title: A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation [in-vivo scRNA-seq]

status: Public on Jan 15 2024

summary: We employed single cell RNA sequencing to interrogate the consequence of conditional Brd4 deletion in the anterior heart field on heart development.

overall_design: Examination of single cell transcriptomes from cardiac progenitors captured at E9.5 from Brd4 floxed homozygous and Brd4 floxed het; Mef2c-AHF-cre hets.  At least 2 biological replicate embryos were analyzed per genotype.

first: Tarja

last: Yvanka de Soysa


title: A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

country: USA

institute: Gladstone Institutes (UCSF)

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation [in-vivo bulk RNA-seq]

summary: We employed bulk RNA sequencing to interrogate the consequence of murine conditional BRD4 deletion in microdissectted E9.5 cardiac and surrounding tissues.

overall_design: Bulk transcriptional analysis of developing cardiac and surroudning structures in E9.5 mouse embryos following conditional deletion of BRD4 in Isl1-expressing cells.

first: Parisha

last: Shah

first: Rajan

last: Jain

first: Arun

last: Padmanabhan

first: Deepak

last: Srivastava


title: An evolutionary epigenetic clock in plants [Biostress]

status: Public on Jan 11 2024

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

type: Methylation profiling by high throughput sequencing

summary: Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~104-108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This ‘epimutation-clock’ is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina, which represent the two primary modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

overall_design: We generated A. thaliana MA lines which were grown under multi-generational biotic stress (repeated exposure to pseudomonas syringe or salicylic acid), as well as their control.  Methylome profilng.

first: Lisa

middle: M

last: Smith

first: Juriaan

last: Ton

first: Frank

last: Johannes


title: Single nucleus RNAseq of mouse astrocytes after traumatic spinal cord injury

status: Public on Jan 09 2024

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We conducted snRNAseq of mouse astrocytes after traumatic spinal cord injury (SCI). These data reveal transcriptomic similarities and differences among astrocytes in healthy spinal cord and after spinal cord injury.

overall_design: Young adult mice, 2 to 4 months of age, were given a full crush SCI. After 28 days, mice with SCI (n=4), and age and sex matched uninjured controls (n=4) were perfused, and tissue samples collected and snRNA extracted and evaluated as described below.

first: Michael

middle: V

last: Sofroniew

first: Vivek

last: Swarep

first: Timothy

last: O'Shea


title: A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation [in-vitro bulk RNA-seq]

summary: We employed bulk RNA sequencing to interrogate the consequence of conditional BRD4 deletion in mouse embryonic stem cell (mESC)-derived cardiac progenitor cells.

overall_design: Bulk transcriptional analysis of cardiac progenitors differentiated from mouse embryonic stem cells (mESCs) that were derived from CMV-CreERT2; Brd4flox/flox mice.


title: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are modified by RORγ expression [II]

status: Public on Jan 07 2024

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

summary: The aim of this study was to test the role of RORγ in the action of the above analogs using murine fibroblasts isolated from the skin of wild type (RORg+/+) and knock out (RORg-/-) mice.

overall_design: mRNA profiles of fibroblasts isolated from the skin of the wild type (WT) and RORg-/- mice treated with CYP11A1- derived vitamin D3 derivatives: 20(OH)D3 and 1,20(OH)2D3 were generated by sequencing. We utilized RNA-sequencing in order to compare the gene expression profiles in wild type and RORγ-/- fibroblasts. Utilizing analysis we compared the gene expression profile of ethanol only treated RORγ-/- fibroblasts with ethanol treated RORγ+/+ fibroblasts. Analysis showed changes in five top canonical pathways including: role of BRCA1 in DNA damage response; Cell cycle: G2/M DNA damage checkpoint regulation; cell cycle control of chromosomal replication; mitotic roles of polo-like kinase; and hepatic fibrosis/ hepatic stellate cell activation. Among ingenuity’s biological functions and diseases and disorders, cancer, gastrointestinal diseases, organismal injury and abnormalities, reproductive system diseases, and hematological diseases are significantly affected. The main cellular functions that are affected are pertinent to liver and kidney inducing hepatotoxicity, renal toxicity, as well as cardiotoxicity.

first: Zorica

last: Janjetovic


title: Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity

status: Public on Jan 13 2024

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing


title: Effect of depletion of LRIG1 on CD8+ tumor infiltrating T cells

status: Public on Jan 02 2024

city: Cleveland

first: Lily

last: Wang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic


title: Nuclear miR-451a activates KDM7A and leads to cetuximab resistance in head and neck squamous cell carcinoma [ChIRP-seq]

status: Public on Jan 01 2024

city: Shanghai City

first: Peisong

last: Zhai

address: Zhizaoju Rd. No.639

country: China

institute: Shanghai Jiao Tong universisy medical school affiliated Shanghai ninth people's hospital

summary: Cetuximab resistance has been a major challenge for head and neck squamous cell carcinoma (HNSCC) during target therapy. Yet the mechanism that caused cetuximab resistance, especially the miRNA regulation therein remains unclear. With growing evidence suggests that miRNAs may function within the cell nucleus and act as “nuclear activating miRNAs” for targeting the promoter region or enhancers related to target genes. They are believed to regulate diseases development including tumorigenesis. This study elucidates a novel mechanism underlying cetuximab resistance in HNSCC involving the nuclear activation of KDM7A transcription via miR-451a. Herein, small RNA sequencing, qRT-PCR and FISH results provide compelling evidence of miR-451a nuclear enrichment with cetuximab treatment. ChIRP-seq, microarray, bioinformatic analysis and dual luciferase reporter assay results show that miR-451a interacts with an enhancer region in KDM7A, activating its expression and further facilitating cetuximab resistance. It is also demonstrated that activation of KDM7A by nuclear miR-451a is induced by cetuximab treatment and is AGO2 dependent. Analyses of HNSCC samples through logistic regression indicated the significance of miR-451a and KDM7A in cetuximab resistance. These discoveries hold promise for the potential utilization of miR-451a and KDM7A as valuable biomarkers for cetuximab resistance and emphasize the function of nuclear activating miRNAs.

overall_design: To investigate the miR-451a interaction with DNA, ChIRP-seq was performed. Biotin labeled miR-451a probe was transfected into CAL27 and HEK293T cells. The cells were treated with cetuximanb for 72 h before ChIRP.

first: Jianjun


title: BRD9-SMAD2/3 orchestrates stemness and tumorigenesis   in pancreatic ductal adenocarcinoma   drives human dilated cardiomyopathy

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

summary: By using a small molecule compound library targeting epigenetic enzymes we have identified BRD9 enzyme for eliminating CSCs. Genomic and proteomic studies revealed that BRD9/BAF complex regulates expression of stemness factors and chemoresistance by cooperating with TGFβ/Activin-SMAD2/3 signalling pathway. Chemical inhibition and genetic loss of function of BDR9 blocks the self-renewal of CSCs, reduces CSC invasiveness and resensitizes PDAC CSCs to conventional therapies. Analyses of chromatin architecture showed that BRD9 regulates the 3D chromatin looping between promoters and enhancers of stemness genes and EMT regulators in CSCs. BRD9 inhibition abrogated tumour formation in mice and eliminated CSCs in tumours from pancreatic cancer patients. Collectively, we uncovered BRD9 enzyme as an attractive therapeutic target for re-sensitizing and eliminating CSCs in pancreatic cancer patients.

first: Yuliang

last: Feng

first: Liuyang

last: Cai

first: Chao-Hui

last: Chang

first: Feng

last: Liu

first: Siim

last: Pauklin


title: Nuclear miR-451a activates KDM7A and leads to cetuximab resistance in head and neck squamous cell carcinoma [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: to investigate the differentially expressed miRNAs in cytoplasm and in nucleus in cetuximab resistant HNSCC cell compared to the sensitive HNSCC cell. We first cultivated cetuximab resistant CAL27 cells, and performed nucleus-cytoplasm seperation to each sample. Small RNA sequencing were performed on cytoplasmic, nuclear and total RNAs of CAL27 and its cetuximab resistant cell line.

last: Zhang


title: Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing

city: Irvine

first: Sergei

last: Butenko

address: Irvine

institute: University of California, Irvine

summary: scRANseq study of different affects of crosslinking of gelatin methacrylate (GelMA) hydrogels on cell responses in skin wounds.

overall_design: Full excisional skin wounds were implanted with GelMA hydrogels of varying crosslinking and stiffness (low crosslinking/soft and high crosslinking/stiff), as well as non-treated wounds. Hydrogels were excised and analyzed by scRNA-seq.

first: Wendy

first: Maksim

last: Plikus

first: Raji

last: Nagala


title: High-throughput sequencing in HNRNPD knock-out SW839 cell lines

city: Hefei

first: Yucong

state: Anhui

address: 443 Huangshan Road

institute: USTC

summary: As HNRNPD regulates the alternative splicing of hundreds of genes, we sought to investigate whether HNRNPD could regulate the biogenesis of circRNAs. To identify the effect of HNRNPD on circRNAs, we performed circRNA sequencing in HNRNPD knockout and wild-type SW839 cells. In addition, to evaluate the impacts of HNRNPD deficiency on circRNA formation, we captured nascent RNA in SW839 and HNRNPD knock-out SW839 cells by immunoprecipitation of 5-ethyluridine (EU) labeling. Comparative analysis of these data, we found the higher expression level of circRNAs in HNRNPD KO SW839 cells.The HNRNPD could influence the circRNA biogenesis.

