Modeling Basins of Attraction for Breast Cancer Using Hopfield Networks

In this report, Hopfield network modeling was used to analyze bulk RNA-Seq data of paired breast tumor and control samples from 70 patients. We characterized the control and tumor attractors with respect to their size and potential energy and correlated the Euclidean distances between the tumor samples and the control attractor with their corresponding clinical data. In addition, we developed a protocol that outlines the key genes involved in tumor state stability. We found that the tumor basin of attraction is larger than that of the control and that tumor samples are associated with a more substantial negative energy than control samples, which is in agreement with previous reports. Moreover, we found a negative correlation between the Euclidean distances from tumor samples to the control attractor and patient overall survival. The ascending order of each node's density in the weight matrix and the descending order of the number of patients that have the target active only in the tumor sample were the parameters that withdrew more tumor samples from the tumor basin of attraction with fewer gene inhibitions. The combinations of therapeutic targets were specific to each patient. We performed an initial validation through simulation of trastuzumab treatment effects in HER2+ breast cancer samples. For that, we built an energy landscape composed of single-cell and bulk RNA-Seq data from trastuzumab-treated and non-treated HER2+ samples. The trajectory from the non-treated bulk s...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research

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Publication date: June 2020Source: European Journal of Surgical Oncology, Volume 46, Issue 6Author(s): Amber Shivarajan, Hiba Fatayer, Nicholas Hobbs, Sami Titi, Nabila Nasir
Source: European Journal of Surgical Oncology (EJSO) - Category: Surgery Source Type: research
In HER2-positive breast cancer patients with brain metastases treated with trastuzumab and capecitabine, tucatinib increased median overall survival from 12 months to 18.1 months in a phase 2 trial.Medscape Medical News
Source: Medscape Hematology-Oncology Headlines - Category: Cancer & Oncology Tags: Hematology-Oncology News Source Type: news
Contributors : Liu Yuan ; Zhu ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensA large-panel gene expression analysis was conducted to identify biomarkers associated with the effectiveness of adding palbociclib to letrozoleCyclin-dependent kinase 4/6 (CDK4/6) inhibitors have demonstrated significant activity in estrogen receptor-positive/human epidermal growth factor receptor 2-negative (ER+/HER2-) advanced breast cancer. Further biomarkers to refine the population beyond ER+/HER2- that benefits remain to be identified. We performed a comprehensive biomarker analysis using patient ...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
Condition:   Metastatic Breast Cancer Intervention:   Drug: Pyrotinib Maleate plus Letrozole Sponsors:   Hunan Cancer Hospital;   Jiangsu HengRui Medicine Co., Ltd. Recruiting
Source: ClinicalTrials.gov - Category: Research Source Type: clinical trials
British Journal of Cancer, Published online: 29 May 2020; doi:10.1038/s41416-020-0908-5Correction: Treatment patterns and survival in HER2-positive early breast cancer: a whole-of-population Australian cohort study (2007–2016)
Source: British Journal of Cancer - Category: Cancer & Oncology Authors: Source Type: research
In this study, we aimed to identify novel lncRNAs that might play critical roles in doxorubicn resistance, which could reveal potential biomarkers of BC. Using a BC dataset (GSE81971), we identified 452 lncRNAs that were upregulated and 659 that were downregulated; furthermore, there were 1896 differentially expressed mRNAs, of which 1137 were upregulated and 758 were downregulated in MCF-7/ADR cells compared with the expression in MCF-7 cells. We constructed an lncRNA–mRNA network by integrating probe reannotation and regulatory interactions. To elucidate the key lncRNAs in BC, we further analyzed dysregulated lncRN...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research
CONCLUSION: The ppStage reflects the prognosis of patients with early breast cancer more accurately than the aStage. PMID: 32472474 [PubMed - as supplied by publisher]
Source: Breast Cancer - Category: Cancer & Oncology Authors: Tags: Breast Cancer Source Type: research
CONCLUSION: Our findings of overexpression of LAT1 in negative HER2 group suggest a role of this protein as prognosticator and drug target in a challenging therapeutic cohort.. PMID: 32458655 [PubMed - in process]
Source: Asian Pacific Journal of Cancer Prevention - Category: Cancer & Oncology Tags: Asian Pac J Cancer Prev Source Type: research
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Source: Asian Pacific Journal of Cancer Prevention - Category: Cancer & Oncology Tags: Asian Pac J Cancer Prev Source Type: research
In conclusion, preoperatively diagnosed non-mass-type DCIS represented an underestimation in approximately 27% of cases. In particular, the presence of a clinically abnormal palpation increases the chance of upstaging to invasive cancer. PMID: 32454975 [PubMed]
Source: Clinical Breast Cancer - Category: Cancer & Oncology Authors: Tags: Mol Clin Oncol Source Type: research
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