechanisms linked to the drop-in locomotor activity in aging, the specific molecule responsible for controlling this decline remains elusive. Here we report that sirtuin 3 (SIRT3), a mitochondrial deacetylase associated with an anti-aging effect, is downregulated in nigral DA neurons of 20-month-old mice, showing the decline in locomotor activity, and that the declined locomotor activity by aging was deteriorated with more serious alteration in the levels of mitochondria-related proteins in mice with genetic deletion of SIRT3 compared to age-matched control mice. Moreover, SIRT3 upregulation through the administration of adeno-associated virus serotype 1 (AAV1) encoding the SIRT3 gene in the substantia nigra (SN) mitigated the age-dependent loss of locomotor activity by the preservation of the nigrostriatal DA system from aging in vivo. Therefore, we conclude that SIRT3 preservation in the nigrostriatal DA system has resistance to age-related locomotor decline, suggesting that SIRT3 upregulation in nigral DA neurons can be useful to preserve locomotor capacity in aging.

overall_design: The substantia nigra was obtained from WT (Intact), GFP-overexpressed (AAV-GFP), and SIRT3-overexpressed (AAV-SIRT3) mice (six mice per group). They were sequenced using 2 x 100bp paired-end Illumina NovaSeq to understand transcriptional changes that occur in the SIRT3-overexpressed substantia nigra.

first: Youngpyo

last: Nam

first: Sehwan

last: Kim

first: Sang

middle: R


title: Cellular Communication Networks in Fibrosis: Single-nucleus Transcriptomic Insights from the MAFLD Pig Model

city: Beijing

first: Kaiyi

last: Zhang

state: Beijing

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary: The aim of this research is to reveal the cellular crosstalk in fibrosis liver using transgenic pigs (TG) expressing humanized risk genes (PNPLA3I148M-GIPRdn-hIAPP) as a MAFLD model. The study uses single-nucleus sequencing to reveal the differentiation and interaction characteristics of various cell populations in the liver during the development of MAFLD. Compared to wild-type pigs (WT), the model pigs showed significantly increased plasma levels of neurotensin and phosphatidylserine, along with insulin resistance and significantly decreased HDL-c levels. After 6 months of high-fat high-sucrose diet induction, the model pigs exhibited obvious liver pathological features, including fat deposition, inflammatory cell aggregation, fibrosis, and blocked insulin signaling pathways. Single-nucleusl transcriptome sequencing identified six main cell types in the liver, and correlation analysis showed similar liver cell clusters, zones, and functions between pigs and humans. Liver cells near the central vein and liver sinusoidal endothelial cells (LSECs) were sensitive to metabolic changes and exhibited impaired function and reduced numbers first. Fibrosis-related pathways and the Rap1 pathway were activated in hepatic stellate cells of the model pigs, while retinol metabolism decreased, and the number of activated hepatic stellate cells increased. The differentiation direction of macrophages in the model pig's liver was markedly different from that in the WT pigs; the former differentiated toward the M1 phenotype, showing high expression of MHC-II antigen presentation molecules, various cytokines, phagosomes, and lysosomal-related genes. In contrast, the macrophages in the WT  pig's liver primarily differentiated toward the M2 phenotype and expressed genes related to immune regulation and injury repair. There was active cell interaction between hepatic stellate cells, endothelial cells, and M1-type macrophages, promoting the development of chronic inflammation and fibrosis through interactions of receptors such as FGFs-FGFRs, PDGFs-PDGFRs, EFNA1-EPHRs, and CXCL12-CXCR4/CXCR7.In conclusion, the transgenic pig model of MAFLD exhibits liver pathological features consistent with MAFLD patients. The receptor interactions between hepatic stellate cells, endothelial cells, and macrophages play a key role in regulating metabolic inflammation and fibrosis development. Remarkable changes in receptor interactions hold promise for application in MAFLD drug development.

overall_design: Triple-transgenic pigs (PNPLA3I148M-GIPRdn-hIAPP) were used as the MAFLD model and wild-type pigs were used as control.  Both groups were induced with a high-fat and high-sugar diet for 6 months. Single-nucleus RNA sequencing was performed on liver samples from both triple-transgenic pig and wild-type pig.

first: Jiakun

last: Miao

first: Yu

last: Yang

first: Shulin


title: Single-cell transcriptome sequencing of macrophages in acute kidney injury(AKI) to chronic kidney dieases(CKD)

first: Weijian

last: YAO

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

summary: Macrophages are key immune cells in AKI and may determine the fate of AKI to CKD progression. Here, by taking advantages of single cell RNA-sequencing technology, we generated a mononuclear macrophage atlas from the initiation of AKI till the progression to CKD.

overall_design: We used a unilateral ischemia-reperfusion renal injury (uIRI) 45minAKI model. The mouse kidney, spleen, and peripheral blood were taken at different time points after surgery, and the kidney, spleen and peripheral blood of normal mice were used as controls. Mononuclear phagocytic cells were sorted by FACS and then performed single cell transcriptome sequencing. 6 mice at each time point.

last: Yao

first: Ying

last: Chen

first: Menghan

last: Liu

first: Li


title: GATA2 up-regulation restores androgen receptor chromatin association and advances darolutamide resistance in prostate cancer

city: Houston

first: Tianyi

last: Zhou

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Darolutamide is an anti-androgen drug clinically used for prostate cancer therapy. Despite its efficacy, potential drug resistance poses significant challenges in the clinical setting. To better understand the molecular changes resulting from prolonged exposure to darolutamide, we developed a darolutamide-resistant model using LNCaP prostate cancer cells. Through ChIP-seq analysis, we found that a temporary treatment of cells with darolutamide effectively disrupts AR binding to chromatin. However, in darolutamide-resistant cells, the chromatin binding of AR is largely restored. By an integrative analysis of ChIP-seq and RNA-seq, we further identified GATA2, a pioneer factor for AR, substantially upregulated in darolutamide-resistant cells. GATA2 plays an essential role in promoting the proliferation of darolutamide-resistant cells and directly contributes to drug resistance. The ablation of GATA2 by siRNA abolished AR's recruitment to chromatin, leading to a significant reduction in gene expression regulated by AR in these resistant cells. Conversely, the overexpression of GATA2 in prostate cancer cells promoted cell proliferation and resistance to darolutamide. This study demonstrates the significance of GATA2 in the development of darolutamide resistance and suggests GATA2 as a promising therapeutic target to overcome this resistance.

