Computational prognostic indicators for breast cancer.
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ABSTRACT:
SUBMITTER: Yang X
PROVIDER: S-EPMC4103923 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
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Project description:Despite the fact that breast cancer was detected in the early stages, the prognosis was not always favorable. In this paper, we examined the impact of clinical and pathological characteristics of patients and the composition of saliva before treatment on overall survival and the risk of recurrence of primary resectable breast cancer. The study included 355 patients of the Omsk Clinical Oncology Center with a diagnosis of primary resectable breast cancer (T1-3N0-1M0). Saliva was analyzed for 42 biochemical indicators before the start of treatment. We have identified two biochemical indicators of saliva that can act as prognostic markers: alkaline phosphatase (ALP) and diene conjugates (DC). Favorable prognostic factors were ALP activity above 71.7 U/L and DC level above 3.93 c.u. Additional accounting for aspartate aminotransferase (AST) activity allows for forming a group with a favorable prognosis, for which the relative risk is reduced by more than 11 times (HR = 11.49, 95% CI 1.43-88.99, p = 0.01591). Salivary AST activity has no independent prognostic value. Multivariate analysis showed that tumor size, lymph nodes metastasis status, malignancy grade, tumor HER2 status, and salivary ALP activity were independent predictors. It was shown that the risk of recurrence decreased with menopause and increased with an increase in the size of the primary tumor and lymph node involvement. Significant risk factors for recurrence were salivary ALP activity below 71.7 U/L and DC levels below 3.93 c.u. before treatment. Thus, the assessment of biochemical indicators of saliva before treatment can provide prognostic information comparable in importance to the clinicopathological characteristics of the tumor and can be used to identify a risk group for recurrence in primary resectable breast cancer.
| S-EPMC9227854 | biostudies-literature
Project description:Breast cancer represents a heterogeneous condition in which the interaction between host immune response and primary oncogenic events can impact disease progression. Ratios of systemic blood-based immunocytes have emerged as clinically-relevant prognostic biomarkers in cancer patients. The NLR (neutrophil-to-lymphocyte ratio) has been shown to be prognostic in a variety of cancers, including breast cancer. However, evaluation of the prognostic value for overall survival (OS) and disease-free survival (DFS) of other key immunocyte ratios-neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), neutrophil-to-white cell count ratio (NWR), lymphocyte-to-white cell count ratio (LWR), monocyte-to-white cell count ratio (MWR), platelet-to-lymphocyte (PLR)-by breast cancer subtypes in a neoadjuvant chemotherapy (NAC) cohort remains to be fully explored. An NAC-treated breast cancer cohort, comprised of Luminal A, Luminal B, HER2-positive, and triple negative/basal breast cancers, treated at a tertiary referral center (minimum 3-year follow-up), was used to calculate immunocyte ratios and immunocyte cut-off values, calculated with >80% specificity (using decision tree modeling). The association with subtype-specific OS, DFS, and tumor grade was analyzed using cut offs calculated using both receiver operating characteristic curves and decision tree modelling. Decision tree calculated ratios showed that LMR (5.29) and MWR (0.06) were significantly associated with Luminal A OS (p = 0.004 and p = 0.022) and DFS (p = 0.004 and p = 0.022), and Luminal B OS (p = 0.027 and p = 0.008) and DFS (p = 0.005 and p = 0.007). NLR (1.79) and LWR (0.30) were significantly associated with HER2-positive OS (p = 0.013 and p = 0.043). NLR (1.79) and NWR (0.62) were significantly associated with DFS (p = 0.035 and p = 0.021). No significant association we observed between any immunocyte ratio in the triple negative cohort. Our results demonstrate the subtype-specific prognostic value of immunocyte ratios in NAC-treated breast cancer patients. Further validation of immunocyte ratios will provide clinicians with a new prognostic aid for disease management and monitoring.