overall_design: We used CRISPR-Cas9 technology to generate HNRNPD knock-out SW839 cell lines for circRNA and nascent RNA sequencing. we extracted total RNA and digested it with RNase R in HNRNPD knock-out and wild-type SW839 cell lines for circRNA sequencing. For nascent RNA-seq, the cell transcription was terminated with 5,6-dichloro-1-β-D- ribofuranosylbenzimidazole (DRB, final concentration 0.5 mM) for 3 hours in HNRNPD knock-out and wild-type SW839 cell lines. Subsequently, the culture media was changed with fresh DMEM medium adding 5-ethyluridine (EU, final concentration 0.25 mM) for another 1 hour. Then the nascent RNA was immunoprecipitated with streptavidin-conjugated magnetic beads and extracted with Trizol reagent. The nascent RNAs were to conduct High-throughput sequencing.

first: Shuhui

first: Liang

last: Chen

first: Ge

last: Shan


title: Transcriptomic and epigenetic dissection of  spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations [Methylation]

status: Public on Jan 26 2024

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: Background: Ependymomas encompass multiple, clinically relevant tumor types based on localization and molecular profiles. Although tumors of the methylation class “spinal ependymoma” (SP-EPN) represent the most common intramedullary neoplasms in children and adults, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical meaning have been described in a large, epigenetically defined series. Methods: We mapped SP-EPN transcriptomes (n=76) to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. In addition, transcriptomic, epigenetic (n=234), genetic (n=140), and clinical analyses (n=115) were integrated for a detailed overview on this entity. Results: Integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord identified mature adult ependymal cells to display highest similarities to SP-EPN. Unsupervised hierarchical clustering of tumor data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype 1 predominantly contained NF2 wild type sequences with regular NF2 expression but revealed more extensive copy number alterations. Subtype 2 harbored previously known germline or sporadic NF2 mutations and was NF2-deficient in most cases, more often showed multilocular disease, and demonstrated a significantly reduced progression-free survival. Conclusion: Based on integrated molecular profiling of a large tumor series we identify two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

overall_design: To investigate the intertumoral heterogeneity of  the  methylation  class  “spinal ependymoma” (SP-EPN) genome-wide DNA methylation profiling  was performed on 234 formalin-fixed paraffin-embedded (FFPE) or frozen tissues. The methylation status of 450,000 or 850,000 CpG sites was analyzed on the iScan system using the HumanMethylation450 BeadChip array or the Infinium MethylationEPIC BeadChip Kit (both Illumina), respectively.

first: Sina

last: Neyazi

first: Erika

last: Yamazawa

first: Tanaka

last: Shota

first: Ulrich

last: Schüller


title: An evolutionary epigenetic clock in plants

first: Zhilin


title: Effect  of different dietary iron contents on liver transcriptome characteristics in Wujin pigs

city: Kunming

first: Peng

last: Ji

address: Fengyuan raod 452

institute: Yunnan Agricultural University

summary: Iron is an important trace element that affects the growth and development of animals and regulates  oxygen transport, hematopoiesis, and hypoxia adaptations. Wujin pig  has unique hypoxic adaptability and iron homeostasis; however, the specific regulatory mechanisms have rarely been reported. This study randomly divided 18 healthy Wujin piglets  into three groups: the control group, supplemented with 100 mg/kg iron (as iron glycinate); the low-iron group, no iron supplementation; and the high-iron group, supplemented with 200 mg/kg iron (as iron glycinate). The pre-feeding period was 5 days, and the formal period was 30 days. Serum was collected from empty stomachs before slaughter and at slaughter to detect changes in the serum iron metabolism parameters. Gene expression in the liver was analyzed via transcriptome analysis to determine the effects of low- and high- iron diets on transcriptome levels. Correlation analysis was performed for apparent serum parameters, and transcriptome sequencing was performed using weighted gene co-expression network analysis to reveal the key pathways underlying hypoxia regulation and iron metabolism. The main results are as follows. (1) Except for the hypoxia-inducible factor 1 (HIF-1) content (between the low- and high-iron groups), significant  differences were not observed among the serum iron metabolic parameters. The serum HIF-1 content of the low-iron group was significantly higher than that of the high-iron group (P<0.05). (2) Sequencing analysis of the liver transcriptome revealed 155 differentially expressed genes (DEGs) between the low-iron  and  control groups, 229 DEGs between the high-iron and control groups, and 279 DEGs between the low- and high-iron groups . Bioinformatics analysis showed that the HIF-1 and transforming growth factor-beta (TGF-β) signaling pathways were the key pathways for hypoxia regulation and iron metabolism.  Four genes were selected for qPCR validation, and the results were consistent with the transcriptome sequencing data. In summary, the serum iron metabolism parameter results showed that under the influence of low- and high-iron diets, Wujin piglets maintain a steady state of physiological and biochemical indices via complex metabolic regulation of the body, which reflects their stress resistance and adaptability. The transcriptome results revealed the effects of low-iron and high-iron diets on the gene expression level in the liver and showed that the HIF-1 and TGF-β signaling pathways were key for regulating hypoxia adaptability and iron metabolism homeostasis under low-iron and high-iron diets. Moreover, HIF-1α and HEPC  were the key genes. The findings provide a theoretical foundation for exploring the regulatory pathways and characteristics of iron metabolism in Wujin pigs.

overall_design:
Three groups piglets were fed with three kinds of iron content feed. Assay rna sequence analysis of liver.
WGZA2, WGZA3, WGZA7 belongs to low-iron group,
WGZB4, WGZB5, WGZB6 belongs to control group,
WGZC2, WGZC7, WGZC8 belongs to high-iron group.

first: Xiaokun

last: Xing

first: Lin

last: Gao

first: Qingcong

last: An


title: Nuclear activating miR-451a induced cetuximab resistance in HNSCC [microarray]

first: Peisong

last: Zhai

summary:
To filter the up-regulated gene induced by miR-451a overexpression and in cetuximab resistant HNSCC cell. We employed whole genome microarray. The HNSCC cell CAL27 was used as a control sample. CAL27_CTX, the cetuximab resistant CAL27 was compared with CAL27. The miR-451a overexpressed CAL27_451a sample was compared with the CAL27_NC sample. CAL27_CTX and CAL27_451A samples were collected after 48h of cetuximab treatment.
The microarray results were taken together with ChIRP-seq analysis and bioinformatics analysis for miR-451a binding and enhancer analysis to eventually find the nuclear acticating target of miR-451a

first: Jianjun


title: Nuclear miR-451a activates KDM7A and leads to cetuximab resistance in head and neck squamous cell carcinoma


title: DNA methylation patterns in IDH-wildtype de novo Glioblastomas at first occurrence (primary) and relapsed (recurrent) disease

status: Public on Dec 31 2023

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

summary: Genome-wide DNA methylation pattern was interrogated in glioblastomas at first diagnosis and at disease relapse, utilizing the Illumina 450K Methylation Bead Array

overall_design: Bisulfite converted genomic DNA from 24 samples (11 primary, 13 recurrent) were subjected to hybridisation with the 450K methylation array

first: Paramita

last: Kundu

first: Arimappamagan

last: Arivazhagan

first: Vani

last: Santosh

first: Paturu

last: Kondaiah


title: Effect of depletion of LRIG1 on polyclonal CD8+ tumor infiltrating T cells and Effect of depletion of LRIG1 on OT1 CD8+ tumor-infiltrating T cells

first: Lily

last: Wang

summary: To investigate the function of LRIG11 in regulating the differentiation of polyclonal CD8 tumor infiltrating T cells during the response to B16melanoma. And, To investigate the function of LRIG1 in regulating the activaiton of ovalbumin specific OT1 CD8+ T cells during the response to B16 tumor stably expresss ovalbumin as surrogate tumor antigen.

overall_design: 3 independent biological replicates of  WT and 2 independent replicates of LRIG1 KO CD8 T cells were sorted from  B16 melanoma tumor tissue, on day 19 post vaccine treatment: each sample is purifed from pooled 4-5 tumor tissues. And for OT1 set WT and LRIG1 KO OT1 T cells were co-transferred at 1:1 ratio into mice which were then inoculated with B16ova tumor. We then sorted OT1 T cells out of tumor tissues on day 7 post exposure to tumors. 3 independent replicates of WT OT1 and 3 independent replicates of LRIG1 KO OT1 T cells were isolated from B16ova tumor tissues: each sample is purified from pooled 2-3 tumor tissues

first: Li

middle: L


title: Synergistic insulation of regulatory domains by developmental genes and clusters of CTCF sites [ChIP-seq]

status: Public on Dec 29 2023

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

summary: The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow certain level of physical crosstalk across regulatory domains, which is at odds with the highly specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites synergistically foster the robust insulation of regulatory domains. Firstly, we found that the TADs containing developmental genes have distinctive features, including the sequential organization of developmental genes and CTCF clusters near TAD boundaries. Most importantly, by genetically dissecting representative loci in mouse embryonic stem cells, we showed that developmental genes and CTCF sites synergistically strengthened the insulation capacity of nearby boundaries through different mechanisms. Namely, while CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the specificity of gene regulation, which in turn might help interpreting the pathological consequences of certain structural variants.

overall_design: Genome-wide binding profiles for RAD21 and H3K27ac  were investigated by ChIP-seq in WT mouse embryonic stem cells (mESC) as well as in transgenic mESC lines containing different genomic re-arrangements (i.e. deletions or inversions). Where indicated the ChIP-seq profiles were generated upon differentiation of the mESC lines into anterior neural progenitors (NPC).

first: Thais

last: Ealo

first: Victor

last: Sanchez-Gaya

first: Endika

last: Haro


title: Transcriptome analysis for differentiated gene expression analysis of TU2218, Vactosertib, and Ramucirumab on VEGF-induced endothelial cell anergy condition

status: Public on Dec 27 2023

city: Seongnam-si, Gyeonggi-do

first: Jihyun

last: Lee

address: 30, Changeop-ro 40beon-gil, Sujeong-gu

country: South Korea

institute: Tiumbio

summary:
Transcriptome analysis of HUVECs treated with TGFβRI or VEGFR2 inhibitors on endothelial cell anergy condition
In this study, the dual inhibitory mechanism of TU2218 was identified using an in vitro analysis mimicking the tumor microenvironment and its anti-tumor effects were analyzed using in vivo mouse syngeneic tumor models. TU2218 directly normalized the activity of damaged T lymphocytes and natural killer cells from TGFβ and suppressed the activity and viability of regulatory T cells. The anergy of endothelial cells induced by VEGF stimulation was completely ameliorated by TU2218, an effect not observed with vactosertib, which only inhibits TGFβ signal.