overall_design: Our research highlights the crucial role of the AR and GATA2 interplay in prostate cancer progression and identifies GATA2 as a potential therapeutic target. Previously GATA2 has been shown to be linked to poor prognosis in prostate cancer, but no clinically applicable GATA2 inhibitor is yet available. K7174, a known proteasome inhibitor that inhibits GATA2, enhanced the killing activity of AML chemotherapeutics in vitro. When we combined K7174 with darolutamide in our study, the prostate cancer cells displayed increased sensitivity to darolutamide. This suggests that such a combination could enhance therapeutic outcomes and has the potential to delay or even prevent the onset of resistance. However, the clinical use of proteasome-targeting agents often comes with substantial side effects. Prostate cancer patients will benefit from future studies on the development of more specific and potent GATA2 inhibitors with less toxicity.

first: Chengtai

last: Yu

first: Yali

last: Han

first: Bin

last: He

first: Qin

last: Feng


title: Effect of hmuY and hmuR or husA and husB genes deletion on Porphyromonas gingivalis gene expression

city: Wrocław

first: Michał

last: Śmiga

address: Fryderyka Joliot-Curie 14a

country: Poland

institute: Faculty of Biotechnology, University of Wrocław

summary: Porphyromonas gingivalis is one of the main etiological agents responsible for initiating and progressing periodontal diseases in humans. P. gingivalis does not synthesize heme, and it uses host hemoproteins as a source of this molecule. The main heme uptake mechanism utilized by P. gingivalis is the Hmu system composed of six proteins where HmuY (hemophore-like protein) and HmuR (TonB-dependant outer membrane heme receptor) play a crucial role in heme supply. The second heme uptake mechanism is the Hus system composed of four proteins, with HusA (hemophore-like protein) and HusB (TonB-dependant outer membrane receptor) supporting heme uptake. Heme and iron starvation influence the P. gingivalis phenotype, therefore the aim was to determine the influence of deletion of HmuY and HmuR (ΔhmuYR strain) or HusA and HusB (ΔhusAB strain) encoding genes on P. gingivalis gene expression.

overall_design: Porphyromonas gingivalis was cultured in heme and iron-rich conditions (Basal medium supplemented with 7.7 µM heme; Hm) or heme and iron-depleted conditions (Basal medium supplemented with 160 μM 2,2-dipyridyl; DIP) until the mid-exponential growth phase (OD600 = 0.5-0.6). Samples were analyzed in three independent biological replicates. Wild-type A7436 strain was cultured in Hm and DIP conditions. ΔhmuYR and ΔhusAB strains were cultured in Hm conditions.

first: Teresa

last: Olczak


title: Lifetime ovulatory years and ovarian cancer gene expression profiles

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary:
Greater ovulatory years is associated with increased ovarian cancer risk. Although ovulation leads to an acute pro-inflammatory local environment, how long-term exposure to ovulation impacts ovarian carcinogenesis is not fully understood.
Thus, we examined the association between gene expression profiles of ovarian tumors and lifetime ovulatory years to enhance understanding of associated biological pathways.

overall_design: Ovarian cancer case-only analysis, association between gene expression profiles of ovarian tumors and lifetime ovulatory years

first: Naoko

last: Sasamoto

first: Shelley

middle: S

last: Tworoger


title: Gene expression in High-Grade Serous Ovarian Cancer (HGSOC) cells

overall_design: Cancer cells <500 micrometers and >500 micrometers from TLS were laser capture microdissected and RNA was extracted. The RNA was analyzed using the NansoString nCounter Human Inflammation Panel v2 assay.

first: Subir

last: Biswas

first: Xiaoqing

first: Jose

last: Conejo-Garcia


title: CircRNA expression profiling in human breast cancer

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We collected 3 paired tumor tissues and adjacent normal tissues collected from patients with node-positive primary breast cancer. Total RNA was extracted from tissues using Trizol reagent. Then total RNA was processed and circRNAs were profiled using RNA-seq technique. Raw read counts were filtered to remove the genes with a zero read count in 3 or more samples, and then normalized with DESeq2 in the statistical program R (version 4.0.1). Differentially expressed genes were screened using following criterions: fold change was larger than 2 and adjusted P value was less than 0.05.

overall_design: The circRNA expression in breast tumors was compared to circRNA expression in adjacent normal breast tissues.

first: Siying


title: Dynamics of gene expression profiling by RNA-Seq and identification of high-risk patients for severe COVID-19 [RNA-Seq]

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

summary: The clinical manifestations of SARS-Co-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of adult patients hospitalized for COVID-19 and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with microbiology-confirmed COVID-19, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 hours of admission and at day 7. There were 2150 differently expressed genes in patients with ARDS at baseline, and 1963 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to the loss of immune regulation. This led in turn to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.

