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Oncotarget Nov 2017Growing evidence indicates that AFAP1-AS1 plays an important role in various cancers, suggesting that it might be a potential cancer biomarker.
BACKGROUND
Growing evidence indicates that AFAP1-AS1 plays an important role in various cancers, suggesting that it might be a potential cancer biomarker.
MATERIALS AND METHODS
A meta-analysis was performed using microarray data obtained via the Affymetrix Human Genome U133 Plus 2.0 platform (found in the GEO database) and data obtained through a systematic search of PubMed and Web of Science. The pooled odds ratio (OR) and hazard ratio (HR) with 95% CI (confidence interval) were used to judge the value of biomarkers.
RESULTS
A total of 30 studies were included in this meta-analysis, comprising a total of 3573 patients. AFAP1-AS1 was significantly linked with overall survival (OS) (HR = 1.58; 95% CI: 1.12-2.23) and recurrence-free survival (RFS) (HR = 2.32, 95% CI: 1.68-3.19). We found that AFAP1-AS1 was a risk factor in the prognoses of lung cancer (pooled HR: 1.54; 95% CI: 1.01-2.34), digestive system cancer (pooled HR: 1.87; 95% CI: 1.45-2.41) and nasopharyngeal carcinoma (HR: 11.82; 95% CI: 5.09-27.46). AFAP1-AS1 was also a risk factor for RFS in breast cancer (pooled HR = 2.90; 95% CI: 1.69-4.98), as well as TNM stage in both esophageal cancer (pooled OR = 1.90; 95% CI: 1.01-3.57) and colorectal cancer (OR = 6.72; 95% CI: 1.92-23.58). AFAP1-AS1 was significantly associated with lymph node metastasis in clear cell carcinoma (OR = 5.04; 95% CI: 2.36-10.78) and distant metastasis in pancreatic cancer (OR = 11.64; 95% CI: 2.13-63.78).
CONCLUSIONS
AFAP1-AS1 can serve as a novel molecular marker predicting tumor progression, patient prognosis and lymph node metastasis in different types of cancers.
PubMed: 29254250
DOI: 10.18632/oncotarget.21830 -
Annual Review of Biomedical Engineering Jul 2021Modeling immunity in vitro has the potential to be a powerful tool for investigating fundamental biological questions, informing therapeutics and vaccines, and providing...
Modeling immunity in vitro has the potential to be a powerful tool for investigating fundamental biological questions, informing therapeutics and vaccines, and providing new insight into disease progression. There are two major elements to immunity that are necessary to model: primary immune tissues and peripheral tissues with immune components. Here, we systematically review progress made along three strategies to modeling immunity: ex vivo cultures, which preserve native tissue structure; microfluidic devices, which constitute a versatile approach to providing physiologically relevant fluid flow and environmental control; and engineered tissues, which provide precise control of the 3D microenvironment and biophysical cues. While many models focus on disease modeling, more primary immune tissue models are necessary to advance the field. Moving forward, we anticipate that the expansion of patient-specific models may inform why immunity varies from patient to patient and allow for the rapid comprehension and treatment of emerging diseases, such as coronavirus disease 2019.
Topics: Adaptive Immunity; Animals; Biophysics; COVID-19; Humans; Immune System; Immunity, Innate; In Vitro Techniques; Lab-On-A-Chip Devices; Lymphocytes; Macrophages; Mice; Microfluidics; SARS-CoV-2; Thymus Gland; Tissue Array Analysis; Tissue Engineering
PubMed: 33872520
DOI: 10.1146/annurev-bioeng-082420-124920 -
Health Technology Assessment... Jun 2019Breast cancer and its treatment can have an impact on health-related quality of life and survival. Tumour profiling tests aim to identify whether or not women need...
BACKGROUND
Breast cancer and its treatment can have an impact on health-related quality of life and survival. Tumour profiling tests aim to identify whether or not women need chemotherapy owing to their risk of relapse.
OBJECTIVES
To conduct a systematic review of the effectiveness and cost-effectiveness of the tumour profiling tests onco DX (Genomic Health, Inc., Redwood City, CA, USA), MammaPrint (Agendia, Inc., Amsterdam, the Netherlands), Prosigna (NanoString Technologies, Inc., Seattle, WA, USA), EndoPredict (Myriad Genetics Ltd, London, UK) and immunohistochemistry 4 (IHC4). To develop a health economic model to assess the cost-effectiveness of these tests compared with clinical tools to guide the use of adjuvant chemotherapy in early-stage breast cancer from the perspective of the NHS and Personal Social Services.
