In-depth proteomic analysis of tissue interstitial fluid for hepatocellular carcinoma serum biomarker discovery

Thrombospondin 2 as a Predictive Biomarker for HCC in Hepatitis C Patients: A Longitudinal Study Following DAA Therapy

This multicentre study investigated the dynamics of thrombospondin 2 (TSP2) levels during direct-acting antiviral (DAA) therapy in hepatitis C virus (HCV) infected patients and evaluated TSP2's potential as a predictive marker for hepatocellular carcinoma (HCC). All 134 participants achieved sustained virological response at 12 weeks (SVR12) with DAA therapy, and serum TSP2 levels significantly decreased from before and after treatment (p < 0.001). During the median follow-up period of 6.0 years, HCC after DAA therapy was observed in 16 patients (11.9%). Patients with serum TSP2 High (≥ 32 ng/mL) at SVR12 had a significantly higher cumulative occurrence of HCC than did those without (26.5% vs. 7.0%, p = 0.0033). A multivariate Cox proportional hazards model identified male gender (HR 4.84, p = 0.005), HCC history (HR 4.61, p = 0.017) and TSP2 High (HR 3.93, p = 0.009) as significant independent predictors of HCC occurrence after DAA therapy. The model had a high concordance index of 0.878. Additionally, combining TSP2 High and FIB-4 High (≥ 3.538) at SVR12 yielded high specificity and negative predictive value (0.941 and 0.917, respectively) for predicting HCC. Kaplan-Meier analysis showed a higher HCC incidence in the TSP2 High + FIB-4 High group (log-rank p < 0.0001). In conclusion, TSP2 may be a promising biomarker for personalised HCC surveillance in DAA-treated hepatitis C patients.

In-Depth Proteomic Analysis of Tissue Interstitial Fluid Reveals Biomarker Candidates Related to Varying Differentiation Statuses in Gastric Adenocarcinoma

The proteomic heterogeneity of gastric adenocarcinoma (GC) has been extensively investigated at the bulk tissue level, which can only provide an average molecular state. In this study, we collected an in-depth quantitative proteomic dataset of tissues and interstitial fluids (ISFs) from both poorly and non-poorly differentiated GC and presented a comprehensive analysis from several perspectives. Comparison of proteomes between ISFs and tissues revealed that ISF exhibited higher abundances of proteins associated with blood microparticles, protein-lipid complexes, immunoglobulin complexes, and high-density lipoprotein particles. Also, consistent and inconsistent protein abundance changes between them were revealed by a correlation analysis. Interestingly, a more pronounced difference between tumors and normal adjacent tissues was found at the ISF level, which accurately reflected tissue properties compared to those of bulk tissue. Two ISF-derived biomarker candidates, calsyntenin-1 (CLSTN1) and prosaposin (PSAP), were identified by distinguishing patients with different differentiation statuses and were further validated in serum samples. Additionally, the silencing of CLSTN1 and PSAP was demonstrated to suppress cell proliferation, migration, and invasion in poorly differentiated gastric cancer cell lines. In summary, the ISF proteome offers a new perspective on tumor biology. This study provides a valuable resource that significantly enhances the understanding of GC and may ultimately benefit clinical practice.

High-throughput proteomics-guided biomarker discovery of hepatocellular carcinoma

Liver cancer stands as the fifth leading cause of cancer-related deaths globally. Hepatocellular carcinoma (HCC) comprises approximately 85%-90% of all primary liver malignancies. However, only 20-30% of HCC patients qualify for curative therapy, primarily due to the absence of reliable tools for early detection and prognosis of HCC. This underscores the critical need for molecular biomarkers for HCC management. Since proteins reflect disease status directly, proteomics has been utilized in biomarker developments for HCC. In particular, proteomics coupled with liquid chromatography-mass spectrometer (LC-MS) methods facilitate the process of discovering biomarker candidates for diagnosis, prognosis, and therapeutic strategies. In this work, we investigated LC-MS-based proteomics methods through recent reference reviews, with a particular focus on sample preparation and LC-MS methods appropriate for the discovery of HCC biomarkers and their clinical applications. We classified proteomics studies of HCC according to sample types, and we examined the coverage of protein biomarker candidates based on LC-MS methods in relation to study scales and goals. Comprehensively, we proposed protein biomarker candidates categorized by sample types and biomarker types for appropriate clinical use. In this review, we summarized recent LC-MS-based proteomics studies on HCC and proposed potential protein biomarkers. Our findings are expected to expand the understanding of HCC pathogenesis and enhance the efficiency of HCC diagnosis and prognosis, thereby contributing to improved patient outcomes.

Research Progress in Isotope Labeling/Tags-Based Protein Quantification and Metrology Technologies

Advanced liquid chromatogram-mass spectrometry (LC-MS) and automated large-scale data processing have made MS-based quantitative analysis increasingly useful for research in fields such as biology, medicine, food safety, and beyond. This is because MS-based quantitative analysis can accurately and sensitively analyze thousands of proteins and peptides in a single experiment. However, the precision, coverage, complexity, and resilience of conventional quantification methods vary as a result of the modifications to the analytic environment and the physicochemical characteristics of analytes. Therefore, specially designed approaches are necessary for sample preparation. Dozens of methods have been developed and adapted for these needs based on stable isotopic labeling or isobaric tagging, each with distinct characteristics. In this review, we will summarize the leading strategies and techniques used thus far for MS-based protein quantification as well as analyze the advantages and shortcomings of different approaches. Additionally, we provide an overview of protein metrology development.

Mass spectrometry-based proteomic analysis of biological stains identifies body fluids specific markers

The identification of biological stains and their tissue resource is an important part of forensic research. Current methods suffer from several limitations including poor sensitivity and specificity, trace samples, and sample destruction. In this study, we profiled the proteomes of menstrual blood, peripheral blood, saliva, semen, and vaginal fluid with mass spectrometry technology. Tissue-enhanced and tissue-specific proteins of each group have been proposed as potential biomarkers. These candidate proteins were further annotated and screened through the combination with the Human Protein Atlas database. Our data not only validates the protein biomarkers reported in previous studies but also identifies novel candidate biomarkers for human body fluids. These candidates lay the foundation for the development of rapid and specific forensic examination methods.

Evaluation of serum thioredoxin as a hepatocellular carcinoma diagnostic marker

Background

Hepatocellular carcinoma (HCC) is one of the most prevalent and fatal malignancies worldwide. Following an increase in reactive oxygen species (ROS), cancer cells enter an oxidative stress state. As a result, these cells experience an increase in antioxidant activity to counteract oxidative stress. The thioredoxin (TRX) system is a ubiquitous mammalian antioxidant system that neutralizes ROS and maintains intracellular reduction oxidation (redox) balance, which is essential for HCC growth. However, the role of TRX protein in HCC remains largely unknown. Hence, we aimed to assess the diagnostic utility of serum TRX in patients with HCC. A total of 50 patients were consecutively recruited in this observational study. They were classified into three groups: an HCC group (25 patients), a cirrhosis group (15 patients with liver cirrhosis on top of chronic HCV infection), and a control group (10 healthy individuals). Serum TRX levels were measured using ELISA.