overall_design: 93 samples (Covid19=60, Covid19_SDRA=33)

first: Alexander

last: Rombauts

first: Lara

last: Nonell


title: Increased YAP transcriptional activity in  in male murine steroidogenic zG adrenocortical cells

status: Public on Dec 30 2024

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

institute: Université de Montréal

summary:
To specifically evaluate the effect of an increase of the transcriptional activity of YAP in mice adrenal gland we generated a mouse mode expressing a constitutively active form of human YAP (YAP5SA) in aldosterone-producing zG cells.
RNAseq analysis on whole adrenal glands were performed on one month male mice

overall_design: RNAseq gene expression profile for WT (Rosa26YAP5SA/+) and mutant mice adrenal glands (Rosa26YAP5SA/+; AScre/+)  (n=3/group)

first: Alexandre

last: Boyer


title: Lats1/2 depletion in male murine steroidogenic zG adrenocortical cells

summary:
In order to understand the role of Hippo pathway in  mice adrenal glands, we inactivated lats1/2 in a transgenic mouse model using the cre recombinase system in aldosterone-producing zG cells.
RNAseq analysis on whole adrenal glands were performed on male mice

overall_design: RNAseq gene expression profile for  WT (Lats1flox/flox;Lats2flox/flox) and KO mice adrenal glands (Lats1flox/flox;Lats2flox/flox;AS-cre) (n=3/group)


title: Hippo signaling regulates zG cell fate in the adrenal cortex of mice

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

overall_design: Refer to individual Series


title: Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19


title: Genotype and expression analyses of FTO and ALKBH5 in renal cell carcinoma cohort from MENA region

status: Public on Dec 29 2024

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: RNA-modifying proteins significantly contribute to cancer progression. Fat mass and obesity-associated protein (FTO) and alkB homolog 5 RNA demethylase (ALKBH5) are RNA-demethylating proteins with opposing roles in renal cell carcinoma (RCC) across different populations. This study evaluates the genotype and expression of FTO and ALKBH5 in RCC patients from the Middle East and Northern Africa (MENA) region. Formalin-fixed paraffin-embedded samples from kidney biopsies of RCC patients and controls were analyzed through targeted DNA sequencing, whole transcriptome profiling, and immunohistochemistry.  Our findings indicated that the rs11075995T variant in FTO is linked to an increased risk of ccRCC. ALKBH5 and FTO protein expression were significantly downregulated in clear cell RCC (ccRCC) and chromophobe RCC (chRCC) but not in papillary RCC (pRCC) patients. In ccRCC, transcriptomic data revealed significant downregulation of FTO (log2FC = -5.2, q <0.001) and ALKBH5 (log2FC = -4.7, q <0.001) compared to controls. A significant negative correlation was found in ccRCC between FTO expression and T allele frequency in rs11075995, suggesting an impact on FTO expression. To our knowledge, this is the first study to examine FTO and ALKBH5 mutations and expression in RCC patients from the MENA region.

overall_design:
Formalin-fixed paraffin-embedded samples from kidney biopsies of RCC patients and controls were analyzed through targeted DNA sequencing to sequence common variant in FTO and ALKBH5 genes.
11 controls, 22  ccRCC, 6 chRCC, and 7 pRCC samples
Abbreviations: (RCC: Renal cell carcinoma, ccRCC: clear cell RCC, chRCC: chromphobe RCC, pRCC: papillary RCC)

first: Muna

middle: A

last: Alhammadi

first: Burcu

middle: Y

last: Ilce

first: Poorna

middle: M

last: Bhamidimarri

first: Amal

last: Bouzid

first: Nival

last: Ali

first: Reem

last: Alhamidi

first: Alaa

last: Hamad

first: Mona

last: Mahfood

first: Abdelaziz

last: Tlili

first: Iman

last: Talaat


title: RNA-seq analysis of kidney cortex of proximal tubular epithelial cell specific I-PpoI expressing mice.

status: Public on Dec 24 2024

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Japan

institute: keio university

summary: For determination of the changes in PTEC gene expression caused by DNA DSBs, RNA-seq analysis was performed.

overall_design: RNA was isolated from the renal cortex from the I-PpoI or WT mice. Total RNA was used to prepare an RNA-seq library using the TruSeq Stranded mRNA LT Sample Prep Kit according to the TruSeq Stranded mRNA Sample Preparation Guide, part #15031047 Rev. E (Illumina, San Diego, CA, USA).

first: Erina

last: Sugita Nishimura

first: Akihito

last: Hishikawa

first: Ran

last: Nakamichi

first: Kaori

last: Hayashi


title: DNA methylation of peripheral blood cells of CKD patients.

status: Public on Dec 27 2024

type: Methylation profiling by genome tiling array

summary: The relationship between DNA methylation changes in peripheral blood cells of CKD and ESKD patients and both DNA damage in renal constituent cells and fatty liver remains unclear. In this study, we analyzed DNA methylation changes in peripheral blood cells of CKD and ESKD patients and examined their associations with DNA damage levels in urinary exfoliated cells and HSI (Hepatic steatosis index).

overall_design: DNA methylation analysis was performed using EPIC array to examine methylation changes in peripheral blood cells of CKD and ESKD patients, and investigate their associations with DNA damage levels in urinary exfoliated cells and HSI (Hepatic steatosis index).


title: Reduced representation of bisulfite sequencing (RRBS) analysis of peripheral blood cells of proximal tubular epithelial cell specific I-PpoI expressing mice.

summary: Using reduced representation bisulfite sequencing (RRBS) analysis, we examined how I-PpoI-induced DSBs affected DNA methylation patterns in peripheral blood cells of 16-week-old I-PpoI mice.

overall_design: RRBS analysis was performed using Zymo-Seq RRBS Library Kit to analyze DNA methylation patterns. Methylated regions were identified using MACS algorithm, and differential methylation was determined by fold change. Motif analysis was conducted on hypermethylated DMRs using MEME suite.


title: Gene expression profile at single cell level of proximal tubular epithelial cell specific I-PpoI expressing mice kidney cortex

summary: To investigate the alterations in cell populations in the kidney after proximal tubular epithelial cell DNA DSBs, we performed single-cell RNA sequencing (scRNA-seq)  on the renal cortex of 16-week-old proximal tubular epithelial cell specific I-PpoI expressing mice.

overall_design: Kidneys were harvested, minced into 1 mm3 cubes, digested using digestion buffer and analyzed using scRNA-seq.


