Serum autoantibody to sideroflexin 3 as a novel tumor marker for oral squamous cell carcinoma

SFXN3 is a Prognostic Marker and Promotes the Growth of Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a heterogeneous disease with rapid progression and frequent mutations. Sideroflexin3 (SFXN3) has been shown to be involved in various neurodegenerative diseases. However, the role of SFXN3 in AML remains unclear. The level and prognostic value of SFXN3 were assessed in pan-cancer, especially AML, based on the data obtained from the TCGA database. The effect and mechanism of SFXN3 in AML were measured by fluorescence-activated cell sorting (FACS), qRT-PCR, western blotting in vitro and in vivo. The correlation between SFXN3 and the infiltration of immune cells in AML was assessed via cibersort and ssGSEA analyses. SFXN3 is expressed at higher levels in AML, and high SFXN3 level is associated with decreased overall survival rate (OSR) in AML. Next, knockdown of SFXN3 results in enhanced cell apoptosis and dropped cell proliferation. Then, knockdown of SFXN3 caused a reduction in the expression of CyclinD1 (CCND1) and nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (NFKB1). Finally, SFXN3 may related to the immunosuppressive state of AML. Increased SFXN3 expression is detected in AML, which indicates a poor prognosis and may link to immunosuppressive state of AML. In addition, SFXN3 can inhibit AML cells apoptosis and promote cell proliferation via enhancing CCND1 and NFKB1 levels.

Identification of iron metabolism-related genes as prognostic indicators for papillary thyroid carcinoma: a retrospective study

Background

The thyroid cancer subtype that occurs more frequently is papillary thyroid carcinoma (PTC). Despite a good surgical outcome, treatment with traditional antitumor therapy does not offer ideal results for patients with radioiodine resistance, recurrence, and metastasis. The evidence for the connection between iron metabolism imbalance and cancer development and oncogenesis is growing. Nevertheless, the iron metabolism impact on PTC prognosis is still indefinite.

Methods

Herein, we acquired the medical data and gene expression of individuals with PTC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Typically, three predictive iron metabolism-related genes (IMRGs) were examined and employed to build a risk score (RS) model via the least absolute shrinkage and selection operator (LASSO) regression, univariate Cox, and differential gene expression analyses. Then we analyzed somatic mutation and immune cell infiltration among RS groups. We also validated the prognostic value of two IMRGs (SFXN3 and TFR2) by verifying their biological function through in vitro experiments.

Results

Based on RS, all patients with PTC were stratified into low- and high-risk groups, where Kaplan-Meier analysis indicated that disease-free survival (DFS) in the high-risk group was much lower than in the low-risk group (P < 0.0001). According to ROC analysis, the RS model successfully predicted the 1-, 3-, and 5-year DFS of individuals with PTC. Additionally, in the TCGA cohort, a nomogram model with RS was developed and exhibited a strong capability to anticipate PTC patients' DFS. In the high-risk group, the enriched pathological processes and signaling mechanisms were detected utilizing the gene set enrichment analysis (GSEA). Moreover, the high-risk group had a significantly higher level of BRAF mutation frequency, tumor mutation burden, and immune cell infiltration than the low-risk group. In vitro experiments found that silencing SFXN3 or TFR2 significantly reduced cell viability.

Conclusion

Collectively, our predictive model depended on IMRGs in PTC, which could be potentially utilized to predict the PTC patients' prognosis, schedule follow-up plans, and provide potential targets against PTC.

A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer

PURPOSE

Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer.

EXPERIMENTAL DESIGN

The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease.

RESULTS

The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.

SFXN3 is Associated with Poor Clinical Outcomes and Sensitivity to the Hypomethylating Therapy in Non-M3 Acute Myeloid Leukemia Patients

BACKGROUND

DNA hypermethylation plays a critical role in the occurrence and progression of acute myeloid leukemia (AML). The mitochondrial serine transporter, SFXN3, is vital for onecarbon metabolism and DNA methylation. However, the impact of SFXN3 on the occurrence and progression of AML has not been reported yet.