overall_design: 18 RNA samples including triplicate-repeated samples for 6 conditions using the Affymetrix Human 2.0 ST platform. The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis.

first: NamHoon

last: Kim

first: Seong-Ho

last: Kang

first: Seung-Hyun

first: Sowon

last: Bae

first: Hun-Taek


title: PRMT5 knockdown changes gene expression in prostate cancer cells

status: Public on Dec 25 2023

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary: PRMT5 is the major type II protein arginine methyltransferase catalyzing the symmetric dimethylation of arginine. Recent reports have indicated that PRMT5 is overexpressed in multiple cancer types, including prostate. However, the exact contribution of PRMT5 to prostate tumorigenesis is unknown. To explore the functional role of PRMT5 in prostate cancer (PCa), we knocked down PRMT5 by lentiviral shRNAs in both AR-dependent LNCaP cells and AR-independent PC3 cells. Our data suggests that PRMT5 regulates PCa cell biology. To further identify PRMT5-regulated genes in PCa, we performed paired-end RNA-seq analysis in PC3 and LNCaP cells with or without PRMT5-knockdown.

overall_design: Quantification of RNA expression in prostate PC3 and LNCaP cancer cells infected with shNC lentivirus or PRMT5-targeting shRNAs to inhibit PRMT5 signaling.

first: Qiang

last: Hu

first: Dean

middle: G

last: Tang


title: Transcriptional effects of SARS-CoV-2 on human  M-CSF-derived macrophages

status: Public on Dec 24 2023

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

institute: CSIC

summary: Analysis of the transcriptional signature of SARS-CoV-2-infected human M-CSF-dependent monocyte-derived macrophages.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were exposed SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1) or nothing (UNT). After 4,12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis.

overall_design: mRNA profiles of human M-CSF-derived macrophages infected with SARS-CoV-2

first: Ángeles

first: Maria

last: Colmenares

first: Miguel

middle: A

last: Vega

first: Angel

last: Corbí


title: Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

institute: Washington State Univ. Spokane

summary: Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including degenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique polyadenylation sites (PASs) expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a meta-analysis of sleep- or circadian-associated PASs with recently described APA-linked brain disorder susceptibility genes.

overall_design: We investigated alternative poly(A) site (APA) usage in the central brain of Long Evans rats for variation (1) over time of day or (2) with increased sleep pressure after sleep deprivation. The animals were maintained on a 12h light: 12h dark cycle. For the time-of-day experiments, 5 replicate libraries from individual rats were prepared from each timepoint; ZT2, 6, 10, 14, 18, or 22. Cycling in specific APAs was evaluated using the meta2d suite of algorithms. To look for APAs affected by sleep pressure, 5 replicate libraries were prepared from individual rats immediately after 6h of sleep-deprivation ("recovery 0" (R0), as well as after 2, 4, 6 or 10h of recovery. APA counts from rats recovering from 6 h SD were contrasted with time-matched controls (R0 vs ZT6, R2 vs ZT8, R4 vs ZT10, R8 vs ZT14). We removed high variation from the first principal component systematically, resulting in improved variance estimates for low read counts. Prcomp (in R) was used to perform PCA and find eigenvectors by way of singular value decomposition. DESeq-2 with "Apeglm" Shrinkage and the Wald Test were used to generate test statistics in R software. The FDRtool was used to determine the Local FDR.

first: Carlos

middle: C

last: Flores

first: Nickolas

last: Pasetto

first: Alexander

last: Dimitrov

first: Hongyang

first: Jon

middle: F

last: Davis

first: Zhihua

last: Jiang

first: Christopher

middle: J

middle: R


title: PRMT5 regulated transcriptome in prostate cancer cells

summary: Compared to intensely studied DNA methylation, protein methylation is less studied. PRMT5 is the major type II protein arginine methyltransferase catalyzing the symmetric dimethylation of arginine. Recent reports have indicated that PRMT5 is overexpressed in multiple cancer types, including prostate. However, the exact contribution of PRMT5 to prostate tumorigenesis is unknown. To explore PRMT5 in prostate cancer (PCa) therapeutically, we utilized a recently developed selective small molecule PRMT5 inhibitor (PRMT5i, EPZ015666) that has shown in vivo potency in MCL models. To understand the molecular mechanisms of action of PRMT5i in PCa, we performed deep RNA-seq analysis in PC3 and LNCaP cells treated with or without PRMT5i at 4 μM for 4 days in vitro.

overall_design: Quantification of RNA expression in prostate PC3 and LNCaP cancer cells treated with PRMT5i to inhibit PRMT5 signaling.


title: Effect of depletion of LRIG1 on CD8+ tumor infiltrating T cells [CITE-Seq]

first: Lily

last: Wang

summary: To investigate the function of LRIG11 in regulating the differentiation of polyclonal CD8 tumor infiltrating T cells during the response to B16melanoma, we isolated CD8 T cells on day 18 post vaccine treatment and examined gene transcription at single cell level

overall_design: WT and LRIG1 KO CD8 T cells were isolated from  pooled B16 melanoma tumor tissues from 8-10 mice for each. Cells were processed using 10x genomics platform for extracting RNA and build single cell library for subsequent RNAseq analysis

first: Li


title: Transcriptome changes caused by Phf6 deletion in Committed leukemic cells from the retroviral-HoxA9 AML mouse model [RNA-seq Committed leukemic cell]

status: Public on Dec 15 2023

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

summary: Hematopoietic conditional knockout (cKO) of Phf6 in a mouse retroviral-HoxA9 AML model led to increased transplantability. We performed bulk RNA-Seq on the 'committed' population (c-Kit+, Ly6C+) sort purified from primary recipients of HoxA9-transduced Ctrl (Vav-Cre/+, Phf6 +/Y marrow transduced with HoxA9) and cKO cells (Vav-Cre/+, Phf6 flox/Y marrow transduced with HoxA9) 8 weeks after transplantation. Our results reveal that Phf6 deletion has minimal effects on the transcriptome of the committed population (see separately deposited series for effects on the transcriptome of leukemia initiating [LIC-e] cells).

overall_design: RNA-Seq of Committed Leukemic cells (c-Kit+, Ly6C+) sort purified from the bone marrow of primary recipient of HoxA9-transduced Ctrl and Phf6 cKO cells 8 weeks after transplantation.

first: S

middle: S

last: Jalnapurkar

last: George

first: V


title: Lineage and ecology define liver tumor evolution in response to treatment

status: Public on Dec 22 2023

city: Bethesda

first: Xin

middle: Wei

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Single-cell transcriptome-based strategy to determine the evolutionary trajectories of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.

overall_design:
scRNA seq was performed on 31 longitudinal samples collected from 11 liver cancer patients undergoing immunotherapy treatment.
*** Due to patient privacy concerns, patient data will be submitted to dbGaP. ***

first: XinWei

first: Lichun

last: Ma


title: RNAseq reveals that Pseudomonas aeruginosa mounts medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Most habitats on earth are colonized by diverse bacterial communities, offering ample opportunities for inter-species interactions. While competition for space and nutrients might often dominate such interactions, little is known about whether bacteria can sense competitors and mount specific responses to withstand their attacks. The competition-sensing hypothesis proposes that bacteria can do so through nutrient stress and cell damage cues. Here, we conducted a replicated RNAseq-transcriptomic study to test this hypothesis. We exposed Pseudomonas aeruginosa to either its own spent medium or to the supernatant of its competitor Burkholderia cenocepacia. Compared to controls, we detected significant changes in the transcriptome of P. aeruginosa that entail both general responses to spent medium and specific responses to the competitor. Specifically, genes encoding various competitive traits, including the type-VI secretion system, the siderophore pyoverdine, and the toxins phenazines and hydrogen cyanide, were upregulated when exposed to the competitor supernatant. Similarly, several stress response and quorum-sensing regulators were overexpressed. Moreover, we found transcriptional responses to vary as a function of iron availability, whereby metabolically more costly responses were launched under iron rich conditions. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when exposed to B. cenocepacia supernatant, integrating both environmental and social cues.

overall_design: Using Illumina High Seq to analyze P.a. gene expression when grown in supernatant of B.c. under high and low iron availabilty. As comparisons P.a. was grown in its own supernatant and in fresh medium only under the same iron treatments. Experiments were performed in triplicates.

first: Anne

last: Leinweber

first: Clémentine

last: Laffont

first: Martina

last: Lardi

first: Leo

last: Eberl

first: Rolf

last: Kümmerli


title: Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome.

status: Public on Dec 18 2023

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

summary: Colletotrichum is a large genus of fungal phytopathogens that cause major economic losses on a wide range of crop plants throughout the world. These pathogenes vary widely in their host specificity and may have either broad or narrow host ranges. Here, we report the first complete genome of the alfalfa (Medicago sativa) pathogen, Colletotrichum destructivum, which will facilitate the genomic analysis of host adaptation and comparison with other members of the Destructivum clade. We identified a specific 1.2Mb region within chromosome 1 displaying all the hallmarks of fungal accessory chromosomes, which may have arisen through the integration of a mini-chromosome into a core chromosome and possibly linked with the pathogenicity of this fungus. We show this region is also a focus for chromosomal rearrangements, which may contribute to generating genetic diversity for adaptive evolution. Finally, we report infection by this fungus of the model legume, Medicago truncatula, providing a novel pathosystem for studying fungal-plant interactions.