title: RNA sequencing of wild-type and FBXO32-knockout hepatocellular carcinoma Huh7 cells

status: Public on Dec 22 2024

city: Chongqing

first: Feng

last: Li

address: No.30, Gaotanyanzheng Street

institute: Army Medical University

summary: FBXO32 is upregulated in multiple human cancers, including hepatocellular carcinoma (HCC), pancreatic ductal adenocarcinoma (PDAC) and cholangiocarcinoma (CCA), and correlated to poor prognosis. Moreover, we demonstrated the tumor-promoting function in these cancers. Here, to explore the associated molecular mechanism of FBXO32 in tumor development, the RNA-seq of FBXO32-knockout Huh7 cells was investigated and analyzed

overall_design: 3 duplicated samples respectively from FBXO32-knockout and wild-type cells of Huh7 were used to perform RNA sequencing

first: Hongqiang

last: Yu

first: Yujun

last: Zhang

first: Fengtian

last: He

first: Leida

first: Chuanming

last: Xie

first: Haojun

last: Xiong


title: An epigenetic timer of gestation length in mice [scRNA-Seq]

status: Public on Dec 20 2024

city: San Francisco

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

summary: Timing mechanisms in biology remain poorly understood. As one prime example, little is known about the mechanisms that specify how long the gestating uterus will remain quiescent before entering labor1. Our lack of insight into this fundamental question, which applies to all mammalian species, also limits investigation into potential causes of preterm labor, a major human pregnancy complication. Here, we provide evidence that gestation length in mice is determined by an epigenetic timer that runs autonomously within the fibroblasts of the pregnant uterus. The timer is set during the peri-implantation period when select genomic loci establish appropriate levels of the repressive histone mark H3K27me3. These loci then progressively lose H3K27me3, thereby scheduling the uterine cell state transitions and associated gene expression changes of late gestation that are the proximal mediators of labor onset. Overwinding of the timer’s peri-implantation setpoint via genetic ablation of the histone demethylase KDM6B delays these transitions and extends gestation length. These results provide insight into how complex tissues employ epigenetic pathways to specify the timing of discrete biological events. We also anticipate that further dissection of the ways such uterine programming controls gestation length may suggest novel approaches for improving human pregnancy outcomes.

overall_design: Single cell RNA-Seq data of inter-implantation sites and implantation site myometrium/endometrium from control mice and Kdm6b cKO mice at sequential timepoints during pregnancy. Samples were multiplexed and sequenced in 7 pools. In the metadata files, inter-implantation sites are referred to as “IIS” and implantation site myometrium/endometrium are referred to as “MYO”. The timepoint refers to the gestation day. The raw data files also include data from non-pregnant mice given 0.2 mg progesterone daily for 3 days prior to sacrifice. These are referred to in the metadata files as “IIS” specimens at the “0” timepoint.

first: Tara

last: McIntyre

first: Adrian

last: Erlebacher


title: Brain-wide neuronal circuit connectome of human glioblastoma [bulk RNA-seq]

city: Philadelphia

first: Yusha

last: Sun

state: PA

address: 415 Curie Boulevard, Clinical Research Building, Room 105

institute: University of Pennsylvania Perelman School of Medicine

summary: This study explores the circuit integration of human glioblastoma organoids (GBOs) in vivo in the adult mouse brain. Here, we performed RNA sequencing analysis of GBOs at baseline conditions and various treatment timepoints of 1 mM acetylcholine (ACh).

overall_design: 3D GBOs were dissociated and reaggregated into organoids of 2000 cells in 96-well U-bottomed plates. ACh was applied to a final concentration of 1 mM for various durations prior to removal of medium and sample lysis for RNA sequencing. Libraries were prepared via a modified Smart-seq3 protocol adapted for bulk samples with sample barcodes and UMIs. This allowed for pooled samples and identification with a unique barcode per sample. Gene expression could be demultiplexed with a provided sample barcode whitelist.


title: A role for fibroblast and mural cell subsets in models of neuropathic pain [scRNA-seq]

status: Public on Dec 19 2024

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

summary: Neuropathic pain is a particularly intractable type of chronic pain that can result from physical nerve damage due to surgery or entrapment. Here, we present data which suggest that a particular subclass of fibroblast and mural cells may be implicated in the sensory neuron dysfunction that is characteristic of this pain state. In a mouse model of traumatic painful neuropathy, we used RNA sequencing, cell sorting and nerve tissue clearing to study mesenchymal lineage cells. We show that Pdgfrb+ fibroblasts and mural cells are increased in number for at least two months post-nerve damage and express high levels of known and putative pro-algesic mediators, which are further upregulated in neuropathy. We go on to demonstrate that a human nerve pericyte line releases a selection of these pro-algesic mediators at protein level. Moreover, conditioned media from stimulated human pericytes induces intra-cellular changes in human induced pluripotent stem cell derived sensory neurons; these changes (phosphorylation of the transcription factor STAT3) have been previously linked to sensory neuron activation. In summary, our data indicate that mesenchymal cell abnormalities should be considered when developing novel strategies to tackle neuropathic pain.

overall_design: Mesenchymal lineage cells extracted from mouse nerve were processed for single cell sequencing 1 week or 2 months after surgically induced nerve injury.

first: Sara

last: Villa-Hernandez

first: Zoe

last: Hore


title: A role for fibroblast and mural cell subsets in models of neuropathic pain [bulkRNA-seq]

overall_design: Pdgfrb+ and Pdgfrb+/Cd146++ cells were extracted from mouse nerve and processed for bulk sequencing 5 days after surgically induced nerve injury.