Results

Higher serum TRX levels were detected in the HCC group than in the cirrhosis and control groups (140.96 ± 12.70 vs 88.33 ± 10.34 vs 73.10 ± 13.22 ng/mL, respectively; P < 0.001). TRX was independently associated with the presence of HCC (P < 0.001). Regarding the detection of HCC, TRX at a cut-off value of 114 ng/mL had superior diagnostic performance to AFP with an AUC of 1.000, sensitivity of 100%, and specificity of 100%, whereas AFP at a cut-off value of 20.5 ng/mL had an AUC of 1.000, sensitivity of 100%, and specificity of 47%.

Conclusion

Thioredoxin has the potential to be an HCC diagnostic marker. The clinical significance of thioredoxin in HCC requires further investigation.

Molecular mechanisms of Thrombospondin-2 modulates tumor vasculogenic mimicry by PI3K/AKT/mTOR signaling pathway

Vasculogenic mimicry (VM) differs from the classical tumor angiogenesis model. VM does not depend on endothelial cells; instead, highly aggressive tumor cells mimic endothelial cells to form a vascular-like channel structure. VM mediated by tumor cells is significantly and positively associated with a poor prognosis and low survival rates in patients with highly aggressive cancer. In the treatment of highly aggressive malignancies, the presence of VM is considered an important reason for the unsatisfactory clinical efficacy of anti-tumor-angiogenesis therapy (e.g., therapy targeting vascular endothelial growth factor A). Many targeted therapeutic drugs based on traditional tumor blood vessels have been used clinically. Although some progress has been made in certain tumors, problems such as drug resistance have restricted the expected therapeutic effects. Thrombospondin 2 (THBS2) is one of the most important genes associated with angiogenesis, and this gene exerts angiogenesis-related functions through the PI3K/AKT signaling pathway. Although the PI3K/AKT/mTOR signaling pathway is closely related to the progression of VM, the mechanism by which the promising biomarker THBS2 participates in and regulates tumor VM by activating the PI3K/AKT/mTOR signaling pathway is unclear. In this review, we analyze the monomer structure and biological activity of THBS2, the structure and potential synthesis mechanisms of VM, and the complex mechanisms between THBS2, the PI3K/AKT/mTOR signaling pathway, and VM.

Application of Intelligent Medical Sensing Technology

With the popularization of intelligent sensing and the improvement of modern medical technology, intelligent medical sensing technology has emerged as the times require. This technology combines basic disciplines such as physics, mathematics, and materials with modern technologies such as semiconductors, integrated circuits, and artificial intelligence, and has become one of the most promising in the medical field. The core of intelligent medical sensor technology is to make existing medical sensors intelligent, portable, and wearable with full consideration of ergonomics and sensor power consumption issues in order to conform to the current trends in cloud medicine, personalized medicine, and health monitoring. With the development of automation and intelligence in measurement and control systems, it is required that sensors have high accuracy, reliability, and stability, as well as certain data processing capabilities, self-checking, self-calibration, and self-compensation, while traditional medical sensors cannot meet such requirements. In addition, to manufacture high-performance sensors, it is also difficult to improve the material process alone, and it is necessary to combine computer technology with sensor technology to make up for its performance shortcomings. Intelligent medical sensing technology combines medical sensors with microprocessors to produce powerful intelligent medical sensors. Based on the original sensor functions, intelligent medical sensors also have functions such as self-compensation, self-calibration, self-diagnosis, numerical processing, two-way communication, information storage, and digital output. This review focuses on the application of intelligent medical sensing technology in biomedical sensing detection from three aspects: physical sensor, chemical sensor, and biosensor.

Epidermal Wearable Biosensors for the Continuous Monitoring of Biomarkers of Chronic Disease in Interstitial Fluid

Healthcare technology has allowed individuals to monitor and track various physiological and biological parameters. With the growing trend of the use of the internet of things and big data, wearable biosensors have shown great potential in gaining access to the human body, and providing additional functionality to analyze physiological and biochemical information, which has led to a better personalized and more efficient healthcare. In this review, we summarize the biomarkers in interstitial fluid, introduce and explain the extraction methods for interstitial fluid, and discuss the application of epidermal wearable biosensors for the continuous monitoring of markers in clinical biology. In addition, the current needs, development prospects and challenges are briefly discussed.

COL3A1, CXCL8, VCAN, THBS2, and COL1A2 are correlated with the onset of biliary atresia

BACKGROUND

Biliary atresia (BA) is a devastating progressive fibro inflammatory disorder in infants. The exact etiology of BA is still unclear. This study aimed screen key genes potentially associated with the occurrence of BA.

METHODS

All BA data was obtained from GSE46960 dataset. The limma package in R language was used for differentially expressed gene (DEG) analyses. gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were performed on the screened DEGs, using "clusterProfiler" package. protein-protein interaction network was built based on STRING Cytoscape software (Bethesda, Rockville, MD). The logistic regression model was constructed based on the selected DEGs.

RESULTS

There were totally 78 DEGs in BA samples compared with normal samples, which were significantly enriched in 200 biological process terms, 37 molecular function terms, 17 cellular component terms, and 18 Kyoto encyclopedia of genes and genomes pathways. Among which, the top 10 genes with the highest importance in protein-protein interaction network were selected. Subsequently, on the basis of the stepwise regression method and 5-fold cross-validation, the logistic regression model constructed based on COL3A1, CXCL8, VCAN, THBS2, and COL1A2 was finally evidenced to predict the BA sample relatively reliably.

CONCLUSIONS

In conclusion, COL3A1, CXCL8, VCAN, THBS2, and COL1A2 are potentially crucial genes in BA. The logistic regression model constructed based on them could predict the BA sample relatively reliably.

Prognostic value of SPARC in hepatocellular carcinoma: A systematic review and meta-analysis

Objective

Hepatocellular carcinoma (HCC) is characterized by a high degree of malignancy, rapid proliferation of tumor cells, and early liver metastasis. Resistance to multiple drugs independent of the high expression of secreted protein acidic and rich in cysteine (SPARC) is associated with a high risk of recurrence and mortality. However, the prognostic value of SPARC in patients with HCC remains unclear. Therefore, we performed a meta-analysis to evaluate the relationship between the expression of SPARC and the prognosis of patients with HCC.

Methods

We searched for relevant articles in the CNKI, PubMed, EMBASE, and Web of Science databases. The 95% confidence intervals (CIs) were calculated for combined overall survival (OS) and disease-free survival (DFS) to assess the prognostic value of expression of SPARC in patients with HCC.

Results

In six of the studies, SPARC expression status was significantly associated with OS (combined hazard ratio [HR], 1.38; 95% CI, 1.0–1.82; Z = 2.27, P = 0.02) but not with DFS (combined HR, 0.79; 95% CI, 0.16–4.00, Z = 0.28, P = 0.78). Therefore, it cannot be assumed that upregulated SPARC expression has an effect on DFS in patients with HCC.

Conclusion

Elevated SPARC expression is associated with a low survival rate but not with DFS in patients with HCC. Further studies are needed to confirm our conclusions.

Registration

INPLASY registration number: INPLASY202180115. https://inplasy.com/inplasy-2021-8-0115/.