| S-EPMC9600104 | biostudies-literature
Project description: Not available
| S-EPMC9547711 | biostudies-literature
Project description:Minichromosome maintenance protein 2 (MCM2) is a highly conserved protein from the MCM protein family that plays an important role in eukaryotic DNA replication as well as in cell cycle progression. In addition, it maintains the ploidy level consistency in eukaryotic cells, hence, mutations or alteration of this protein could result in the disintegration of the fine-tuned molecular machinery that can lead to uncontrolled cell proliferation. Moreover, MCM2 has been found to be an important marker for progression and prognosis in different cancers. Therefore, we aimed to analyze the MCM2 expression and the associated outcome in breast cancer (BC) patients based on the publicly available online databases. In this study, server-based gene expression analyses indicate the upregulation of MCM2 (p < 10-6; fold change>2.0) in various BC subtypes as compared to the respective normal tissues. Besides, the evaluation of histological sections from healthy and cancer tissues showed strong staining signals indicating higher expression of MCM2 protein. The overexpression of MCM2 was significantly correlated to promoter methylation and was related to patients' clinical features. Further, mutation analysis suggested missense as the predominant type of mutation (71.4%) with 18 copy-number alterations and 0.2% mutation frequency in the MCM2 gene. This study revealed a significant correlation (Cox p ≤ 0.05) between the higher MCM2 expression and lower patient survival. Finally, we identified the co-expressed genes with gene ontological features and signaling pathways associated in BC development. We believe that this study will provide a basis for MCM2 to be a significant biomarker for human BC prognosis.
| S-EPMC7530310 | biostudies-literature
Project description:Triple negative breast cancers (TNBCs) are highly heterogeneous and aggressive without targeted treatment. Here, we aim to systematically dissect TNBCs from a prognosis point of view by building a subnetwork atlas for TNBC prognosis through integrating multi-dimensional cancer genomics data from The Cancer Genome Atlas (TCGA) project and the interactome data from three different interaction networks. The subnetworks are represented as the protein-protein interaction modules perturbed by multiple genetic and epigenetic interacting mechanisms contributing to patient survival. Predictive power of these subnetwork-derived prognostic models is evaluated using Monte Carlo cross-validation and the concordance index (C-index). We uncover subnetwork biomarkers of low oncogenic GTPase activity, low ubiquitin/proteasome degradation, effective protection from oxidative damage, and tightly immune response are linked to better prognosis. Such a systematic approach to integrate massive amount of cancer genomics data into clinical practice for TNBC prognosis can effectively dissect the molecular mechanisms underlying TNBC patient outcomes and provide potential opportunities to optimize treatment and develop therapeutics.
| S-EPMC5342106 | biostudies-literature
Project description:PurposeThe purpose of this study was to investigate if human-extracted MRI tumor phenotypes of breast cancer could predict receptor status and tumor molecular subtype using MRIs from The Cancer Genome Atlas project.Materials and methodsOur retrospective interpretation study utilized the analysis of HIPAA-compliant breast MRI data from The Cancer Imaging Archive. One hundred and seven preoperative breast MRIs of biopsy proven invasive breast cancers were analyzed by 3 fellowship-trained breast-imaging radiologists. Each study was scored according to the Breast Imaging Reporting and Data System lexicon for mass and nonmass features. The Spearman rank correlation was used for association analysis of continuous variables; the Kruskal-Wallis test was used for associating continuous outcomes with categorical variables. The Fisher-exact test was used to assess correlations between categorical image-derived features and receptor status. Prediction of estrogen receptor (ER), progesterone receptor, human epidermal growth factor receptor, and molecular subtype were performed using random forest classifiers.ResultsER+ tumors were associated with the absence of rim enhancement (P = 0.019, odds ratio [OR] 5.5), heterogeneous internal enhancement (P = 0.02, OR 6.5), peritumoral edema (P = 0.0001, OR 10.0), and axillary adenopathy (P = 0.04, OR 4.4). ER+ tumors were smaller than ER- tumors (23.7 mm vs 29.2 mm, P = 0.02, OR 8.2). All of these variables except the lack of axillary adenopathy were also associated with progesterone receptor+ status. Luminal A tumors (n = 57) were smaller compared to nonLuminal A (21.8 mm vs 27.5 mm, P = 0.035, OR 7.3) and lacked peritumoral edema (P = 0.001, OR 6.8). Basal like tumors were associated with heterogeneous internal enhancement (P = 0.05, OR 10.1), rim enhancement (P = 0.05, OR6.9), and perituomral edema (P = 0.0001, OR 13.8).ConclusionsHuman extracted MRI tumor phenotypes may be able to differentiate those tumors with a more favorable clinical prognosis from their more aggressive counterparts.