title: Neuronal Deficiency of Cytochrome c Oxidase Engineered by Mitochondrial DNA Editing Recapitulates Amyotrophic Lateral Sclerosis [snRNA-seq]

status: Public on Dec 18 2024

first: Kexin

address: No. 15, Datun Road, Chaoyang District, Beijing, China

institute: Peking Union Medical College

summary: Amyotrophic lateral sclerosis (ALS) is categorized into 10% familial and 90% sporadic cases. While the space of 10% familial ALS is crowded with mutations in many genes of diverse functions, most ALS-associated mutations could not faithfully recapitulate the disease phenotype in animal models. Remarkably, nearly half of sporadic ALS patients exhibit defective mitochondrial respiratory complex Ⅳ (CⅣ). To establish the causal role of defective CⅣ in inducing ALS, we employed TALE-based mtDNA editing to mimic ALS-linked mutations in CⅣ compared to other respiratory complexes in rat neurons and demonstrated that mutations exclusively introduced to mtDNA-encoded CⅣ subunits are sufficient to cause a full spectrum of ALS-like phenotypes, including selective motor neuron loss, SOD1 overexpression and cytosolic TDP-43 aggregation. These findings reveal a broad basis for sporadic ALS, provide critical insights into the selective motor neuron vulnerability, and present a faithful animal model for advancing ALS therapy.

overall_design: To investigate the effects of mitochondrial respiratory complex Ⅳ deficiency in rat neurons , the spinal cord WT and COXⅢNeuN-Cre rats, were dissected , and the RNA was isolated to perform the  single-nucleus RNA sequencing study (n=3 per group).

first: M

last: Cheng

first: D

last: Lv

first: X

last: Tong

first: K


title: A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics

city: New Orleans

first: Amitabh

last: Pandey

state: LA

address: 1430 Tulane Ave

department: Medicine, Section of Cardiology

institute: Tulane University School of Medicine

summary: Single-cell RNA-seq (scRNAseq) struggles to capture the cellular heterogeneity of transcripts within individual cells due to the prevalence of highly abundant and ubiquitous transcripts, which obscure the detection of biologically distinct transcripts expressed at up to several orders of magnitude lower levels. To address this challenge, we introduce single-cell CRISPRclean (scCLEAN), a molecular method that globally recomposes scRNAseq libraries, providing a benefit that cannot be recapitulated with deeper sequencing. scCLEAN utilizes the programmability of CRISPR/Cas9 to target and remove less than 1% of the transcriptome while redistributing approximately half of reads, shifting the focus toward less abundant transcripts. We then experimentally apply scCLEAN to both heterogeneous immune cells and homogenous vascular smooth muscle cells to demonstrate its ability to uncover novel biological signatures in different biological contexts. We further emphasize scCLEAN’s versatility by applying it to a third-generation sequencing method, single-cell MAS-Seq, to increase transcript-level detection and discovery. Here we show, the projected utility of scCLEAN across a wide array of human tissues and cell types, indicating which contexts this technology proves beneficial and those in which its application is not advisable.

overall_design: This study generated scRNAseq using two primary cell samples derived from healthy human donors- PBMCs and vascular smooth muscle cells. For all samples, standard sample prep was completed per the manufacturer's protocol for 10X or PacBio, respectively, for the PBMCs and 10X Genomics for the VSMCs. Samples were aliquoted to allow for the standard prep and a prep using scCLEAN, which is a CRISPR/Cas9 based delpetion protocol that removes redundant reads to redistribute reads to allow for improved readouts. For VSMCs, matched donors were used for the isolation of coronary and pulmonary arteries, with a total of 4 donors utilized. For computational analysis, donors were pooled together using CellRanger for analysis using Seurat, Scanpy, MAGIC, PHATE, randomly, scFATES, and CellRank packages in R or python, as appropriate.


title: Neuronal Deficiency of Cytochrome c Oxidase Engineered by Mitochondrial DNA Editing Recapitulates Amyotrophic Lateral Sclerosis

last: Li

overall_design: To investigate the effects of mitochondrial respiratory complex Ⅳ deficiency in rat neurons , the spinal cord and brain of WT, COXⅢNeuN-Cre rats, were dissected , and the RNA was isolated to perform the bulk RNA-sequencing study (n=4/6 per group).

first: Man

first: Dan

first: Xiwen

first: Yuanwu

last: Ma

first: Xiaorong


title: Brain-wide neuronal circuit connectome of human glioblastoma

summary: This study explores the circuit integration of human glioblastoma organoids (GBOs) in vivo in the adult mouse brain. We performed single cell RNA sequencing (scRNA-seq) to understand the cell state diversity of malignant tumor cells in GBOs at baseline and after stimulation by 1 mM acetylcholine (ACh) for 1 hour. Sliced neocortical organoids (SNOs) were also sequenced to study gene expression properties of neural stem cells (NSCs).

overall_design: 3D GBOs were either not treated or treated with 1 mM ACh for 1 hour, upon which they were dissociated to single cells and sorted into lysis-buffer containing 96-well plates. 3D SNOs were processed the same way without treatment. Whole cell scRNAseq libraries were performed via a modified Smart-seq3 protocol with cell barcodes. Therefore, cells could be pooled together and identified with a unique barcode. Gene expression data could be demultiplexed with a provided barcode whitelist.

first: Sun

last: Yusha


title: Single cell sequencing datasets of tibial nerves from diabetic neuropathy (DPN) patients and traumatic limb amputation (TLA) patients.

city: Shanghai

first: Xiangyun

last: Yao

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital

summary: To understand the cellular diversity and alterations in the pathogenesis of diabetic neuropathy (DPN), weenrolled 4 DPN patients, 3 traumatic limb amputation (TLA) patients at the Department of Orthopedic Surgery of Shanghai Sixth People’s Hospital, Shanghai, China.

overall_design: Tibial nerves were collected during amputation surgeries in patients suffering from diabetic peripheral neuropathy (DPN) or patients with traumatic limb amputation (TLA). Nerve samples isolated from TLA patients were set as control group. Tibial nerves from donors were rapidly frozen on liquid nitrogen in the operating room and stored until tissue digestion. The sequencing data for 4 DPN samples were named as "DPN_Sample 1-4" and the sequencing data for 3 TLA samples were named as "TLA_Sample 1-3".

first: Lingchi

last: Kong


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus [RNA-Seq]

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

summary: MYT1L Syndrome mouse model displays obesity as observed in MYT1L patients. Utilizing this mouse model, ATAC-seq and RNA-seq on adult mouse hypothalamus reveals molecular alternations related to feeding behaviors, which might contribute to obesity phenotype.

