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At least 19 recordsLinked to original sources
PubMed2025

Proteomic-based biomarker discovery reveals panels of diagnostic biomarkers for early identification of heart failure subtypes.

BACKGROUND: Limited access to echocardiography can delay the diagnosis of suspected heart failure (HF), which in turn postpones the initiation of optimal guideline-directed medical therapy. Although natriuretic peptides like B-type natriuretic peptide (BNP) are valuable biomarkers for diagnosing and managing HF, the utility of combining BNP with other blood-based biomarkers to predict subtypes of new-onset HF remains underexplored. OBJECTIVES: This study sought to investigate and evaluate the diagnostic significance of adding blood-based biomarkers to BNP for identifying heart failure with preserved ejection fraction (HFpEF) or reduced ejection fraction (HFrEF), with the goal of enhancing diagnostic assays beyond BNP measurements. METHODS: We identified candidate blood protein biomarkers using untargeted proteomics workflows from a cohort of individuals recruited to the STOP-HF trial who were at risk of HF and subsequently developed either HFpEF or HFrEF over time ("HF progressors"; n = 40). Candidate biomarkers were verified in an independent cohort (n = 52) from a community-based rapid access HF diagnostic clinic. The biological processes associated with these proteins were assessed, and the diagnostic values of biomarker panels were evaluated using a machine learning approach. RESULTS: Within HF progressors, we identified 3 proteins associated with HFpEF development: vascular cell adhesion protein 1 (VCAM1), insulin-like growth factor 2 (IGF2), and inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3). Additionally, 4 proteins were linked to HFrEF development: C-reactive protein (CRP), interleukin-6 receptor subunit beta (IL6RB), phosphatidylinositol-glycan-specific phospholipase D (PHLD), and noelin (NOE1). These findings were verified in an independent cohort to distinguish HF subtypes from controls. Moreover, a random forest algorithm demonstrated that combining these candidate biomarkers with BNP measurement significantly improved the prediction of HF subtypes. CONCLUSIONS: We identified candidate proteins linked to HFpEF and HFrEF in a longitudinal HF progressor cohort and validated them in a community-based cohort. Adding these proteins to BNP led to a significant improvement in HF subtype prediction. Study results have clinical implications for blood-based screening of HF subtypes using panels of biomarkers, particularly in resource-limited settings.

Humans↗
PubMed2006

Finding diagnostic biomarkers in proteomic spectra.

In seeking to find diagnostic biomarkers in proteomic spectra, two significant problems arise. First, not only is there noise in the measured intensity at each m/z value, but there is also noise in the measured m/z value itself. Second, the potential for overfitting is severe: it is easy to find features in the spectra that accurately discriminate disease states but have no biological meaning. We address these problems by developing and testing a series of steps for pre-processing proteomic spectra and extracting putatively meaningful features before presentation to feature selection and classification algorithms. These steps include an HMM-based latent spectrum extraction algorithm for fusing the information from multiple replicate spectra obtained from a single tissue sample, a simple algorithm for baseline correction based on a segmented convex hull, a peak identification and quantification algorithm, and a peak registration algorithm to align peaks from multiple tissue samples into common peak registers. We apply these steps to MALDI spectral data collected from normal and tumor lung tissue samples, and then compare the performance of feature selection with FDR followed by classification with an SVM, versus joint feature selection and classification with Bayesian sparse multinomial logistic regression (SMLR). The SMLR approach outperformed FDR+SVM, but both were effective in achieving good diagnostic accuracy with a small number of features. Some of the selected features have previously been investigated as clinical markers for lung cancer diagnosis; some of the remaining features are excellent candidates for further research.

Algorithms↗
PubMed2026

Key hub genes and pathways associated with HCV-related hepatocellular carcinoma as potential diagnostic biomarkers.

