Promising Biomarkers For Cancer Diagnosis Research Articles

A panel sequencing dataset of peripheral blood gene variations in pan-cancer

Circulating cell-free DNA (cfDNA) in the peripheral blood is a promising biomarker for cancer diagnosis and prognosis. Somatic mutations identified in cancers have been used to detect therapeutic targets for clinical transformation and individualize drug selection, while germline variants can predict a patient’s risk of developing cancer and drug sensitivity. However, no platform has been developed to analyze, calculate, integrate, and friendly visualize these pan-cancer cfDNA mutations deeply. In this work, we performed panel sequencing encompassing 1,115 cancer-related genes across 16,659 cancer patients, spanning 27 cancer types. We detected 496 germline variants in leukocytes and 11,232 somatic mutations in the cfDNA of all patients. CPGV (Cancer Peripheral blood Gene Variations), a database constructed from this dataset, is the first pan-cancer cfDNA database that encompasses somatic mutations, germline variants, and further comparative analyses of mutations across different cancer types. It bears great promise to serve as a valuable resource for cancer research.

N6-methyladenosine modified circPAK2 promotes lymph node metastasis via targeting IGF2BPs/VEGFA signaling in gastric cancer.

Circular RNAs (circRNAs) have emerged as key regulators of cancer occurrence and progression, as well as promising biomarkers for cancer diagnosis and prognosis. However, the potential mechanisms of circRNAs implicated in lymph node (LN) metastasis of gastric cancer remain unclear. Herein, we identify a novel N6-methyladenosine (m6A) modified circRNA, circPAK2, which is significantly upregulated in gastric cancer tissues and metastatic LN tissues. Functionally, circPAK2 enhances the migration, invasion, lymphangiogenesis, angiogenesis, epithelial-mesenchymal transition (EMT), and metastasis of gastric cancer in vitro and in vivo. Mechanistically, circPAK2 is exported by YTH domain-containing protein 1 (YTHDC1) from the nucleus to the cytoplasm in an m6A methylation-dependent manner. Moreover, increased cytoplasmic circPAK2 interacts with Insulin-Like Growth Factor 2 mRNA-Binding Proteins (IGF2BPs) and forms a circPAK2/IGF2BPs/VEGFA complex to stabilize VEGFA mRNA, which contributes to gastric cancer vasculature formation and aggressiveness. Clinically, high circPAK2 expression is positively associated with LN metastasis and poor prognosis in gastric cancer. This study highlights m6A-modified circPAK2 as a key regulator of LN metastasis of gastric cancer, thus supporting circPAK2 as a promising therapeutic target and prognostic biomarker for gastric cancer.

LINK-A: unveiling its functional role and clinical significance in human tumors.

LINK-A, also recognized as LINC01139, has emerged as a key oncological lncRNA in cancer. LINK-A is upregulated in solid and liquid tumor samples, including breast cancer, ovarian cancer, glioma, non-small-cell lung cancer, and mantle cell lymphoma. Notably, LINK-A is involved in regulating critical cancer-related pathways, such as AKT and HIF1α signaling, and is implicated in a range of oncogenic activities, including cell proliferation, apoptosis, epithelial-mesenchymal transition (EMT), cell invasion and migration, and glycolysis reprogramming. LINK-A's differential expression and its correlation with clinical features enable it to be a promising biomarker for cancer diagnosis, prognosis, and the stratification of tumor progression. Additionally, LINK-A's contribution to the development of resistance to cancer therapies, including AKT inhibitors and immunotherapy, underscores its potential as a therapeutic target. This review provides a comprehensive overview of the available data on LINK-A, focusing on its molecular regulatory pathways and clinical significance. By exploring the multifaceted nature of LINK-A in cancer, the review aims to offer a valuable resource for future research directions, potentially guiding the development of novel therapeutic strategies targeting this lncRNA in cancer treatment.

DNA Logical Device Combining an Entropy-Driven Catalytic Amplification Strategy for the Simultaneous Detection of Exosomal Multiplex miRNAs In Situ.