OBJECTIVE

In this study, we hypothesized that SFXN3 indicates a poor prognosis and suggested tailored treatment for AML patients.

METHODS

We used GEPIA and TCGA repository data to analyze the expression of SFXN3 and its correlation with survival in AML patients. RT-qPCR was used to detect the SFXN3 level in our enrolled AML patients and volunteers. Additionally, Whole Genome Bisulfite Sequencing (WGBS) was used to detect the genomic methylation level in individuals.

RESULTS

Through the TCGA and GEPIA databases, we found that SFXN3 was enriched in AML patients, predicting shorter survival. Furthermore, we confirmed that SFXN3 was primarily overexpressed in AML patients, especially non-M3 patients, and that high SFXN3 in non-M3 AML patients was found to be associated with poor outcomes and frequent blast cells. Interestingly, non-M3 AML patients with high SFXN3 levels who received hypomethylating therapy showed a higher CR ratio. Finally, we found that SFXN3 could promote DNA methylation at transcription start sites (TSS) in non-M3 AML patients. These sites were found to be clustered in multiple vital cell functions and frequently accompanied by mutations in DNMT3A and NPM1.

CONCLUSION

In conclusion, SXFN3 plays an important role in the progression and hypermethylation in non-M3 AML patients and could be a potential biomarker for indicating a high CR rate for hypomethylating therapy.

Prediction of prognosis and immunotherapy response of amino acid metabolism genes in acute myeloid leukemia

Background

Amino acid (AA) metabolism plays a crucial role in cancer. However, its role in acute myeloid leukemia (AML) is still unavailable. We screened out AA metabolic genes, which related to prognosis, and analyzed their correlation with tumor immune microenvironment in AML.

Methods

We evaluated 472 amino acid metabolism-related genes in 132 AML patients. The predictive risk model was developed according to differentially expressed genes, univariate Cox and LASSO analyses. We validated the risk signature by survival analysis and independence tests. Single-sample gene set enrichment analysis (ssGSEA), tumor immune microenvironment (TME), tumor mutation burden (TMB), functional enrichment, and the IC50 of drugs were assessed to explore the correlations among the risk model, immunity, and drug sensitivity of AML.

Results

Six amino acid metabolism-related genes were confirmed to develop the risk model, including TRH, HNMT, TFEB, SDSL, SLC43A2, and SFXN3. The high-risk subgroup had an immune "hot" phenotype and was related to a poor prognosis. The high-risk group was also associated with more activity of immune cells, such as Tregs, had higher expression of some immune checkpoints, including PD1 and CTLA4, and might be more susceptible to immunotherapy. Xenobiotic metabolism, the reactive oxygen species (ROS) pathway, fatty acid metabolism, JAK/STAT3, and the inflammatory response were active in the high-risk subgroup. Furthermore, the high-risk subgroup was sensitive to sorafenib, selumetinib, and entospletinib. ssGSEA discovered that the processes of glutamine, arginine, tryptophan, cysteine, histidine, L-serine, isoleucine, threonine, tyrosine, and L-phenylalanine metabolism were more active in the high-risk subgroup.

Conclusion

This study revealed that AA metabolism-related genes were correlated with the immune microenvironment of AML patients and could predict the prognosis and immunotherapy response of AML patients.

Non-coding RNA-mediated high expression of SFXN3 as a prognostic biomarker associated with paclitaxel resistance and immunosuppressive microenvironment in head and neck cancer

Chemoresistance is the leading cause of poor prognosis in head and neck squamous cell carcinoma (HNSC); however, promising biomarkers to identify patients for stratified chemotherapy are lacking. Sideroflexin 3 (SFXN3) is an important mitochondrial serine transporter during one-carbon metabolism, which is involved in the proliferation of cancer cells. However, the specific role of SFXN3 in HNSC remains unknown. In this study, we performed expression and survival analysis for SFXN3 in pan-cancer using data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) and found that SFXN3 served as a potential oncogene in HNSC. Notably, SFXN3 expression was found to be positively associated with enriched tumor-infiltrating macrophages, other immune suppressive cells, and immune checkpoint expression and resistance to paclitaxel. Gene, clinical, and immune variables included in the univariate and multivariate analyses showed that SFXN3 expression was an independent risk factor. Moreover, the LINC01270/hsa-miR-29c-3p/SFXN3 axis was identified as the most likely upstream non-coding RNA-related pathway of SFXN3 in HNSC using bioinformatic analysis, expression analysis, correlation analysis, and survival analysis. Taken together, our findings demonstrated that a non-coding RNA-mediated high expression of SFXN3 is a prognostic biomarker and is associated with the immunosuppressive microenvironment in HNSC.