BACKGROUND: Hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC) remains a major global health challenge, with high morbidity and mortality despite recent therapeutic advances. Early detection and identification of reliable molecular biomarkers are essential to improve patient outcomes. Therefore, the present study aimed to investigate key hub genes and pathways associated with HCV-related HCC as potential diagnostic biomarkers. METHODS: The datasets GSE69715 and GSE62232 were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were recognized according to an adjusted p-value and a log fold change (logFC). The GEO2R tool facilitated the identification of common DEGs across the two datasets. Pathways were explored using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Furthermore, protein-protein interactions (PPIs) were assessed through Cytoscape. The target genes were confirmed through a GEPIA analysis. RESULTS: A total of 421 common DEGs were identified, and 80 hub genes were subsequently determined through GEO and PPI network analyses, respectively. The GO and KEGG pathways analysis presented DEGs were enhanced in metabolic pathways, cellular components, extracellular exosome, detoxification of copper ion and monooxygenase activity. The GEPIA analysis indicated a notable variation in the expression levels of four specific genes -CDKN2A, CDK1, CCNB1, and TOP2A-when comparing normal samples to tumor samples. CONCLUSION: The present study discovered novel genes by expression variation in HCV-related hepatocellular carcinoma development. These findings suggest that CDKN2A, CDK1, CCNB1, and TOP2A are promising candidates for diagnostic biomarkers and present a valuable opportunity for the early identification of HCV-HCC, which could lead to improved treatment outcomes.

Bioinformatics↗
PubMed2024

Comprehensive Proteomic Analysis Reveals Distinct Features and a Diagnostic Biomarker Panel for Early Pregnancy Loss in Histological Subtypes.

Early pregnancy loss (EPL) is a common event in human reproduction and is classified into histological subtypes such as hydropic abortion (HA) and hydatidiform moles, including complete hydatidiform moles (CHMs) and partial hydatidiform moles (PHMs). However, accurate diagnosis and improved patient management remain challenging due to high rates of misdiagnosis and diverse prognostic risks. Therefore, diagnostic biomarkers for EPL are urgently needed. Our study aimed to identify biomarkers for EPL through comprehensive proteomic analysis. Ten CHMs, six PHMs, ten HAs, and 10 normal control products of conception were used to obtain a proteomic portrait. Parallel reaction monitoring-targeted proteomic and regression analyses were used to verify and select the diagnostic signatures. Finally, 14 proteins were selected and a panel of diagnostic classifiers (DLK1, SPTB/COL21A1, and SAR1A) was built to represent the CHM, PHM, and normal control groups (area under the receiver operating characteristic curve = 0.900, 0.804/0.885, and 0.991, respectively). This high diagnostic power was further validated in another independent cohort (n = 148) by immunohistochemistry (n = 120) and Western blot analyses (n = 28). The protein SPTB was selected for further biological behavior experiments in vitro. Our data suggest that SPTB maintains trophoblast cell proliferation, angiogenesis, cell motility, and the cytoskeleton network. This study provides a comprehensive proteomic portrait and identifies potential diagnostic biomarkers. These findings enhance our understanding of EPL pathogenesis and offer novel targets for diagnosis and therapeutic interventions.

Humans↗
PubMed1997

Identification of the MN/CA9 protein as a reliable diagnostic biomarker of clear cell carcinoma of the kidney.

The MN/CA9 protein is a tumor-associated antigen that has been shown to have diagnostic utility in identifying cervical dysplasia and carcinoma. MN/CA9 expression is limited to very few normal tissues. We have now extended those observations to further investigate expression of the MN/CA9 protein in histological sections and fine-needle aspiration biopsy smears of normal kidney, benign renal cell lesions, all categories of renal cell carcinomas (clear/granular/spindle cell, chromophilic cell, chromophobic cell, and collecting duct cell RCCs), metastatic RCCs, and non-renal cell clear cell adenocarcinomas. We have found that high levels of MN/CA9 expression is seen in all primary RCCs, cystic RCCs, and metastatic RCCs, with the exception of two cases of the chromophobe cell type, which were MN/CA9 negative. Identical MN/CA9 immunostaining was also observed in the aspiration cytological smears. In contrast, all benign lesions, including pyelonephritis, renal cysts, adenomas, oncocytomas, and normal kidney, did not express the MN/CA9 protein. Thus, we conclude that MN/CA9 protein expression could serve as a valuable adjunct to the cytological and histological diagnosis of benign renal cysts versus cystic RCC, adenoma versus RCC, and oncocytoma versus granular cell RCC. Diffuse membraneous staining of all RCCs (with the exception of chromophobic cell RCC) suggests that MN/CA9 protein expression might have an important clinical utility in the early detection and treatment of RCC. Absence of MN/CA9 expression in non-renal cell clear cell adenocarcinoma also indicates that MN/CA9 protein expression may be used as a differential diagnostic biomarker of metastatic clear cell RCC.

