Identification of novel serum biomarkers in child nephroblastoma using proteomics technology

Wilms' Tumor: A Review of Clinical Characteristics, Treatment Advances, and Research Opportunities

Nephroblastoma is a complex childhood cancer with a generally favorable prognosis, well-defined incidence, and demographic profile but with significant challenges in terms of recurrence and long-term health outcomes. Although the management of this pathology has evolved, leading to improved survival rates, continued research into the long-term effects of treatment and the genetic factors influencing its development is still required. The survival landscape for Wilms tumor is evolving, with emerging research focusing on therapeutic biomarkers and genetic predispositions that influence treatment efficacy and survival rates. Identifying predictors for treatment response, such as specific genetic markers and histologic features, emerges as a critical area of study that could refine future interventions. The management of Wilms tumor is complex, taking into account the stage of the disease, histological classification, and individual patient factors, including age and the presence of syndromic associations. As treatment paradigms evolve, the integration of precision medicine approaches may enhance the ability of clinicians to personalize treatment to improve long-term survival outcomes for a broader range of patients. Recent advances in technology, including machine-learning approaches, have facilitated the identification of therapeutic biomarkers that correlate with clinical outcomes. This innovative method enhances the ability to integrate clinical and genetic data to predict disease trajectory and therapeutic response.

A novel machine learning algorithm selects proteome signature to specifically identify cancer exosomes

Non-invasive early cancer diagnosis remains challenging due to the low sensitivity and specificity of current diagnostic approaches. Exosomes are membrane-bound nanovesicles secreted by all cells that contain DNA, RNA, and proteins that are representative of the parent cells. This property, along with the abundance of exosomes in biological fluids makes them compelling candidates as biomarkers. However, a rapid and flexible exosome-based diagnostic method to distinguish human cancers across cancer types in diverse biological fluids is yet to be defined. Here, we describe a novel machine learning-based computational method to distinguish cancers using a panel of proteins associated with exosomes. Employing datasets of exosome proteins from human cell lines, tissue, plasma, serum, and urine samples from a variety of cancers, we identify Clathrin Heavy Chain (CLTC), Ezrin, (EZR), Talin-1 (TLN1), Adenylyl cyclase-associated protein 1 (CAP1), and Moesin (MSN) as highly abundant universal biomarkers for exosomes and define three panels of pan-cancer exosome proteins that distinguish cancer exosomes from other exosomes and aid in classifying cancer subtypes employing random forest models. All the models using proteins from plasma, serum, or urine-derived exosomes yield AUROC scores higher than 0.91 and demonstrate superior performance compared to Support Vector Machine, K Nearest Neighbor Classifier and Gaussian Naive Bayes. This study provides a reliable protein biomarker signature associated with cancer exosomes with scalable machine learning capability for a sensitive and specific non-invasive method of cancer diagnosis.

A novel machine learning algorithm selects proteome signature to specifically identify cancer exosomes

Non-invasive early cancer diagnosis remains challenging due to the low sensitivity and specificity of current diagnostic approaches. Exosomes are membrane-bound nanovesicles secreted by all cells that contain DNA, RNA, and proteins that are representative of the parent cells. This property, along with the abundance of exosomes in biological fluids makes them compelling candidates as biomarkers. However, a rapid and flexible exosome-based diagnostic method to distinguish human cancers across cancer types in diverse biological fluids is yet to be defined. Here, we describe a novel machine learning-based computational method to distinguish cancers using a panel of proteins associated with exosomes. Employing datasets of exosome proteins from human cell lines, tissue, plasma, serum and urine samples from a variety of cancers, we identify Clathrin Heavy Chain (CLTC), Ezrin, (EZR), Talin-1 (TLN1), Adenylyl cyclase-associated protein 1 (CAP1) and Moesin (MSN) as highly abundant universal biomarkers for exosomes and define three panels of pan-cancer exosome proteins that distinguish cancer exosomes from other exosomes and aid in classifying cancer subtypes employing random forest models. All the models using proteins from plasma, serum, or urine-derived exosomes yield AUROC scores higher than 0.91 and demonstrate superior performance compared to Support Vector Machine, K Nearest Neighbor Classifier and Gaussian Naive Bayes. This study provides a reliable protein biomarker signature associated with cancer exosomes with scalable machine learning capability for a sensitive and specific non-invasive method of cancer diagnosis.