DESIGN
A systematic review and health economic analysis were conducted.
REVIEW METHODS
The systematic review was partially an update of a 2013 review. Nine databases were searched in February 2017. The review included studies assessing clinical effectiveness in people with oestrogen receptor-positive, human epidermal growth factor receptor 2-negative, stage I or II cancer with zero to three positive lymph nodes. The economic analysis included a review of existing analyses and the development of a de novo model.
RESULTS
A total of 153 studies were identified. Only one completed randomised controlled trial (RCT) using a tumour profiling test in clinical practice was identified: Microarray In Node-negative Disease may Avoid ChemoTherapy (MINDACT) for MammaPrint. Other studies suggest that all the tests can provide information on the risk of relapse; however, results were more varied in lymph node-positive (LN+) patients than in lymph node-negative (LN0) patients. There is limited and varying evidence that onco DX and MammaPrint can predict benefit from chemotherapy. The net change in the percentage of patients with a chemotherapy recommendation or decision pre/post test ranged from an increase of 1% to a decrease of 23% among UK studies and a decrease of 0% to 64% across European studies. The health economic analysis suggests that the incremental cost-effectiveness ratios for the tests versus current practice are broadly favourable for the following scenarios: (1) onco DX, for the LN0 subgroup with a Nottingham Prognostic Index (NPI) of > 3.4 and the one to three positive lymph nodes (LN1-3) subgroup (if a predictive benefit is assumed); (2) IHC4 plus clinical factors (IHC4+C), for all patient subgroups; (3) Prosigna, for the LN0 subgroup with a NPI of > 3.4 and the LN1-3 subgroup; (4) EndoPredict Clinical, for the LN1-3 subgroup only; and (5) MammaPrint, for no subgroups.
LIMITATIONS
There was only one completed RCT using a tumour profiling test in clinical practice. Except for onco DX in the LN0 group with a NPI score of > 3.4 (clinical intermediate risk), evidence surrounding pre- and post-test chemotherapy probabilities is subject to considerable uncertainty. There is uncertainty regarding whether or not onco DX and MammaPrint are predictive of chemotherapy benefit. The MammaPrint analysis uses a different data source to the other four tests. The Translational substudy of the Arimidex, Tamoxifen, Alone or in Combination (TransATAC) study (used in the economic modelling) has a number of limitations.
CONCLUSIONS
The review suggests that all the tests can provide prognostic information on the risk of relapse; results were more varied in LN+ patients than in LN0 patients. There is limited and varying evidence that onco DX and MammaPrint are predictive of chemotherapy benefit. Health economic analyses indicate that some tests may have a favourable cost-effectiveness profile for certain patient subgroups; all estimates are subject to uncertainty. More evidence is needed on the prediction of chemotherapy benefit, long-term impacts and changes in UK pre-/post-chemotherapy decisions.
STUDY REGISTRATION
This study is registered as PROSPERO CRD42017059561.
FUNDING
The National Institute for Health Research Health Technology Assessment programme.
Topics: Breast Neoplasms; Chemotherapy, Adjuvant; Cost-Benefit Analysis; Female; Humans; Prognosis; Quality-Adjusted Life Years; Technology Assessment, Biomedical; Treatment Outcome
PubMed: 31264581
DOI: 10.3310/hta23300 -
Biochemistry and Biophysics Reports Mar 2024Papillary thyroid cancer (PTC) is a prevalent kind of thyroid cancer (TC), with the risk of metastasis increasing faster than any other malignancy. So, understanding the...
The role of MAPK, notch and Wnt signaling pathways in papillary thyroid cancer: Evidence from a systematic review and meta-analyzing microarray datasets employing bioinformatics knowledge and literature.