Adult↗
PubMed2025

Discovery of novel diagnostic biomarkers of hepatocellular carcinoma associated with immune infiltration.

OBJECTIVE: Diagnosis of hepatocellular carcinoma (HCC) remains challenging for clinicians. Machine learning approaches and big data analyses are viable strategies for identifying HCC diagnostic markers. MATERIALS AND METHODS: In this study, we downloaded mRNA expression profiles of HCC from the GEO database and used random forest and machine learning algorithms, such as least absolute shrinkage and selection operator, to screen for reliable diagnostic genes. Disease Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis enrichment analyses were performed to explore differential gene functions and disease pathways. CIBERSORT was performed to calculate the immune cell infiltration of HCC and the correlation between diagnostic genes and immune cells. Cell experiments were performed to evaluate the function of R-spondin 3 (RSPO3) in HCC cells. Immunohistochemical staining was used to evaluate the protein expression of CD138, CD206 and iNOS. RESULTS: The results indicated that extracellular matrix protein 1 (ECM1), Niemann-Pick C1-Like 1 (NPC1L1) and RSPO3 were down-regulated in HCC compared with the normal group (p&#x2009;<&#x2009;0.05), which was validated in clinical tissue samples. Moreover, ECM1, NPC1L1 and RSPO3 had high diagnostic values (AUC > 0.75) for HCC in both training and test groups. Immuno-infiltration analysis revealed that ECM1 and RSPO3 were highly positively correlated with neutrophil and macrophage M2 levels, whereas they were negatively correlated with Tregs. RSPO3-si affected cell proliferation and apoptosis in HCC. Furthermore, RSPO3 exhibited a positive correlation with tumour progression, the proportion of plasma cells and M2 macrophages in mice, while showing a negative association with M1 macrophages. CONCLUSION: The present study identified ECM1, NPC1L1 and RSPO3 as new diagnostic biomarkers for HCC based on normal and diseased samples from HCC, meanwhile the pro-oncogenic function of RSPO3 and its regulation on immune infiltration have been confirmed.

Carcinoma, Hepatocellular↗
PubMed2026

Urinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy. Yet, no rapid, non-invasive biomarkers are available for diagnosis or screening. Urine represents an ideal analyte matrix due to its accessibility, low invasiveness, longitudinal sampling, and the kidney's central role in filtration. Here, we integrated proteomic, lipidomic, and metabolomic analyses of urine from ccRCC patients and controls to identify diagnostic biomarkers. Multi-omics profiling revealed urogenital metabolic dysregulation in ccRCC, including increased lipid metabolism, altered mitochondrial respiration signatures, and elevated urinary lipid content. We identified three urinary protein biomarkers: serum amyloid A1 (SAA1), haptoglobin (HP), and lipocalin 15 (LCN15). Using a parallel reaction monitoring mass spectrometry workflow, we developed a rapid and sensitive assay and combined these markers into a diagnostic UrineScore. The UrineScore achieved 0.96 in an area under the receiver operating characteristic curve analysis in the discovery cohort, and 0.95 in an independent validation cohort. Together, these results support the feasibility of multi-omics-guided urinary biomarker discovery and represent a step toward accessible diagnostic platforms for ccRCC.

