High throughput differential identification of TMPRSS2-ERG fusion genes in prostate cancer patient urine

Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent

Simple Summary

Men of African origin have a 2–3 times greater chance of developing prostate cancer than those of European origin, and of patients that are diagnosed with the disease, men of African descent are 2 times more likely to die compared to white men. Men of African origin are still greatly underrepresented in genetic studies and clinical trials. This, unfortunately, means that new discoveries in cancer treatment are missing key information on the group with a greater chance of mortality. A fusion gene is a hybrid gene formed from two previously independent genes. Fusion genes have been found to be common in all main types of human cancer. The objective of this study was to increase our knowledge of fusion genes in prostate cancer using computational approaches and to compare fusion genes between men of African and European origin. This identified novel gene fusions unique to men of African origin and suggested that this group has a greater number of fusion genes.

Abstract

Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a western lifestyle and of African descent, suggesting risk factors that are genetic, environmental, and socioeconomic in nature. In the USA, African American (AA) men are disproportionately affected, on average suffering from a higher grade of the disease and at a younger age compared to men of European descent (EA). Fusion genes are chimeric products formed by the merging of two separate genes occurring as a result of chromosomal structural changes, for example, inversion or trans/cis-splicing of neighboring genes. They are known drivers of cancer and have been identified in 20% of cancers. Improvements in genomics technologies such as RNA-sequencing coupled with better algorithms for prediction of fusion genes has added to our knowledge of specific gene fusions in cancers. At present AA are underrepresented in genomic studies of prostate cancer. The primary goal of this study was to examine molecular differences in predicted fusion genes in a cohort of AA and EA men in the context of prostate cancer using computational approaches. RNA was purified from prostate tissue specimens obtained at surgery from subjects enrolled in the study. Fusion gene predictions were performed using four different fusion gene detection programs. This identified novel putative gene fusions unique to AA and suggested that the fusion gene burden was higher in AA compared to EA men.

Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel

Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.

The Role of Suspension Array Technology in Rapid Detection of Foodborne Pollutants: Applications and Future Challenges

Food safety is an important livelihood issue, which has always been focused attention by countries and governments all over the world. As food supply chains are becoming global, food quality control is essential for consumer protection as well as for the food industry. In recent years, a great part of food analysis is carried out using new techniques for rapid detection. As the first biochip technology that has been approved by the Food and Drug Administration (FDA), there is an increasing interest in suspension array technology (SAT) for food and environmental analysis with advantages of rapidity, high accuracy, sensitivity, and throughput. Therefore, it is important for researchers to understand the development and application of this technology in food industry. Herein, we summarized the principle and composition of SAT and its application in food safety monitoring. The utility of SAT in detection of foodborne microorganisms, residues of agricultural and veterinary drugs, genetically modified food and allergens in recent years is elaborated, and the further development direction of SAT is envisaged.

A review of current clinical biomarkers for prostate cancer: towards personalised and targeted therapy

Background:

Prostate cancer is the most commonly diagnosed cancer in men and it is responsible for about 10% of all cancer mortality in Canadian men. The current ‘gold standard’ for the diagnosis of prostate cancer is a prostate biopsy and the decision on when to biopsy a patient with non-suspicious Digital Rectal Examination (DRE) result and total prostate specific antigen (tPSA) of 4–10 ng/ml can be challenging. In order to shift the treatment paradigm of prostate cancer toward more personalised and targeted therapy, there is the need for a clear system that makes its detection binary so as to decrease the rate of inaccurate detections. Therefore in recent years, there have been several investigations into the development of various biomarkers with high sensitivity and specificity for screening, early detection and personalised patient-specific targeted medicine from diagnosis to treatment of the disease.

Materials and methods:

This paper reports on nine currently available clinical biomarkers used in screening for early detection and diagnosis, to reduce the number of unnecessary biopsies, in risk assessment of aggressive disease and in monitoring treatment response of prostate cancer.

Conclusion:

Current clinical prostate cancer biomarkers have the potential for a personalised risk assessment of aggressive disease and the risk of developing distant metastatic disease and have been proven to be useful tools to guide clinicians in personalised patient-specific targeted treatment and in the shared decision making between patients and their physicians regarding prostate biopsy and treatment. Using biomarkers to select patients with a significant probability of aggressive prostate cancer would potentially avoid premature death from the disease, while at the same time would safely preclude patients who do not require unnecessary invasive intervention.

Bio-barcode detection technology and its research applications: A review

With the rapid development of nanotechnology, the bio-barcode assay (BCA), as a new diagnostic tool, has been gradually applied to the detection of protein and nucleic acid targets and small-molecule compounds. BCA has the advantages of high sensitivity, short detection time, simple operation, low cost, good repeatability and good linear relationship between detection results. However, bio-barcode technology is not yet fully formed as a complete detection system, and the detection process in all aspects and stages is unstable. Therefore, studying the optimal reaction conditions, optimizing the experimental steps, exploring the multi-residue detection of small-molecule substances, and preparing immuno-bio-barcode kits are important research directions for the standardization and commercialization of BCA. The main theme of this review was to describe the principle of BCA, provide a comparison of its application, and introduce the single-residue and multi-residue detection of macromolecules and single-residue detection of small molecules. We also compared it with other detection methods, summarized its feasibility and limitations, expecting that with further improvement and development, the technique can be more widely used in the field of stable small-molecule and multi-residue detection.

Quantitative Single-Cell Analysis of Isolated Cancer Cells with a Microwell Array

The heterogeneous nature of tumor-cell populations suggests that quantitative analysis at the single-cell level may provide better insights into cancer biology. Specifically, detection of multiple biomarkers from a single cell offers important initial information about cellular behavior. However, conventional approaches limit biomarker detection at the single-cell level. Here, we fabricated a polymer microwell array to capture single cells from prostate-cancer cell lines and quantitatively analyzed the expression of three different cancer-related biomarkers, CD44, EpCAM, and PSMA, without a membrane protein-extraction step. The resulting information on cell-surface biomarker distributions was compared with that from other standard analytical techniques. Interestingly, a large variation in CD44-expression levels was observed when the cell-proliferation cycle was modulated. On the other hand, the expression levels of EpCAM in three different cell lines are consistent among the different analytical methods with the exception of the microarray, where it has a different substrate material to adhere to. This observation clearly emphasizes that biomarker choice and environmental control are critical for properly understanding the single-cell state.

Dual-wavelength digital holographic phase and fluorescence microscopy combining with Raman spectroscopy for micro-quartz pieces-based dual-channel encoded suspension array

Dual-wavelength digital holographic phase and fluorescence microscopy (DW-DHPFM), combining with Raman spectroscopy, is designed to achieve the detection and analysis of biomolecules with a new dual-channel encoding method. This employs the Raman reporter molecules assembled micro-quartz pieces (MQPs) as microcarriers of suspension array (SA). The dual-wavelength digital holographic phase microscopy (DW-DHPM) and Raman spectroscopy are served as the decoding platforms, and the fluorescence microscopy is used to quantify target analytes. Considering the independence between encoding and label signal, the above two encoding channels could effectively avoid the crosstalk in immunoassay process, and the combination of two encoding methods expand the encoding capacity with a considerable magnitude. Accurate and stable decoding abilities are verified by multiplexed immunoassay experiment and the quantitative analysis of targets with high-sensitivity is confirmed by concentration gradient experiments.

Fast and accurate decoding of Raman spectra-encoded suspension arrays using deep learning

A deep learning network called “residual neural network” (ResNet) was used to decode Raman spectra-encoded suspension arrays (SAs).