Exosomal miRNAs are considered promising biomarkers for cancer diagnosis, but their accuracy is severely compromised by the low content of miRNAs and the large amount of exosomal miRNAs released from normal cells. Here, we presented a dual-specific miRNA's logical recognition triggered by an entropy-driven catalysis (EDC)-enhanced system in exosomes for accurate detection of liver cancer-cell-derived exosomal miR-21 and miR-122. Taking advantage of the accurate analytical performance of the logic device, the excellent membrane penetration of gold nanoparticles, and the outstanding amplification ability of the EDC reaction, this method exhibits high sensitivity and selectivity for the detection of tumor-derived exosomal miRNAs in situ. Moreover, due to its excellent performance, this logic device can effectively distinguish liver cancer patients from healthy donors by determining the amount of cancer-cell-derived exosomal miRNAs. Overall, this strategy has great potential for analyzing various types of exosomes and provides a viable tool to improve the accuracy of cancer diagnosis.

A Magnetically Driven Tandem Chip Enables Rapid Isolation and Multiplexed Profiling of Extracellular Vesicles.

The protein phenotypes of extracellular vesicles (EVs) have emerged as promising biomarkers for cancer diagnosis and treatment monitoring. However, the technical challenges in rapid isolation and multiplexed molecular detection of EVs have limited their clinical practice. Herein, we developed a magnetically driven tandem chip to achieve streamlined rapid isolation and multiplexed profiling of surface protein biomarkers of EVs. Driven by magnetic force, the magnetic nanomixers not only act as tiny stir bars to promote mass transfer and enhance reaction efficiency of EVs, but also transport on communicating vessels of the tandem chip continuously and expedite the assay workflow. We designed cyclic surface enhancement of Raman scattering (SERS) tags to bind with target EVs and then release them by exonuclease I, eliminating steric hindrance and amplifying the SERS signal of multiple protein biomarkers on EVs. Due to the excellent assay performance, six breast cancer biomarkers were detected simultaneously on EVs using only 10 μL plasma within 1.5 h. The unweighted SUM signature offers great accuracy in discriminating breast cancer patients from healthy donors. Overall, the dynamic magnetic driving tandem chip offers a new avenue to advance the clinical application of EV-based liquid biopsy.

A Magnetically Driven Tandem Chip Enables Rapid Isolation and Multiplexed Profiling of Extracellular Vesicles

AbstractThe protein phenotypes of extracellular vesicles (EVs) have emerged as promising biomarkers for cancer diagnosis and treatment monitoring. However, the technical challenges in rapid isolation and multiplexed molecular detection of EVs have limited their clinical practice. Herein, we developed a magnetically driven tandem chip to achieve streamlined rapid isolation and multiplexed profiling of surface protein biomarkers of EVs. Driven by magnetic force, the magnetic nanomixers not only act as tiny stir bars to promote mass transfer and enhance reaction efficiency of EVs, but also transport on communicating vessels of the tandem chip continuously and expedite the assay workflow. We designed cyclic surface enhancement of Raman scattering (SERS) tags to bind with target EVs and then release them by exonuclease I, eliminating steric hindrance and amplifying the SERS signal of multiple protein biomarkers on EVs. Due to the excellent assay performance, six breast cancer biomarkers were detected simultaneously on EVs using only 10 μL plasma within 1.5 h. The unweighted SUM signature offers great accuracy in discriminating breast cancer patients from healthy donors. Overall, the dynamic magnetic driving tandem chip offers a new avenue to advance the clinical application of EV‐based liquid biopsy.

