Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31278500_1.fastq.gz | Fastqsanger.gz | |||
| SRR31278500_2.fastq.gz | Fastqsanger.gz | |||
| SRR31278498_1.fastq.gz | Fastqsanger.gz | |||
| SRR31278498_2.fastq.gz | Fastqsanger.gz | |||
| SRR31278499_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Immune checkpoint blockade therapy has been successfully applied in clinical settings as a standard therapy for many cancer types, but its clinical efficacy is restricted to patients with immunologically hot tumors. Various strategies to modify the tumor microenvironment (TME), such as Toll-like receptor (TLR) agonists, have been explored but have not been successful. Here, we identified a mechanism of acquired resistance to combination treatment consisting of an agonist for multiple TLRs, OK-432 (Picibanil), and PD-1 blockade. Adding the TLR agonist failed to convert the TME from immunogenically cold to hot. The combination treatment did not augment antitumor immunity, particularly CD8+ T cell responses, in multiple animal models. The failure was attributed to the coactivation of innate suppressive cells, such as CD11b+ Gr1+ Ly6C- Ly6G+ myeloid-derived suppressor cells (MDSCs) expressing CXCR2, through high CXCL1 production by macrophages in the TME upon OK-432 treatment. Thus, a triple combination treatment with OK-432, PD-1 blockade, and a CXCR2 neutralizing antibody overcame the resistance induced by MDSCs, resulting in a far stronger antitumor effect than that of any dual combination or single treatment. The accumulation of MDSCs was similarly observed in the pleural effusion of lung cancer patients after OK-432 administration. We propose that successful combination cancer immunotherapy stimulating innate immunity against immunologically cold tumors requires modulation of unwanted activation of innate immune suppressive cells, including MDSCs.
2025-01-15 | GSE281467 | GEO
Project description:Immune checkpoint blockade therapy has been successfully applied in clinical settings as a standard therapy for many cancer types, but its clinical efficacy is restricted to patients with immunologically hot tumors. Various strategies to modify the tumor microenvironment (TME), such as Toll-like receptor (TLR) agonists, have been explored but have not been successful. Here, we identified a mechanism of acquired resistance to combination treatment consisting of an agonist for multiple TLRs, OK-432 (Picibanil), and PD-1 blockade. Adding the TLR agonist failed to convert the TME from immunogenically cold to hot. The combination treatment did not augment antitumor immunity, particularly CD8+ T cell responses, in multiple animal models. The failure was attributed to the coactivation of innate suppressive cells, such as CD11b+ Gr1+ Ly6C- Ly6G+ myeloid-derived suppressor cells (MDSCs) expressing CXCR2, through high CXCL1 production by macrophages in the TME upon OK-432 treatment. Thus, a triple combination treatment with OK-432, PD-1 blockade, and a CXCR2 neutralizing antibody overcame the resistance induced by MDSCs, resulting in a far stronger antitumor effect than that of any dual combination or single treatment. The accumulation of MDSCs was similarly observed in the pleural effusion of lung cancer patients after OK-432 administration. We propose that successful combination cancer immunotherapy stimulating innate immunity against immunologically cold tumors requires modulation of unwanted activation of innate immune suppressive cells, including MDSCs.
2025-01-15 | GSE281466 | GEO
Project description:Contact lens-related ocular surface complications occur more often in teenagers and young adults. The purpose of this study was to determine changes in tear proteome of young patients wearing glasses (GL), orthokeratology lenses (OK), and soft contact lenses (SCL). Twenty-two young patients (10-26 years of age) who were established (> 3 years) GL (n=10), OK (n=6), and SCL (n=6) wearers were recruited. Tears were collected via Schirmer strips. Proteomic data were collected using a data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) workflow. Tear proteome composition and abundance were compared across different correction groups and between the children (age <18 years) and young adults (age 18 years) GL wearers. We identified 3406 protein groups in tears. Among proteins identified in 80% of tear samples, 8 proteins were upregulated, and 11 proteins were down-regulated in the SCL group compared to the OK group. Eighty-two proteins were differentially expressed in children and young adults GL wearers, among which 67 proteins were upregulated, and 15 proteins were downregulated in children. These 82 proteins were involved in 1 inflammation, 9 immune, and 1 glycoprotein metabolic biological processes. As teenagers and young adults have the highest risk of developing contact lens-related complications, this work highlights the importance of understanding ocular responses to contact lens wear across different ages.
2022-11-07 | PXD029188 | Pride
Project description:We present a tool for processing NGS DNA-seq BAM files to quantify peaks and create coverage tracks from ChIP-seq, NS-seq, ATAC-seq, OK-seq, END-seq and replication timing data
2020-05-17 | GSE131417 | GEO
Project description:The OK cell line derived from kidney of a female opossum Didelphys virginiana has proven to be a useful model in which to investigate the unique regulation of ion transport and membrane trafficking mechanisms in the proximal tubule (PT). Sequence data and comparison of the transcriptome of this cell line to eutherian mammal PTs would further broaden the utility of this culture model. However, genomic sequence for Didelphys virginiana is not available and although a draft genome sequence for the opossum Monodelphis domestica (sequenced in 2012 by the Broad Institute) exists, its relatedness and similarity of the transcriptome to the Didelphys virginiana species is not known. The Monodelphis domestica sequence is not highly annotated, and the majority of transcripts are predicted rather than experimentally validated. Using deep RNA sequencing of the Didelphys virginiana OK cell line we characterized its transcriptome using de novo transcriptome assembly and alignment to the Monodelphis domestica genome. The quality of the de novo assembled transcriptome was assessed by the extent of homology to sequences in nucleotide and protein databases. Gene expression levels in the OK cell line, from both the de novo transcriptome and genes aligned to the Monodelphis domestica genome, were compared to publicly available rat kidney nephron segment expression data. Our studies demonstrate the expression in OK cells of numerous PT specific ion transporters and other key proteins relevant for rodent and human PT function. The sequence and expression data reported here provide a new and important resource for studies on the regulation of PT mRNA and protein expression.
2017-08-07 | GSE94443 | GEO
Project description:During each cell division, tens of thousands of DNA replication origins are coordinately activated to ensure the complete duplication of the entire human genome. However, the progression of replication forks can be challenged by numerous factors. One such factor is transcription-replication conflict (TRC), which can either be co-directional or head-on and the latter has been revealed as more dangerous for genome integrity. In order to study the direction of replication fork movement and TRC, we developed a bioinformatics tool, called OKseqHMM, to direct measure the replication fork directionality (RFD) as well as replication initiation and termination, along human genome obtained by sequencing of Okazaki fragments (OK-Seq) and related techniques. We have gathered and analyzed OK-seq data from a large number of organisms including yeast, mouse and human, to generate high-quality RFD profiles and determine initiation zones and termination zones by using Hidden Markov Model (HMM) algorithm (all tools and data are available at https://github.com/CL-CHEN-Lab/OK-Seq). In addition, we have extended our analysis to data obtained by related techniques, such as eSPAN and TrAEL-seq, which also contain RFD information. Our works, therefore, provide an important tool and resource for the community to further study TRC and genome instability, in a wide range of cell line models and growth conditions, which is of prime importance for human health.
2022-12-31 | GSE193547 | GEO
Project description:We previously demonstrated that OK cells cultured under orbital shear stress have morphological and functional features that more closely resemble the proximal tubule in vivo. This study was designed to identify progressive transcriptional changes with increasing exposure time to shear stress and to compare the transcriptome of cells cultured under shear stress vs static conditions.
2020-09-29 | GSE155315 | GEO