Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA310101 | ENA |
REPOSITORIES: ENA
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Project description:Background: Resistance to trastuzumab remains a common challenge to HER-2 positive breast cancer. Up until now, the underlying mechanism of trastuzumab resistance is still unclear. tRNA-derived small non-coding RNAs (tDRs), a new class of small non-coding RNA (sncRNAs), have been observed to play an important role in cancer progression. However, the relationship between tDRs and trastuzumab resistance is still unknown. Methods: We detected the levels of tDRs expression in normal breast epithelial cell lines, trastuzumab-sensitive and -resistant breast cancer cell lines using high-throughput sequencing. qRT-PCR was conducted to validate the differentially expressed tDRs in serums from trastuzumab-sensitive and -resistant patients. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the power of specific tDRs. Progression-free survival (PFS) was analyzed using Cox-regression. Furthermore, Gene Ontology (GO) and pathway analyses indicated the potential mechanism underlying tDR-mediated trastuzumab resistance. Results: Our sequence results showed that tDRs were differentially expressed in the HBL-100, SKBR3, and JIMT-1 cell lines. tDR-1960 and tDR-1969 were found significantly upregulated in trastuzumab-resistant patients compared to sensitive individuals, and the ROC analysis showed that tDR-1960 and tDR-1969 were correlated with trastuzumab resistance. In a multivariate analysis, higher levels of tDR-1960 and tDR-1969 expression were associated with significantly shorter PFS in patients with metastatic HER-2 positive breast cancer. Additionally, the GO analysis indicated that tDR-1960 and tDR-1969 were mainly involved in the cellular response to drug, which may partially explain the molecular mechanism underlying trastuzumab resistance in HER-2 positive breast cancer. Conclusion: we comprehensively analyzed tDRs in trastuzumab-sensitive and -resistant breast cancer. Our results suggest that tDR-1960 and tDR-1969 play important roles in trastuzumab resistance. Patients with high levels of tDR-1960 and tDR-1969 expression benefitted less from trastuzumab-based therapy than those that express lower-levels of these tDRs. tDR-1960 and tDR-1969 may be potential biomarkers and intervention targets in the clinical treatment of trastuzumab-resistant breast cancer.
2018-06-30 | GSE107473 | GEO
Project description:Purpose: The goal of our study is to identify the differentially expressed genes between cispaltin sensitive and cisplatin resistance gastric cancer cell line. Methods: Transcriptome sequencing of cisplatin sensitive and cisplatin resistance KATOIII cells were generated by Illumina HiSeq TM, for triplicates Results : Using an optimized data analyzed workflow, we mapped 57773 genes and were found 5966 differentially expressed genes between cisplatin sensitive KATOIII and cisplatin resistance KATO/DDP cell lines.
2021-10-22 | GSE186205 | GEO
Project description:The intention was to detect genes that are determining trastuzumab efficiency in HER2-positive breast cancer cell lines with different resistance phenotypes. While BT474 should be sensitive to the drug treatment, HCC1954 is expected to be resistant due to a PI3K mutation. The cell line BTR50 has been derived from BT474 and was cultured to be resistant as well. Based on RNA-Seq data, we performed differential expression analyses on these breast cancer cell lines with and without trastuzumab treatment. In detail, five separate tests were performed, namely resistant cells vs. wild type, i.e. HCC1954 and BTR50 vs. BT474, respectively, and untreated vs. drug treated cells. The significant genes of the first two tests should contribute to resistance. The significant genes of the test BT474 vs. its drug treated version should contribute to the trastuzumab effect. To exclude false positives from the combined gene set (#64), we removed ten genes that were also significant in the test BTR50 vs. its drug treated version. This way we ended up with 54 genes that are very likely to determine trastuzumab efficiency in HER2-positive breast cancer cell lines. mRNA profiles of human breast cancer cell lines were generated by deep sequencing using Illumina HiSeq 2000. The cell lines BT474 and HCC1954 were analyzed with and without trastuzumab treatment. HCC1954 is known to be trastuzumab resistant. Additionally, the cell line BTR50 was generated as resistant version of BT474, and was analyzed with and without trastuzumab as well.
2015-04-21 | E-GEOD-55005 | biostudies-arrayexpress
Project description:The clinical performance of trastuzumab in the treatment of ErbB2-positive gastric cancer is severely hampered by the emergence of molecular resistance. The glycosylation landscape of ErbB2’s extracellular domain, and the molecular mechanisms through which it tunes gastric cell malignancy, including the acquisition of trastuzumab resistance, remain elusive. We show that the expression of ErbB2 sialylated glycoforms holds clinical utility in the prediction of clinical outcome and stratification of gastric cancer patients. In-depth glycoproteomic and glycomic analysis of ErbB2 extracellular region disclosed a site-specific profile in gastric cancer cells. We further demonstrate that ST6Gal1 sialyltransferase specifically targets ErbB2 N-glycosylation sites within the trastuzumab binding domain. Moreover, the abrogation of ST6Gal1-mediated α2,6-sialylation reshapes ErbB2 glycome and sensitizes gastric cancer cells to trastuzumab-induced cytotoxicity through receptor membrane stabilization and a downregulation of ErbB2 activation. Overall, this data demonstrates that aberrant sialylation tunes the molecular resistance of ErbB2-driven gastric cancer cells to trastuzumab.
2021-05-11 | PXD017609 | Pride
Project description:Differentially expressed genes in normal gastric mucosa and gastric cancer tissues
| PRJNA487176 | ENA
Project description:Our novel drug imaging technique revealed that trastuzumab, which is representative antibody drug for breast and gastric cancer in clinical, distributed heterogeneously inside tumor even though its target receptor, HER2 (Human epidermal growth factor receptor 2) expressed homogeneously. For identifying a predominant regulator of trastuzumab tumor delivery in the tumor site, we tried tumor region-specific microarray analysis according to trastuzumab distribution in patient derived xenograft model.
2019-11-01 | GSE121787 | GEO
Project description:Differentially Expressed Genes between Drought-tolerant and Drought-sensitive Barley Genotypes
| PRJNA115549 | ENA
Project description:We established an acquired trastuzumab-resistant model in vitro from a trastuzumab-sensitive, HER2-amplified breast-cancer cell line. A multi-omic strategy was implemented to obtain gene, proteome, and phosphoproteome signatures associated with acquired resistance to trastuzumab in HER2-positive breast cancer, followed by validation in human clinical samples.
2020-06-01 | PXD010574 | Pride
Project description:We compared gene expression profiles in trastuzumab-sensitive NCI-N87 cell line versus four trastuzumab-resistant cell lines (N87-TR1, N87-TR2, N87-TR3, N87-TR4) by microarray analysis in order to identify groups of genes associated with a specific signaling pathway or biological process.
2017-02-13 | GSE77346 | GEO
Project description:Differentially Expressed Genes between Drought-tolerant and Drought-sensitive Barley Genotypes
2015-12-02 | E-GEOD-15970 | ExpressionAtlas