Humans↗
PubMed2026

Human Wings Apart-Like Protein as a Serum Diagnostic Biomarker in Cervical Cancer: An Integrative Bioinformatics Analysis with Serum Validation.

Cervical cancer remains a major threat to women's health worldwide, and reliable serum biomarkers for early detection and therapeutic stratification remain limited. Human wings-apart-like (hWAPL) protein has been implicated in cervical carcinogenesis, but its diagnostic and clinical value has not been fully elucidated. To address this gap, this study integrated public multi-omics datasets, including The Cancer Genome Atlas, GEPIA2, the Human Protein Atlas, and single-cell transcriptomic data, to characterize hWAPL expression, clinicopathological associations, immune infiltration, co-expression networks, post-translational modifications, and drug sensitivity predictions. These findings were evaluated in an independent single-center serum cohort comprising 89 patients with histologically confirmed cervical squamous cell carcinoma and 89 healthy female controls. Serum hWAPL and squamous cell carcinoma antigen (SCC) levels were measured, and diagnostic performance was assessed by receiver operating characteristic curve analysis. In silico, hWAPL was broadly upregulated across multiple malignancies, particularly cervical cancer, enriched in malignant epithelial cells and monocytes/macrophages, and associated with shorter progression-free interval, predicted reduced sensitivity to cisplatin, paclitaxel, and 5-fluorouracil, and predicted sensitivity to MCL-1 and Wee1 inhibitors. In the serum cohort, hWAPL levels were significantly higher in patients than controls and discriminated cervical cancer with an area under the curve of 0.961, exceeding SCC alone. Combining hWAPL with SCC further improved diagnostic performance (area under the curve, 0.974; sensitivity, 93.3%; specificity, 95.5%). These findings suggest that serum hWAPL is a potential novel diagnostic biomarker for cervical squamous cell carcinoma whose performance is enhanced by SCC, whereas the observed associations with chemoresistance and immune microenvironment remodeling are hypothesis-generating and require experimental confirmation.

Humans↗
PubMed2025

Development and validation of blood-based diagnostic biomarkers for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) using EpiSwitch&#xae; 3-dimensional genomic regulatory immuno-genetic profiling.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating, multifactorial disorder characterised by profound fatigue, post-exertional malaise, cognitive impairments, and autonomic dysfunction. Despite its significant impact on quality of life, ME/CFS lacks definitive diagnostic biomarkers, complicating diagnosis and management. Recent evidence highlights potential blood tests for ME/CFS biomarkers in immunological, genetic, metabolic, and bioenergetic domains. Chromosome conformations (CCs) are potent epigenetic regulators of gene expression and cross-tissue exosome signalling. We have previously developed an epigenetic assay, EpiSwitch&#xae;, that employs an algorithm-based CCs analysis. Using EpiSwitch&#xae; technology, we have shown the presence of disease-specific CCs in peripheral blood mononuclear cells (PBMCs) of patients with amyotrophic lateral sclerosis (ALS), rheumatoid arthritis (RA), prostate and colorectal cancers, diffuse Large B-cell lymphoma and severe COVID-19. In a recent paper, we have identified a profile of systemic chromosome conformations in cancer patients reflective of the predisposition to respond to immune checkpoint inhibitors, PD-1/PD-L1 antagonists, with 85% accuracy. In this Retrospective case/control study (EPI-ME, Epigenetic Profiling Investigation in Myalgic Encephalomyelitis), we used whole blood samples retrospectively collected from n&#x2009;=&#x2009;47 patients with severe ME/CFS and n&#x2009;=&#x2009;61 age-matched healthy control patients to perform whole-genome 3D DNA screening for CCs correlating to ME/CFS diagnosis. We identified a 200-marker model for ME/CFS diagnosis (Episwitch&#xae;CFS test). First testing on the retrospective independent validation cohort demonstrated a strong systemic ME/CFS signal with a sensitivity of 92% and a specificity of 98%.Pathways analysis revealed several likely contributors to the pathology of ME/CFS, including interleukins, TNF&#x3b1;, neuroinflammatory pathways, toll-like receptor signalling and JAK/STAT. Comparison with pathways involved in the action of Rituximab and glatiramer acetate (Copaxone) (therapies with potential in ME/CFS treatment) identified IL2 as a shared pathway with clear patient clustering, indicating a possibility of a potential responder group for targeted treatment.