overall_design: Colletotrichum destructivum LARS709 (Cd709) was grown in vitro (in PDB) or inoculated on Medicago sativa for 48h or 72h.

first: Nicolas

last: Lapalu

last: Simon

first: Antoine

last: Lu

first: Peter-Louis

last: Plaumann

first: Joëlle

last: Amselem

first: Sandrine

last: Pigné

first: Annie

last: Auger

first: Jean-Félix

last: Dallery

first: Christian

last: Koch

first: Richard

last: O'Connell


title: Chromatin accessibility changes caused by Phf6 deletion in Leukemia-initiating cells from the retroviral-HoxA9 AML mouse model [ATAC-Seq LICe]

first: Vikram

last: Paralkar

summary: Hematopoietic conditional knockout (cKO) of Phf6 in a mouse retroviral-HoxA9 AML model led to increased transplantability and accumulation of a c-Kit+ Ly6C- population that we termed the 'Leukemia Initiating Cell-Enriched' (LIC-e) population. We performed bulk ATAC-Seq on the LIC-e population sort purified 4 days after transduction of Ctrl (Vav-Cre/+, Phf6 +/Y) or cKO (Vav-Cre/+, Phf6 flox/Y) marrow retrovirally transduced with HoxA9.

overall_design: ATAC-Seq of LIC-e cells (c-Kit+, Ly6C-) sort purified from bone marrow of Ctrl and Phf6 cKO marrow 4 days after retroviral transduction with HoxA9 transgene.

first: S

last: Jalnapurkar

last: George

first: V


title: The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction

status: Public on Dec 13 2023

city: Rochester

first: Andrew

last: Samuelson

state: NY

address: 601 Elmwood Ave

department: Biomedical Genetics

institute: University of Rochester Medical Center

summary: Dietary restriction (DR), the process of decreasing overall food consumption over an extended period of time, has been shown to increase longevity across evolutionarily diverse species and delay the onset of age-associated diseases in humans. In Caenorhabditis elegans, the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP), which function as obligate heterodimers, and the forkhead box transcription factor A ortholog (PHA-4) are both necessary for the full physiological benefits of DR. However, the adaptive transcriptional response to DR and the role of MML-1::MXL-2 and PHA-4 remains elusive. We identified the transcriptional signature of C. elegans DR, using the eat-2 genetic model, and demonstrate broad changes in metabolic gene expression in eat-2 DR animals, which requires both mxl-2 and pha-4. While the requirement for these factors in DR gene expression overlaps, we found many of the DR genes exhibit an opposing change in relative gene expression in eat-2;mxl-2 animals compared to wild-type, which was not observed in eat-2 animals with pha-4 loss. We further show functional deficiencies of the mxl-2 loss in DR outside of lifespan, as eat-2;mxl-2 animals exhibit substantially smaller brood sizes and lay a proportion of dead eggs, indicating that MML-1::MXL-2 has a role in maintaining the balance between resource allocation to the soma and to reproduction under conditions of chronic food scarcity. While eat-2 animals do not show a significantly different metabolic rate compared to wild-type, we also find that loss of mxl-2 in DR does not affect the rate of oxygen consumption in young animals. The gene expression signature of eat-2 mutant animals is consistent with optimization of energy utilization and resource allocation, rather than induction of canonical gene expression changes associated with acute metabolic stress -such as induction of autophagy after TORC1 inhibition.  Consistently, eat-2 animals are not substantially resistant to stress, providing further support to the idea that chronic DR may benefit healthspan and lifespan through efficient use of limited resources rather than broad upregulation of stress responses, and also indicates that MML-1::MXL-2 and PHA-4 may have different roles in promotion of benefits in response to different pro-longevity stimuli.

overall_design: C. elegans hermaphrodite N2 (WT), eat-2(ad465), mxl-2(tm1516), or eat-2(ad465);mxl-2(tm1516) animals were grown on dsRNA-expressing HT115 E coli for feeding-based RNAi for daf-16, pha-4, or empty-vector (EV) control. All combinations of these conditions were tested, and at least two biological replicate experiments were performed, each consisting of a separate synchronized population of animals. Animals were raised at 16 degrees C from L1 to L4, then transferred to 20 degrees C for the remainder of the experiment. Approximately 3000 total animals were collected at day 2 of adulthood for RNA isolation from populations that were synchronized at L1 and then treated with FUdR at L4 to prevent formation of progeny. Libraries for RNA-Seq were prepared and sequenced on a HiSeq2500 v4 in 1x100bp mode at the University of Rochester Genomics Research Center.

first: Adam

middle: B

last: Cornwell

first: Manjunatha

last: Thondamal

first: Yun

last: Zhang

first: David

middle: W

last: Johnson

first: Juilee

last: Thakar


title: Transcriptome atlas of injection site response reveals initial mechanisms of mRNA vaccine immunity

status: Public on Dec 14 2023

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: Precise immunological mechanisms of mRNA vaccines have still not been fully elucidated, especially the initial immune responses at the injection site. Here, by constructing a single-cell atlas of injection site responses of mRNA vaccine, we show that stromal inflammatory responses and type I interferon responses dominate initial transcriptional reactions elicited by mRNA vaccines at the injection site. Tracking down the fates of the delivered mRNA revealed that injection site fibroblasts are highly enriched with the delivered mRNA, and they express IFN-β specifically in response to the mRNA component, not to the LNP. Accordingly, migratory dendritic cells highly expressing interferon stimulated genes (mDC_ISG) were found specifically in muscle and draining lymph nodes of mRNA vaccine injected mice, compared to the empty LNP injected mice. Co-administration of IFN-β and LNP robustly induced mDC_ISGs at the injection site and substantially enhanced antigen-specific CD8 T cell responses. Collectively, these data elucidate earliest mechanisms of the mRNA vaccine and highlight the underappreciated immunogenic role of the mRNA component in the mRNA vaccine.

overall_design: We performed single cell RNA sequencing on the mRNA vaccine or empty LNP injected muscle tissues, draining lymph nodes and peripheral blood cells.

first: Jinah

last: Yeo

first: Seongryong

last: Kim


title: R7-dependent transcription in the developing Drosophila retina

status: Public on Dec 07 2023

city: Austin

first: John

middle: Calvin

last: Aldrich

state: TX

address: 1601 Trinity St. Bldg B

department: Neurology

institute: University of Texas at Austin, Dell Medical School

summary: Color vision in Drosophila is mediated by photoreceptors R7 and R8, which express various combinations of opsins Rh3, Rh4, Rh5 and Rh6 depending on their cellular identity. Most ommatidia are classified as either “pale” or “yellow” subtypes with pale ommatidia coordinately expressing Rh3 and Rh5—in R7 and R8 cells respectively—while yellow express Rh4 and Rh6. Subtype identity is established initially in R7 photoreceptors via a stochastic mechanism then transmitted to the R8 via an inductive signal to ensure paired opsin expression.  To identify factors that may be involved in this process, we used RNA-Seq to detect genes that are differentially expressed in sevenless mutant retinas at 40 hours after puparium formation. Since loss of sevenless prevents R7 recruitment and specification, we reasoned that this approach would allow us to identify genes that are enriched in R7 cells during this critical time point. Furthermore, since it has previously been established that in the absence of R7 most R8s will adopt the yellow Rh6-expressing identity, this gives us the opportunity to identify genes which may inductive mechanism occurring in R8 cells.

overall_design: Replicate samples (four per genotype) were prepared from dissected 40 hour apf female pupal retinas from w[1118] control or w[*] sev[14] animals. Normalized count data from RNA-Seq was used to identify differentially espressed transcripts.

first: Lauren

last: Vanderlinden

first: Thomas

last: Jacobsen

first: Cheyret

last: Wood

first: Laura

last: Saba

first: Steven

last: Britt


title: Multiomics analysis of immune-related adverse events in melanoma patients treated with immune checkpoint inhibitors

status: Public on Dec 01 2023

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

institute: Hopitaux universitaires de Geneve

summary: Immune checkpoint inhibitors (ICIs) are a standard-of-care for the treatment of advanced melanoma, but their use is limited by immune-related adverse events (irAEs). Proteomic analysis and multiplex cytokine/chemokine assay from serum at baseline and at irAEs onset in 82 patients indicated aberrant T-cell activity with differential expression of Type I and III immune signatures. This was in line with an increase in the proportions of monocytes and decrease of IL-17A producing CD4+ T-cells in the peripheral blood in single cell RNA sequencing. Multiplex immunohistochemistry on ICI-induced skin rash and inflamed colon showed increase in the proportion of CD4+ T-cells with IL-17A expression. Anti-IL17A antagonistic mAbs were administered in two patients with severe myocarditis, colitis and skin rash with resolution of the irAE. This study demonstrates the potential role of Type III CD4+ T-cells in the irAEs development and provides proof-of-principle evidence to support a clinical trial examining anti-IL17A in their management.

overall_design:
PBMCs from 6 melanoma patients receiving combination anti-CTLA4 and anti-PD1 at baseline and at AE onset or at 2nd infusion.
This submission does not contain raw data files as the fastq files contain protected patient information. Fastq files can be provided upon request.