Apolipoprotein C1 promotes glioblastoma tumorigenesis by reducing KEAP1/NRF2 and CBS-regulated ferroptosis

Glioblastoma (GBM), a malignant brain tumor, is a world-wide health problem because of its poor prognosis and high rates of recurrence and mortality. Apolipoprotein C1 (APOC1) is the smallest of apolipoproteins, implicated in many diseases. Recent studies have shown that APOC1 promotes tumorigenesis and development of several types of cancer. In this study we investigated the role of APOC1 in GBM tumorigenesis. Using in silico assays we showed that APOC1 was highly expressed in GBM tissues and its expression was closely related to GBM progression. We showed that APOC1 protein expression was markedly increased in four GBM cell lines (U251, U138, A172 and U87) compared to the normal brain glia cell lines (HEB, HA1800). In U251 cells, overexpression of APOC1 promoted cell proliferation, migration, invasion and colony information, which was reversed by APOC1 knockdown. APOC1 knockdown also markedly inhibited the growth of GBM xenografts in the ventricle of nude mice. We further demonstrated that APOC1 reduced ferroptosis by inhibiting KEAP1, promoting nuclear translocation of NRF2 and increasing expression of HO-1 and NQO1 in GBM cells. APOC1 also induced ferroptosis resistance by increasing cystathionine beta-synthase (CBS) expression, which promoted trans-sulfuration and increased GSH synthesis, ultimately leading to an increase in glutathione peroxidase-4 (GPX4). Thus, APOC1 plays a key role in GBM tumorigenesis, conferring resistance to ferroptosis, and may be a promising therapeutic target for GBM.

Lysosomal dysfunction and autophagy blockade contribute to autophagy-related cancer suppressing peptide-induced cytotoxic death of cervical cancer cells through the AMPK/mTOR pathway

Background

Autophagy is an intracellular process through which intracellular components are recycled in response to nutrient or growth factor deficiency to maintain homeostasis. We identified the peptide autophagy-related cancer-suppressing peptide (ARCSP), a potential antitumor peptide that disrupts intracellular homeostasis by blocking autophagic flux and causes cytotoxic death.

Methods

The proliferative ability of ARCSP-treated cervical cancer cells was examined by the CCK8, EdU, and colony formation assays. The TUNEL assay was used to detect apoptosis. Mitochondrial function was evaluated based on the mitochondrial membrane potential. Autophagic flux was detected by immunofluorescence and confocal microscopy. The autophagy-related proteins AMPK, Raptor, mTOR, p62, LC3B, atg7, Rab7, LAMP1, LAMP2, and cathepsin D were detected by Immunoblotting. The antitumor effect of ARCSP was explored in vivo by establishing a transplant tumor model in nude mice.

Results

The results demonstrated that ARCSP induced cell death and inhibited proliferation. ARCSP induced AMPK/mTOR activation, resulting in the accumulation of the proteins LC3B, p62 and Atg7. ARCSP also blocked autophagosome-lysosome fusion by inhibiting endosomal maturation and increasing the lysosomal pH. The accumulation of nonfused autophagosomes exacerbated cytotoxic death, whereas knocking down Atg7 reversed the cytotoxic death induced by ARCSP. ARCSP-treated cells exhibited increased cytotoxic death after cotreatment with an autophagy inhibitor (Chloroquine CQ). Furthermore, the tumors of ARCSP-treated nude mice were significantly smaller than those of untreated mice.

Conclusions

Our findings demonstrate that ARCSP, a novel lethal nonfused autophagosome inducer, might cause mitochondrial dysfunction and autophagy-related cytotoxic death and is thus a prospective agent for cancer therapy.

Screening and identification of non-inflammatory specific protein markers in Wilms' tumor tissues

Wilms' tumor is one of the most common malignancies in children, and early diagnosis is critical for its subsequent treatment and prognosis. Our previous study employed proteomics to investigate protein markers in the serum of Wilms' tumor children. The present study aimed to identify specific protein markers in Wilms' tumor. Proteomic comparison of Wilms' tumor with normal kidney tissues and the sera of systemic inflammatory response syndrome (SIRS) controls was performed. Surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF-MS) identified a protein with m/z 8350 as specific to Wilms' tumor. The target protein was purified using sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and identified as profilin-1 by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF). Its expression was validated using real-time polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Our data identify profilin-1 as a potential protein marker for Wilms' tumor and demonstrate the feasibility of the above procedures for screening and identification of tumor-specific protein markers.