Exploration of aminopeptidase N as new biomarker for early diagnosis of thyroid cancer

False-positive diagnosis and overdiagnosis are ongoing issues in clinical diagnosis of thyroid cancer. Identifying new disease markers is crucial for early diagnosis and improved treatment. Aminopeptidase N (APN) is a promising biomarker for cancer diagnosis due to its critical roles in tumor invasion, metastasis, angiogenesis, and other processes. However, its potential as biomarker for thyroid cancer diagnosis needs further investigation. This study developed an ultra-sensitive near-infrared fluorescence probe, LAN-apn, to investigate the expression level of APN in thyroid cancer and evaluate its potential as biomarker of thyroid cancer. LAN-apn could accurately and sensitively determine APN through fluorescence method (DL = 0.069 ng/mL) and colorimetric method (DL = 4.5 ng/mL). In addition, LAN-apn allowed for successful fluorescence imaging of APN in thyroid cancer cells and thyroid cancer tumors both in vivo and in vitro, and confirmed that APN was significantly upregulated in thyroid cancer. Therefore, APN may become a new biomarker for thyroid cancer diagnosis, and LAN-apn could be used as a new imaging tool for the study of APN-thyroid cancer relationship and the early diagnosis of thyroid cancer.

Simultaneous Recognition of Over- and Under-Expressed MicroRNAs Using Nanopore Decoding.

This paper describes a strategy for simultaneous recognition of over- and under-expressed microRNAs (miRNAs) using the method of signal classification-based nanopore decoding. MiRNA has attracted attention as a promising biomarker for cancer diagnosis owing to its cancer-type-specific expression patterns. While nanopore technology has emerged as a simple and label-free method to detect miRNAs and their expression patterns, recognizing patterns involving simultaneous over/under-expression is still challenging due to the inherent working principles. Here, inspired by the sequence design for DNA computation with nanopore decoding, we designed diagnostic DNA probes targeting two individual over/under-expressed miRNAs in the serum of oral squamous cell carcinoma. Through nanopore measurements, our designed probes exhibited characteristic current signals depending on the hybridized miRNA species, which were plotted on the scatter plot of duration versus current blocking ratio. The classified signals reflected the relative abundance of target miRNAs, thereby enabling successful pattern recognition of over/under-expressed miRNAs, even when using clinical samples. We believe that our method paves the way for miRNA-targeting simple diagnosis as a liquid biopsy.

Abstract 2302: Detection of tumor-associated methylation and mutation signatures for early colorectal cancer diagnosis

Abstract Introduction: The ability to identify epigenetic signatures, together with genetic alterations, has expanded the translational utility of genomic sequencing in clinical settings. Epigenetic changes may appear at very early stages before diagnosis. Thus, they could be used as epigenetic biomarkers for early detection or risk of cancer development. Circulating cell-free DNA (cfDNA) profiling has emerged as a promising biomarker for cancer diagnosis and prognosis. Herein, we developed targeted next-generation sequencing (NGS) based assays for assessing multiple DNA methylated and mutated regions in both low-quantity (plasma cfDNA) and low-quality formalin-fixed paraffin-embedded (FFPE) tissue for colorectal cancer (CRC) detection. Methods: For the OptiSeqTM CRC methylation panel, we assessed the methylation status of CpG dinucleotides in 42 genes. With this panel, we profiled 6 CRC samples (matching cfDNA and FFPE), 2 primary colon tumors with adjacent normal, and 6 advanced adenomas (AA) FFPE tissue DNA. For healthy individuals, we profiled 12 normal colon FFPE samples and 31 plasma cfDNA (26 matching buffy coat DNA samples). For the OptiSeqTM CRC mutation panel, the mutation status was assessed in 43 genes. Here, we profiled 6 CRC samples (matching cfDNA and FFPE), 19 CRC plasma cfDNA, 4 AA FFPE and 42 healthy individuals’ plasma cfDNA (26 matching buffy coat DNA samples). The analytical and clinical performance for both panels (separately and combined) were calculated using advanced adenoma (AA), CRC, and cancer-free individuals. Results: For CRC cfDNA samples, clinical samples testing showed that the methylation panel had a sensitivity of 50% (95% CI: 13.9-86.0) and specificity of 100% (95% CI: 86.2-100) while the mutation panel yielded the sensitivity 88% (95% CI: 67.7-96.8) and specificity 100% (95% CI: 89.5-100). Combining the mutation panel with the methylation panel, the sensitivity increased to 100% (95% CI: 51.6-100) and specificity to 100% (95% CI: 65.1-93.3). For AA FFPE samples, the methylation panel analysis yielded a sensitivity of 100% (95% CI: 39.5-100.0) and a specificity of 100% (95% CI: 67.8-100). Conclusion: We have developed and validated the targeted NGS-based panels to detect clinically relevant mutation and methylation patterns and demonstrate its potential as a highly sensitive assay for early CRC diagnosis. Citation Format: Pushpinder Bains, Mikhail Kulak, Zhen Cui, Alisha Babu, Stella Tran, Bongyong Lee, Aiguo Zhang, Michael Sha. Detection of tumor-associated methylation and mutation signatures for early colorectal cancer diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2302.