overall_design: We have 3 biological replicates per genotype for ATAC-seq and 6(Het)/5(WT) replicates for RNA-seq on adult mouse hypothalamus

first: Jiayang

last: Chen


title: Evidence for a lipofibroblast-to-Cthrc1pos myofibroblast reversible switch during the development and resolution of lung fibrosis

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: Question addressed in the study:   Genetic lineage tracing of alpha smooth muscle actin-positive (ACTA2+) cells in the context of bleomycin-induced pulmonary fibrosis in mice has shown that activated myofibroblasts (aMYFs) differentiate into lipofibroblasts (LIFs) during fibrosis resolution. However, the heterogeneity of the different mesenchymal cell subclusters during fibrosis formation and their contribution to the aMYFs as well as the fate of aMYFs during fibrosis resolution are still unclear.    Materials and methods:  Two-month-old Tg(Acta2-CreERT2); tdTomatoflox mice were used to label Acta2pos cells before (Tam-Bleo condition) or after (Bleo-Tam condition) bleomycin administration. Using scRNA-seq, the origin and fate of Acta2pos cells converging on the aMYF/Cthrc1pos myofibroblast lineage, were analyzed at the peak of fibrosis formation (day 14) as well as during resolution (day 60). Mining of human IPF scRNA-seq data was also carried out. The function of resident mesenchymal cells derived from saline or bleomycin-injured lungs during fibrosis formation or resolution in supporting AT2 progenitor cell renewal was assessed using alveolar organoid assays.    Results:  By employing the dimensionality reduction and UMAP visualization MYF/Cthrc1pos cells were identified and characterized in three scRNA-seq conditions: Saline, Tam-Bleo and Bleo-Tam. Acta2pos cells isolated from saline-treated mice revealed the presence of Acta2pos cells in the expected airway and vascular smooth muscle cells, but also in alveolar fibroblasts, peribronchial and adventitial fibroblasts as well as in a restricted number of Cthrc1pos cells indicating a primed pro-fibrotic status of the non-injured lung. In Tam-Bleo lungs, minimal contribution of these cells to the Cthrc1pos pool was observed. By contrast, labeling of Acta2pos cells following bleo administration (Bleo-Tam) led to massive labeling of Cthrc1pos cells, which following fine clustering were grouped into 4 subclusters named F1-F4. Interestingly, cells in cluster F1 were identified as Cthrc1low and displayed a strong LIF signature (LIFhigh) while cells in cluster F2 were LIFlow and Cthrc1high. Examination of F1 and F2 subclusters during fibrosis resolution suggested that F2 transition back to an F1 status and eventually differentiate into Cthrc1low LIFhigh alveolar fibroblasts. Analysis of the alveolar fibroblast cluster revealed the presence of three subclusters (A, B and C). Cluster C appeared only in Bleo-Tam and displayed a fibrotic signature (Sfrp1, Eln, Ltbp2, Spp1high). These cells, which originate from Acta2neg alveolar fibroblasts are suggested to differentiate into the Cthrc1low LIFhigh F1 subcluster. Data mining of human scRNA-seq from fibrotic lungs supported the conservation of the heterogeneity of the CTHRC1pos population. Alveolosphere assays indicated that resident mesenchymal cells did not reacquire their stem cell niche function at day 60, during fibrosis resolution.    Answer to the question:  Our results support a LIF-to-aMYF reversible switch during fibrosis formation and resolution.

overall_design: Two-month-old Tg(Acta2-CreERT2); tdTomatoflox mice were used to label Acta2pos cells before (Tam-Bleo condition) bleomycin administration. Using scRNA-seq, the origin and fate of Acta2pos cells converging on the aMYF/Cthrc1pos myofibroblast lineage, were analyzed at the  fibrosis resolution (day 60)

first: Arun

last: Lingampally

first: Saverio

last: Bellusci


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus [ATAC-Seq]


title: Investigating the transcriptional regulatory role of FBXA-215

status: Public on Dec 15 2024

city: Cambridge

first: Miguel

middle: Vasconcelos

last: Almeida

address: Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

overall_design: Refer to individual Series


title: Investigating the transcriptional regulatory role of FBXA-215 [young Adults]

summary: We identified a Mariner transposase helix-turn-helix (HTH) DNA-binding domain that was captured in the Caenorhabditis genus by a subset of F-box genes, which we refer to as F-box A2 genes. The origin of F-box A2 genes likely occurred through a single transposase capture event, followed by an increase in copy number. We focused on fbxa-215, a F-box A2 gene highly expressed in the C. elegans germline and embryos, and that localizes to germ granules in embryos. The HTH domain of FBXA-215 is required for fertility and displays predominantly a signature of purifying selection, highlighting the importance of this domain. As the HTH domain of FBXA-215 is related to the DNA-binding HTH domain of transposases, we reasoned that FBXA-215 may bind to DNA in C. elegans and thus regulate gene expression at the transcriptional level. We performed mRNA sequencing of young adults and embryos to test this, but found no clear deregulation of protein-coding genes and transposable elements upon complete deletion of fbxa-215.

overall_design: To test whether FBXA-215 has a role in regulating gene expression at the transcriptional level, we have sequenced mRNAs of mixed-staged embryos and young adults of wild-type N2 and fbxa-215(syb4404) mutants grown at 20 and 25oC.

middle: V

first: Jonathan

last: Price

first: Eric

last: Miska


title: MYT1L loss leads to chromatin structures and transcriptome alterations in mouse hypothalamus