End-to-end design of wearable sensors

Wearable devices provide an alternative pathway to clinical diagnostics by exploiting various physical, chemical and biological sensors to mine physiological (biophysical and/or biochemical) information in real time (preferably, continuously) and in a non-invasive or minimally invasive manner. These sensors can be worn in the form of glasses, jewellery, face masks, wristwatches, fitness bands, tattoo-like devices, bandages or other patches, and textiles. Wearables such as smartwatches have already proved their capability for the early detection and monitoring of the progression and treatment of various diseases, such as COVID-19 and Parkinson disease, through biophysical signals. Next-generation wearable sensors that enable the multimodal and/or multiplexed measurement of physical parameters and biochemical markers in real time and continuously could be a transformative technology for diagnostics, allowing for high-resolution and time-resolved historical recording of the health status of an individual. In this Review, we examine the building blocks of such wearable sensors, including the substrate materials, sensing mechanisms, power modules and decision-making units, by reflecting on the recent developments in the materials, engineering and data science of these components. Finally, we synthesize current trends in the field to provide predictions for the future trajectory of wearable sensors.

Diagnostic and Prognostic Roles of Thrombospondin-2 in Digestive System Cancers

BACKGROUND

Cancers of digestive system have high case-fatality rate. It is important to find more appropriate methods in diagnosing and predicting gastrointestinal malignances. And thrombospondin-2 (TSP-2) was reported to have the functions, although results were not identical. So we performed this meta-analysis to clarify the significance of TSP-2 in this area.

METHODS

PubMed, Embase, Web of Science, Cochrane Library, and Clinicaltrial.gov were searched for relevant studies. Data were extracted from these involved records. For the meta-analysis of diagnostic test, bivariate mixed effect model was used to estimate diagnostic accuracy. For prognosis part, HRs and their 95% CIs were pooled to compare the overall survival (OS) and disease-free survival (DFS) between patients with high TSP-2 and low TSP-2.

RESULTS

Nine records were eligible for the analysis of diagnostic test. Pooled results were as follows: sensitivity 0.60 (0.52, 0.68), specificity 0.96 (0.91, 0.98), positive likelihood ratio (PLR) 15.4 (7.3, 32.2), negative likelihood ratio (NLR) 0.42 (0.34, 0.50), and diagnostic odds ratio (DOR) 37 (18, 76). While in prognosis part, 10 articles were included. Patients with increased TSP-2 had shorter OS (HR = 1.64, 95% CI = 1.21-2.22); however, no difference was found in DFS between TSP-2 high and low groups (HR = 1.44, 95% CI = 0.28-7.33).

CONCLUSIONS

TSP-2, as a diagnostic marker, has a high specificity but a moderate sensitivity. Meanwhile, it plays a role in predicting OS. Therefore, making TSP-2 a routine assay could be beneficial to high-risk individuals and patients with digestive malignances.

Identification of potential modifier genes in Chinese patients with Wilson disease

The mutations in modifier genes may contribute to some inherited diseases including Wilson disease (WD). This study was designed to identify potential modifier genes that contribute to WD. A total of 10 WD patients with single or no heterozygous ATP7B mutations were recruited for whole-exome sequencing (WES). Five hundred and thirteen candidate genes, of which the genetic variants present in at least two patients, were identified. In order to clarify which proteins might be involved in copper transfer or metabolism processes, the isobaric tags for relative and absolute quantitation (iTRAQ) was performed to identify the differentially expressed proteins between normal and CuSO4-treated cell lines. Thirteen genes/proteins were identified by both WES and iTRAQ, indicating that disease-causing variants of these genes may actually contribute to the aberrant copper ion accumulation. Additionally, the c.86C > T (p.S29L) mutation in the SLC31A2 gene (coding CTR2) has a relative higher frequency in our cohort of WD patients (6/191) than reported (0.0024 in gnomAD database) in our healthy donors (0/109), and CTR2S29L leads to increased intracellular Cu concentration and Cu-induced apoptosis in cultured cell lines. In conclusion, the WES and iTRAQ approaches successfully identified several disease-causing variants in potential modifier genes that may be involved in the WD phenotype.

Recent Progress in Microneedles-Mediated Diagnosis, Therapy, and Theranostic Systems

Theranostic system combined diagnostic and therapeutic modalities is critical for the real-time monitoring of disease-related biomarkers and personalized therapy. Microneedles, as a multifunctional platform, are promising for transdermal diagnostics and drug delivery. They have shown attractive properties including painless skin penetration, easy self-administration, prominent therapeutic effects, and good biosafety. Herein, an overview of the microneedles-based diagnosis, therapies, and theranostic systems is given. Four microneedles-based detection methods are concluded based on the sensing mechanism: i) electrochemistry, ii) fluorometric, iii) colorimetric, and iv) Raman methods. Additionally, robust microneedles are suitable for implantable drug delivery. Microneedles-assisted transdermal drug delivery can be primarily classified as passive, active, and responsive drug release, based on the release mechanisms. Microneedles-assisted oral and implantable drug delivery mechanisms are also presented in this review. Furthermore, the key frontier developments in microneedles-mediated theranostic systems as the major selling points are emphasized in this review. These systems are classified into open-loop and closed-loop theranostic systems based on the indirectness and directness of feedback between the transdermal diagnosis and therapy, respectively. Finally, conclusions and future perspectives for next-generation microneedles-mediated theranostic systems are also discussed. Taken together, microneedle-based systems are promising as the new avenue for diagnosis, therapy, and disease-specific closed-loop theranostic applications.

Thrombospondin-2 as a diagnostic biomarker for distal cholangiocarcinoma and pancreatic ductal adenocarcinoma

PURPOSE

Distal cholangiocarcinoma and pancreatic ductal adenocarcinoma are malignancies with poor prognoses that can be difficult to distinguish preoperatively. Thrombospondin-2 has been proposed as a novel diagnostic biomarker for early pancreatic ductal adenocarcinoma. The aim of the present study was to evaluate thrombospondin-2 as a diagnostic and prognostic biomarker in combination with current biomarker CA 19-9 for distal cholangiocarcinoma and pancreatic ductal adenocarcinoma.

METHODS

Thrombospondin-2 was measured in prospectively collected serum samples from patients who underwent surgery with a histopathological diagnosis of distal cholangiocarcinoma (N = 51), pancreatic ductal adenocarcinoma (N = 52) and benign pancreatic diseases (N = 27) as well as healthy blood donors (N = 52) using an enzyme-linked immunosorbent assay.

RESULTS

Thrombospondin-2 levels (ng/ml) were similar in distal cholangiocarcinoma 55 (41-77) and pancreatic ductal adenocarcinoma 48 (35-80) (P = 0.221). Thrombospondin-2 + CA 19-9 had an area under the curve of 0.92 (95% CI 0.88-0.97) in differentiating distal cholangiocarcinoma and pancreatic ductal adenocarcinoma from healthy donors which was superior to CA 19-9 alone (P < 0.001). The diagnostic value of adding thrombospondin-2 to CA 19-9 was larger in early disease stages. Thrombospondin-2 did not provide additional value to CA 19-9 in differentiating the benign disease group; however, heterogeneity was notable in the benign cohort. Three of five patients with autoimmune pancreatitis patients had greatly elevated thrombospondin-2 levels. Thrombospondin-2 levels had no correlation with prognoses.