Bottom-Up Signal Boosting with Fractal Nanostructuring and Primer Exchange Reaction for Ultrasensitive Detection of Cancerous Exosomes.

Exosomes are emerging as promising biomarkers for cancer diagnosis, yet sensitive and accurate quantification of tumor-derived exosomes remains a challenge. Here, we report an ultrasensitive and specific exosome sensor (NPExo) that initially leverages hierarchical nanostructuring array and primer exchange reaction (PER) for quantitation of cancerous exosomes. This NPExo uses a high-curvature nanostructuring array (bottom) fabricated by single-step electrodeposition to enhance capturing of the target exosomes. The immuno-captured exosome thus provides abundant membrane sites to insert numerous cholesterol-DNA probes with a density much higher than that by immune pairing, which further allows PER-based DNA extension to assemble enzyme concatemers (up) for signal amplification. Such a bottom-up signal-boosting design imparts NPExo with ultrahigh sensitivity up to 75 particles/mL (i.e., <1 exosome per 10 μL) and a broad dynamic range spanning 6 orders of magnitude. Furthermore, our sensor allows monitoring subtle exosomal phenotypic transition and shows high accuracy in discrimination of liver cancer patients from healthy donors via blood samples, suggesting the great potential of NPExo as a promising tool in clinical diagnostics.

Improving SERS biosensors for the analysis of ovarian cancer-derived small extracellular vesicles.

Small extracellular vesicles (sEVs) are lipid bilayer vesicles that carry key molecules (e.g., proteins, DNAs, RNAs, and lipids) for cell-to-cell communication, being regarded as promising biomarkers for cancer diagnosis. However, the detection of sEVs is still challenging due to their unique characteristics such as size and phenotype heterogeneity. The surface-enhanced Raman scattering (SERS) assay is a promising tool for sEV analysis as it shows the advantages of robustness, high sensitivity, and specificity. Previous studies proposed different "sandwich" immunocomplex assembling strategies and various capturing probes for sEV detection by the SERS assay. However, no studies have reported the effect of immunocomplex assembling strategies and capturing probes on the analysis of sEVs using this assay. Hence, to achieve the highest performance of the SERS assay for analysing ovarian cancer-derived sEVs, we first assessed the presence of ovarian cancer markers such as EpCAM on cancer cells and sEVs by using flow cytometry and immunoblotting. We found that cancer cells and their derived sEVs present EpCAM and therefore EpCAM was used to functionalise SERS nanotags for the comparison study of "sandwich" immunocomplex assembling strategies. Then, we compared three types of capturing probes (magnetic beads conjugated with anti-CD9, CD63, or CD81 antibodies) for sEV detection. Our study showed the strategy of pre-mixing of sEVs with SERS nanotags and the anti-CD9 capturing probe would achieve the best performance with the minimum detection of sEVs down to 1.5 × 105 particles per μL and with high specificity in distinguishing sEVs from different ovarian cancer cell lines. We further profiled the surface protein biomarkers (EpCAM, CA125, and CD24) on ovarian cancer-derived sEVs in both PBS and plasma (sEVs spiked in healthy plasma) using the improved SERS assay, showing high sensitivity and specificity. As such, we anticipate that our improved SERS assay has the potential to be used clinically as one of the effective detection methods of ovarian cancer.

