Cancer biomarker discovery
Cancer is a multigene disorder that arises from gene mutations as well as changes in transcriptional, epigenetic, and proteomic profiles. These changes can serve as valuable biomarkers for both early detection/diagnosis and the development of individualized therapy. Mutations in several known oncogenes (e.g., EGFR, HER2, KRAS) and tumor suppressor genes (e.g., TP53, PTEN, PI3K) are already being used as biomarkers to guide therapies in breast, ovarian, lung, and prostate cancers, among others.
Next-Generation Sequencing (NGS) analysis has greatly facilitated cancer biomarker discovery of circulating nucleic acids within blood, urine, saliva, pleural effusions, and cerebrospinal fluid (i.e., noninvasive liquid biopsies), which can contain tumor-derived genetic information (Siravenga et al. 2017). The sequencing of entire genomes or thousands of mutations simultaneously in a cost-effective manner with NGS can serve as a powerful tool in biomarker detection and discovery. The molecular profiles gathered from circulating tumor DNA (ctDNA) can be further complemented with those obtained through analysis of circulating tumor cells (CTCs), as well as RNA, proteins, and lipids contained within cell-derived vesicles, such as exosomes.
Recent advances in cancer biology have highlighted the importance of exosomes as carriers of genetic and biological messages between cancer cells and their immediate and distant environments. Cancer cells secrete exosomes containing diverse molecules that can be transferred to recipient cells and vice versa to induce a plethora of biological processes, including angiogenesis, metastasis formation, and therapeutic resistance. Therefore, the molecular cargo of exosomes represents a rich source for novel cancer biomarker discovery (Sundararajan et al. 2018).
We provide innovative technologies to speed up your cancer biomarker discovery workflow, including our SMARTer ThruPLEX Plasma-Seq Kit (Figure 1), designed to construct NGS libraries from DNA present within body fluids such as cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA). Our chemistry has been optimized to work efficiently with blood samples and is compatible with leading target enrichment platforms for whole-exome sequencing or specific gene panels. Moreover, our SMARTer ThruPLEX technology has been successfully employed and cited by a number of groups, including Murtaza et al., Xia et al., and Patel et al., who demonstrated the applicability of noninvasive monitoring of tumor chemo-resistance by sequencing ctDNA from liquid biopsies in various types of cancers.
Tools to accelerate cancer biomarker discovery from exosome molecular cargo, such as microRNAs, include our Capturem Exosome Isolation Kit (Cell Culture), which allows fast (<30 minutes) and easy isolation of exosomes from cell culture media. Our SMARTer smRNA-Seq Kit for Illumina provides a streamlined and fast NGS workflow for the global analysis of small RNAs (smRNAs) from picogram amounts of RNA extracted from exosomes, plasma, and serum. Indeed, Guelfi et al. successfully utilized our SMARTer smRNA-Seq Kit to carry out NGS-based miRNA profiling for noninvasive biomarker discovery in the diagnosis of prostate cancer (Guelfi et al. 2017).
Siravegna G. et al. Integrating liquid biopsies into the management of cancer. Nat. Rev. Clin. Oncol. 14, 531–548 (2017).
Sundararajan V. et al. The versatile role of exosomes in cancer progression: diagnostic and therapeutic implications. Cell. Oncol. 41, 223–252 (2018).
Publications citing the use of the SMARTer ThruPLEX-Plasma Seq Kit for noninvasive monitoring of tumor chemoresistance and the SMARTer smRNA-seq Kit for miRNA profiling in prostate cancer diagnosis
Guelfi, G. et al. Next generation sequencing of urine exfoliated cells: an approach of prostate cancer microRNAs research. Sci. Rep. 8, 7111 (2018).
Mayrhofer, M. et al. Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis. Genome Med. 10, 85–98 (2018).
Mouliere, F. et al. Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients. EMBO. 12, e9323 (2018).
Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108–112 (2013).
Patel, K. M. et al. Association of plasma and urinary mutant DNA with clinical outcomes in muscle invasive bladder cancer. Sci. Rep. 7, 5554 (2017).
Xia, Y. et al. Copy number variations in urine cell free DNA as biomarkers in advanced prostate cancer. Oncotarget 7, 35818–35831 (2016).
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