A systematic review of proteomic biomarkers in oral squamous cell cancer

BACKGROUND

Head and neck squamous cell cancer (HNSCC) is the most common cancer associated with chewing tobacco, in the world. As this is divided in to sites and subsites, it does not make it to top 10 cancers. The most common subsite is the oral cancer. At the time of diagnosis, more than 50% of patients with oral squamous cell cancers (OSCC) had advanced disease, indicating the lack of availability of early detection and risk assessment biomarkers. The new protein biomarker development and discovery will aid in early diagnosis and treatment which lead to targeted treatment and ultimately a good prognosis.

METHODS

This systematic review was performed as per PRISMA guidelines. All relevant studies assessing characteristics of oral cancer and proteomics were considered for analysis. Only human studies published in English were included, and abstracts, incomplete articles, and cell line or animal studies were excluded.

RESULTS

A total of 308 articles were found, of which 112 were found to be relevant after exclusion. The present review focuses on techniques of cancer proteomics and discovery of biomarkers using these techniques. The signature of protein expression may be used to predict drug response and clinical course of disease and could be used to individualize therapy with such knowledge.

CONCLUSIONS

Prospective use of these markers in the clinical setting will enable early detection, prediction of response to treatment, improvement in treatment selection, and early detection of tumor recurrence for disease monitoring. However, most of these markers for OSCC are yet to be validated.

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray

: Breast cancer (BRCA) remains the leading cause of cancer morbidity and mortality worldwide. In the present study, we identified novel biomarkers expressed during estradiol and tamoxifen treatment of BRCA. The microarray dataset of E-MTAB-4975 from Array Express database was downloaded, and the differential expressed genes (DEGs) between estradiol-treated BRCA sample and tamoxifen-treated BRCA sample were identified by limma package. The pathway and gene ontology (GO) enrichment analysis, construction of protein-protein interaction (PPI) network, module analysis, construction of target genes-miRNA interaction network and target genes-transcription factor (TF) interaction network were performed using bioinformatics tools. The expression, prognostic values, and mutation of hub genes were validated by SurvExpress database, cBioPortal, and human protein atlas (HPA) database. A total of 856 genes (421 up-regulated genes and 435 down-regulated genes) were identified in T47D (overexpressing Split Ends (SPEN) + estradiol) samples compared to T47D (overexpressing Split Ends (SPEN) + tamoxifen) samples. Pathway and GO enrichment analysis revealed that the DEGs were mainly enriched in response to lysine degradation II (pipecolate pathway), cholesterol biosynthesis pathway, cell cycle pathway, and response to cytokine pathway. DEGs (MCM2, TCF4, OLR1, HSPA5, MAP1LC3B, SQSTM1, NEU1, HIST1H1B, RAD51, RFC3, MCM10, ISG15, TNFRSF10B, GBP2, IGFBP5, SOD2, DHF and MT1H) , which were significantly up- and down-regulated in estradiol and tamoxifen-treated BRCA samples, were selected as hub genes according to the results of protein-protein interaction (PPI) network, module analysis, target genes-miRNA interaction network and target genes-TF interaction network analysis. The SurvExpress database, cBioPortal, and Human Protein Atlas (HPA) database further confirmed that patients with higher expression levels of these hub genes experienced a shorter overall survival. A comprehensive bioinformatics analysis was performed, and potential therapeutic applications of estradiol and tamoxifen were predicted in BRCA samples. The data may unravel the future molecular mechanisms of BRCA.