Overexpression of FNDC4 constrains ovarian cancer progression by promoting cell apoptosis and inhibiting cell growth.

Hepatocellular carcinoma is one of the most common malignant tumors in the world. It has been reported that fibronection type III domain containing family plays an important role in the formation and development of a variety of tumors, but the role of FNDC4 is still unclear. In our study, we found that FNDC4 was highly expressed in normal liver tissues but abnormally expressed at low levels in liver cancer tissues. Enhanced apoptosis and decreased proliferation were shown in the FNDC4 overexpression model in HepG2 cells. In addition, FNDC4 was negatively correlated with AFP, a tumor marker of HCC, and other cancer-related genes such as AHSA1, GDF1, GPC3 and MDK. In addition, we found that FNDC4 was associated with the abundance of several tumor-infiltrating lymphocytes and the expression of chemokines and immunostimulators, and FNDC4 was enriched in response to transforming growth factor β. These results indicated that FNDC4 plays a key role in hepatocellular carcinoma progression and might be a promising biomarker for cancer diagnosis.

Label-free and low-background FEN1 sensing based on cleavage-induced ligation of bifunctional dumbbell DNA and in-situ signal readout

Flap endonuclease 1 (FEN1) is overexpressed in various types of human tumor cells and has been recognized as a promising biomarker for cancer diagnosis in recent years. In this work, a label-free fluorescent nanosensor for FEN1 detection was developed based on cleavage-induced ligation of bifunctional dumbbell DNA and in-situ signal readout by copper nanoparticles (CuNPs). The dumbbell DNA was rationally designed with a FEN1 cleavable 5′ flap for target recognition and AT-riched stem-loop template for CuNPs formation. In the presence of FEN1, 5′ overhanging DNA flap of dumbbell DNA was effectively removed to form a linkable nick site. After the ligation by T4 DNA ligase, the dumbbell DNA changed to exonuclease-resisted closed structure which enabled in-situ generation of fluorescent CuNPs that served as signal source for target quantification. The low background attributed to synergic digestion by exonucleases facilitated the highly sensitive detection of FEN1 with limit of detection of 0.007 U/mL. Additionally, the sensor was extended to the assay of FEN1 inhibitor (aurintricarboxylic acid) with reasonable results. Last but not least, the normal cells and tumor cells were distinguished unambiguously by this sensor according to the detected concentration difference of cellular FEN1, which indicates the robustness and practicability of this nanosensor.

A novel urokinase plasminogen activator receptor-targeted peptide-based probe for in-vivo molecular imaging of glioblastoma.

The urokinase plasminogen activator receptor (uPAR) is a promising biomarker for cancer diagnosis and therapy. We herein fabricated a new type of uPAR-targeted imaging probe Al18F-NOTA-VC and preliminarily evaluated its potential application in PET imaging of the glioma model in vivo. Peptide VC was synthesized and identified by MALDI-TOF-MS. The IC50 between VC/precursor NOTA-VC and uPAR was then determined before the synthesis and purification of Al18F-NOTA-VC, followed by further studies of in-vitro properties of Al18F-NOTA-VC. Meanwhile, the AE105-based probe followed a similar procedure in-vitro test. Finally, the PET imaging properties, including uPAR-targeting ability and the metabolism of Al18F-NOTA-VC, were investigated. The VC and NOTA-VC were obtained successfully and demonstrated a good affinity with uPAR. Followed by Al18F labeling successfully, excellent properties, including the serum stability, water solubility, and specificity of Al18F-NOTA-VC, were obtained in-vitro test compared with AE105 based probe. An excellent tumor uptake and renal excretion data of Al18F-NOTA-VC were acquired from in-vivo U87MG tumor model PET imaging, consistent with the subsequent biodistribution study. In addition to the excellent specificity and high tumor/normal tissue contrast for uPAR-targeted PET imaging of U87MG tumor, Al18F-NOTA-VC possessed promising clearance ability by renal system route. These excellent properties facilitated Al18F-NOTA-VC to be a promising imaging agent for uPAR high-expressing tumors and, thus, provided a paradigm for developing peptide-based probes for uPAR-associated disease diagnosis.