first: Cheng

last: Phil

first: Dimitriou

last: Florentia


title: Immune checkpoint inhibitor monotherapy is sufficient to promote microenvironmental normalization via Type I interferon pathway in PD-L1+ expressing head and neck cancer

city: Suwon-si

first: Ji-Hye

last: Choi

state: Gyeonggi-do

address: World cup-ro

institute: Ajou university

summary: Immune checkpoint blockers (ICBs) targeting programmed death 1(PD-1) are considered effective first-line therapy against PD-1 ligand (PD-L1)-expressing head and neck squamous cell carcinoma (HNSCC). However, associated changes in tumor microenvironment (TME) and mechanisms remain elusive. Oral tumors in C57/BL6 mice were induced by administering 7,12-dimethylbenzanthracene into the buccal mucosa. Single-cell suspension was isolated from tumor tissue; proliferating cells were injected subcutaneously into the left flank of mice to establish Ajou Oral Cancer (AOC) cell lines. Subsequently, a syngeneic PD-L1-expressing HNSCC xenograft model was developed by injecting AOC cells into the buccal or tongue area. The model recapitulated human HNSCC molecular features and showed reliable in vivo tumorigenicity with significant PD-L1 expression. ICB monotherapy induced global changes in TME, including vascular normalization. Furthermore, the anti-tumor effect of ICB monotherapy was superior to those of other therapeutic agents, including cisplatin and anti-vascular endothelial growth factor receptor 2 inhibitors. The ICB-induced anti-tumorigenicity and TME normalization were alleviated by blocking the Type I interferon pathway.In summary, ICB monotherapy is sufficient to induce TME normalization in the syngeneic model; the Type-I interferon pathway is indispensable in realizing ICB effects. Furthermore, these results explain the underlying mechanism of the efficacy of ICB monotherapy against HNSCC expressing PD-L1 in the KEYNOTE-048 trial. This model can assist future research on HNSCC immunotherapy.

overall_design: Transcriptome profiling from 4 cell lines of Ajou Oral Cancer (AOC, n=2) and 2 metastatic lymph node tumors (LNC, n=2)

first: Jeon

middle: Y

last: Jang

first: Bok-Soon

last: Lee

first: Mei

last: Huang

first: Chorong

last: Seo

first: Yoo

last: Shin

first: Hyun

last: Woo

first: Chul-Ho


title: RNA helicase DDX5 mediates adaptive response to multi-kinase inhibitors in liver cancer

city: West Lafayette

first: Ourania

middle: M

last: Andrisani

state: IN

address: 625 Harrison Street

department: DEPARTMENT OF BASIC MEDICAL SCIENCES

institute: Purdue University

summary: Earlier studies linked sorafenib effectiveness to induction of ferroptosis. Herein we demonstrate sorafenib and mTKIs downregulate DDX5 in vitro and in vivo. To understand the effect of DDX5 downregulation, we compared TCGA-derived HCCs expressing low vs. high DDX5 focusing on ferroptosis-related genes. Glutathione Peroxidase 4 (GPX4), a key ferroptosis regulator, was significantly overexpressed in DDX5LOW HCCs. Importantly, DDX5-knockdown (DDX5KD) HCC cell lines lacked lipid peroxidation by GPX4 inhibition, indicating DDX5 downregulation suppresses ferroptosis. RNAseq analyses comparing wild type vs. DDX5KD cells in the presence or absence of sorafenib, identified a unique set of genes repressed by DDX5 and upregulated by sorafenib. This set significantly overlaps genes from Wnt/β-catenin and non-canonical NF-κB pathways, including NF-κB inducing Kinase required for non-canonical NF-κB activation. Pharmacologic inhibition of these pathways in combination with sorafenib reduced DDX5KD cell viability. Mechanistically, sorafenib-mediated NF-κB activation induced NRF2 transcription, while DDX5KD extended NRF2 half/life by stabilizing p62/SQSTM1, leading to enhanced expression of GPX4 and ferroptosis escape. Conclusion: Sorafenib/mTKI-mediated DDX5 downregulation results in adaptive mTKI resistance by enhancing NRF2 expression, leading to ferroptosis escape. We propose inhibition of the pathways leading to NRF2 expression will enhance the therapeutic effectiveness of sorafenib/mTKIs.

overall_design: HepAD38WT and HepAD38-DDX5KD cells were treated with Sorafenib (7.5 μM) for 3 days prior to harvesting. Three independent biological replicates were prepared for RNA isolation and RNA sequencing. Total RNA submitted to Novogene for quality assessment and next-generation sequencing. Paired-end 2x50 bp sequencing performed using a HiSeq2500 system (Illumina).

first: Zhili

last: Li

first: Jiazeng

last: Sun

first: Naimur

last: Rahman

first: Bingyu

last: Yan

first: Sagar

last: Utturkar

first: Nadia

last: Atallah Lanman

first: Majid

last: Kazemian

first: Claude

last: Caron de Fromentel

first: Massimo

last: Levrero


title: Synergistic insulation of regulatory domains by developmental genes and clusters of CTCF sites

first: Alvaro

last: Rada-Iglesias

summary: The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow certain level of physical crosstalk across regulatory domains, which is at odds with the highly specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites synergistically foster the robust insulation of regulatory domains. Firstly, we found that the TADs containing developmental genes have distinctive features, including the sequential organization of developmental genes and CTCF clusters near TAD boundaries. Most importantly, by genetically dissecting representative loci in mouse embryonic stem cells, we showed that developmental genes and CTCF sites synergistically strengthened the insulation capacity of nearby boundaries through different mechanisms. Namely, while CTCF sites prevent undesirable enhancer-gene contacts (i.e. physical insulation), developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the specificity of gene regulation, which in turn might help interpreting the pathological consequences of certain structural variants.

overall_design: Capture-C experiments were performed to investigate enhancer-gene contacts within specific loci (i.e. Gbx2/Asb18 or Six3/Six2) in WT mouse embryonic stem cells (mESC) as well as in transgenic mESC lines containing different genomic re-arrangements (i.e. deletions or inversions). Where indicated the Capture-C experiments were performed upon differentiation of the mESC lines into anterior neural progenitors (NPC).

first: Thais

last: Ealo

first: Victor

last: Sanchez-Gaya

first: Endika

last: Haro


title: Cohesin composition and dosage independently affect early development in zebrafish

status: Public on Nov 29 2023

city: Dunedin

first: Michael

last: Meier

state: Region

address: 56 Hanover St

department: Pathology

country: New Zealand

institute: University of Otago

summary: Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition, we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA-sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2, but not rad21 mutants, implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies.

overall_design: Tailbuds obtained from wild type and stag2b(nz207) were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.

first: David

last: Tatarakis

first: Thomas

last: Schilling

first: Julia

last: Horsfield

first: Benjamin

last: Martin


title: single-nuclei RNA-sequencing (snRNA-seq) of murine tumors derived from the orthotopic transplantation of PDAC KPC T-LOH organoids in C57BL/6j mice following 2-week treatment with Neratinib or vehicle

status: Public on Nov 30 2023

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: We investigated the effect of Neratinib treatment on murine PDAC tumors

overall_design: 8 samples in total - 4 vehicle-treated; 4-neratinib treated

first: Gianluca

last: Mucciolo

first: Wenlong

last: Li

first: Muntadher

last: Jihad


address: 56 Hanoverstr

institute: Otago University

overall_design: RNA-seq analysis was performed on tailbud samples from wild type zebrafish embryos, as well as those with homozygous and heterozygous rad21 mutations, and homozygous stag2b mutations. The dataset includes both, baseline samples as well as, samples treated with Wnt agonist (2.5 μM 6-bromoindirubin-3’-oxime).

first: Anastasia

last: Labudina

first: Gregory

last: Gimenez

first: Jisha

last: Antony


title: Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

city: Amsterdam

first: Ruben

last: Schep

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: We sought to find if epigenetic drugs had chromatin context-dependent effects on CRISPR-Cas9 efficiency and DNA double-strand break repair. We performed a multiplexed drug screen in a reporter cell line containing 19 sequencing based pathway reporters. This submission contains high throughput sequencing data of the pathway reporters, their mapping and mutation readout. It also contains the raw pA-DamID data for H3K27me3, H3K9me2, H3K9me3 and "Dam-only" samples in RPE-1 cells.

overall_design:
The samples are pA-DamID experiments, as described in (van Schaik , 2022), where DNA-protein interactions are measured. Here we profile H3K27me3, H3K9me2, H3K9me3 and Dam only in hTERT RPE-1 cells. The Dam only samples are used as controls for DNA accessibility. These data were used in this study to compare DNA repair outcomes of DNA double strand breaks in different chromatin states in RPE-1.

ChIP-seq experiments have been performed using H3K27ac and H3K27me3 antibodies. 3 biological replicates are provided.


title: Next Generation Sequencing of a repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

summary: A putative EAF3/MRG15 ortholog N1617, containing chromo and MRG domain, is a partner of Ash1 in Magnaporthe oryzae

overall_design: Examination of 3 different mutants in Magnaporthe oryzae strain

first: Zeng

last: Tao


title: Repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae

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

overall_design: Refer to individual Series


title: Yeast EndoG prevents genome instability by degrading extranuclear DNA species

status: Public on Dec 20 2023

city: Boston

first: Xin

last: Wang

state: MA

address: 300 Longwood Ave,

institute: Boston children's hospital

summary: In metazoans mitochondrial DNA (mtDNA) or retrotransposon cDNA released to cytoplasm are degraded by nucleases to prevent sterile inflammation. It remains unknown whether degradation of these DNA also prevents nuclear genome instability. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. In non-dividing stationary phase cells, Pol4-mediated non-homologous end-joining increases, resulting in frequent insertions of 1-3 nucleotides, and insertions of mtDNA (NUMTs) or retrotransposon cDNA.  Yeast EndoG (Nuc1) nuclease limits insertion of cDNA and transfer of very long mtDNA (>10 kb) to the nucleus, where it forms unstable circles, while promoting the formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of extranuclear DNA to nucleus in aging or meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating extranuclear DNA preserve genome stability.