Wilms tumor-suppressing peptide inhibits proliferation and induces apoptosis of Wilms tumor cells in vitro and in vivo

BACKGROUND

Our previous study identified a Wilms tumor-suppressing peptide (WTSP) that was upregulated in healthy children, but downregulated in children with Wilms tumor (WT). This study aimed to investigate the effect of WTSP on WT growth in vivo and in vitro.

METHODS

WTSP was synthesized by solid-phase synthesis of FOMC-protected amino acids. Cell growth curve, cytotoxicity, and apoptosis of WTSP-treated human WT cell line (SK-NEP-1) were determined by cell count, Cell Counting Kit-8 assay, and flow cytometry. The expression of key proteins of four WT-associated signaling pathways was determined by real-time PCR and western blotting. The WT xenograft mouse model was established by the armpit injection of SK-NEP-1 cells. The TUNEL assay was used to detect apoptosis in mouse tumor cells.

RESULTS

WTSP inhibited the proliferation of SK-NEP-1 cells in a dose- and time-dependent manner, and it arrested SK-NEP-1 cells in G2/M phase. WTSP-treated cells exhibited a low expression of PCNA and Bcl-2 and high expression of Bax. The expression of β-catenin was markedly changed after WTSP treatment. WTSP-treated mice had significantly smaller tumors than untreated mice.

CONCLUSION

Our findings indicated an anti-tumor effect of WTSP, which is correlated with Wnt/β-catenin pathway. This newly identified peptide may exert a therapeutic effect of WT in the future.

Apolipoprotein C1 (APOC1) as a novel diagnostic and prognostic biomarker for gastric cancer

Background

Gastric cancer (GC) is a common malignant cancer in the worldwide, especially in China. Patients with GC have poor prognosis, which is mainly due to lack of early diagnosis. Up to now, there is no good biomarker to detect GC at early stage. Apolipoprotein C1 (APOC1), a component of both triglyceride-rich lipoproteins and high-density lipoproteins, is reported to be involved in numerous biological processes.

Methods

Expression of APOC1 mRNA was analyzed by in silicon assay. Concentration of APOC1 in serum was measured by ELISA assay. Expression of APOC1 protein in GC tissue array was checked by immunohistochemistry.

Results

It was firstly found that concentration of APOC1 in serum was significantly higher in GC than that in control. Expression of APOC1 protein was also higher in GC than that in adjacent issues of GC and normal tissues using tissues array by immunohistochemistry. In addition, the expression of APOC1 is significantly associated with clinical stage (P=0.011), tumor classification (P=0.010), as well as with the lymph node metastasis (P=0.048). Area under the curve (AUC) of receiver operating characteristic (ROC) curve of APOC1 was 0.803. Furthermore, elevated APOC1 expression in GC was found to be correlated with decreased overall survival (P=0.00214).

Conclusions

All these results suggested that APOC1 might be a potential serum biomarker to diagnose GC and a potential prognostic marker for GC.

Identification of differentially expressed inflammatory factors in Wilms tumors and their association with patient outcomes

The present study aimed to identify differentially expressed inflammatory factors observed in Wilms tumors (WT), and to investigate the association of these factors with clinical stage, pathological type, lymph node metastasis and vascular involvement of WT. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry was performed to screen differentially expressed proteins among WT and normal tissue pairs. Upregulated proteins in WT were separated and purified by solid phase extraction and Tricine SDS-PAGE, respectively. Following in-gel digestion, the peptide mixture was subjected to liquid chromatography mass spectrometry to identify proteins on the basis of their amino acid sequences. Immunohistochemistry was used to confirm the expression of differentially expressed inflammatory proteins. Of the proteins that were upregulated in WT, two proteins with mass/charge (m/z) ratio of 12,138 and 13,462 were identified as macrophage migration inhibitory factor (MIF) and C-X-C motif ligand 7 (CXCL7) chemokine, respectively. The expression of these two proteins was increased in WT compared with adjacent normal tissues and normal renal tissues, and increased with increasing clinical stage. In addition, their expression was significantly increased in patients with unfavorable pathological type, lymph node metastasis and vascular involvement compared with the groups with favorable type, and without lymph node metastasis or vascular involvement (P<0.05). Increased pro-inflammatory MIF and CXCL7 expression in WT is closely associated with the clinical stage, pathological type, lymph node metastasis and vascular involvement, and may represent biomarkers for the clinical diagnosis of WT.