Quantification-Promoted Discovery of Glycosylated Exosomal PD-L1 as a Potential Tumor Biomarker.

Exosomal programmed cell death ligand 1 (exoPD-L1) has emerged as a promising biomarker for cancer diagnosis and immunotherapy outcome prediction. However, the existing quantitation methods are incapable of addressing the heterogeneity of exoPD-L1 glycosylation, which has been demonstrated to be the institutional basis for PD-L1/PD-1 interaction and the crucial participant in inhibiting the activity of CD8+ T cells. Herein, an aptamer- and lectin-induced proximity ligation assay combined with quantitative real-time polymerase chain reaction for precise quantitation of glycosylated exoPD-L1 is developed. Leveraging the metabolism-free lectin labeling of glycosylation, the glycosylation-independent aptamer tagging of PD-L1, and excellent selectivity of dual-recognition, this method enables glycosylated exoPD-L1 quantitation with high sensitivity and selectivity in a wash-free manner. As a result, this method is able to distinguish the levels of glycosylated exoPD-L1 between healthy donors and cancer patients with sensitivity and specificity of 100%. Compared with the total circulating exoPD-L1 level, glycosylated exoPD-L1 is for the first time identified to be a more reliable biomarker for tumor diagnosis. Overall, this strategy holds a great potential for revealing the significance of exoPD-L1 glycosylation and converting glycosylated exoPD-L1 into a reliable clinical indicator.

CircFBXO7/miR-96-5p/MTSS1 axis is an important regulator in the Wnt signaling pathway in ovarian cancer

BackgroundCircRNAs are a novel class of evolutionarily conserved noncoding RNA molecules that form covalently closed continuous loop structures without 5′ caps and 3′ poly(A) tails. Accumulating evidence suggests that circRNAs play important regulatory roles in cancer and are promising biomarkers for cancer diagnosis and prognosis, as well as targets for cancer therapy. In this study, we identify and explore the role of a novel circRNA, circFBXO7, in ovarian cancer.MethodsrRNA-depleted RNA-sequencing was performed to identify differentially expressed circRNAs between ovarian cancerous and normal tissues. qRT-PCR and single-molecule RNA in-situ hybridization was used to quantify circFBXO7 expression in tumor tissues. The association of circFBXO7 expression with patient prognosis was evaluated by Kaplan–Meier survival analysis. The biological function of circFBXO7 was also investigated using loss-of-function and gain-of-function assays in vivo and in vitro. Luciferase reporter and TOP/FOP-Flash reporter assays were then conducted together with RNA immunoprecipitation and western blot to assess the circFBXO7/miR-96-5p/MTSS1/Wnt/β-catenin axis.ResultscircFBXO7 was downregulated in ovarian cancer which was associated with poor prognosis. Biologically, circFBXO7 overexpression significantly suppressed ovarian cancer cell proliferation, migration, and invasion in vitro, and inhibited tumor growth and metastasis in vivo, whereas its knockdown exerted an opposite role. Mechanistically, circFBXO7 functioned as a competing endogenous RNA for miR-96-5p to regulate the expression of MTSS1. Consequently, downregulation of MTSS1 led to excessive accumulation of β-catenin and increased phosphorylation of GSK3β, leading to the translocation of β-catenin to the nucleus, thereby activating the Wnt/β-catenin signaling pathway and ultimately promoting ovarian cancer progression.ConclusionsOur findings indicate that circFBXO7 acts as a bone fide tumor suppressor in ovarian cancer and that the circFBXO7/miR-96-5p/MTSS1 axis is an important regulator in the Wnt/β-catenin signaling pathway which may provide a promising target for ovarian cancer therapy.