Diagnostic accuracy of serum biomarkers for head and neck cancer: A systematic review and meta-analysis

Serum biomarkers could be helpful to characterize head and neck squamous cell carcinoma (HNSCC). Thus, the purpose of this systematic review and meta-analysis was to determine the diagnostic capability of serum biomarkers in the assessment of HNSCC patients. Studies were gathered by searching LILACS, PubMed, Science Direct, Scopus and Web of Science up to April 10th, 2015. Studies that focused on serum biomarkers in the diagnosis of HNSCC compared with controls were considered. Sixty-five studies were identified, and the sample size included 9098 subjects. Combined biomarkers demonstrated improved accuracy than those tested individually. Therefore, 12.8% of single and 34.3% of combined indicated that serum biomarkers discriminate patients with HNSCC from controls. The combined biomarkers with better diagnostic capability included Epidermal growth factor receptor (EGFR)+Cyclin D1 and squamous cell cancer-associated antigen (SCCA)+EGFR+Cyclin D1. Beta2-microglobin may also be a promising single biomarker for future studies. Serum biomarkers can be potentially useful in the diagnosis of HNSCC. However, further research is required to validate these biomarkers.

Circulating Anti-Matrix Metalloproteinase-7 Antibodies May Be a Potential Biomarker for Oral Squamous Cell Carcinoma

PURPOSE

The present study was conducted to evaluate the diagnostic and prognostic values of serum autoantibody against matrix metalloproteinase-7 (MMP-7) in patients with oral squamous cell carcinoma (OSCC).

MATERIALS AND METHODS

Anti-MMP-7 antibodies were measured in sera from 204 patients with OSCC and 212 normal controls using enzyme-linked immunosorbent assay, and clinicopathologic characteristics were correlated. Prognostic consequence was assessed with Kaplan-Meier curve and log-rank tests using Cox proportional hazard models. To check whether anti-MMP-7 antibody was related to tumor associated antigen, real-time polymerase chain reaction and western blot were used to measure MMP-7 mRNA and protein expression in tumor tissues from all 204 patients with OSCC.

RESULTS

Serum anti-MMP-7 antibody was higher in patients with OSCC (P < .05), and those with poorly differentiated tumors had more anti-MMP-7 antibody than those with well to moderate tumor differentiation (P < .01, P < .01, respectively). Patients with OSCC at late TNM stages (III, IV) and lymph node metastases had relatively higher serum anti-MMP-7 antibody levels than those with earlier stages (I, II) and those who lacked lymph node metastases (P < .05 for the 2 comparisons). OSCC prediction sensitivity as measured by receiver operating characteristics analysis was 0.485 and specificity was 0.896 (area under the curve, 0.761; 95% confidence interval, 0.716 to 0.806). Cox analysis showed that serum anti-MMP-7 antibody positivity independently predicted poor overall survival in patients with OSCC (hazard ratio, 1.82; 95% confidence interval, 1.07 to 4.61). MMP-7 mRNA and protein expression was increased in tumor tissues from patients with OSCC and high serum anti-MMP-7 antibody.

CONCLUSION

Serum anti-MMP-7 antibody might be a novel diagnostic and prognostic biomarker for OSCC.

Proteomics of microparticles with SILAC Quantification (PROMIS-Quan): a novel proteomic method for plasma biomarker quantification

Unbiased proteomic analysis of plasma samples holds the promise to reveal clinically invaluable disease biomarkers. However, the tremendous dynamic range of the plasma proteome has so far hampered the identification of such low abundant markers. To overcome this challenge we analyzed the plasma microparticle proteome, and reached an unprecedented depth of over 3000 plasma proteins in single runs. To add a quantitative dimension, we developed PROMIS-Quan-PROteomics of MIcroparticles with Super-Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantification, a novel mass spectrometry-based technology for plasma microparticle proteome quantification. PROMIS-Quan enables a two-step relative and absolute SILAC quantification. First, plasma microparticle proteomes are quantified relative to a super-SILAC mix composed of cell lines from distinct origins. Next, the absolute amounts of selected proteins of interest are quantified relative to the super-SILAC mix. We applied PROMIS-Quan to prostate cancer and compared plasma microparticle samples of healthy individuals and prostate cancer patients. We identified in total 5374 plasma-microparticle proteins, and revealed a predictive signature of three proteins that were elevated in the patient-derived plasma microparticles. Finally, PROMIS-Quan enabled determination of the absolute quantitative changes in prostate specific antigen (PSA) upon treatment. We propose PROMIS-Quan as an innovative platform for biomarker discovery, validation, and quantification in both the biomedical research and in the clinical worlds.

