Performance of a Logistic Regression Model Using Paired miRNAs to Stratify Abnormal Mammograms for Benign Breast Lesions
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE255660 | GEO | 2026/03/01
REPOSITORIES: GEO
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Project description:For successful treatment of breast cancer, early and efficient diagnosis is paramount. However, the diagnosis of breast cancer in the earliest stage, stage 1, is challenging as small tumors are often left undetected by conventional imaging techniques. Additionally, 8 out of 10 breast masses are classified as benign which causes unnecessary psychological stress and increased costs to the medical system. To improve the detection of early-stage breast cancer, development of non-invasive approaches should be explored. Here, we investigated the potential of extracellular vesicles (EVs) to report on a breast cancer diagnosis. EVs contain unique cancer-associated proteins from the parental cell and have the potential to be used for early detection of tumor growth. We isolated EVs from healthy (19), benign (19), and early-stage breast cancer (86) patient plasma samples using size exclusion chromatography. Mass spectrometry analysis identified 94 significantly changed proteins in the plasma EVs from breast cancer patients . Using a cohort of pre- and post-surgery breast cancer patients, we identified enolase 1 as a promising biomarker for breast cancer detection. Enolase 1 was further validated using a larger cohort of healthy and breast cancer patients, by high-throughput ELISA of plasma, and was found to be elevated in breast cancer patient plasma at all stages, including Stage 1. Furthermore, enolase-1 plasma levels decreased post-operatively upon tumor removal. An enolase 1 liquid blood biopsy could be used to support breast cancer screening for the identification of high-risk individuals promoting the diagnosis of breast cancer at the very earliest and treatable stage. Furthermore, plasma-enolase 1 can decipher between individuals with a benign or cancerous mass, it could therefore be used alongside current imaging practices to direct physician decisions to carry out only necessary needle biopsy procedures.
2025-01-31 | MSV000097016 | MassIVE
Project description:BACKGROUND: In patients with suspicious pulmonary lesions, bronchoscopy is frequently non-diagnostic. This often results in additional invasive testing, including surgical biopsy, although many patients have benign disease. We sought to validate an airway gene-expression classifier for lung cancer in patients undergoing diagnostic bronchoscopy. METHODS: Two multicenter prospective studies (AEGIS 1 and 2) enrolled 1357 current or former smokers undergoing bronchoscopy for suspected lung cancer. Bronchial epithelial cells were collected from normal appearing mucosa in the mainstem bronchus during bronchoscopy. Patients without a definitive diagnosis from bronchoscopy were followed for 12 months. A gene-expression classifier was used to assess the risk of lung cancer, and its performance was evaluated. RESULTS: A total of 298 patients from AEGIS 1 and 341 from AEGIS 2 met criteria for analysis. Bronchoscopy was non-diagnostic for cancer in 272 of 639 patients (43%; 95%CI, 39-46%). The gene expression classifier correctly identified 431 of 487 patients with cancer (89% sensitivity; 95%CI, 85-91%), and 72 of 152 patients without cancer (47% specificity; 95%CI, 40-55%). The combination of the classifier and bronchoscopy had a sensitivity of 97% (95%CI, 95-98%), which was independent of size, location, stage, and histological subtype of lung cancer. In patients with an intermediate pre-test risk (10-60%) of lung cancer, the NPV of the classifier was 91% (95%CI 75-98%). CONCLUSIONS: In patients with an intermediate risk of lung cancer and a non-diagnostic bronchoscopy, a gene-expression classification of “low-risk” warrants consideration of a more conservative diagnostic approach that could reduce unnecessary invasive testing in patients with benign disease. 680 CEL files from 639 BEC specimens, 152 benign and 487 malignant samples
2015-05-17 | E-GEOD-66499 | biostudies-arrayexpress
Project description:BACKGROUND: In patients with suspicious pulmonary lesions, bronchoscopy is frequently non-diagnostic. This often results in additional invasive testing, including surgical biopsy, although many patients have benign disease. We sought to validate an airway gene-expression classifier for lung cancer in patients undergoing diagnostic bronchoscopy. METHODS: Two multicenter prospective studies (AEGIS 1 and 2) enrolled 1357 current or former smokers undergoing bronchoscopy for suspected lung cancer. Bronchial epithelial cells were collected from normal appearing mucosa in the mainstem bronchus during bronchoscopy. Patients without a definitive diagnosis from bronchoscopy were followed for 12 months. A gene-expression classifier was used to assess the risk of lung cancer, and its performance was evaluated. RESULTS: A total of 298 patients from AEGIS 1 and 341 from AEGIS 2 met criteria for analysis. Bronchoscopy was non-diagnostic for cancer in 272 of 639 patients (43%; 95%CI, 39-46%). The gene expression classifier correctly identified 431 of 487 patients with cancer (89% sensitivity; 95%CI, 85-91%), and 72 of 152 patients without cancer (47% specificity; 95%CI, 40-55%). The combination of the classifier and bronchoscopy had a sensitivity of 97% (95%CI, 95-98%), which was independent of size, location, stage, and histological subtype of lung cancer. In patients with an intermediate pre-test risk (10-60%) of lung cancer, the NPV of the classifier was 91% (95%CI 75-98%). CONCLUSIONS: In patients with an intermediate risk of lung cancer and a non-diagnostic bronchoscopy, a gene-expression classification of “low-risk” warrants consideration of a more conservative diagnostic approach that could reduce unnecessary invasive testing in patients with benign disease.