Identification of novel key regulatory lncRNAs in gastric adenocarcinoma

BackgroundStomach adenocarcinoma (STAD) is one of the most common and deadly cancers worldwide. Recent evidence has demonstrated that dysregulation of long noncoding RNAs (lncRNA) is associated with different hallmarks of cancer. lncRNAs also were suggested as novel promising biomarkers for cancer diagnosis and prognosis. Despite these previous investigations, the expression pattern, diagnostic role, and hallmark association of lncRNAs in STAD remain unclear.ResultsIn this study, The STAD lncRNA-mRNA network was constructed based on RNAs that differentially expressed among tumor and normal samples and had a strong expression correlation with others. The high degree nodes of the network were associated with overall survival. In addition, we found that the hubs’ regulatory roles have previously been confirmed in different types of cancers by literature. For example, the HCG22 hub inhibited cell proliferation and invasion and induced apoptosis in oral squamous cell carcinoma (OSCC) cells. The levels of PCNA, Vimentin, and Bcl2 were decreased and E-cadherin and Bax expression was elevated in OSCC cells after HCG22 overexpression. Additionally, HCG22 overexpression inhibited the Akt, mTOR, and Wnt/β-catenin pathways.Then lncRNAs were mapped to their related GO terms and cancer hallmarks. Based on these mappings, we predict the hallmarks that might be associated with each lncRNA. Finally, the literature review confirmed our prediction.Among the 20 lncRNAs of the STAD network, 11 lncRNAs (LINC02560, SOX21-AS1, C5orf66-AS1, HCG22, PGM5-AS1, NALT1, ENSG00000241224.2, TINCR, MIR205HG, HNF4A-AS1, ENSG00000262756) demonstrated expression correlation with overall survival (OS). Based on expression analysis, survival analysis, hallmark associations, and literature review, LINC02560, SOX21-AS1, C5orf66-AS1, HCG22, PGM5-AS1, NALT1, ENSG00000241224.2, TINCR, MIR205HG, HNF4A-AS1 plays a regulatory role in STAD. For example, our prediction of association between C5orf66-AS1 expression dysregulation and “sustaining proliferative signal” and “Activating invasion and metastasis” has been confirmed in STAD, OSCC and cervical cancer. Finally, we developed a lncRNA signature with SOX21-AS1 and LINC02560, which classified patients into high and low-risk subgroups with significantly different survival outcomes. The mortality rate of the high-risk patients was significantly higher compared to the low-risk patients (28/1% vs 60.13).ConclusionThese findings help in designing more precise and detailed experimental studies to find STAD biomarkers and therapeutic targets.

Highly sensitive and reliable detection of microRNA for clinically disease surveillance using SERS biosensor integrated with catalytic hairpin assembly amplification technology

MicroRNAs (miRNAs) play an important regulatory role in several diseases, especially as a class of promising biomarkers for cancer diagnosis and prognosis. Here, a biosensor based on surface enhanced Raman spectroscopy (SERS) combined with catalytic hairpin assembly (CHA) amplification technology was developed for ultra-sensitive detection of miRNA-21 and miRNA-155 in breast cancer serum. By using CHA strategy, the extremely low concentration of target microRNA in human serum can be significantly amplified through the re-hybridization with thousands of hairpin probes to trigger amplification cycles. Besides, a sandwich SERS sensing chip with numerous hot spots and signal self-calibration was built through the linkage between two-dimensional Au–Si substrate and upper Ag@4-MBA@Au core-shell nanoparticles. Using this specially-designed biosensing platform, a low detection limit of 0.398 fM and 0.215 fM with a dynamic range from 1 fM to 10 nM can be achieved for the detection of miRNA-21 and miRNA-155, respectively. Additionally, the analysis of these two miRNAs in serum samples is capable of identifying the breast cancer subjects from normal ones with 100% of accuracy, as well as potentially evaluating the molecular types and prognosis for breast cancer. These results demonstrate that the proposed SERS with CHA technology would be an alternative method for highly sensitive and reliable detection of miRNA biomarkers contributing to breast cancer diagnosis and prognosis.