Proteomics in pediatric cystic craniopharyngioma

Adamantinomatous craniopharyngioma (ACP) is still often burdened by a poor prognosis in children as far as the risk of recurrence and the quality of life are concerned. Therefore, many efforts are now dedicated to investigate the molecular characteristics of this tumor aiming at finding new therapeutic options. ACP is prevalently a cystic lesion so that an increasing number of researches are focused on the analysis of its cystic content. In the present article, the main results of the current proteomic analysis (PA) on the ACP fluid are summarized. Both "bottom-up" and "top-down" approaches have been utilized. In the bottom-up approach, proteins and peptides are enzymatically or chemically digested prior to liquid chromatography and mass spectrometry analyses. The bottom-up approach pointed out several proteins of the inflammation (namely, α2-HS-glycoprotein, α1-antichymotrypsin and apolipoproteins) as possibly involved in the genesis and growth of the cystic component of ACP. The top-down strategy analyzes proteins and peptides in the intact state, making it particularly suitable for the identification of peptides and low molecular weight proteins and for the characterization of their possible isoforms and post-translational modifications. The top-down approach disclosed the presence of the thymosin β family. Thymosin β4, in particular, which is involved in the cytoskeleton organization and migration of several tumors, could play a role in the progression of ACP. Finally, PA was utilized to investigate alterations in cyst fluid character after treatment with interferon-α. The analyzed samples showed a progressive reduction of the levels of α-defensins (proteins involved in the inflammatory-mediated response) after the intracystic injection of interferon-α, thus reinforcing the hypothesis that inflammation contributes to ACP cyst pathogenesis. Additional studies on the solid component of ACP are still necessary to further validate the previous results and to identify possible markers for targeted therapy.

Identification of proteins associated with pediatric bilateral Wilms tumor

Wilms tumor (WT) is the most common cancer that primarily develops in abdominal solid organ of children. It has no incipient symptom, and the most frequent symptoms are a painless, palpable abdominal mass. Proteomics technology was used to select the differentially expressed proteins of bilateral Wilms tumor (BWT). Ten serum samples of children with BWT were chosen, 20 serum samples of children with unilateral WT (UWT) and 20 serum samples of healthy children were selected, and proteomics technology was used to detect and collect data. Using bioinformatics, the data were analyzed and 10 difference peaks were obtained (P<0.01). Non-linear support vector machine was used to classify and to select the composite pattern with the highest Youdens index, and one differentially expressed protein with m/z of 5,648 kDa was obtained. A significantly high expression in children with BWT was obtained, and the expression intensity was also significantly (3,889.36±1,796.83) higher for children with BWT compared to those with UWT (2,886.81±1,404.65) and healthy children (432.21±730.42). Matrix-assisted laser desorption ionization/time-of-flight ionization/time-of-flight mass spectrometry was used for identification of the peak, and the peak was further identified as apolipoprotein C-III (APO C-III) by western blot analysis. In conclusion, to the best of our knowledge, a differentially expressed protein of APO C-III of BWT was obtained through proteomics technology for the first time, and it is expected to be a new marker for the early diagnosis and prognosis of BWT.

Screening and identification of post-traumatic stress-related serum factors in children with Wilms' tumors

Wilms' tumors are one of the most common malignant, solid intra-abdominal tumors observed in children. Although potential tumor markers have been found, inflammatory cytokines interfere with the process of specific protein identification. The present study was undertaken to identify post-traumatic stress-related factors of Wilms' tumors and to verify the accuracy of early-stage tumor-specific serum protein markers. Serum samples were screened for differentially-expressed proteins using surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). Potential markers were isolated and purified using solid-phase extraction (SPE) and SDS-PAGE. Following enzymatic digestion of the protein samples, the peptide fragments were detected with high performance liquid chromatography-mass spectrometry. The obtained peptide mass fingerprint was searched in the Swiss-Prot protein sequence database via the Mascot search engine. Differentially-expressed proteins were verified using western blot analysis. Differentially-expressed proteins with a mass/charge of 5,816 were screened out using SELDI-TOF-MS, and significant differences between the tumor and control groups, and the trauma and control groups were observed. Target proteins were isolated and purified using SPE and SDS-PAGE. Thioredoxin 1 (Trx1) was found to be differentially expressed. In the serum of children with Wilms' tumors, there was an increase in the level of the post-traumatic stress-related inflammatory factor, Trx1, as compared with the normal control group. Thus, the results of this study indicate that Trx1 presents a potential post-traumatic stress-related factor of Wilms' tumors.