| S-EPMC6387644 | biostudies-literature
Project description:Background. The diagnosis, treatment, and long-term management of cancer can present individuals with a multitude of stressors at various points in that trajectory. Psychosocial distress may appear early in the diagnostic process and have negative effects on compliance with treatment and subsequent quality of life. Purpose. The aim of the study was to determine early-phase predictors of distress before any medical treatment. Method. Consistent with the goals of the study, 123 newly diagnosed breast cancer patients (20 to 74 years old) completed multiple indicators of knowledge about breast cancer management and treatment, attitudes toward cancer, social support, coping efficacy, and distress. Results. SEM analysis confirmed the hypothesized model. Age was negatively associated with the patient's knowledge (β = - 0.22), which, in turn, was positively associated with both attitudes toward breast cancer (β = 0.39) and coping self-efficacy (β = 0.36). Self-efficacy was then directly related to psychological distress (β = - 0.68). Conclusions. These findings establish indicators of distress in patients early in the cancer trajectory. From a practical perspective, our results have implications for screening for distress and for the development of early interventions that may be followed by healthcare professionals to reduce psychological distress.
| S-EPMC4517964 | biostudies-literature
Project description:ObjectivesWe evaluated breast cancer (BC) care quality indicators (QIs) in clinical pathways and integrated health care processes.MethodsFollowing protocol registration (Prospero no: CRD42021228867), relevant documents were identified, without language restrictions, through a systematic search of bibliographic databases (EMBASE, Scopus, Web of Science, MEDLINE), health care valuable representatives and the World Wide Web in April 2021. Data concerning QIs, measurement tools and compliance standards were extracted from European and North American sources in duplicate with 98% reviewer agreement.ResultsThere were 89 QIs found from 22 selected documents (QI per document mean 13.5 with standard deviation 11.9). The Belgian (38 QIs) and the EUSOMA (European Society of Breast Cancer Specialists) (34 QIs) documents were the ones that best reported the QIs. No identical QI was identified in all the documents analysed. There were 67/89 QIs covering processes (75.3%) and 11/89 (12.4%) for each structure and outcomes QIs. There were 21/89 QIs for diagnosis (30.3%), 43/89 for treatment (48.3%), and 19/89 for staging, counselling, follow-up and rehabilitation (21.4%). Of 67 process QIs and 11 outcome QIs, 20/78 (26%) did not report a minimum standard of care. Shared decision making was only included as a QI in the Italian document.ConclusionMore than half of countries have not established a national clinical pathway or integrated breast cancer care process to achieve the excellence of BC care. There was heterogeneity in QIs for the evaluation of BC care quality. Over two-thirds of the clinical pathways and integrated health care processes did not provide a minimum auditable standard of care for compliance, leaving open the definition of best practice. There is a need for harmonisation of BC care QIs.
| S-EPMC8322135 | biostudies-literature
Project description:The aim of this study was to determine the impact that age and comorbidity status have on both overall and bladder cancer-specific survival of bladder cancer patients. We obtained medical information pertaining to a population of 528 patients with newly diagnosed bladder cancer from Chung-Ang University Hospital cancer registry. The Adult Comorbidity Evaluation-27 (ACE-27) test, which has been previously validated in adult cancer patients, was used to assess comorbidity. We evaluated differences in the demographic and clinical characteristics of included patients, as well as differences in the treatments they received after categorizing them by age. The median age at the time of bladder cancer diagnosis of the entire cohort was 63 years, and the median follow-up time was 97 months. Of the 528 patients who were included in our study, 303 had at least one comorbid condition and 249 died during the follow-up period. When patients were stratified by age, we found that older patients had a higher proportion of severe comorbidities (P < 0.01) than younger patients, and that a lower proportion of them underwent radical cystectomy for invasive bladder cancer (IBC) (P < 0.01). By multivariate analysis, we found that older age was predictive of lower overall survival (OS) and bladder cancer-specific survival (BCSS) rates among patients with superficial bladder cancer (SBC) and of lower OS rates among patients with IBC. We also found that moderate-severe comorbidity status and treatment through a bladder-conserving approach were predictive of lower OS and cancer-specific survival rates among patients with IBC. The disparity between overall deaths and bladder cancer deaths was shown in SBC and increased along with age and higher comorbidity. Age and comorbidity were found to be independent predictive factors of OS and BCSS among bladder cancer patients, and explained the disparity that we observed between overall bladder cancer-specific mortality rates.
| S-EPMC3739310 | biostudies-other
Project description:There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.
2019-05-06 | PXD013397 | Pride