Integrative Analysis of 5-Hydroxymethylcytosine and Transcriptional Profiling Identified 5hmC-Modified lncRNA Panel as Non-Invasive Biomarkers for Diagnosis and Prognosis of Pancreatic Cancer.

Pancreatic adenocarcinoma (PAAD) is the fourth leading cause of cancer-related deaths worldwide. 5-Hydroxymethylcytosine (5hmC)-mediated epigenetic regulation has been reported to be involved in cancer pathobiology and has emerged to be promising biomarkers for cancer diagnosis and prognosis. However, 5hmC alterations at long non-coding RNA (lncRNA) genes and their clinical significance remained unknown. In this study, we performed the genome-wide investigation of lncRNA-associated plasma cfDNA 5hmC changes in PAAD by plotting 5hmC reads against lncRNA genes, and identified six PAAD-specific lncRNAs with abnormal 5hmC modifications compared with healthy individuals. Then we applied machine-learning and Cox regression approaches to develop predictive diagnostic (5hLRS) and prognostic (5hLPS) models using the 5hmC-modified lncRNAs. The 5hLRS demonstrated excellent performance in discriminating PAAD from healthy controls with an area under the curve (AUC) of 0.833 in the training cohort and 0.719 in the independent testing cohort. The 5hLPS also effectively divides PAAD patients into high-risk and low-risk groups with significantly different clinical outcomes in the training cohort (log-rank test p = 0.04) and independent testing cohort (log-rank test p = 0.0035). Functional analysis based on competitive endogenous RNA (ceRNA) and enrichment analysis suggested that these differentially regulated 5hmC modified lncRNAs were associated with angiogenesis, circulatory system process, leukocyte differentiation and metal ion homeostasis that are known important events in the development and progression of PAAD. In conclusion, our study indicated the potential clinical utility of 5hmC profiles at lncRNA loci as valuable biomarkers for non-invasive diagnosis and prognostication of cancers.

Decreased Expression of circ_0000160 in Breast Cancer With Axillary Lymph Node Metastasis.

Background: Circular RNAs (circRNAs) have been shown to play important roles in the development and progression of human cancers. Emerging evidence shows that circRNAs have the potential to be promising biomarkers for cancer diagnosis and prognosis. However, the roles of circRNAs in breast cancer axillary lymph node metastasis (ALNM) remain to be determined. Methods: Transcriptome sequencing was utilized to screen the differentially expressed circRNAs in three breast cancer tissues with ALNM and three without ALNM. Differentially expressed circRNAs were further verified by quantitative real-time PCR. Moreover, receiver operating characteristic (ROC) curve analysis was performed to calculate the value of circRNAs to distinguish breast cancer tissues with ALNM and those without ALNM. To explore the potential mechanism of the circRNAs, a circRNA–miRNA–mRNA network was constructed based on the CircInteractome, circBank, and mirDIP online software. Results: In total, 31 differentially expressed circRNAs were identified by transcriptome sequencing; among them, 21 were upregulated and 10 were downregulated in breast cancer with ALNM compared to those without ALNM. Circ_0000160 was validated to be downregulated in breast cancer tissues with ALNM compared with those without ALNM. The ROC curve showed the ability of circ_0000160 to distinguish breast cancer tissues with ALNM and those without ALNM, with an area under the curve of 0.7435. Furthermore, bioinformatics analysis revealed that the predicted mRNAs for circ_0000160 may be related to lymph node metastasis. The predicted mRNAs for circ_0000160 may be involved in many cancer-related pathways. Conclusion: A decreased expression of circ_0000160 was found in breast cancer with axillary lymph node metastasis. Circ_0000160 may have the potential to distinguish breast cancer with axillary lymph node metastasis from those without axillary lymph node metastasis.