overall_design: To study NUMT formation in yeast, we developed a high-throughput amplicon sequencing based method called Break-Ins (Break Insertions) which allows screening of hundreds of thousands of NHEJ products simultaneously for the events carrying NUMTs . We used yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus. This DSB can only be repaired by NHEJ; only the cells that repaired the break imprecisely, altering the HO recognition site, can survive continuous HO induction and form colonies.Cells from an overnight saturated YEPD culture were washed twice with YEP-Raffinose, inoculated into 10 ml YEP-Raffinose and incubated overnight at 30 °C. When the density of the culture was ~2×107 cells/ml, ~1×107 cells were spread on a YEP-galactose 150mm plate and incubated at 30 °C for 5 days. Each culture was spread on 5-7 plates. Some slow growing strains were incubated 1-3 more days. Colony number was counted. Colony numbers were estimated by counting a representative sector of one plate per genotype and multiplying to cover all plates. Cells were collected using a spreader after adding 5 ml water onto each plate. Cells were pooled and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl. The construction of the sequencing library was adapted from Illumina’s amplicon sequencing protocol #15044223 Rev. B. Two rounds of PCR were performed to construct the sequencing library. For each sample, 3.2 μl genomic DNA, 0.5 μl 10 μM primers and 12.5 μl KAPA HiFi HotStart ReadyMix (Roche, 7958927001) was used for the first round of PCR for a total volume of 25 μl. The forward primers are 66-mers that contain (5’ to 3’): 33 bases Illumina adapter sequence (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG), 3 bases unique home index, and 30 bases (GCATAGTCGGGTTTTTCTTTTAGTTTCAGC) targeting the Mata locus which is located 12-41 bp upstream the HO cleavage site. The reverse primers are 66-mers that contain (5’ to 3’): 34 bases Illumina adapter sequence (GTCTCGTGGGCTCGGAGATGTG TATAAGAGACAG), 3 bases unique home index, and 29 bases (CAACCACTCTACAAAAC CAAAACCAGGGT) targeting the MATa locus which is located 15-43 bp downstream the HO cleavage site. The following conditions were used for the first round of PCR: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 18μl PCR product was purified with 20μl AMPure XP beads (Beckman Coulter, A63880) and eluted with 52.5 μl 10 mM Tris pH 8.5. For the second round of PCR, 5 μl purified PCR product, 5 μl Nextera XT V2 Index (Illumina, FC-131-2001) primer N7xx, 5 μl index primer S5xx, and 25 μl KAPA HiFi HotStart ReadyMix were used. The total volume of PCR is 50 μl. The following conditions were used for PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 40 μl PCR product was purified with 48 μl AMPure XP beads and eluted with 27.5 μl 10 mM Tris pH 8.5. The DNA concentration of each sample was determined with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850) and the average size of the DNA was determined with TapeStation. The DNA was diluted to 4 nM using 10 mM Tris pH 8.5. An equal amount of DNA was pooled from ~20 samples into the library. The pooled library and PhiX library (Illumina, FC‐110‐3001) were denatured with 0.2 M NaOH separately and diluted with pre-chilled HT1 to 12 pM. 540μl pooled library and 60 μl PhiX were mixed, incubated at 96 °C for 2 min and immediately placed in an ice-water bath for 5 min. The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003). The cluster density was ~1100 K/mm2.

first: Yang

last: Yu

first: Kaifu

last: Chen

first: Grzegorz

last: Ira


title: EGFR-activated cancer-associated myofibroblasts promote metastasis in pancreatic cancer


title: Next Generation Sequencing of Two H3K36 methyltransferases during growth mycelia in the Magnaporthe oryzae

summary: Di- and tri-methylation of lysine 36 on histone H3 (H3K36me2/3) are catalyzed by SET2 histone methyltransferase which play an important role in transcriptional elongation.we reveal a novel mechanism by which H3K36me2 and H3K36me3 associates with opposite transcriptional activity and Ash1 is required for the normal distribution of facultative heterochromatic modifications and stable maintenance of transcriptional silencing in eukaryotes.

overall_design: Examination of 2 different mutants in Magnaporthe oryzae strain


title: Transcriptome changes caused by Phf6 deletion in Leukemia-initiating cells from the retroviral-HoxA9 AML mouse model [RNA-seq LICe]

first: Vikram

last: Paralkar

summary: Hematopoietic conditional knockout

overall_design: RNA-Seq of LIC-e cells

first: S

last: Jalnapurkar

last: George

first: V


title: Genome-wide mapping of Two H3K36 methyltransferases during growth mycelia in the Magnaporthe oryzae

overall_design: Examination of H3K36 di/tri-methylation of  Pyricularia oryzae. Two biological replicates were performed.


title: Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex [H3K27ac]

status: Public on Nov 28 2023

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 180,000 cells.  For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes, and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than  promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species, and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity help uncover functional  cis-regulatory elements and enhance our ability  to interpret genetic variants contributing to neurological disease and traits.

overall_design: Analysis of single cell H3K27ac Droplet-based Paired-Tag + Gene Expression (10x Genomics) of motor cortex from human

first: Nathan

last: Zemke


title: Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [RNA-seq]

status: Public on Nov 27 2023

city: South San Francisco

first: Tim

last: Sterne-Weiler

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: Accurate detection and quantification of mRNA isoforms from nanopore long-read sequencing remains challenged by technical noise, particularly in single cells. To address this, we introduce Isosceles, a computational toolkit that outperforms other methods in isoform detection sensitivity and quantification accuracy across single-cell, pseudo-bulk and bulk resolution levels, as demonstrated using synthetic and biologically-derived datasets. Isosceles improves the fidelity of single-cell transcriptome quantification at the isoform-level, and enables flexible downstream analysis.  As a case study, we apply Isosceles, uncovering coordinated splicing within and between neuronal differentiation lineages.  Isosceles is suitable to be applied in diverse biological systems, facilitating studies of cellular heterogeneity across biomedical research applications.

overall_design: RNA-seq sequencing of ovarian cancer cell lines using PromethION and MinION platforms used for benchmarking the Isosceles package.

first: Michal

last: Kabza

first: Alexander

last: Ritter

first: Ashley

last: Byrne

first: Kostianna

last: Sereti

first: Daniel

last: Le

first: William

last: Stephenson

first: Timothy


title: Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles


title: Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [scRNA-seq]

overall_design: scRNA-seq sequencing of a mix of three ovarian cancer cell lines using PromethION and Illumina platforms used for benchmarking the Isosceles package.


title: The androgen receptor in mesenchymal progenitors regulates skeletal muscle mass via Igf1 expression in male mice.

status: Public on Nov 22 2023

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: Androgens exert their effects primarily by binding to the androgen receptor (AR), a ligand-dependent nuclear receptor. While androgens have anabolic effects on skeletal muscle, previous studies reported that AR functions in myofibers to regulate skele- tal muscle quality, rather than skeletal muscle mass. Therefore, the anabolic effects of androgens are exerted via nonmyofiber cells. In this context, the cellular and molecular mechanisms of AR in mesenchymal progenitors, which play a crucial role in maintaining skeletal muscle homeostasis, remain largely unknown. In this study, we demonstrated expression of AR in mesenchymal progenitors and found that targeted AR ablation in mesenchymal progenitors reduced limb muscle mass in mature adult, but not young or aged, male mice, although fatty infiltration of muscle was not affected. The absence of AR in mesenchymal progenitors led to remarkable perineal muscle hypotrophy, regard- less of age, due to abnormal regulation of transcripts associated with cell death and extracellular matrix organization. Additionally, we revealed that AR in mesenchymal progenitors regulates the expression of insulin-like growth factor 1 (Igf1) and that IGF1 administration prevents perineal muscle atrophy in a paracrine manner. These findings indicate that the anabolic effects of androgens regulate skeletal muscle mass via, at least in part, AR signaling in mesenchymal progenitors.

overall_design:
To investigate the role of AR in mesenchymal progenitors, PDGFRα-CreER and ARL2/Y mice were crossed to selectively delete AR gene in mesenchymal progenitors expressing PDGFRα.
To determine the effects of AR on gene expression, we performed RNA-Seq from PDGFRα+ cells in LA/BC muscles of both control (PDGFRα-CreER;AR+/Y)  and mutant (PDGFRα-CreER;ARL2/Y) mice.
To determine the AR target genes, we used CUT&RUN method for AR and trimethylated lysine 4 from histone H3 (H3K4me3) in mesenchymal progenitors isolated from C57BL/6J male mice treated with DHT 2 hours before sampling.

first: Yuuki

last: Imai


title: A map of signaling responses in human airway epithelium [time_course]

status: Public on Nov 17 2023

first: Kalki

last: Kukreja

address: 200 Longwood Avenue

institute: Harvard University

summary: Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling–response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of all epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal-cell and secretory-cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses.

overall_design: Human bronchial epithelial cells were cultured at air-liquid interface without treatment to drive differentiation into a pseudo- stratified epithelium that recapitulates the physiological cell types of the airway, after which the luminal cells were stripped through calcium depletion, leaving the remaining basal cells to regenerate the tissue. Cells were sampled for sequencing at timepoints beginning immediately post-stripping up to 2 weeks of differentiation. A "never-stripped" well was included as  control. At each timepoint, the composition of the tissue was analyzed by scRNA-Seq and imaging. Cells (n=2 donors) were run in two separate experiments.

first: Katherine

last: Mccauley

first: Aron

last: Jaffe

first: Allon

last: Klein


title: CD23+IgG1+ memory B cells are poised to switch to pathogenic IgE production in food allergy

status: Public on Nov 16 2023

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

institute: Yale University

summary: Food allergy is caused by allergen-specific IgE but little is known about the B cell memory of persistent responses. Here we describe in pediatric peanut allergy a population of CD23+IgG1 memory B cells that contains peanut-specific clones and generates IgE plasma cells on activation. Through single cell transcriptomics and B cell receptor (BCR) sequencing, we characterized FCER2/CD23+ IgG1 memory B cells co-expressing IL4R, IL13RA1, IGHE and carrying highly mutated BCRs. Further we found that peanut allergen (Ara h 2)-specific B cells were mostly IgG1 memory cells, carried highly mutated BCRs compared to diphtheria toxin-specific B cells, and expressed FCER2 and germlin IGHE. Our findings suggest that CD23+IgG1+ memory B cells transcribing IGHE are a unique memory population containing precursors for pathogenic IgE in food allergy.