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


title: Pol II degradation activates cell death independently from the loss of transcription [DKO_wasting_RNAseq]

status: Public on Dec 13 2024

city: Worcester

first: Michael

last: Lee

address: 368 Plantation Street

institute: UMASS Chan Medical School

summary: Pol II-mediated transcription is essential for eukaryotic life. While loss of transcription is thought to be universally lethal, the associated mechanisms promoting cell death are not yet known. Here, we show that death following loss of Pol II is not caused by loss of gene expression. Instead, death occurs in response to the loss of Pol II protein itself. Loss of Pol II protein exclusively activates apoptosis, and using functional genomics, we identified a previously uncharacterized pathway, which we call the Pol II Degradation-dependent Apoptotic Response (PDAR). Using the genetic dependencies of PDAR, we identify clinically used drugs that owe their efficacy to a PDAR-dependent mechanism. Our findings unveil a novel apoptotic pathway that contributes to the efficacy of a wide array of anti-cancer therapies.

overall_design:
RNA-seq profiling of U2OS cells treated with 1 µM triptolide for 0 or 1 days, and U2OS-BAX-BAK1 -/- cells treated with 1 µM triptolide for 0, 2, 4, 6, 8, or 10 days.
RNA-seq profiling of U2OS and U2OS-BAX-BAK1 -/- cells treated with 1 µM triptolide short timecourse (0,4,8,24 hours).

first: Nicholas

last: Harper

first: Gavin

last: Birdsall

first: Megan

middle: E

last: Honeywell

first: Athma

last: Pai


title: Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

city: Chapel Hill

first: Justin

last: Waldern

state: NC

address: 250 Bell Tower Dr

department: Biology

institute: The University of North Carolina at Chapel Hill

summary: Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these two sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene, specifically exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE-JuMP strategy, to characterize both secondary and tertiary interactions in the pre-mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly-paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data also identified multiple long-range interactions between non-pairing nucleotides. Genome wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and that additional interactions are key components of the mechanism.

overall_design: SHAPE-MaP, DMS, and SHAPE-JuMP probing of HIPK3 circularization constructs.

first: Colin

last: Taylor

first: Catherine

last: Giannetti

first: Patrick

last: Irving

first: Scott

last: Allen

first: Mingyi

last: Zhu

first: Rolf

last: Backofen

first: Dave

last: Mathews

first: Kevin

last: Weeks

first: Alain

last: Laederach


title: ISWI chromatin remodeler SMARCA5 is essential for meiotic gene expression and male fertility in mammals

status: Public on Dec 05 2024

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

institute: Yale University

summary: Regulation of the transcriptome to promote meiosis is important for sperm development and fertility. However, how chromatin remodeling directs the transcriptome during meiosis in male germ cells is largely unknown. Here, we demonstrate that the ISWI family ATP-dependent chromatin remodeling factor SMARCA5 (SNF2H) plays a critical role in regulating meiotic prophase progression during spermatogenesis. Males with germ cell-specific depletion of SMARCA5 are infertile and unable to form sperm. Loss of Smarca5 results in failure of meiotic progression with abnormal spermatocytes beginning at the pachytene stage and an aberrant global increase in chromatin accessibility, especially at genes important for meiotic prophase.

overall_design: ATAC-seq from sorted cKIT+ spermatogonia, scRNA-seq from whole testes

first: Shubhangini

last: Kataruka

first: Shannon

last: Rainsford


title: Investigating the transcriptional regulatory role of FBXA-215 [embryos]

first: Miguel

last: Almeida

first: Jonathan

last: Price

first: Eric

last: Miska


title: An Unbiased Approach to Identifying Cellular Reprogramming-Inducible Enhancers [ChIP-seq]

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

summary: Cellular reprogramming of somatic cells towards induced pluripotency is a multistep stochastic process mediated by the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM), which orchestrate global epigenetic and transcriptional changes. We performed a large-scale analysis of integrated ChIP-seq, ATAC-seq and RNA-seq data and revealed the spatiotemporal highly dynamic pattern of OSKM DNA binding during reprogramming. We found that OSKM show distinct temporal patterns of binding to different classes of pluripotency-related enhancers. Genes involved in reprogramming are regulated by the coordinated activity of multiple enhancers, which are sequentially bound by OSKM for strict transcriptional control. Based on these findings, we developed an unbiased approach to identify Reprogramming-Inducible Enhancers (RIEs), constructed enhancer-traps and isolated cells undergoing reprogramming in real time. We used a representative RIE taken from the Upp1 gene fused to GFP and isolated cells at different time-points during reprogramming and found that they have unique developmental capacities as they are reprogrammed with high efficiency due to their distinct molecular signatures. In conclusion, our experiments have led to the development of an unbiased method to identify and isolate reprogrammable cells in real time by exploiting the functional dynamics of OSKM, which can be used as efficient reprogramming biomarkers.

overall_design: We performed ChIP-seq for Nanog in Embryonic Stem Cells (ESCs).

first: Dimitrios

first: Eleftheria

last: Klagkou

first: Giannis

last: Vatsellas

last: Thanos


title: MYLIP attenuates hypoxia tolerance by inducing K27-linked polyubiquitination and subsequent proteasomal degradation of HIF-α

status: Public on Dec 04 2024

city: 武汉

first: li

last: jun

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

summary: Hypoxia tolerance is mainly controlled by the hypoxia signaling pathway and HIF-1α/2α serve as master regulators in this pathway. Here we identify MYLIP, an E3 ubiquitin ligase thought to specifically target lipoprotein receptors, as a negative regulator of HIF-1α/2α. MYLIP interacts with HIF-1α/2α and catalyzes K27-linked polyubiquitination at lysine 118/442 (HIF-1α) or lysine 117 (HIF-2α). This modification induces proteasomal degradation of HIF-1α, resulting in inhibition of hypoxia signaling. Furthermore, Mylip-deficient bluntsnout bream, zebrafish and mice are more tolerant to hypoxia. These findings reveal a role for MYLIP in regulating hypoxia signaling and identify a target for developing fish strains with high hypoxia tolerance for the benefit of the

overall_design: M. amblycephala (2 mpf) of similar weight were selected for hypoxia experiments.  The flask was filled with 200 ml of water.  Three M. amblycephala were placed in a flask under normoxia (21% O2) or hypoxia (5% O2) for 2 hours.  These above sampled fish were euthanized by a concentration of 0.3 mg/L MS-222, and the brain was dissected and immediately stored in liquid nitrogen for total RNA extraction.  Experiments were repeated five times (n = 5 per group).  Clustering of indexed samples was performed on a cBot cluster generation system using the TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions.    After cluster generation, the library preparations were sequenced on an Illumina Hiseq 4000 platform and paired-end 150bp reads were generated.  Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1).  DESeq provides statistical routines to determine differential expression in digital gene expression data using a model based on the negative binomial distribution.  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach to control for the false discovery rate.  Genes with an adjusted P value < 0.05 found by DESeq were considered to be differentially expressed.