Detection of Serum Protein Biomarkers for the Diagnosis and Staging of Hepatoblastoma

The present study aimed to identify serum biomarkers for the detection of hepatoblastoma (HB). Serum samples were collected from 71 HB patients (stage I, n = 19; stage II, n = 19, stage III, n = 19; and stage IV, n = 14) and 23 age- and sex-matched healthy children. Differential expression of serum protein markers were screened using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), and the target proteins were isolated and purified using HPLC and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), SEQUEST, and bioinformatics analysis. Differential protein expression was confirmed by enzyme-linked immunosorbent analysis (ELISA). SELDI-TOF-MS screening identified a differentially expressed protein with an m/z of 9348 Da, which was subsequently identified as Apo A–I; its expression was significantly lower in the HB group as compared to the normal control group (1546.67 ± 757.81 vs. 3359.21 ± 999.36, respectively; p < 0.01). Although the expression level decreased with increasing disease stage, pair-wise comparison revealed significant differences in Apo A–I expression between the normal group and the HB subgroups (p < 0.01). ELISA verified the reduced expression of Apo A–I in the HB group. Taken together, these results suggest that Apo A–I may represent a serum protein biomarker of HB. Further studies will assess the value of using Apo A–I expression for HB diagnosis and staging.

Screening and identification of apolipoprotein A-I as a potential hepatoblastoma biomarker in children, excluding inflammatory factors

The aim of the present study was to identify a child hepatoblastoma serum biomarker that is unaffected by inflammatory factors, with the ultimate aim of finding an effective method for the early diagnosis of hepatoblastoma. The magnetic bead-based weak cation exchange chromatography technique was used to process serum harvested from 30 children with hepatoblastoma, 20 children with systemic inflammatory response syndrome (SIRS) and 20 healthy children. Proteins differentially expressed in SIRS were excluded from consideration as biomarkers for hepatoblastoma. Proteins differentially expressed in hepatoblastoma and healthy controls were screened using surface-enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS). Target proteins were purified by SDS-PAGE, and matrix-assisted laser desorption/ionization (MALDI)-TOF-MS was used to determine their amino acid sequences. Protein matches were searched in the SwissProt database. Quantitative polymerase chain reaction (qPCR) and ELISA were employed to confirm the expression of target proteins. Following screening to exclude inflammatory factors, SELDI-TOF-MS revealed a protein with a mass-to-charge ratio of 9,348 Da that was expressed at significantly lower levels in the serum of children with hepatoblastoma compared with healthy controls (P<0.01). Sequence analysis identified this protein as apolipoprotein A-1 (Apo A-I). qPCR and ELISA confirmed that the expression of Apo A-I mRNA and protein were significantly lower in children with hepatoblastoma compared with healthy controls (P<0.05). These results indicate that Apo A-I is a non-inflammatory protein marker for hepatoblastoma with the potential for use in early diagnosis of hepatoblastoma. In addition, the present study demonstrates the feasibility of proteomic screening for the identification of proteins that can serve as markers for a specific tumor.

Identification of apolipoprotein C-I as a potential Wilms' tumor marker after excluding inflammatory factors

Wilms' tumor is one of the most common malignant tumors observed in children, and its early diagnosis is important for late-stage treatment and prognosis. We previously screened and identified protein markers for Wilms' tumor; however, these markers lacked specificity, and some were associated with inflammation. In the current study, serum samples from children with Wilms' tumors were compared with those of healthy controls and patients with systemic inflammatory response syndrome (SIRS). After exclusion of factors associated with inflammation, specific protein markers for Wilms' tumors were identified. After comparing the protein peak values obtained from all three groups, a protein with a m/z of 6438 Da was specified. Purification and identification of the target protein using high-pressure liquid chromatography (HPLC) and two-dimensional liquid chromatography-linearion trap mass spectrometry(2D-LC-LTQ-MS) mass spectrometry, respectively, revealed that it was apolipoprotein C-I (APO C-I). Thus, APO C-I is a specific protein marker for Wilms' tumor.