overall_design:
Sampling of peanut allergic (PA) and non-allergic, non-atopic (non-PA) subjects

UPDATE: [09-26-2024] The following supplementary files were updated:
GSE208235_bcr_gex.tsv
GSE208235_data_integrated_annotated_clusters_over.rds
GSE208235_filtered_sequences.tsv

first: Maria

last: Lafaille

first: Miyo

last: Ota

first: Kenneth

last: Hoehn


title: Whole transcriptomic analysis of liver tissue from high-intake fed compared to normally-fed lion-head geese

city: Guangzhou

first: Xinheng

last: Zhang

address: 483 Wushan Road

institute: South China Agricultural University

summary: Lion-head goose is the only large goose species in China, and it was one of the largest goose species in the world. Our previous study firstly reported a chromosome-level genome assembly of Lion-head goose (Anser cygnoides), a native breed in South China, through the combination of PacBio, Bionano, and Hi-C technologies. The fat content of foie gras is augmented during its preparation due to the special feeding regimen. Lion-head geese have a strong tolerance of massive energy intake and show a priority of fat accumulation in liver tissue. In this study, we studied for the first time the important differential genes that regulate fatty liver in Lion-head goose. After high-intake feeding, the fatty livers of Lion-head geese were distinctly characterized. The revelation of gene regulation is an important basis for the study of liver development and molecular characteristics for the Lion-head goose. To analyze the excellent fatty liver performance of Lion-head goose at the molecular level, we performed whole transcriptome analysis by high-throughput RNA sequencing to analyze the key regulatory genes that determine the fatty livers in high-intake feeding group compared with the normal livers in normally-fed Lion-head geese. We identified 716 differentially expressed mRNAs, 145 differentially expressed circRNAs, and 39 differentially expressed lncRNAs in the fatty livers in high-intake feeding group compared with the normal livers in normally-fed Lion-head geese, including upregulated and downregulated genes, respectively. GO enrichment analysis showed that these genes were significantly enriched in molecular function, involved in extracellular regions, DNA-binding transcription factor activity, extracellular matrix, heme binding and other life activities. We chose differentially expressed genes involved in either upregulation or downregulation, and we additionally confirmed the accuracy of sequencing at the RNA level. In summary, our research suggested that these differentially expressed genes may play important roles in fatty liver development in Lion-head goose. However, the functions and mechanisms of these significantly differentially expressed genes should be investigated in future studies.

overall_design: Animal Handling and Sample Collection, Total RNA-seq and Quality Control, Preparing and Constructing cDNA library, Transcriptome sequence data analysis, Analysis of differentially expressed genes, Function enrichment analysis of DEGs, Quantitative Real Time-PCR (qRT-PCR) verification

first: Jie

last: Kong

first: Ziqi

last: Yao

first: Junpeng

last: Chen

first: Qiqi

last: Zhao


title: Dapagliflozin protects against chronic heart failure in mice via inhibiting macrophage-mediated inflammation, independent of SGLT2

status: Public on Nov 14 2023

city: Wuhan

first: Qing

middle: Qing

last: Wu

address: Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan 430060, P.R. of China.

institute: Renmin Hospital of Wuhan University


title: Mouse kidney endotoxin time course

status: Public on Nov 15 2023

city: Indianapolis

first: Takashi

last: Hato

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: Time course of endotoxin-induced acute kidney injury in mice

overall_design: C57BL/6J male mice were subjected to a single-dose, 4 mg/kg LPS (E. coli serotype 0111:B4) tail vein i.v. or vehicle saline in a volume of 300 ul. Kidney tissues were harvested at 0, 1, 4, 8, 16, 28, or 48 hours post-LPS injection and total RNA-seq was performed.


title: Dapagliflozin protects against chronic heart failure in mice via inhibiting macrophage-mediated inflammation, independent of SGLT2 [scRNA-Seq]

summary: The specific mechanism of sodium-glucose cotransporter 2 (SGLT2) inhibitor in heart failure (HF) needs to be elucidated.Based on single-cell RNA sequencing dapagliflozin causes significant differences in the gene expression profile of macrophages and fibroblasts.

overall_design: Single cell RNA-sequence experiments: Heart tissues were harvested from mice 2 weeks post myocardial infarction (MI) surgery. sham surgery + NS (Sham-NS), MI + NS (MI-NS) , and MI + dapagliflozin (MI-DAPA).

first: Qizhu

last: Tang

first: Qingqing


title: Genome-wide mapping of a repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae

first: mengting

last: xu

first: Zeng

last: Tao


title: Two H3K36 methyltransferases differentially associate with transcriptional activity and Ash1 is required for facultative heterochromatin and transcriptional silencing


title: dsRNA immunoprecipitation sequencing on a murine model of endotoxin-induced acute kidney injury

status: Public on Nov 10 2023

summary: To investigate the extent of A-to-I RNA editing during endotoxemia in the kidney, we performed immunoprecipitation of dsRNA species, followed by stranded total RNA-seq on cytoplasmic and nuclear fractions of mouse kidneys.

overall_design: C57BL/6J male mice were subjected to a single-dose, 4 mg/kg LPS (E. coli serotype 0111:B4) tail vein i.v. or vehicle saline in a volume of 300 ul. Kidney tissues were harvested at 0, 1, 4, 16, or 28 hours post-LPS injection, minced, and fractionated into cytoplasmic and nuclear compartments. Each fraction was immunoprecipitated using the anti-dsRNA monoclonal antibody J2 or IgG isotype control. cDNA library was prepared using the Clontech SMARTer Stranded Total RNA-Seq Kit v2.


title: ABIN1 is a negative regulator of effector functions in cytotoxic T cells

status: Public on Nov 01 2023

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: The main objective of the data analysis presented here is the investigation of the role of ABIN1 in antigenic responses of primary T cells. For this purpose, T cells from ABIN1-deficient mouse strain (GTKO) and WT mice were analyzed under different activation conditions. The effect of P38 MAPK inhibitor SB203580 (p38 inhibitor/p38i) was also analyzed. The results suggest that ABIN1 is a negative regulator of TCR-mediated activation and expression of the key effector molecules in primary CD8+ T cells, at least partly via the inhibition of the p38 pathway.

overall_design: Two RNAseq experiments were made. The first one compares the activation of CD8+ T cells in WT and ABIN1 GTKO mice under different conditions (anti-CD3ε/CD28 beads at 1:1 or 4:1 beads-to-cell ratios or without beads). The second one compares the effect of p38 inhibitor (P38 MAPK inhibitor SB203580) on activated of CD8+ T cells in WT and ABIN1 GTKO mice. The first experiment concerns replicates 6-9, the second one replicates 17-19.

first: Sarka

last: Janusova

first: Ondrej

last: Stepanek


title: Development of a hepatic cryoinjury model to study liver regeneration

status: Public on Nov 09 2023

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

summary: We developed a new model to study liver regeneration based on cryoinjury. Hepatic cryoinjury induced a localised necrotic and apoptotic lesion characterised by inflammation and infiltration of innate immune cells. Following this initial phase, we observed fibrosis, which resolved as regeneration re-established homeostasis in 30 days. Importantly, this approach enables the comparison of healthy and injured parenchyma with an individual animal, providing unique advantages to previous models. These datasets include Bulk RNA-seq of livers collected at sham, 1 dpci, 3 dpci, and 7 dpci.

overall_design: Adult zebrafish were cryoinjured, collection of samples for Bulk RNA-seq was done at different time points, including sham, 1, 3 and 7 days-post cryoinjury (dpci)

first: Marcos

last: Sande-Melon

first: David

last: Bergemann

first: Juan

last: González-Rosa


title: Expression data from mouse rGAS6-stimulated BMDMs

status: Public on Oct 31 2023

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: To determine the mechanism by which ATF3 regulated the survival/proliferation of MerTK+ cardiac macrophages, microarray was performed to identify gene expression differences in MerTK+ macrophages from WT and ATF3-CKO mice under the HR state.

overall_design:
GAS6-induced MerTK+ macrophages of WT or ATF3-CKO mice were harvested 24 hours following HR and performed to further analysis.
For microarray profiling, the BMDMs total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix GeneChip, Santa Clara CA, USA), which contains 65957 gene-level probe sets.

first: Yulin

last: Li

first: Yihui

last: Shao


title: The PA3040-PA3042 operon influences biofilm formation and bacteriophage survival in Pseudomonas aeruginosa

status: Public on Oct 30 2023

city: Odense M

first: Magnus

middle: Zimmermann

last: Østergaard

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Bacteriophages (hereafter “phages”) are ubiquitous predators of bacteria in the natural world, but interest is growing in their development into antibacterial therapy as complement or replacement for antibiotics. However, bacteria have evolved a huge variety of anti-phage defense systems allowing them to resist phage lysis to a greater or lesser extent, and in pathogenic bacteria these inevitably impact phage therapy outcomes. In addition to dedicated phage defense systems, some aspects of the general stress response also impact phage susceptibility, but the details of this are not well known. In order to elucidate these factors in the opportunistic pathogen Pseudomonas aeruginosa, we used the laboratory-conditioned strain PAO1 as host for phage infection experiments as it is naturally poor in dedicated phage defense systems. Screening by transposon insertion sequencing indicated that the uncharacterized operon PA3040-PA3042 was potentially associated with resistance to lytic phages. However, we found that its primary role appeared to be in regulating biofilm formation. Its expression was highly growth-phase dependent and responsive to phage infection and cell envelope stress.

overall_design: We generated a Pseudomonas aeruginosa transposon sequencing library and challenged with 4 different bacteriophages to identify genes involved in survival against phage attack. Samples correspond to transposon libraries treated with 1 of 4 phages or control in biological triplicates.