CONCLUSIONS

Serum thrombospondin-2 in combination with CA 19-9 has potential as a biomarker for distal cholangiocarcinoma and pancreatic cancer.

SPARC Overexpression Promotes Liver Cancer Cell Proliferation and Tumor Growth

Background: Secreted protein acidic and rich in cysteine (SPARC) plays an important role in cancer development. The roles of SPARC in the liver hepatocellular carcinoma (LIHC) are unclear. Methods: GEPIA2 and UALCAN were used to analyze the SPARC mRNA expression levels in LIHC based on the TCGA database. The GEO database was used to verify the analysis results. Immunohistochemical (IHC) analysis was used to investigate the SPARC protein levels in LIHC tissues. The Kaplan-Meier (KM) plotter was used to analyze the correlation between SPARC and prognosis. The serum SPARC levels were measured by ELISA. CCK8 and murine xenograft models were used to investigate the effect of SPARC on the liver cancer growth in vitro and in vivo. SPARC-correlated genes were screened by LinkedOmics. Results: Based on the TCGA and GEO databases, the analysis showed that the SPARC mRNA expression levels were increased in tumor tissues and peripheral blood mononuclear cell (PBMC) from LIHC compared to normal controls. The IHC analysis showed an increased level of SPARC in LIHC tissues compared to adjacent non-tumor tissues. However, we found that the serum SPARC levels were lower in LIHC than those in healthy controls. The KM plotter showed that there was no significant correlation between the SPARC mRNA levels and overall survival. However, in sorafenib-treated LIHC patients, the high SPARC expression predicts favorable prognosis. Furthermore, the endogenous SPARC overexpression promotes liver cancer cell proliferation in vitro and tumor growth in vivo, while there was no significant effect of exogenous SPARC treatment on liver cancer cell proliferation. Function enrichment analysis of SPARC-correlated genes indicated a critical role of interaction with an extracellular matrix in SPARC-promoting cancer cell proliferation. Conclusion: SPARC mRNAs were increased in LIHC tumor tissues, and SPARC overexpression may promote the liver cancer growth. Further studies are needed to clarify the potential prognostic value of SPARC, both in tissues and in circulation.

Hepatocellular Carcinoma in 2021: An Exhaustive Update

Primary liver cancer is a challenging global health concern with an estimated more than a million persons to be affected annually by the year 2025. The commonest type is hepatocellular carcinoma (HCC), which has been increasing in incidence the world over, mostly due to chronic viral hepatitis B infection. In the last decade, paradigm changes in the etiology, understanding of molecular biology, and pathogenesis, including the role of gut microbiota; medical and surgical treatments, and outcome trends are notable. The application of omics-based technology has helped us unlock the molecular and immune landscape of HCC, through which novel targets for drug treatment such as immune-checkpoint inhibitors have been identified. Novel tools for the surveillance and diagnosis of HCC include protein-, genomics-, and composite algorithm-based clinical/biomarker panels. Magnetic resonance imaging-based novel techniques have improved HCC diagnosis through ancillary features that enhance classical criteria while positron emission tomography has shown value in prognostication. Identification of the role of gut microbiota in the causation and progression of HCC has opened areas for novel therapeutic research. A select group of patients still benefit from modified surgical and early interventional radiology treatments. Improvements in radiotherapy protocols, identification of parameters of futility among radiological interventions, and the emergence of novel first-line systemic therapies that include a combination of antiangiogenic and immune-checkpoint inhibitors have seen a paradigm change in progression-free and overall survival. The current review is aimed at providing exhaustive updates on the etiology, molecular biology, biomarker diagnosis, imaging, and recommended treatment options in patients with HCC.

Beyond liquid biopsy: Toward non-invasive assays for distanced cancer diagnostics in pandemics

Liquid biopsy technologies have seen a significant improvement in the last decade, offering the possibility of reliable analysis and diagnosis from several biological fluids. The use of these technologies can overcome the limits of standard clinical methods, related to invasiveness and poor patient compliance. Along with this there are now mature examples of lab-on-chips (LOC) which are available and could be an emerging and breakthrough technology for the present and near-future clinical demands that provide sample treatment, reagent addition and analysis in a sample-in/answer-out approach. The possibility of combining non-invasive liquid biopsy and LOC technologies could greatly assist in the current need for minimizing exposure and transmission risks. The recent and ongoing pandemic outbreak of SARS-CoV-2, indeed, has heavily influenced all aspects of life worldwide. Ordinary tasks have been forced to switch from “in presence” to “distanced”, limiting the possibilities for a large number of activities in all fields of life outside of the home. Unfortunately, one of the settings in which physical distancing has assumed noteworthy consequences is the screening, diagnosis and follow-up of diseases.

In this review, we analyse biological fluids that are easily collected without the intervention of specialized personnel and the possibility that they may be used -or not-for innovative diagnostic assays. We consider their advantages and limitations, mainly due to stability and storage and their integration into Point-of-Care diagnostics, demonstrating that technologies in some cases are mature enough to meet current clinical needs.

Identifying the biomarkers and pathways associated with hepatocellular carcinoma based on an integrated analysis approach

BACKGROUND AND AIMS

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. The molecular mechanism underlying HCC is still unclear. In this study, we conducted a comprehensive analysis to explore the genes, pathways and their interactions involved in HCC.

METHODS

We analysed the gene expression datasets corresponding to 488 samples from 10 studies on HCC and identified the genes differentially expressed in HCC samples. Then, the genes were compared against Phenolyzer and GeneCards to screen those potentially associated with HCC. The features of the selected genes were explored by mapping them onto the human protein-protein interaction network, and a subnetwork related to HCC was constructed. Hub genes in this HCC specific subnetwork were identified, and their relevance with HCC was investigated by survival analysis.

RESULTS

We identified 444 differentially expressed genes (177 upregulated and 267 downregulated) related to HCC. Functional enrichment analysis revealed that pathways like p53 signalling and chemical carcinogenesis were eriched in HCC genes. In the subnetwork related to HCC, five disease modules were detected. Further analysis identified six hub genes from the HCC specific subnetwork. Survival analysis showed that the expression levels of these genes were negatively correlated with survival rate of HCC patients.

CONCLUSIONS

Based on a systems biology framework, we identified the genes, pathways, as well as the disease specific network related to HCC. We also found novel biomarkers whose expression patterns were correlated with progression of HCC, and they could be candidates for further investigation.