Papillary thyroid cancer (PTC) is a prevalent kind of thyroid cancer (TC), with the risk of metastasis increasing faster than any other malignancy. So, understanding the role of PTC in pathogenesis requires studying the various gene expressions to find out which particular molecular biomarkers will be helpful. The authors conducted a comprehensive search on the PubMed microarray database and a meta-analysis approach on the remaining ones to determine the differentially expressed genes between PTC and normal tissues, along with the analyses of overall survival (OS) and recurrence-free survival (RFS) rates in patients with PTC. We considered the associated genes with MAPK, Wnt, and Notch signaling pathways. Two GEO datasets have been included in this research, considering inclusion and exclusion criteria. Nineteen genes were found to have higher differences through the meta-analysis procedure. Among them, ten genes were upregulated, and nine genes were downregulated. The expression of 19 genes was examined using the GEPIA2 database, and the Kaplan-Meier plot statistics were used to analyze RFS and the OS rates. We discovered seven significant genes with the validation: PRICKLE1, KIT, RPS6KA5, GADD45B, FGFR2, FGF7, and DTX4. To further explain these findings, it was discovered that the mRNA expression levels of these seven genes and the remaining 12 genes were shown to be substantially linked with the results of the experimental literature investigations on the PTC. Our research found nineteen panels of genes that could be involved in the PTC progression and metastasis and the immune system infiltration of these cancers
PubMed: 38371530
DOI: 10.1016/j.bbrep.2023.101606 -
Ultrasound in Obstetrics & Gynecology :... Jun 2019Fetal aberrant right subclavian artery (ARSA) is a relatively common sonographic finding. Several studies have reported a significant association between ARSA and Down...
OBJECTIVES
Fetal aberrant right subclavian artery (ARSA) is a relatively common sonographic finding. Several studies have reported a significant association between ARSA and Down syndrome, as well as 22q11.2 microdeletion. The objective of this study was to assess the risk of abnormal chromosomal microarray analysis (CMA) findings in a large cohort of pregnancies with fetal ARSA as an isolated, as well as a non-isolated, sonographic anomaly. A secondary objective was to review the literature, examining the frequency of chromosomal microarray aberrations in fetuses with isolated ARSA.
METHODS
Data from all pregnancies referred for invasive testing and CMA due to sonographic diagnosis of fetal ARSA, between 2013 and 2017, were obtained retrospectively from the computerized database of the Israeli Ministry of Health. The rate of clinically significant CMA findings in these fetuses was compared to that in a local control population of 2752 low-risk pregnancies with normal ultrasound and serum screening results. In addition, a literature search was conducted in PubMed, from inception to February 2018, of original studies in the English language describing the frequency and nature of microscopic and submicroscopic aberrations in fetuses with isolated ARSA.
RESULTS
Of 246 pregnancies with isolated ARSA that underwent CMA analysis, a clinically significant finding was detected in one (0.4%) pregnancy (trisomy 21). This rate did not differ significantly from that in the control population (P = 0.1574). Of 22 fetuses with non-isolated ARSA, one (4.5%) additional case of trisomy 21 was noted. The frequency of trisomy 21 in this cohort also did not differ from that in the control population (relative risk, 5.5 (95% CI, 0.8-37.6)). The literature search yielded 13 additional relevant papers, encompassing 333 cases of isolated ARSA. Of 579 cases overall (including those of the present study), 13 (2.2%) cases of trisomy 21 were detected, with no cases of 22q11.2 microdeletion.
CONCLUSION
While an association may exist between non-isolated ARSA and Down syndrome, isolated ARSA might better serve as a soft marker for Down syndrome, rather than a routine indication for invasive prenatal testing. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
Topics: Cardiovascular Abnormalities; Cohort Studies; Down Syndrome; Female; Humans; Israel; Microarray Analysis; Pregnancy; Subclavian Artery; Ultrasonography, Prenatal
PubMed: 30584678
DOI: 10.1002/uog.20208 -
Frontiers in Physiology 2022Cancer is one of the top causes of death globally. Recently, microarray gene expression data has been used to aid in cancer's effective and early detection. The use of...