Humans↗
PubMed1996

Expression of the MN antigen in cervical papanicolaou smears is an early diagnostic biomarker of cervical dysplasia.

A new tumor-associated antigen, MN, has been shown to be expressed in virtually all cervical carcinomas and the majority of cervical intraepithelial neoplasia, but not in normal cervices (S. Y. Liao et al., Am. J. Pathol., 145: 598-609, 1994). Therefore, we postulated that the exfoliative cells in cervical Papanicolaou (Pap) smears would reflect the MN immunoreactivity seen in the tissue sections, and high levels of MN expression in the exfoliative cells would indicate the presence of dysplasia in the cervix. A total of 305 cervical Pap smears, with histological confirmation, representing all categories of the Bethesda System, were immunohistologically examined. We found that high levels of MN expression in exfoliative cells were not restricted to the dysplastic cells but were observed also in the normal endocervical cells (NECs) when dysplasia was present in the tissue biopsies. Overall, the rates of positive MN immunostaining of the dysplastic cells in low- and high-grade squamous intraepithelial lesions and invasive carcinoma were 35 (65%) of 54, 44 (77%) of 57, and 12 (92%) of 13, respectively. However, diffuse MN immunoreactivity of the atypical and/or dysplastic endocervical columnar cells was seen in all cases (100%) of adenocarcinoma in situ (AIS; n = 23) and adenocarcinomas (n = 8). In the groups with cytological diagnoses of atypical squamous cells or atypical glandular cells of undetermined significance (ASCUS and AGUS, respectively), MN positivity was seen in 47% of ASCUS (22/47) and 55% of AGUS (12/22). Dysplastic tissues were identified in all MN-positive cases. In contrast, all MN-negative atypical Pap smears were confirmed histologically to be benign cervix with one exception, in which the cytological diagnosis was ASCUS and focal low-grade squamous intraepithelial lesions were found in the cervix. The study also included 89 cases with cytological diagnoses of within normal limits/benign cellular changes. Among these, 10 Pap smears expressed diffuse MN antigen in the NEC, and dysplasia (8 cases of low-grade squamous intraepithelial lesions, 2 AIS) was found in the cervices. None of MN-negative cases with "within normal limits" cytology contained dysplastic cervices. Therefore, it would seem that diffuse MN antigen expression in the NEC may be an indicator of cervical dysplasia. Thus, MN antigen might serve as an early biomarker of cervical neoplasia. The combination of detection via cytology and MN immunostaining resulted in no false negatives and also discriminated between cellular atypia due to benign reactive changes versus cellular atypia due to dysplasia in the category of ASCUS and AGUS. In particular, it was found in the AGUS group that diffuse MN immunostaining restricted to atypical columnar cells was diagnostic for AIS. These findings indicate that MN antigen expression is an important diagnostic biomarker of glandular neoplasia and a valuable adjunct to cytological diagnosis of ASCUS and AGUS.

Adult↗
PubMed2026

ceRNA network of lncRNAs and mRNAs in OSF-to-OSCC progression: Diagnostic biomarkers and functional pathways.