Laser ionization mass spectrometry in oral squamous cell carcinoma

Biomarker research in oral squamous cell carcinoma (OSCC) aims for screening/early diagnosis and in predicting its recurrence, metastasis and overall prognosis. This article reviews the current molecular perspectives and diagnosis of oral cancer with proteomics using matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) mass spectrometry (MS). This method shows higher sensitivity, accuracy, reproducibility and ability to handle complex tissues and biological fluid samples. However, the data interpretation tools of contemporary mass spectrometry still warrant further improvement. Based on the data available with laser-based mass spectrometry, biomarkers of OSCC are classified as (i) diagnosis and prognosis, (ii) secretory, (iii) recurrence and metastasis, and (iv) drug targets. Majority of these biomarkers are involved in cell homeostasis and are either physiologic responders or enzymes. Therefore, proteins directly related to tumorigenesis have more diagnostic value. Salivary secretory markers are another group that offers a favourable and easy strategy for non-invasive screening and early diagnosis in oral cancer. Key molecular inter-related pathways in oral carcinogenesis are also intensely researched with software analysis to facilitate targeted drug therapeutics. The review suggested the need for incorporating 'multiple MS or tandem approaches' and focusing on a 'group of biomarkers' instead of single protein entities, for making early diagnosis and treatment for oral cancer a reality.

Identification of anti-α-enolase autoantibody as a novel serum marker for endometriosis

Diagnosis of endometriosis needs invasive maneuvers. New serum marker that possesses both high sensitivity and high specificity has long been desired. To establish novel serum marker for endometriosis, serum autoantibodies (autoAbs) were investigated using proteomic approach. AutoAbs in sera of endometriotic patients and healthy controls were analyzed using a mesothelial cell line, 2-DE and Western blotting. Proteins in reacted spots were identified using MALDI TOF-MS with MASCOT analysis. ELISAs were established using recombinant proteins and autoAb-titers were estimated in sera of endometriotic patients, disease and healthy controls. Several autoAbs were identified. Anti-α-enolase (Eno1)-autoAb levels in endometriotic patients were significantly elevated compared with both healthy and disease controls. Sensitivity and specificity of serum anti-Eno1-autoAb was nearly comparable to serum CA125. When anti-Eno1-autoAb and CA125 assays were combined, diagnostic sensitivity and accuracy improved. Serum anti-Eno1-autoAb can be a new serum endometriotic marker and it is useful as a supplement assay for CA125. This study validates further clinical evaluation of this novel marker.

A joint detection of CEA and CA-50 levels in saliva and serum of patients with tumors in oral region and salivary gland

OBJECTIVE

To detect the levels of carcinoembryonic antigen (CEA) and carcinoma associated antigen CA-50 in the patients with oral or salivary malignant tumors.

METHODS

The concentrations of salivary CEA and CA-50 were assayed in 80 patients of oral and salivary malignant tumors, 40 patients of benign tumors and 80 health controls. In 80 patients with malignant tumors, serum CEA and CA-50 were also assayed by enzyme-linked immunoabsorbent assay and immunoradiometric analysis, respectively.

RESULTS

Salivary CEA and CA-50 levels were significantly higher in malignant tumors than in benign tumors and in health controls, respectively (P < 0.001). Only 7 cases and 3 cases of 80 patients with malignant tumors were found having increased serum CEA and CA-50 levels, respectively.

CONCLUSIONS

The measurement of CEA and CA-50 levels in saliva were more sensitive than in serum. This may be more useful as prognostic indicators in early diagnosis of oral and salivary malignant tumors.