Cancer is one of the top causes of death globally. Recently, microarray gene expression data has been used to aid in cancer's effective and early detection. The use of DNA microarray technology to uncover information from the expression levels of thousands of genes has enormous promise. The DNA microarray technique can determine the levels of thousands of genes simultaneously in a single experiment. The analysis of gene expression is critical in many disciplines of biological study to obtain the necessary information. This study analyses all the research studies focused on optimizing gene selection for cancer detection using artificial intelligence. One of the most challenging issues is figuring out how to extract meaningful information from massive databases. Deep Learning architectures have performed efficiently in numerous sectors and are used to diagnose many other chronic diseases and to assist physicians in making medical decisions. In this study, we have evaluated the results of different optimizers on a RNA sequence dataset. The Deep learning algorithm proposed in the study classifies five different forms of cancer, including kidney renal clear cell carcinoma (KIRC), Breast Invasive Carcinoma (BRCA), lung adenocarcinoma (LUAD), Prostate Adenocarcinoma (PRAD) and Colon Adenocarcinoma (COAD). The performance of different optimizers like Stochastic gradient descent (SGD), Root Mean Squared Propagation (RMSProp), Adaptive Gradient Optimizer (AdaGrad), and Adaptive Momentum (AdaM). The experimental results gathered on the dataset affirm that AdaGrad and Adam. Also, the performance analysis has been done using different learning rates and decay rates. This study discusses current advancements in deep learning-based gene expression data analysis using optimized feature selection methods.
PubMed: 36246115
DOI: 10.3389/fphys.2022.952709 -
Journal of Materials Science. Materials... Jul 2021Microneedles (MNs) are minimally invasive tridimensional biomedical devices that bypass the skin barrier resulting in systemic and localized pharmacological effects....
Microneedles (MNs) are minimally invasive tridimensional biomedical devices that bypass the skin barrier resulting in systemic and localized pharmacological effects. Historically, biomaterials such as carbohydrates, due to their physicochemical properties, have been used widely to fabricate MNs. Owing to their broad spectrum of functional groups, carbohydrates permit designing and engineering with tunable properties and functionalities. This has led the carbohydrate-based microarrays possessing the great potential to take a futuristic step in detecting, drug delivery, and retorting to biologicals. In this review, the crucial and extensive summary of carbohydrates such as hyaluronic acid, chitin, chitosan, chondroitin sulfate, cellulose, and starch has been discussed systematically, using PRISMA guidelines. It also discusses different approaches for drug delivery and the mechanical properties of biomaterial-based MNs, till date, progress has been achieved in clinical translation of carbohydrate-based MNs, and regulatory requirements for their commercialization. In conclusion, it describes a brief perspective on the future prospects of carbohydrate-based MNs referred to as the new class of topical drug delivery systems.
Topics: Administration, Cutaneous; Animals; Biocompatible Materials; Biological Products; Carbohydrates; Cellulose; Chitin; Chitosan; Chondroitin Sulfates; Dermatology; Drug Delivery Systems; Humans; Hyaluronic Acid; Materials Testing; Mice; Microarray Analysis; Needles; Skin; Swine
PubMed: 34331594
DOI: 10.1007/s10856-021-06559-x -
Journal of Ovarian Research Apr 2019The expression of PD-L1 has been reported in ovarian cancer. However, the prognostic role of PD-L1 expression in ovarian carcinoma remained controversial. This study was... (Meta-Analysis)
Meta-Analysis
BACKGROUND
The expression of PD-L1 has been reported in ovarian cancer. However, the prognostic role of PD-L1 expression in ovarian carcinoma remained controversial. This study was performed to assess the prognostic value of PD-L1 expression on ovarian cancer.
METHODS
The PubMed, Embase, EBSCO, and Cochrane Library databases were searched to identify available publications. The pooled odds ratio (OR) or hazard ratios (HRs: multivariate analysis) with their 95% confidence intervals (95% CIs) were calculated in this analysis. A bioinformatics study based on The Cancer Genome Atlas (TCGA) sequencing and microarray datasets was used to further validate the results of PD-L1 mRNA expression. Kaplan-Meier (KM) survival curves were performed to evaluate the prognostic effect of PD-L1 mRNA expression.
RESULTS
Twelve studies with 1630 ovarian cancers regarding PD-L1 immunohistochemical expression were identified. Meta-analysis showed that PD-L1 protein expression was not associated with tumor grade, clinical stage, lymph node status, tumor histology, overall survival (OS), and progression-free survival (PFS). TCGA data showed no association between PD-L1 mRNA expression and ovarian cancer. Further validation using microarray data suggested that no association between PD-L1 mRNA expression and OS was found in large independent patient cohorts (1310 cases). PD-L1 mRNA expression was significantly linked to worse PFS in 1228 patients with ovarian cancer (227458_at: HR = 1.55, 95% CI = 1.28-1.88, P < 0.001; 223834_at: HR = 1.41, 95% CI = 1.14-1.75, P = 0.0015).