Microneedle Arrays for Sampling and Sensing Skin Interstitial Fluid

Dermal interstitial fluid (ISF) is a novel source of biomarkers that can be considered as an alternative to blood sampling for disease diagnosis and treatment. Nevertheless, in vivo extraction and analysis of ISF are challenging. On the other hand, microneedle (MN) technology can address most of the challenges associated with dermal ISF extraction and is well suited for long-term, continuous ISF monitoring as well as in situ detection. In this review, we first briefly summarise the different dermal ISF collection methods and compare them with MN methods. Next, we elaborate on the design considerations and biocompatibility of MNs. Subsequently, the fabrication technologies of various MNs used for dermal ISF extraction, including solid MNs, hollow MNs, porous MNs, and hydrogel MNs, are thoroughly explained. In addition, different sensing mechanisms of ISF detection are discussed in detail. Subsequently, we identify the challenges and propose the possible solutions associated with ISF extraction. A detailed investigation is provided for the transport and sampling mechanism of ISF in vivo. Also, the current in vitro skin model integrated with the MN arrays is discussed. Finally, future directions to develop a point-of-care (POC) device to sample ISF are proposed.

Distribution of serum Thrombospondin-2, a novel tumor marker, in general population and cancer patients in China

PURPOSE

Distribution of serum thrombospondin-2 in general population and cancer patients in China have not been reported.

METHODS

This study evaluated the expression level of serum thrombospondin-2 in general population and various cancer patients, the 95% confidence interval was used for the derivation of reference range. The comparison of the expression levels in controls for age and gender was performed. The associations between candidate biomarkers (thrombospondin-2 [THBS2]) expression and tumor metastasis status were also explored.

RESULTS

125 healthy controls and 193 various cancer patients were enrolled. The mean ± SD in serum THBS2 levels in general population was 42.37 ± 12.24 ng/ml, there was no significant sex and age difference, the reference range is 18.37-66.36 ng/ml. Most cancer patients present a decreased serum THBS2 level except hepatoma and lymphoma which most patients showed a relatively high level of THBS2. There was no statistical difference of serum THBS2 level between metastasis and non-metastasis group in breast, lung, cervical, colorectal cancer, nasopharyngeal carcinoma and hepatoma (P > 0.05) while a significant negative correlation was observed in ovarian cancer (P = 0.0209).

CONCLUSIONS

The distribution of serum THBS2 displayed an obvious heterogeneity among various cancers comparing to health controls, ovarian cancer patients detected with low THBS2 expression may be more prone to develop metastasis in China.

Minimally Invasive Biospecimen Collection for Exposome Research in Children's Health

PURPOSE OF REVIEW

The advent of low-volume biosampling and novel biomarker matrices offers non- or minimally invasive approaches to sampling in children. These new technologies, combined with advancements in mass spectrometry that provide high sensitivity, robust measurements of low-concentration exposures, facilitate the application of untargeted metabolomics in children's exposome research. Here, we review emerging sampling technologies for alternative biomatrices-dried capillary blood, interstitial fluid, saliva, teeth, and hair-and highlight recent applications of these samplers to drive discovery in population-based exposure research.

RECENT FINDINGS

Biosampling and biomarker technologies demonstrate potential to directly measure exposures during key developmental time periods. While saliva is the most traditional of the reported biomatrices, each technology has key advantages and disadvantages. For example, hair and teeth provide retrospective analysis of past exposures, and dried capillary blood provides quantitative measurements of systemic exposures that can be more readily compared with traditional venous blood measurements. Importantly, all technologies can or have the potential to be used at home, increasing the convenience and parental support for children's biosampling. This review describes emerging sample collection technologies that hold promise for children's exposome studies. While applications in metabolomics are still limited, these novel matrices are poised to facilitate longitudinal exposome studies to discover key exposures and windows of susceptibility affecting children's health.

Biomarker Identification for Liver Hepatocellular Carcinoma and Cholangiocarcinoma Based on Gene Regulatory Network Analysis

Background:

Liver hepatocellular carcinoma (LIHC) and cholangiocarcinoma (CHOL) are two main histological subtypes of primary liver cancer with a unified molecular landscape, and feed-forward loops (FFLs) have been shown to be relevant in these complex diseases.

Objective:

To date, there has been no comparative analysis of the pathogenesis of LIHC and CHOL based on regulatory relationships. Therefore, we investigated the common and distinct regulatory properties of LIHC and CHOL in terms of gene regulatory networks.

Method:

Based on identified FFLs and an analysis of pathway enrichment, we constructed pathway-specific co-expression networks and further predicted biomarkers for these cancers by network clustering.

Resul:

We identified 20 and 36 candidate genes for LIHC and CHOL, respectively. The literature from PubMed supports the reliability of our results.

Conclusion:

Our results indicated that the hsa01522-Endocrine resistance pathway was associated with both LIHC and CHOL. Additionally, six genes (SPARC, CTHRC1, COL4A1, EDIL3, LAMA4 and OLFML2B) were predicted to be highly associated with both cancers, and COL4A2, CSPG4, GJC1 and ADAMTS7 were predicted to be potential biomarkers of LIHC, and COL6A3, COL1A2, FAP and COL8A1 were predicted to be potential biomarkers of CHOL. In addition, we inferred that the Collagen gene family, which appeared more frequently in our overall prediction results, might be closely related to cancer development.

Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth

We previously reported that human carboxylesterase 1 (CES1), a serine esterase containing a unique N-linked glycosyl group at Asn79 (N79 CES1), is a candidate serological marker of hepatocellular carcinoma (HCC). CES1 is normally present at low-to-undetectable levels in normal human plasma, HCC tumors, and major liver cancer cell lines. To investigate the potential mechanism underlying the suppression of CES1 expression in liver cancer cells, we took advantage of the low detectability of this marker in tumors by overexpressing CES1 in multiple HCC cell lines, including stable Hep3B cells. We found that the population of CES1-overexpressing (OE) cells decreased and that their doubling time was longer compared with mock control liver cancer cells. Using interactive transcriptome, proteome, and subsequent Gene Ontology enrichment analysis of CES1-OE cells, we found substantial decreases in the expression levels of genes involved in cell cycle regulation and proliferation. This antiproliferative function of the N79 glycan of CES1 was further supported by quantitative real-time polymerase chain reaction, flow cytometry, and an apoptosis protein array assay. An analysis of the levels of key signaling target proteins via Western blotting suggested that CES1 overexpression exerted an antiproliferative effect via the PKD1/PKCμ signaling pathway. Similar results were also seen in another HCC cell line (PLC/RFP/5) after transient transfection with CES1 but not in similarly treated non-HCC cell lines (e.g., HeLa and Tera-1 cells), suggesting that CES1 likely exerts a liver cell-type-specific suppressive effect. Given that the N-linked glycosyl group at Asn79 (N79 glycan) of CES1 is known to influence CES1 enzyme activity, we hypothesized that the post-translational modification of CES1 at N79 may be linked to its antiproliferative activity. To investigate the regulatory effect of the N79 glycan on cellular growth, we mutated the single N-glycosylation site in CES1 from Asn to Gln (CES1-N79Q) via site-directed mutagenesis. Fluorescence 2-D difference gel electrophoresis protein expression analysis of cell lysates revealed an increase in cell growth and a decrease in doubling time in cells carrying the N79Q mutation. Thus our results suggest that CES1 exerts an antiproliferative effect in liver cancer cells and that the single N-linked glycosylation at Asn79 plays a potential regulatory role. These functions may underlie the undetectability of CES1 in human HCC tumors and liver cancer cell lines. Mass spectrometry data are available via ProteomeXchange under the identifier PXD021573.