Proteomic characterization of pediatric craniopharyngioma intracystic fluid by LC-MS top-down/bottom-up integrated approaches

The combination of top-down and bottom-up platforms was utilized for the LC-MS proteomic characterization of the intracystic fluid of adamantinomatous craniopharyngioma pediatric brain tumor disease. Proteins and peptides characterization was achieved by high-resolution LC-ESI-LTQ-Orbitrap-MS analysis while low-resolution LC-ESI-IT-MS was applied for the complete screening of the samples and the evaluation of the protein distribution within patients. Top-down analyses were applied to liquid/liquid extracted samples while bottom-up analyses were performed after trypsin digestion of both untreated and pretreated samples. The two proteomic approaches were complementary for the characterization of the proteome of craniopharyngioma intracystic fluid. Proteins and peptides involved in inflammation, mineralization processes and lipid transport were identified, in agreement with the calcium flecks, cholesterol granules and bone residues characteristic of this fluid. Apolipoprotein A-I, A-II, C-I and J, hemoglobin fragments, ubiquitin, α-2-HS-glycoprotein or fetuin A, α-1-antichymotrypsin, vitamin D binding protein, and α-1-acid glycoprotein were characterized. These data could be relevant for the comprehension of the processes involved in the pathogenesis of the disease and the development of the cyst and could contribute to the individuation of therapeutic targets for the reduction of the cyst volume delaying and/or avoiding invasive surgical treatments.

Kidney protein profiling of Wilms' tumor patients by analysis of formalin-fixed paraffin-embedded tissue samples

Wilms' tumor (nephroblastoma, WT) is the most frequent renal cancer in children. However, molecular details leading to WT have not been characterized sufficiently yet. Proteomic studies might provide new insights but are hampered by limited availability of fresh frozen tissue specimen. Therefore, we tested formalin-fixed paraffin-embedded (FFPE) tissue sections routinely collected for pathological inspection for their use in in-depth-proteomic analyses of WT samples in comparison to fresh frozen specimen. The overlap of the proteins identified was over 65%. Thus we used FFPE material from 7 patients for tandem mass spectrometry based comparison of the proteomes of WT and healthy renal tissues. We detected 262 proteins, which were differentially expressed in tumor compared to healthy renal tissue. The majority of these proteins displayed lower levels in the tumor tissue and only 30% higher levels. For selected candidates data were confirmed by immunohistochemical staining. Correlation analysis of blastemal proportions in WT and protein intensities revealed candidates for tumor stratification.

CONCLUSION

This proof of principle proteomic study of FFPE tissue sections from WT patients demonstrates that these archived tissues constitute a valuable resource for larger in-depth proteomic studies to identify markers to follow chemotherapy efficiency or for stratification of tumor subtypes.

Advances in MALDI mass spectrometry in clinical diagnostic applications

The concept of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was first reported in 1985. Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. These technologies are high-throughput and sensitive. Emerging evidence has shown that they are not only useful in qualitative and quantitative analyses of proteins, but also of other types of biomolecules, such as DNA, glycans, and metabolites. Recently, parallel fragmentation monitoring (PFM), which is a method comparable to selected reaction monitoring, has been reported. This highlights the potentials of MALDI-TOF/TOF tandem MS in quantification of metabolites. Here we critically review the applications of the major MALDI MS technologies, including MALDI-TOF MS, MALDI-TOF/TOF MS, SALDI-TOF MS, MALDI-QqQ MS, and SELDI-TOF MS, to the discovery and quantification of disease biomarkers in biological specimens, especially those in plasma/serum specimens. Using SELDI-TOF MS as an example, the presence of systemic bias in biomarker discovery studies employing MALDI-TOF MS and its possible solutions are also discussed in this chapter. The concepts of MALDI, SALDI, SELDI, and PFM are complementary to each other. Theoretically, all these technologies can be combined, leading to the next generation of the MALDI MS technologies. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming.

Identification of serum protein biomarkers in biliary atresia by mass spectrometry and enzyme-linked immunosorbent assay

OBJECTIVE

There is an urgent need to identify noninvasive and convenient biomarkers for early diagnosis of biliary atresia (BA). The aim of the present study was to identify potential protein biomarkers for BA.

METHODS

Serum samples from 42 infants with BA, 38 infants with non-BA neonatal cholestasis (NC), and 36 healthy controls (HC) were randomly divided into a training set and a test set. Serum proteomic profiles were measured using surface-enhanced desorption/ionization time-of-flight mass spectrometry. Candidate biomarkers were purified using high-performance liquid chromatography, identified using liquid chromatography tandem mass spectrometry, and validated using enzyme-linked immunosorbent assay.