middle: Z

first: Clare

middle: L

last: Kirkpatrick


title: A map of signaling responses in human airway epithelium II

status: Public on Oct 27 2023

first: Kalki

last: Kukreja

overall_design: Human bronchial epithelial cells (hBECs) were cultured at air-liquid interface (ALI) without treatment to drive differentiation into a pseudo-stratified epithelium that recapitulates the physiological cell types of the airway, after which the luminal cells were stripped through calcium depletion, leaving the remaining basal cells to regenerate the tissue. This was done in the presence of a signaling agonist for OSM or IFNG added to each well at a dosage 10- to 100-fold greater than the IC50. One condition was kept as a control. After 2 weeks of differentiation, the final composition of the tissue was analyzed by scRNA-Seq and imaging. Three donors were included in the study and were pooled and sequenced together.

first: Katherine

last: Mccauley

first: Aron

last: Jaffe

first: Allon

last: Klein


title: A map of signaling responses in human airway epithelium

status: Public on Oct 26 2023

overall_design: Human bronchial epithelial cells were cultured at air-liquid interface (ALI) without treatment to drive differentiation into a pseudo- stratified epithelium that recapitulates the physiological cell types of the airway. The differentiated luminal cells were then stripped through calcium depletion, leaving the remaining basal cells to regenerate the tissue. This was done in the presence of a signaling agonist added to each well at a dosage 10- to 100-fold greater than the IC50. One condition was kept unperturbed for control. After 2 weeks of differentiation, the final composition of the tissue was analyzed by scRNA-Seq and imaging. Cells were run in two separate experiments: donor #429581 was collected individually; donors #221175 and #323353 were pooled and captured simultaneously, except for one condition (ActA) for which we only collected donor #323353. We call these two experiments as ali12 and ali13 respectively in the metadata files.


title: Bulk RNA-Seq analysis of TCF1 Reporter eGFP+ and TCF1 Reporter eGFP- CD8+ T cells generated with different metabolic manipulations and isolated from in vitro co-culture with HKP1-ova-GFP mouse lung adenocarcinoma cells

status: Public on Oct 19 2023

city: New York

first: Vivek

last: Mittal

address: 525 East 68th Street, W412

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine

summary: To investigate how metabolic manipulation alters differentiation and the transcriptional landscape in tumor-specific CD8+ T cells, we isolated OT-I+ CD8+ T cells from spleens of transgenic OT-I+ Tcf7GFP+ mice expressing a TCF1 eGFP Reporter, and activated them for one day on plates coated with 2μg/ml of both anti-CD3 and anti-CD28 in the presence of 50U/mL mouse IL-2. We then treated them with equal volumes of DMSO vehicle control, 3μM glucose 6-phosphate dehydrogenase agonist AG1, 25μM glucose 6-phosphate dehydrogenase inhibitor G6PDi-1, or 2mM hexokinase inhibitor 2-DG, and expanded them for 1 more day on anti-CD3/anti-CD28 coated plates in the presence of 50U/mL mouse IL-2. We subsequently co-cultured these cells with HKP1-ova-GFP tumor cells at a 5:1 T cell:tumor cell ratio for an additional 4 days with continuing drug treatment in the presence of 50U/mL mouse IL-2, passing cultures every other day. At day 6 post-initial-stimulation, CD8+ T cells were harvested, filtered by passing through a 70uM cell strainer, washed, and stained for CD8β and Thy1.2. Samples were dyed with DAPI at 0.2μg/mL, and sorted on a Becton-Dickinson FACS Aria II sorter for DAPI- CD8β + Thy1.2+ eGFP+ or DAPI- CD8β + Thy1.2+ eGFP- cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of sorted cells, comparing across treatment groups and TCF1 eGFP Reporter expression.

overall_design: Comparative gene expression profiling of biological replicates of OT-I+ TCF1 Reporter eGFP+ and OT-I+ TCF1 Reporter eGFP- CD8+ T cells isolated from in vitro co-culture with HKP1-ova-GFP mouse lung adenocarcinoma cells in the presence of different metabolism-altering drugs (DMSO, AG1, G6PDi-1, 2-DG) at 6 days post-initial-stimulation. Grouped by treatment and TCF1 eGFP Reporter expression. DMSO eGFP+ [n=2]; DMSO eGFP- [n=2]; AG1 eGFP+ [n=2]; AG1 eGFP- [n=2]; G6PDi-1 eGFP+ [n=2]; G6PDi-1 eGFP- [n=2]; 2-DG eGFP+ [n=2].

first: Geoffrey

last: Markowitz


title: Bulk RNA-Seq analysis of CD8+ T cells from treatment-naïve matched tumor-bearing lungs and spleens from the HKP1 orthotopic mouse lung adenocarcinoma model

summary: To investigate how gene expression profiles change in CD8+ T cells based on time, tumor burden, and tissue localization, we orthotopically implanted the mouse lung adenocarcinoma HKP1 cell line expressing luciferase into syngeneic C57BL/6 mice by tail vein injections. Tumor growth was monitored by bioluminescence imaging. A separate cohort of mice received no tumor implantation. At days 7, 17, and 24 post tumor implantation, mice were euthanized and CD8+ T cells sorted from tumor-bearing lungs and spleens, or matched naive lungs and spleens. We then performed gene expression profiling analysis using data obtained from RNA-seq of sorted cells, comparing across time, tumor burden, and tissue localization.

overall_design: Comparative gene expression profiling of CD8+ T cells isolated from naïve lungs, naïve spleens, tumor-bearing lungs, or spleens of tumor-bearing mice, grouped by time post-tumor implantation (naïve [n=3], day 7 [n=6], day 17 [n=6], and day 24 [n=5]) and tumor burden (naïve [n=3], day 7 [n=6], low [n=6], high [n=5]).


title: MYC oncogene reprograms the local tissue microenvironment during prostate carcinogenesis

status: Public on Oct 16 2023

city: Chicago

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

summary: To investigate the casual sequelae of MYC activation in the prostate tumor microenvironment (TME), we modeled MYC activation in the prostate TME using the transgenic Hi-Myc mouse model of prostate cancer.

overall_design: We carried out scRNA-seq from each prostate lobe (anterior, dorsal, lateral, and ventral) of the MYC-driven mouse model of prostate cancer (Hi-MYC) in 6 month old mice in both FVB/NJ (N = 2) and C57BL/6J (N =2) mouse strains, as well as age-matched wild type animals (FVB/NJ N =2, C57BL/6J N = 3). Additionally we performed scRNA-seq analysis in the dorsal and lateral lobes of 10 month (+/- 6 weeks) old mice FVB/NJ Hi-Myc mice (N = 2) and age matched WT dorsal and lateral lobes (N = 2).

middle: K

first: Rulin

last: Wang

first: Srinivasan

last: Yegnasubramanian


title: Discovery and characterization of the first known biological lanthanide chelator

city: Berkeley

first: Norma

middle: Cecilia

last: Martinez-Gomez

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary: Many bacteria secrete metallophores, low-molecular weight organic compounds that bind ions with high selectivity and affinity, in order to access essential metals from the environment. The biosynthetic machinery to produce metallophores as well as their structures have been elucidated for iron, zinc, nickel, molybdenum, and copper specific molecules. No lanthanide-specific metallophore has been discovered despite the knowledge that lanthanide metals (Ln) have recently been revealed to be essential cofactors for certain alcohol dehydrogenases across a diverse range of phyla. Here, we report the biosynthetic machinery for, the structure of, and the physiological relevance of the first known lanthanophore, methylolanthanin. The structure of methylolanthanin exhibits a unique 4-hydroxybenzoate moiety which has not previously been described in other metallophores. We find that production of methylolanthanin is required for normal levels of Ln accumulation in the methylotrophic bacterium Methylobacterium extorquens AM1, while overexpression of the molecule greatly increases bioaccumulation. Our results provide a clearer understanding of how Ln-utilizing bacteria sense, scavenge, and store Ln; essential processes in the environment where Ln are poorly bioavailable. Beyond Ln, we anticipate our study to be a starting point for understanding how organisms acquire other f-block metals, the actinides. More broadly, the discovery of a lanthanophore opens doors for study of how biosynthetic gene clusters are repurposed for new functions, how metallophores acquire their metal specificity, and the complex relationship between metal homeostasis and fitness.

overall_design: To better understand the impacts of Ln solubility on methylotrophy in M. extorquens AM1, we assessed the growth and transcriptomic changes of a mutant lacking the lanthanide-dependent methanol dehydrogenase MxaFI (dmxaF) when grown with methanol and either soluble NdCl3 or poorly soluble Nd2O3. Gene expression profiling analysis was perfomed on two strains (WT, mxaF) with data from RNA-seq of each condition (NdCl3 or Nd2O3) with three biological replicates per condition, with the WT strain serving as a reference.

first: Alexa

last: Zytnick

first: Sophie

last: Gutenthaler-Tietze

first: Allegra

middle: T

last: Aron

first: Zachary

last: Reitz

first: Manh

last: Phi

first: Nathan

last: Good

first: Lena

last: Daumann

middle: C


title: Single-cell transcriptome profiling of mouse cardio-pharyngeal development under maternal diabetes mellitus

city: San Francisco

first: Tomohiro

last: Nishino

state: California

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

summary: We employed single cell RNA sequencing to interrogate the consequence of maternal diabetes in cardiac and craniopharyngeal development

overall_design: Examination of single cell RNA sequnecing from craniopharyngeal and cardiac cells captured at E10.5 fetues from vehicle pre-treated or streptozoticine pre-treated females.  At least 3 biological replicate embryos were analyzed per genotype.

first: Angelo

last: Pelonero

first: Deepak

last: Srivastava


title: Single-cell profiling of mouse cardio-pharyngeal development under maternal diabetes mellitus

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

overall_design: Refer to individual Series