Low Levels of SPARC are Associated with Tumor Progression and Poor Prognosis in Human Endometrial Carcinoma

Background

SPARC (secreted protein acidic and rich in cysteine), also known as osteonectin, BM-40, and 43 K protein, is a matricellular protein associated with various tumor progressions. The aim of this research was to investigate the prognostic value of SPARC in endometrial carcinoma (EC) and its function in cancer cell invasion and metastasis.

Methods

From both mRNA and protein levels, SPARC expression in normal endometrial tissue and EC tissue, normal endometrial cells and 4 EC cell lines (KLE, HEC-1A, HEC-1B, Ishikawa) were evaluated by immunohistochemistry (IHC) or immunocytochemistry (ICC), quantitative real-time PCR (qRT-PCR) and Western blotting. RNA interference mediated by lentivirus was performed to get the stable SPARC down-expressing cells. The functional analysis techniques in vitro and in vivo were used to detect the effects of SPARC knockdown on EC cell proliferation, apoptosis, invasion and metastasis.

Results

The expressions of SPARC in EC tissues and cells were much lower than those in normal endometrial cells and tissues; meanwhile, its low expression was closely related to the malignant clinicopathological characteristics of EC. SPARC knockdown could inhibit apoptosis, promote the process of EMT and improve the proliferation and invasion capacities of EC cells in vitro and in vivo.

Conclusion

The low expression of SPARC was detected in EC tissues and cells, which was positively correlated with the poor prognosis of EC patients. SPARC acted as a tumor suppressor gene that hindered EC progression, which proposed a new therapeutic strategy for EC treatment.

The use of minimally invasive biomarkers for the diagnosis and prognosis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a common cause of cancer-related deaths worldwide. Despite advances in systemic therapies, patient survival remains low due to late diagnosis and frequent underlying liver diseases. HCC diagnosis generally relies on imaging and liver tissue biopsy. Liver biopsy presents limitations because it is invasive, potentially risky for patients and it frequently misrepresents tumour heterogeneity. Recently, liquid biopsy has emerged as a way to monitor cancer progression in a non-invasive manner. Tumours shed content into the bloodstream, such as circulating tumour cells (CTCs), circulating nucleic acids, extracellular vesicles and proteins, that can be isolated from biological fluids of patients with HCC. These biomarkers provide knowledge regarding the genetic landscape of tumours and might be used for diagnostic or prognostic purposes. In this review, we summarize recent literature on circulating biomarkers for HCC, namely CTCs, circulating tumour DNA (ctDNA), RNA, extracellular vesicles and proteins, and their clinical relevance in HCC.

Quantitative proteomics identifies a plasma multi-protein model for detection of hepatocellular carcinoma

More efficient biomarkers are needed to facilitate the early detection of hepatocellular carcinoma (HCC). We aimed to identify candidate biomarkers for HCC detection by proteomic analysis. First, we performed a global proteomic analysis of 10 paired HCC and non-tumor tissues. Then, we validated the top-ranked proteins by targeted proteomic analyses in another tissue cohort. At last, we used enzyme-linked immunosorbent assays to validate the candidate biomarkers in multiple serum cohorts including HCC cases (HCCs), cirrhosis cases (LCs), and normal controls (NCs). We identified and validated 33 up-regulated proteins in HCC tissues. Among them, eight secretory or membrane proteins were further evaluated in serum, revealing that aldo-keto reductase family 1 member B10 (AKR1B10) and cathepsin A (CTSA) can distinguish HCCs from LCs and NCs. The area under the curves (AUCs) were 0.891 and 0.894 for AKR1B10 and CTSA, respectively, greater than that of alpha-fetoprotein (AFP; 0.831). Notably, combining the three proteins reached an AUC of 0.969, which outperformed AFP alone (P < 0.05). Furthermore, the serum AKR1B10 levels dramatically decreased after surgery. AKR1B10 and CTSA are potential serum biomarkers for HCC detection. The combination of AKR1B10, CTSA, and AFP may improve the HCC diagnostic efficacy.

New Blood Biomarkers for the Diagnosis of AFP-Negative Hepatocellular Carcinoma

An early diagnosis of hepatocellular carcinoma (HCC) followed by effective treatment is currently critical for improving the prognosis and reducing the associated economic burden. Alpha-fetoprotein (AFP) is the most widely used biomarker for HCC diagnosis. Based on elevated serum AFP levels as well as typical imaging features, AFP-positive HCC (APHC) can be easily diagnosed, but AFP-negative HCC (ANHC) is not easily detected due to lack of ideal biomarkers and thus mainly reliance on imaging. Imaging for the diagnosis of ANHC is probably insufficient in sensitivity and/or specificity because most ANHC tumors are small and early-stage HCC, and it is involved in sophisticated techniques and high costs. Moreover, ANHC accounts for nearly half of HCC and exhibits a better prognosis compared with APHC. Therefore, the diagnosis of ANHC in clinical practice has been a critical issue for the early treatment and prognosis improvement of HCC. In recent years, tremendous efforts have been made to discover new biomarkers complementary to AFP for HCC diagnosis. In this review, we systematically review and discuss the recent advances of blood biomarkers for HCC diagnosis, including DNA biomarkers, RNA biomarkers, protein biomarkers, and conventional laboratory metrics, focusing on their diagnostic evaluation alone and in combination, in particular on their diagnostic performance for ANHC.

HKR3 regulates cell cycle through the inhibition of hTERT in hepatocellular carcinoma cell lines

Hepatocellular carcinoma is a malignant disease with improved hepatic regeneration and survival, and is activated by human telomere transferase (hTERT). hTERT is expressed during early fetal development and switched off in most adult tissues, but it becomes reactivated in HCC. The exact mechanism regulating these expression changes remains unknown during HCC progress. We evaluated the relationship between hTERT expression and human kruppel-related 3 (HKR3) and cell cycle-related factors in HCC cell lines. Following transfection for hTERT knockdown and HKR3 overexpression, proteomic and transcriptomic analyses related to hTERT were performed using liquid chromatography/mass spectrometry (LC/MS) and RNA sequencing (RNAseq) in HCC cell lines. The expression levels of hTERT, HKR3, and cell cycle-related factors were measured using western blotting, and tumor growth were evaluated via cell proliferation and cell cycle assays. Transcriptomic and proteomic analyses showed that HKR3, hTERT and cyclin-dependent kinase inhibitor 2A (CDKN2A) were correlated. Up-regulation of HKR3 expression decreased hTERT and cyclin activation and suppressed the G1/S phase of the cell cycle through CDKN2A activation. Our results suggest that HKR3 induced regulation of cell cycle through hTERT inhibition and CDKN2A activation. Our results will facilitate further exploration of the pathways regulating human telomerase activity in HCC cell lines.