RESULTS

A total of 2 protein peaks (m/z with 8697 and 9098  Da) with differential expression levels were found using surface-enhanced desorption/ionization time-of-flight mass spectrometry. These peaks were then analyzed by a support vector machine to construct a classification model in the training set. The sensitivity and specificity of the model were 94.1% and 91.8%, respectively, in the test set. One candidate biomarker (9098  Da) was identified as Apo C-II, and was found to be downregulated in BA samples compared with HC samples, and upregulated in BA samples compared with NC samples. The other candidate biomarker (8697  Da) was identified as Apo C-III, and was found to be upregulated in BA compared with NC and HC.

CONCLUSIONS

Apo C-II and Apo C-III may be potential protein biomarkers of BA and may be useful in distinguishing infants with BA from healthy and NC infants. Further studies with additional populations or using prediagnostic serum are needed to confirm the importance of these findings as diagnostic markers of infants with BA.

Clinicopathological pattern and Annexin A2 and Cdc42 status in patients presenting with differentiation and lymphnode metastasis of esophageal squamous cell carcinomas

Annexin A2 and Cdc42 were identified by 2-dimensional electrophoresis (2-DE) and MALDI-TOF-MS between esophageal squamous cell carcinomas (ESCC) and corresponding normal esophagus mucosa in our previous study. To assess clinico-pathological pattern and Annexin A2 and Cdc42 status with respect to cell differentiation and lymphnode metastasis in patients with ESCC. The expression of Annexin A2 and Cdc42 in 22 pairs of fresh ESCC and matched tissues were detected by qRT-PCR and western blot, respectively. And it was further confirmed by immunohistochemistry with 175 pairs of formalin-fixed, paraffin-embedded ESCC. Results showed that Annexin A2 expression was significantly down-regulated, and Cdc42 was up-regulated in ESCC compared to matched control on both mRNA and protein level (P < 0.05), which was in accordance with our previous results on proteomics data. Additionally, Annexin A2 and Cdc42 expression was significantly correlated with lymphoid node metastasis (P < 0.05) and pathological differentiation (P < 0.05). Taken together, we proposed that the aberrant expression of Annexin A2 and Cdc42 played a role in carcinogenesis, differentiation and metastasis of ESCC, which implied its potential target for clinical biomarkers in differentiation and lymph node metastasis.

Identification of potential serum biomarkers for Wilms tumor after excluding confounding effects of common systemic inflammatory factors

Wilms tumor is the most common pediatric tumor of the kidney. Previous studies have identified several serum biomarkers for Wilms tumor; however, they lack sufficient specificity and may not adequately distinguish Wilms tumor from confounding conditions. To date, no specific protein biomarker has been confirmed for this pediatric tumor. To identify novel serum biomarkers for Wilms tumor, we used proteomic technologies to perform protein profiling of serum samples from pre-surgery and post-surgery patients with Wilms tumor and healthy controls. Some common systemic inflammatory factors were included to control for systemic inflammation. By comparing protein peaks among the three groups of sera, we identified two peaks (11,526 and 4,756 Da) showing significant differential expression not only between pre-surgery and control sera but also between pre-surgery and post-surgery sera. These two peaks were identified as serum amyloid A1 (SAA1) and apolipoprotein C-III (APO C-III). Western blot analysis confirmed that both proteins were expressed at higher levels in pre-surgery sera than in post-surgery and control sera. Using the method of leave-1-out for cross detection, we demonstrate that detection of these two candidate biomarkers had high sensitivity and specificity in discriminating pre-surgery sera from post-surgery and normal control sera. Taken together, these findings suggest that SAA1 and APO C-III are two potential biomarkers for Wilms tumor.

Effect of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry on identifying biomarkers of laryngeal carcinoma

The aim is to study the serum protein fingerprint of patients with laryngeal carcinoma (LC) and to screen for protein molecules closely related to LC during the onset and progression of the disease with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Serum samples from 68 patients with LC and 117 non-cancer control samples (75 healthy volunteers and 42 Vocal fold polyps). Q10 protein chips and PBSII-C protein chips reader (Ciphergen Biosystems Inc.) were used. The protein fingerprint expression of all the Serum samples and the resulting profiles between cancer and non-cancer groups were analyzed with Biomarker Wizard system. A group of proteomic peaks were detected. Three differently expressed potential biomarkers were identified with the relative molecular weights of 5,915, 6,440 and 9,190 Da. Among the three peaks, the one with m/z 6,440 was down-regulated, and the other two peaks with m/z 5,915 and 9,190 were up-regulated in LC. This diagnostic model could distinguish LC patients from controls with a sensitivity of 92.1% and a specificity of 91.9%. Moreover, blind test data showed a sensitivity of 86.7% and a specificity of 89.1%. The data suggested that SELDI technology could be used to screen proteins with altered expression levels in the serum of LC patients. These protein peaks were considered as specific serum biomarkers of LC and have the potential value for further investigation.