BACKGROUND: Oral submucous fibrosis (OSF) is a chronic potentially malignant disorder that can progress to oral squamous cell carcinoma (OSCC). Although dysregulated non-coding RNAs have been implicated in oral carcinogenesis, the competing endogenous RNA (ceRNA)-mediated regulatory mechanisms underlying OSF-to-OSCC progression remain poorly understood. This study aimed to identify candidate regulatory molecules and construct a putative lncRNA-miRNA-mRNA network associated with malignant transformation. METHODS: Publicly available microarray datasets (GSE117973 and GSE125866) were analyzed to identify differentially expressed genes between OSF and OSCC. Differentially expressed transcripts were classified into mRNAs and lncRNAs based on public transcript annotations. Highly correlated lncRNA-mRNA pairs were identified using Pearson correlation analysis and integrated with multiMiR-supported miRNA-mRNA interactions obtained from public databases to construct a putative ceRNA regulatory network. Functional characterization focused on apoptosis, epithelial-mesenchymal transition (EMT), and immune checkpoint-related pathways. Receiver operating characteristic (ROC) analysis was performed to evaluate diagnostic performance, and selected biomarkers were externally validated using The Cancer Genome Atlas (TCGA) OSCC cohort. RESULTS: Integrated transcriptomic analysis identified several dysregulated mRNAs and lncRNAs associated with OSF-to-OSCC progression. Network analysis highlighted TBC1D3B, RREB1, TEAD3, SREBF1, TMEM41B, FOXK2, and KIAA1958 as prominent hub genes within the putative regulatory network. Functional analyses demonstrated significant associations with apoptosis-, EMT-, and immune checkpoint-related genes, suggesting potential involvement in multiple biological processes contributing to malignant transformation. Several hub genes exhibited strong diagnostic performance, with ROC analysis yielding AUC values ranging from 0.891 to 1.000, indicating excellent discrimination between OSF and OSCC samples. External validation using TCGA further supported the relevance of the identified biomarkers in OSCC. CONCLUSIONS: This study provides a comprehensive transcriptomic framework describing putative lncRNA-miRNA-mRNA regulatory interactions associated with OSF progression to OSCC. The identified hub genes and regulatory networks represent candidate biomarkers for early detection and provide a foundation for future mechanistic and experimental validation. As the proposed ceRNA interactions are computationally inferred, further biological validation is required before clinical application.

RNA, Long Noncoding↗
PubMed2026

Exploring the Translation of Organ-on-a-Chip Technology for Human-Relevant Diagnostic Biomarkers.

Microphysiological systems (MPSs) are gaining traction as a viable alternative model for toxicity studies. Further characterization is necessary to explore the full translational potential of MPSs to human physiology, along with the utility of these platforms to serve as a diagnostic tool. Multiomics analyses have emerged as a key means for identifying host biomarkers associated with chemical and drug exposure. Correlations between published human omics and MPS technology omics data will inform the potential of organ chips to accurately represent human responses and provide an alternative approach for improved biomarker discovery for toxicity assessment and exposure identification. To interrogate these potential overlaps, TissUse Chip3 multiorgan chips (MOCs) seeded with kidney organoids, liver organoids, and respiratory tract tissue were exposed to low, therapeutic, and toxic doses of acetaminophen (n = 4 for each condition) for 24 h and subjected to proteomic and metabolomic analysis. The data from our organ chips are largely consistent with biomarkers and dysregulations identified in published human omics data, in vitro and in vivo data, to include the identification of several known acetaminophen metabolites and biotransformation products. These data suggest that organ chips may be a suitable surrogate for human biomarker identification and drug or hazardous chemical exposure diagnosis.

Humans↗
PubMed2006

Analysis of potential diagnostic biomarkers in cerebrospinal fluid of idiopathic normal pressure hydrocephalus by proteomics.