Serum soluble VSIG4 as a surrogate marker for the diagnosis of lymphoma-associated hemophagocytic lymphohistiocytosis

Lymphoma-associated haemophagocytic lymphohistiocytosis (L-HLH) is characterized by excessively activated macrophages and cytotoxic T lymphocytes, but few reliable markers for activated macrophages are available clinically. This study, designed to discover novel biomarkers for the diagnosis of lymphoma patients with L-HLH, was initiated between 2016 and 2018. Fifty-seven adult lymphoma patients were enrolled - 39 without HLH and 18 with HLH. The differential serum protein expression profile was first screened between lymphoma patients with and without L-HLH by a quantitative mass spectrometric approach. Soluble V-set and immunoglobulin domain-containing 4 (sVSIG4), specifically expressed by macrophages, was significantly upregulated in the L-HLH group. Subsequently, sVSIG4 concentration was confirmed by enzyme-linked immunosorbent assay to be significantly increased in lymphoma patients with L-HLH. When it was exploited for the diagnosis of lymphoma patients with L-HLH, the area under a receiver operating characteristic curve was 0·98 with an optimal cut-off point of 2195 pg/ml and the corresponding sensitivity and specificity were 94·44% and 94·87% respectively. In addition, the one-year overall survival was significantly worse in patients with a sVSIG4 concentration above 2195 pg/ml compared with those below 2195 pg/ml (5·3% vs. 72·2%, P < 0·0001). sVSIG4 may be a surrogate marker of activated macrophages for the diagnosis of lymphoma patients with L-HLH.

Review of the Application of Nanovesicles and the Human Interstitial Fluid in Gastrointestinal Premalignant Lesion Detection, Diagnosis, Prognosis and Therapy

Premalignant lesions arise from cells that abnormally proliferate and have a tendency to become cancerous. Developing methods to specifically target and remove these premalignant lesions is imperative to the prevention of malignant progression into gastrointestinal (GI) tumors. However, accurate detection and diagnosis of GI precancerous lesions is challenging, as these lesions show little or no structural change. Thus, this prevents early intervention and reduces the success rate of therapy. In this review, we performed a systematic analysis of the technological advancements in the combined application of nanovesicles (NVs) and the human interstitial fluid (HIF) to specifically target GI premalignant lesions. NVs, which include quantum dots (QDs), are small membranous vehicles of a nanometer diameter that are widely used as drug delivery vectors, therapeutic effectors and diagnostic sensors. HIF is the fluid that is present in human interstitial tissues (HITs) in which signaling molecules and agents travel and can be found throughout the body. HIF is exploited by tumor cells for their invasion, migration and spread. Because the HITs span the entire submucosa of the gastrointestinal tract, they have been increasingly targeted in GI tumor therapy. The challenges involved in the combined application of NVs and HIF in the detection, diagnosis, prognosis and therapy of GI premalignant lesions are also discussed.

IGF2 enhanced the osteo-/dentinogenic and neurogenic differentiation potentials of stem cells from apical papilla

OBJECTIVES

In dental tissue engineering, niche is important for maintaining stem cell function and regenerating the dental tissues. However, there is limited knowledge for the growth factors in niche to maintain the function of stem cells. In this study, we investigated the effect of IGF2, a growth factor in stem cells from apical papilla (SCAPs) niche, on differentiation and proliferation potentials of SCAPs.

MATERIALS AND METHODS

Recombinant human IGF2 protein (rhIGF2) was used. Cell counting kit-8 assay, Carboxyfluorescein succinimidyl ester assay, alkaline phosphatase (ALP) activity, Alizarin Red staining, quantitative calcium analysis, immunofluorescence staining and real-time RT-PCR were performed to investigate the cell proliferation and differentiation potentials of SCAPs. And proteomic analysis was used to identify the differential secreted proteins.

RESULTS

By ALP activity assay, we found that 5 ng/mL rhIGF2 might be the optimal concentration for treatment. Then, Alizarin Red staining, quantitative calcium analysis and osteogenesis-related gene expression results showed that 5 ng/mL rhIGF2 could enhance the osteo-/dentinogenic differentiation potentials in SCAPs. Immunofluorescence staining and real-time RT-PCR results showed that neurogenic markers were significantly induced by 5 ng/mL rhIGF2 in SCAPs. Then, CCK-8 assay and CFSE assay results showed that 5 ng/mL rhIGF2 could enhance the cell proliferation in SCAPs. Furthermore, proteomic analysis showed that IGF2 could induce some secreted proteins which function related to the osteogenesis, neurogenesis and cell proliferation.

CONCLUSIONS

Our results identified that IGF2 might be the potential mediator in niche to promote SCAP function and dental tissue regeneration.

Thrombospondin-2 is a Highly Specific Diagnostic Marker and is Associated with Prognosis in Pancreatic Cancer

BACKGROUND

Thrombospondin-2 (TSP-2) has been reported as an early diagnostic marker for pancreatic ductal adenocarcinoma (PDAC) in Caucasian populations. This study was designed to validateTSP-2 as a diagnostic marker in a large Taiwan cohort and to investigate the association of TSP-2 with the clinical outcomes of PDAC patients.

METHODS

The serum TSP-2 levels in 263 PDAC patients and 230 high-risk individuals (HRIs) were measured via an enzyme-linked immunosorbent assay. The sensitivity, specificity, and accuracy of TSP-2 as a diagnostic marker to discriminating PDAC patients from HRIs and correlations between TSP-2 levels and prognosis of PDAC patients were analyzed.

RESULTS

Serum TSP-2 levels were significantly higher in patients with PDAC (44.90 ± 40.70 ng/ml) than in the HRIs (17.52 ± 6.23 ng/ml). At a level of ≥ 29.8 ng/ml, TSP-2 exhibited 100% specificity, 55.9% sensitivity, 100% positive predictive value (PPV), and 66.5% negative predictive value (NPV) for discriminating PDAC patients from HRIs. The Cox regression analysis showed that higher serum TSP-2 levels were significantly associated with poor outcomes in PDAC patients (hazard ratio = 1.54, 95% confidence interval = 1.143-2.086, P = 0.005). Combining the carbohydrate antigen 19-9 (CA19-9) (cutoff value of 62.0 U/ml) and TSP-2 (cutoff value of 29.8 ng/ml) levels yielded 98.7% specificity, 90.5% sensitivity, 98.8% PPV, and 90.1% NPV for discriminating patients with PDAC from HRIs.

CONCLUSIONS

TSP-2 is a highly specific diagnostic marker and an independent prognostic marker in patients with PDAC. A combined biomarker panel, including TSP-2 and CA19-9, may facilitate future PDAC screening.

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues Using PCT-SWATH

PURPOSE

To rapidly identify protein abundance changes in biopsy-level fresh-frozen hepatocellular carcinoma (HCC).

EXPERIMENTAL DESIGN

The pressure-cycling technology (PCT) is applied and sequential window acquisition of all theoretical mass spectra (SWATH-MS) workflow is optimized to analyze 38 biopsy-level tissue samples from 19 HCC patients. Each proteome is analyzed with 45 min LC gradient. MCM7 is validated using immunohistochemistry (IHC).

RESULTS

A total of 11 787 proteotypic peptides from 2579 SwissProt proteins are quantified with high confidence. The coefficient of variation (CV) of peptide yield using PCT is 32.9%, and the R² of peptide quantification is 0.9729. Five hundred forty-one proteins showed significant abundance change between the tumor area and its adjacent benign area. From 24 upregulated pathways and 13 suppressed ones, enhanced biomolecule synthesis and suppressed small molecular metabolism in liver tumor tissues are observed. Protein changes based on α-fetoprotein expression and hepatitis B virus infection are further analyzed. The data altogether highlight 16 promising tumor marker candidates. The upregulation of minichromosome maintenance complex component 7 (MCM7) is further observed in multiple HCC tumor tissues by IHC.