CONCLUSIONS
Meta-analysis showed that PD-L1 may not be a prognostic factor for ovarian cancer. But a bioinformatics study showed that PD-L1 expression was significantly associated with worse PFS of ovarian cancer. More clinical studies are needed to further validate these findings.
Topics: B7-H1 Antigen; Computational Biology; Female; Humans; Ovarian Neoplasms; Prognosis
PubMed: 31039792
DOI: 10.1186/s13048-019-0512-6 -
Urologic Oncology Mar 2021The present systematic review aimed to identify prognostic values of tissue-based biomarkers in patients treated with neoadjuvant systemic therapy (NAST), including...
PURPOSE
The present systematic review aimed to identify prognostic values of tissue-based biomarkers in patients treated with neoadjuvant systemic therapy (NAST), including chemotherapy (NAC) and checkpoint inhibitors (NAI) for urothelial carcinoma of the bladder (UCB).
MATERIAL AND METHODS
The PubMed, Web of Science, and Scopus databases were searched in August 2020 according to the PRISMA statement. Studies were deemed eligible if they compared oncologic or pathologic outcomes in patients treated with NAST for UCB with and without detected pretreatment tissue-based biomarkers.
RESULTS
Overall, 44 studies met our eligibility criteria. Twenty-three studies used immunohistochemistry (IHC), 19 - gene expression analysis, three - quantitative polymerase chain reaction (QT PCR), and two - next-generation sequencing (NGS). According to the currently available literature, predictive IHC-assessed biomarkers, such as receptor tyrosine kinases and DNA repair pathway alterations, do not seem to convincingly improve our prediction of pathologic response and oncologic outcomes after NAC. Luminal and basal tumor subtypes based on gene expression analysis showed better NAC response, while claudin-low and luminal-infiltrated tumor subtypes did not. In terms of NAI, PD-L1 seems to maintain value as a predictive biomarker, while the utility of both tumor mutational burden and molecular subtypes remains controversial. Specific genomic alterations in DNA repair genes have been shown to provide significant predictive value in patient treated with NAC. QT PCR quantification of specific genes selected through microarray analysis seems to classify cases regarding their NAC response.
CONCLUSION
We believe that the present systematic review may offer a robust framework that will enable the testing and validation of predictive biomarkers in future prospective clinical trials. NGS has expanded the discovery of molecular markers that are reflective of the mechanisms of the NAST response.
Topics: Biomarkers, Tumor; Carcinoma, Transitional Cell; Humans; Neoadjuvant Therapy; Prognosis; Urinary Bladder Neoplasms
PubMed: 33423937
DOI: 10.1016/j.urolonc.2020.12.019 -
Biomedicine Hub 2017The aim of the study is to review biotechnology advances in gene expression profiling on prostate cancer (PCa), focusing on experimental platform development and gene... (Review)
Review
OBJECTIVES
The aim of the study is to review biotechnology advances in gene expression profiling on prostate cancer (PCa), focusing on experimental platform development and gene discovery, in relation to different study designs and outcomes in order to understand how they can be exploited to improve PCa diagnosis and clinical management.
METHODS
We conducted a systematic literature review on gene expression profiling studies through PubMed/MEDLINE and Web of Science between 2000 and 2016. Tissue biopsy and clinical gene profiling studies with different outcomes (e.g., recurrence, survival) were included.
RESULTS
Over 3,000 papers were screened and 137 full-text articles were selected. In terms of technology used, microarray is still the most popular technique, increasing from 50 to 70% between 2010 and 2015, but there has been a rise in the number of studies using RNA sequencing (13% in 2015). Sample sizes have increased, as well as the number of genes that can be screened all at once, but we have also observed more focused targeting in more recent studies. Qualitative analysis on the specific genes found associated with PCa risk or clinical outcomes revealed a large variety of gene candidates, with a few consistent cross-studies.
CONCLUSIONS
The last 15 years of research in gene expression in PCa have brought a large volume of data and information that has been decoded only in part, but advancements in high-throughput sequencing technology are increasing the amount of data that can be generated. The variety of findings warrants the execution of both validation studies and meta-analyses. Genetic biomarkers have tremendous potential for early diagnosis of PCa and, if coupled with other diagnostics (e.g., imaging), can effectively be used to concretize less-invasive, personalized prediction of PCa risk and progression.
PubMed: 31988908
DOI: 10.1159/000472146