BACKGROUND: The pathogenesis of idiopathic normal pressure hydrocephalus (INPH) is unknown, and the syndrome of INPH remains a diagnostic and therapeutic challenge. The present study investigated the disease-specific proteins that aid in the diagnosis and treatment of INPH and thus to study their role in the disease process. METHODS: A comparative proteomic analysis was used for clinical screening of cerebrospinal fluid (CSF) proteins in 15 patients with INPH and compared with 12 normal subjects. Furthermore, enzyme linked immunosorbent assay (ELISA) was performed for comparison with CSF proteins between individual INPH patients and controls. RESULTS: Seven proteins and their isoforms, including leucine-rich alpha-2-glycoprotein (LRG), alpha1-antichymotrypsin, apolipoprotein D, apolipoprotein J, haptoglobin alpha1, serum albumin, and alpha-1-microglobulin/bikunin precursor showed significant changes in CSF of INPH patients compared with controls by proteomic analysis. And significant higher CSF levels of LRG in INPH patients compared with controls were found by ELISA. CONCLUSIONS: These results indicate that there are significant differences in the expression of certain proteins in the CSF of patients with INPH and normal subjects. In particular, the CSF level assay of LRG suggests that LRG is a specific biomarker for INPH and has potential use in the diagnosis and indication for CSF shunting.

Aged↗
PubMed2000

Expression of MN/CA9 protein in Papanicolaou smears containing atypical glandular cells of undetermined significance is a diagnostic biomarker of cervical dysplasia and neoplasia.

BACKGROUND: Despite the enormous impact that Papanicolaou (Pap) smear screening has had on the incidence of cervical carcinoma in developed countries, there is still an unacceptably high frequency of occurrence of this cancer. In part, this is due to human error associated with cytologic diagnoses of Pap smears. Also, the use of new sampling devices, such as the cytobrush, has increased the complexity of diagnosing benign and neoplastic cervical cytology. This is particularly apparent in the diagnosis of atypical glandular cells of undetermined significance (AGUS). Approximately 40% of AGUS diagnoses have a corresponding significant lesion at biopsy follow-up, and 60% do not. There is clearly a need for an adjunct to cytologic diagnosis that can readily identify AGUS smears that are diagnostic of significant lesions. The authors have identified the MN/CA9 antigen as a strong candidate for an adjunct biomarker. METHODS: A total of 245 Pap smears of all AGUS diagnostic categories with histologic confirmation were studied. The median age of the patients was 39 years. The Bethesda system classification (AGUS-favor reactive, AGUS-not otherwise specified, and AGUS-favor neoplastic) was used. All of the Pap smears were decolorized and immunostained with monoclonal antibody to MN/CA9 antigen by the immunoperoxidase technique. The results of MN/CA9 immunoreactivity were correlated with the histologic data in a semiblinded fashion. RESULTS: The follow-up biopsies showed that a high percentage (70%) of patients had low and high grade cervical intraepithelial neoplasia lesions, respectively (CIN I and CIN II or III). Clinically significant lesions-adenocarcinoma in situ/carcinoma (AIS/CA) and CIN II or III-were found in 50% of the cases. Among these, 11% were AIS/CA. In the three subcategories of AGUS diagnosis, the AGUS-not otherwise specified showed the broadest range of lesions in the follow-up biopsies. Three patterns of MN/CA9 immunoreactivity were observed in the Pap smears: 1) atypical cells, 2) normal endocervical cells only, and 3) all cells negative. All Pap smears that were MN/CA9 positive were histologically confirmed to be clinically significant lesions or CIN I; in addition, there were a very small number (n = 12) of cases of atypia. None of the benign lesions showed MN/CA9 expression in the corresponding Pap smears. Furthermore, the pattern of atypical cell immunostaining identified all cases with significant lesions (AIS/CA and CIN II or III) in the cervices. Conversely, the majority of CIN I cases (82%) and all cases of atypia showed positive immunostaining restricted to normal endocervical cells only. CONCLUSIONS: There is a clear association between MN/CA9 immunostaining of atypical cells and the presence of significant lesions in the cervix. Similarly, there is a clear association between lack of expression of MN/CA9 and the absence of cervical lesions. However, the screen does not allow discrimination between CIN I and atypia. The authors also found that, based on the combined patterns of morphology and immunostaining, they are able to discriminate between AIS and CIN II or III in AGUS Pap smear diagnoses. Thus, expression of the MN/CA9 antigen is indeed a discriminator of significant lesions in AGUS Pap smear diagnoses.