first: Jun

last: Li

first: Jing

last: Wang

first: Wuhan

last: Xiao


title: Differential behavior responses and genetic alteration underpinning exercise effectiveness in stress-susceptible mice

city: Seoul

first: Dong-Joo

last: Hwang

address: 1239, Yangjae-daero, Songpa-gu

department: Institute of Sport Science

institute: Korea National Sport University

summary: Stress susceptibility varies across individuals, influenced by genetic, molecular, and environmental factors. Considering the individual differences in response to stress, however, approaches for exercise treatment as an antidepressant and anxiolytic intervention are also not exempt from variability in effectiveness among individuals, and insight into the biology of those variations can be gained by examining the individual adaptation to exercise. Here, we investigated the efficacy of voluntary wheel running (VWR) exercise as a disease-modifying intervention for stress-susceptible (SS) mice subjected to chronic restraint stress (CRST). Multidimensional behavior analysis revealed significant variability in the efficacy of VWR among individuals, with some mice showing substantial behavior phenotypic improvements (e.g., behavior despair, anhedonia, aversion to open space, and compulsive behavior) (SES) while others displayed limited or no benefits (SER). Furthermore, transcriptomic analysis of the ventral hippocampus (vHPC), a critical brain region involved in emotional regulation and processing, demonstrated that SES mice exhibited molecular signatures promoting adaptive changes by restoring cellular repair, energy availability, and synaptic plasticity observed in SS mice, whereas SER mice exhibited limited behavior resilience and distinct transcriptomic profiles enriched in structural adaptation without functional resilience and glia cell differentiation, particularly marked by astrocyte activation or differentiation. These findings suggest that while VWR can alleviate multiple concurrent behavior symptoms in stress-susceptible mice; however, its efficacy is influenced by distinct biological processes. Collectively, our work highlights the importance of a multivariate framework for behavior assessment and genetic underpinnings to better understand the often-overlooked variability in response to stress and the therapeutic efficacy of exercise in stress-related disorders.

overall_design: To investigate the efficacy of voluntary wheel running (VWR) exercise as a disease-modifying intervention for stress-susceptible (SS) mice subjected to chronic restraint stress (CRST), multidimensional behavior analysis was performed to segregate the individual mice into effective mice to exercise (SES mice) showing substantial behavior phenotypic improvements (e.g., behavior despair, anhedonia, aversion to open space, and compulsive behavior) while others displayed limited or no benefits (SER mice). We then performed transcriptomic analysis of the ventral hippocampus (vHPC), a critical brain region involved in emotional regulation and processing. Comparative gene expression profiling analysis of RNA-seq data for Control (C), stress-susceptible (SS), effective responder to VWR (SES), and ineffective responder to VWR (SER).

first: Dongjoo

first: Jieun

last: Kim

first: Joonyong

last: Cho

first: Junghoon

last: Koo

first: Yongchul

last: Jang

first: Taekyung


title: Drosophila epidermal cells are intrinsically mechanosensitive and modulate nociceptive behavioral outputs

city: Seattle

first: Jay

middle: Z

last: Parrish

state: WA

address: 3747 W Stevens Way NE

institute: University of Washington

summary: Somatosensory neurons (SSNs) that detect and transduce mechanical, thermal, and chemical stimuli densely innervate an animal’s skin. However, although epidermal cells provide the first point of contact for sensory stimuli. our understanding of roles that epidermal cells play in SSN function, particularly nociception, remains limited. Here, we show that stimulating Drosophila epidermal cells elicits activation of SSNs including nociceptors and triggers a variety of behavior outputs, including avoidance and escape. Further, we find that epidermal cells are intrinsically mechanosensitive and that epidermal mechanically evoked calcium responses require the store-operated calcium channel Orai. Epidermal cell stimulation augments larval responses to acute nociceptive stimuli and promotes prolonged hypersensitivity to subsequent mechanical stimuli. Hence, epidermal cells are key determinants of nociceptive sensitivity and sensitization, acting as primary sensors of noxious stimuli that tune nociceptor output and drive protective behaviors.

overall_design: Larvae with cytoplasmic GFP expressed in different epidermal subsets were microdissected and dissociated in collagenase type I into single cell suspensions, and pools of 10 single GFP-positive cells were collected and processed for Smart-Seq2 RNA-Seq analysis.

first: Jiro

last: Yoshino

first: Sonali

last: Mali

first: Claire

last: Williams

first: Takeshi

last: Morita

first: Chloe

last: Emerson

first: Christopher

last: Arp

first: Sophie

last: Miller

first: Chang

last: Yin

first: Lydia

last: The

first: Chikayo

last: Hemmi

first: Mana

last: Motoyoshi

first: Kenichi

last: Ishii

first: Kazuo

last: Emoto

first: Diana

last: Bautista


title: Dexamethasone-stimulated DNA methylation in peripheral blood

status: Public on Dec 01 2024

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: Genome-wide DNA methylation profiling was conducted on 199 individuals (398 samples, pre- and post-treatment with Dex) recruited at the Max Planck Institute of Psychiatry (MPIP). Whole blood samples were analyzed using the Illumina EPIC v1 DNA Methylation Beadchip to obtain comprehensive DNA methylation profiles.

overall_design: Bisulphite converted DNA from the 398 samples were hybridised to the Illumina EPIC v1 methylation Beadchip .

first: Elisabeth

middle: B

last: Binder