CONCLUSIONS AND CLINICAL RELEVANCE

The practicality of rapid proteomic analysis of biopsy-level fresh-frozen HCC tissue samples with PCT-SWATH has been demonstrated and promising tumor marker candidates including MCM7 are identified.

Contribution of the plasma and lymph Degradome and Peptidome to the MHC Ligandome

Every biological fluid, blood, interstitial fluid and lymph, urine, saliva, lacrimal fluid, nipple aspirate, and spinal fluid, contains a peptidome-degradome derived from the cellular secretome along with byproducts of the metabolic/catabolic activities of each parenchymal organ. Clement et al. (J Proteomics 78:172-187, 2013), Clement et al. (J Biol Chem 291:5576-5595, 2016), Clement et al. (PLoS One 5:e9863, 2010), Clement et al. (Trends Immunol 32:6-11, 2011), Clement et al. (Front Immunol 4:424, 2013), Geho et al. (Curr Opin Chem Biol 10, 50-55, 2006), Interewicz et al. (Lymphology 37:65‑72, 2004), Leak et al. (Proteomics 4:753‑765, 2004), Popova et al. (PLoS One 9:e110873, 2014), Zhou et al. (Electrophoresis 25:1289‑1298, 2004), D'Alessandro et al. (Shock 42:509‑517, 2014), Dzieciatkowska et al. (Shock 42:485‑498, 2014), Dzieciatkowska et al. (Shock 35:331‑338, 2011), Jordan et al. (J Surg Res 143:130‑135, 2007), Peltz et al. (Surgery 146:347‑357, 2009), Zurawel et al. (Clin Proteomics 8:1, 2011), Ling et al. (Clin Proteomics 6:175‑193, 2010), Sturm et al. (Nat Commun 4:1616, 2013). Over the last decade, qualitative and quantitative analysis of the biological fluids peptidome and degradome have provided a dynamic measurement of tissue homeostasis as well as the tissue response to pathological damage. Proteomic profiling has mapped several of the proteases and resulting degradation by-products derived from cell cycle progression, organ/tissue remodeling and cellular growth, physiological apoptosis, hemostasis, and angiogenesis. Currently, a growing interest lies in the degradome observed during pathological conditions such as cancer, autoimmune diseases, and immune responses to pathogens as a way to exploit biological fluids as liquid biopsies for biomarker discovery Dzieciatkowska et al. (Shock 42:485-498, 2014), Dzieciatkowska et al. (Shock 35:331-338, 2011), Ling et al. (Clin Proteomics 6:175-193, 2010), Ugalde et al. (Methods Mol Biol 622:3-29, 2010), Quesada et al. (Nucleic Acids Res 37:D239‑243, 2009), Cal et al. (Front Biosci 12, 4661-4669, 2007), Shen et al. (PLoS One 5:e13133, 2010a), Antwi et al. (Mol Immunol 46:2931-2937, 2009a), Antwi et al. (J Proteome Res 8:4722‑4731, 2009b), Bedin et al. (J Cell Physiol 231, 915‑925, 2016), Bery et al. (Clin Proteomics 11:13, 2014), Bhalla et al. (Sci Rep 7:1511, 2017), Fan et al. (Diagn Pathol 7:45, 2012a), Fang et al. (Shock 34:291‑298, 2010), Fiedler et al. (Clin Cancer Res 15:3812‑3819, 2009), Fredolini et al. (AAPS J 12:504‑518, 2010), Greening et al. (Enzymes 42:27‑64, 2017), He et al. (PLoS One 8:e63724, 2013), Huang et al. (Int J Gynecol Cancer 28:355‑362, 2018), Hashiguchi et al. (Med Hypotheses 73:760‑763, 2009), Liotta and Petricoin (J Clin Invest 116:26‑30, 2006), Petricoin et al. (Nat Rev Cancer 6:961‑967, 2006), Shen et al. (J Proteome Res 9:2339‑2346, 2010a), Shen et al. (J Proteome Res 5:3154‑3160, 2006), Smith (Clin Proteomics 11:23, 2014), Wang et al. (Oncotarget 8:59376‑59386, 2017), Yang et al. (Clin Exp Med 12:79‑87, 2012a), Yang et al. (J Clin Lab Anal 26:148‑154, 2012b), Yang et al. (Anat Rec (Hoboken) 293:2027‑2033, 2010), Zapico-Muniz et al. (Pancreas 39:1293‑1298, 2010), Villanueva et al. (Mol Cell Proteomics 5:1840‑1852, 2006), Robbins et al. (J Clin Oncol 23:4835‑4837, 2005), Klupczynska et al. (Int J Mol Sci 17:410, 2016). In this review, we focus on the current knowledge of the degradome/peptidome observed in two main biological fluids (plasma and lymph) during physiological and pathological conditions and its importance for immune surveillance.

N-glycan signatures identified in tumor interstitial fluid and serum of breast cancer patients: association with tumor biology and clinical outcome

Particular N‐glycan structures are known to be associated with breast malignancies by coordinating various regulatory events within the tumor and corresponding microenvironment, thus implying that N‐glycan patterns may be used for cancer stratification and as predictive or prognostic biomarkers. However, the association between N‐glycans secreted by breast tumor and corresponding clinical relevance remain to be elucidated. We profiled N‐glycans by HILIC UPLC across a discovery dataset composed of tumor interstitial fluids (TIF, n = 85), paired normal interstitial fluids (NIF, n = 54) and serum samples (n = 28) followed by independent evaluation, with the ultimate goal of identifying tumor‐related N‐glycan patterns in blood of patients with breast cancer. The segregation of N‐linked oligosaccharides revealed 33 compositions, which exhibited differential abundances between TIF and NIF. TIFs were depleted of bisecting N‐glycans, which are known to play essential roles in tumor suppression. An increased level of simple high mannose N‐glycans in TIF strongly correlated with the presence of tumor infiltrating lymphocytes within tumor. At the same time, a low level of highly complex N‐glycans in TIF inversely correlated with the presence of infiltrating lymphocytes within tumor. Survival analysis showed that patients exhibiting increased TIF abundance of GP24 had better outcomes, whereas low levels of GP10, GP23, GP38, and coreF were associated with poor prognosis. Levels of GP1, GP8, GP9, GP14, GP23, GP28, GP37, GP38, and coreF were significantly correlated between TIF and paired serum samples. Cross‐validation analysis using an independent serum dataset supported the observed correlation between TIF and serum, for five of nine N‐glycan groups: GP8, GP9, GP14, GP23, and coreF. Collectively, our results imply that profiling of N‐glycans from proximal breast tumor fluids is a promising strategy for determining tumor‐derived glyco‐signature(s) in the blood. N‐glycans structures validated in our study may serve as novel biomarkers to improve the diagnostic and prognostic stratification of patients with breast cancer.