Adult↗
PubMed2000

New peptide labels containing covalently bonded platinum(II) centers as diagnostic biomarkers and biosensors.

[reaction: see text] Water- and acid-resistant arylplatinum(II) complexes have been covalently bonded to the N-terminus of L-valine, thus providing organometallic biomolecules with excellent stability properties. Owing to the (195)Pt nucleus (I = (1)/(2)), these building blocks are potentially versatile biomarkers (e.g., MRI). Moreover, they display efficient in vitro biosensor characteristics since they detect SO(2) gas selectively and fully reversibly by an instantaneous change of the spectroscopic properties including a diagnostic (195)Pt NMR signal.

Biomarkers↗
PubMed2006

Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers.

PURPOSE: An estimated 4% to 7% of the population will develop a clinically significant thyroid nodule during their lifetime. In many cases, preoperative diagnoses by needle biopsy are inconclusive. Thus, there is a clear need for improved diagnostic tests to distinguish malignant from benign thyroid tumors. The recent development of high-throughput molecular analytic techniques should allow the rapid evaluation of new diagnostic markers. However, researchers are faced with an overwhelming number of potential markers from numerous thyroid cancer expression profiling studies. MATERIALS AND METHODS: To address this challenge, we have carried out a comprehensive meta-review of thyroid cancer biomarkers from 21 published studies. A gene ranking system that considers the number of comparisons in agreement, total number of samples, average fold-change and direction of change was devised. RESULTS: We have observed that genes are consistently reported by multiple studies at a highly significant rate (P < .05). Comparison with a meta-analysis of studies reprocessed from raw data showed strong concordance with our method. CONCLUSION: Our approach represents a useful method for identifying consistent gene expression markers when raw data are unavailable. A review of the top 12 candidates revealed well known thyroid cancer markers such as MET, TFF3, SERPINA1, TIMP1, FN1, and TPO as well as relatively novel or uncharacterized genes such as TGFA, QPCT, CRABP1, FCGBP, EPS8 and PROS1. These candidates should help to develop a panel of markers with sufficient sensitivity and specificity for the diagnosis of thyroid tumors in a clinical setting.

Biomarkers, Tumor↗
PubMed2026

Integrated multi-omics identification of m6A-SNP-related diagnostic biomarkers in amyotrophic lateral sclerosis.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) lacks reliable and minimally invasive biomarkers for early diagnosis. m6A-associated single-nucleotide polymorphisms (m6A-SNPs) may influence RNA methylation and gene expression, offering opportunities to identify clinically relevant diagnostic markers. METHODS: We integrated eQTLGen cis-eQTL data, RMVar m6A-SNP annotations, and ALS transcriptomic datasets to identify m6A-SNP-related genes. Random Forest and LASSO regression were combined to screen robust diagnostic markers. A nomogram was constructed and validated using independent cohorts. Immune infiltration, predicted m6A modification sites, and potential RBP-SNP interactions were assessed. Peripheral blood samples from ALS patients were used for exploratory validation of gene expression and global m6A levels. RESULTS: We identified 109 ALS-associated m6A-SNP-related genes with cis-eQTL signals and narrowed these to seven candidate diagnostic markers (TMED5, OXR1, BRI3, FEM1C, SUZ12, EIF2AK4, and TJAP1). The seven-gene model outperformed the individual markers in the training cohort and retained moderate discrimination in the independent validation cohort. ALS samples showed differences in inferred immune-cell composition, including monocytes, neutrophils, and T-cell subsets. The selected SNP loci were located near predicted m6A sites and annotated RBP-binding regions. Exploratory clinical validation showed significant upregulation of FEM1C and SUZ12 at both mRNA and protein levels, accompanied by reduced global m6A modification. CONCLUSIONS: Through multi-omics integration and exploratory clinical validation, this study identifies m6A-SNP-related candidate markers associated with ALS. The findings support further evaluation of m6A-related signatures for ALS discrimination and molecular characterization, while larger independent cohorts and additional calibration are required before clinical application.

Humans↗