2015-05-17 | GSE66499 | GEO
Project description:Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. In epigenome-wide analyses we identified 58 differentially methylated CpG sites associated with breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer (q-value < 0.05), using linear mixed effects models adjusted for history of breast biopsy, age, age of the baby, cell type proportion estimates, array chip, and subject as random effect. Nearly all sites associated with breast cancer diagnosis were hypomethylated in cases compared with controls, and CpG sites were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has promise as a biospecimen for prospective assessment of disease risk, and for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.
2019-12-06 | GSE133918 | GEO
Project description:The study accrued 49 subjects, and 48 underwent a tumor biopsy. and MP based therapy was administered to 35 patients. Study therapy was not given in 13 subjects either due to insufficient tumor on biopsy (n=8) or due to worsening cancer related symptoms after biopsy (n=5) . The demographics of evaluable patients (n=35) are M/F (59%/41%), with and age range was 34-78 (median 63 years). Time from first diagnosis of mPC to biopsy ranged from 5.8-26.7 months (median 16.1 months). Patients had 1-6 prior regimens with a median of 2. The most common IHC targets were topoisomerase 1 or 2, thymidylate synthase, ERCC1 and SPARC. Only commercially available agents were prescribed. Common regimens/agents recommended were FOLFIRI, FOLFOX, irinotecan and doxorubicin. Response rate was 9% , overall median survival of 6 months and 1 year survival was 21%.
2014-12-31 | GSE64462 | GEO
Project description:Breast cancer (BC) is the second leading cause of death in Canadian women. Despite this, non-invasive early detection methods for BC have yet to be developed. Cells release various types of extracellular vesicles (EVs) as intercellular signals into biofluids, such as blood, reflecting the physiological state of the origin cell. It is by transmitting bioactive molecules between cells that EVs may regulate multiple pathologies in human diseases, including cancer. The detection of protein biomarkers present on the surface of EVs in depleted or enriched biofluids could enable the early diagnosis of BC. Therefore, we used two different approaches to study the surfactome of EVs from cancerous and non-cancerous cells. We found several potential biomarkers that may be involved in the early diagnosis of BC.
2024-05-21 | PXD048074 | Pride
Project description:Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset. Fresh frozen pre-treatment surgical biopsy samples from breast cancer patients were analyzed on Affymetrix HGU133A.
2014-04-17 | E-GEOD-46184 | biostudies-arrayexpress
Project description:This study will collect de-identified tumor samples, with correlated clinical/demographic data and tissue histology, from patients selected or scheduled for pre-treatment tumor biopsy or who have had a recent pre-treatment tumor biopsy. These specimens and clinical data may be used in subsequent studies for the development and validation of a diagnostic test.
| 2348584 | ecrin-mdr-crc
Project description:We report an initial understanding of the modular immune response to a P. vivax malaria challenge after protection with PvRAS. By contrasting blood samples drawn at baseline, following immunization but pre-challenge, and at the first day of diagnosis of malaria in affected subjects.
2017-12-31 | GSE85263 | GEO
Project description:Purpose: Multiple studies from last decades have shown that the microenvironment of carcinomas plays an important role in the initiation, progression and metastasis of cancer. Our group has previously identified novel cancer stroma gene expression signatures associated with outcome differences in breast cancer by gene expression profiling of two tumors of fibroblasts as surrogates for physiologic stromal expression patterns. The aim of this study is to find additional new types of tumor stroma gene expression patterns. Results: 53 tumors were sequenced by 3SEQ with an average of 29 million reads per sample. Both the elastofibroma (EF) and fibroma of tendon sheath (FOTS) gene signatures demonstrated robust outcome results for survival in the four breast cancer datasets. The EF signature positive breast cancers (20-33% of the cohort) demonstrated significantly better outcome for survival. In contrast, the FOTS signature positive breast cancers (11-35% of the cohort) had a worse outcome. The combined stromal signatures of EF, FOTS, and our previously identified DTF, and CSF1 signatures characterize, in part, the stromal expression profile for the tumor microenvironment for between 74%-90% of all breast cancers. Conclusions: We defined and validated two new stromal signatures in breast cancer (EF and FOTS), which are significantly associated with prognosis.
2013-11-21 | GSE42948 | GEO