Identification of new biomarkers of low-dose GH replacement therapy in GH-deficient patients

CONTEXT

GH secretion peaks at puberty and continues to be secreted in adulthood, albeit at a declining rate. Profound GH deficiency (GHD) in adults with pituitary disease is associated with symptoms that improve with GH substitution, but it is important to tailor the GH dose to avoid overtreatment. Measurement of serum IGF-I levels is an important clinical tool in this regard, but it is well recognized that some patients receiving GH treatment do not show an increase in IGF-I.

OBJECTIVE

The objective of the study was to identify novel serum biomarkers of GH treatment in adults with GHD.

DESIGN AND PATIENTS

Eight patients with profound GHD as a consequence of a pituitary adenoma or its treatment were evaluated before and 3 months after GH replacement therapy (0.2-0.4 mg/d).

MAIN OUTCOME MEASURES

Serum proteomic changes were studied using two-dimensional gel electrophoresis and mass spectrometry. Protein profiles were analyzed and compared in serum samples obtained before and after GH treatment.

RESULTS

The levels of six serum protein spots were significantly altered after GH substitution. These proteins were identified as five isoforms of haptoglobin (decreased in posttreatment samples) and one isoform of apolipoprotein A-I (increased in posttreatment samples). Importantly, changes in the levels of the identified proteins were associated with decreases in fat mass and increases in lean mass in all patients. These results were independent of serum IGF-I levels.

CONCLUSIONS

Evaluation of the identified proteins provides a novel alternative to traditional markers of GH status, such as serum IGF-I levels, to assess GH therapy in GH deficient adults.

Proteomic identification of differentially-expressed proteins in esophageal cancer in three ethnic groups in Xinjiang

The Objective is to identify candidate biomarkers for Squamous cell carcinoma (ESCC) in three ethnics in Xinjiang as well as reveal molecular mechanism. Proteins from 15 pairs of ESCC and matching adjacent normal esophageal tissues (five pairs in each ethnic of Kazakh, Uygur and Han) were separated by 2-DE and differentially proteins were identified by matrix-assisted laser desorption/ionization time-of-flight MS. After identified by Mascot database, some of interesting proteins were confirmed in the other 175 pairs of ESCC by immuno histochemistry. Comparison of patterns revealed 20 proteins significantly changed, of which 12 protein with concordantly increased, such as ACTB protein, COMT protein, Syntaxin binding protein Pyruvate Kinase (PKM2), Cathepsin D, Chromosome 1 open reading frame 8, Heat shock protein 27, Cdc42, Proteosome, LLDBP, Immunoglobulin, TNF receptor associated factor 7; and eight protein spots with concordantly decreased intensity in ESCC, such as Adenylate kinase 1, General transcription factor II H, Smooth muscle protein, Trangelin, Early endosome antigen 1, Annexin A2, Fibrin beta, Tropomyosin. There were a significant difference in protein overexpression of PKM2 (74.9%) and Cathepsin D (85.1%) in ESCC compared to adjacent tissues (P < 0.05) by immunohistochemistry. Further, overexpression of Cathepsin D was obvious difference in Hazakh ESCC (94.7%) than that in Uygur (78.6%) (P < 0.05). Interestingly, the overexpression of Cathepsin D was reversely associated with ESCC differentiation (P < 0.05). Twenty proteins differentially-expressed between ESCC and normal tissues were identified. Cathepsin D and PKM2 were for the first time observed to be dysregulated in Kazakh's ESCC. Moreover, Cathepsin D may play a complicated role both in carcinogenesis and cell-differentiation of ESCC.

Profiling for novel proteomics biomarkers in neurodevelopmental disorders

Protein biomarker discovery from biological fluids, such as serum, has been widely applied to disorders such as cancer and has more recently also been utilized in neuro-psychiatric disorders with relatively clear biological causes, such as Alzheimer's disease and schizophrenia. The application of the associated technologies for the identification of protein biomarker signatures in neurodevelopmental disorders, such as autism spectrum disorder and attention deficit hyperactivity disorder, is comparatively less well established. The aim of this article is to provide an overview of the various protocols available for such analysis, discuss reports in which these techniques have been previously applied in biomarker discovery/validation in neurodevelopmental disorders, and consider the future development of this area of research.