{"title":"Ion mobility spectrometry and ion mobility-mass spectrometry in clinical chemistry.","authors":"Kyle E Lira, Jody C May, John A McLean","doi":"10.1016/bs.acc.2024.10.003","DOIUrl":"10.1016/bs.acc.2024.10.003","url":null,"abstract":"<p><p>Advancements in clinical chemistry have major implications in terms of public health, prompting many clinicians to seek out chemical information to aid in diagnoses and treatments. While mass spectrometry (MS) and hyphenated-MS techniques such as LC-MS or tandem MS/MS have long been the analytical methods of choice for many clinical applications, these methods routinely demonstrate difficulty in differentiating between isomeric forms in complex matrices. Consequently, ion mobility spectrometry (IM), which differentiates molecules on the basis of size, shape, and charge, has demonstrated unique advantages in the broad application of stand-alone IM and hyphenated IM instruments towards clinical challenges. Here, we highlight representative IM applications and approaches and describe contemporary commercial offerings of IM technology and how these can be, or are currently being, applied to the field of clinical chemistry.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"124 ","pages":"123-160"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Preface.","authors":"Gregory S Makowski","doi":"10.1016/S0065-2423(25)00025-3","DOIUrl":"https://doi.org/10.1016/S0065-2423(25)00025-3","url":null,"abstract":"","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"125 ","pages":"xi-xii"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143485330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shereen M Aleidi, Abeer Malkawi, Hiba Al Fahmawi, Anas M Abdel Rahman
{"title":"Metabolomics of nephrotic syndrome.","authors":"Shereen M Aleidi, Abeer Malkawi, Hiba Al Fahmawi, Anas M Abdel Rahman","doi":"10.1016/bs.acc.2025.04.004","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.04.004","url":null,"abstract":"<p><p>This chapter reviews the emerging role of metabolomics in nephrotic syndrome (NS), a kidney disorder characterized by proteinuria, hypoalbuminemia, edema, and hyperlipidemia. Metabolomics provides valuable insights into the complex metabolic changes associated with NS, including disruptions in lipid, amino acid, and energy metabolism and oxidative stress markers. Through untargeted and targeted approaches, metabolomics enables the discovery of novel potential biomarkers that could enhance diagnosis, monitor disease progression, and personalize treatment strategies. Despite challenges such as methodological variability and the need for extensive computational resources, advancements in metabolomics technology and data integration are poised to improve our understanding of NS. Integrating metabolomics with genomics and proteomics may enable a comprehensive molecular profile of NS, offering new opportunities for precision medicine and improved patient outcomes.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"127 ","pages":"63-84"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Gel electrophoresis-based proteoform separation and analysis.","authors":"Paul Dowling, Kay Ohlendieck","doi":"10.1016/bs.acc.2025.04.002","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.04.002","url":null,"abstract":"<p><p>Proteomics using gel electrophoresis (GE) for efficient protein separation prior to mass spectrometry is a frequently employed and proteoform-centric analysis tool of biomedical chemistry. Isolated molecular species can be visualized by various protein staining techniques and their characterization being combined with protein interaction analyses and the determination of dynamic post-translational modifications. This chapter describes the bioanalytical usefulness of one-dimensional GE (1D-GE) approaches, including the gel electrophoresis liquid chromatography (GeLC) mass spectrometry method, as well as commonly used two-dimensional gel electrophoresis (2D-GE) techniques, including fluorescence difference GE (DIGE) for sophisticated comparative studies. The ways in which advanced protein identification and gel-based proteomics can help to discover novel biomarker candidates is discussed.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"127 ","pages":"119-171"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"From nonexistence to novel applications: Nullomers and related k-mer based concepts in bioinformatics.","authors":"Candace S Y Chan, Ilias Georgakopoulos-Soares","doi":"10.1016/bs.acc.2025.06.009","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.06.009","url":null,"abstract":"<p><p>Underrepresented k-mer sequences, provide insights into evolutionary constraints, molecular mechanisms, and organismal fitness. Analysis of these sequences have broad applications across genomics and proteomics, such as in biomarker development, cancer diagnostics, phylogenetic analysis, synthetic biology and novel drug discovery. Absent sequences (nullomers and neomers) show promise for cancer detection and tissue-of-origin identification using nucleic acids derived from liquid biopsies, while quasi-primes serve as genomic fingerprints that offer potential for evolutionary studies for understanding trait evolution, and in metagenomics, as biomarkers of organismal presence. The chapter also discusses computational challenges associated with analyzing absent sequences and highlights available k-mer based resources and databases. With the continuous expansion of genomic and proteomic data, absent sequences present an innovative framework for addressing fundamental biological questions and advancing applications in basic and translational research.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"129 ","pages":"191-206"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gabriel C Nwokolo, Robert A Falconer, Francis M Barnieh
{"title":"Aminopeptidase N (CD13): Bridging physiology, pathology and therapeutic potential.","authors":"Gabriel C Nwokolo, Robert A Falconer, Francis M Barnieh","doi":"10.1016/bs.acc.2025.07.002","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.07.002","url":null,"abstract":"<p><p>Aminopeptidase N (CD13) is a multifunctional protein recognized for its diverse roles as an enzyme, receptor, and signalling molecule, attributes that have earned it classification as a \"moonlighting\" protein. Its involvement in key biological processes such as inflammation, angiogenesis, cell migration, tissue invasion, and the propagation and survival of cancer cells has spurred significant interest in its potential as a therapeutic target. This interest extends beyond oncology to include conditions such as hypertension and rheumatoid arthritis. Consequently, substantial research efforts have been directed toward exploring strategies for leveraging CD13 in clinical interventions. This chapter comprehensively reviews this protein with the aim of improving current understanding of this protein, with a particular focus on its tissue-specific expression and functional roles. Special attention is given to the physiological and pathological diversity of CD13 activity, which offers critical insights into opportunities for selective targeting and disease-specific therapeutic applications.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"129 ","pages":"207-269"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chrisanna Dobrowolski, Shu Min Lao, Fadi Kharouf, Paula Parnizari Croci, Joan Wither, Dafna D Gladman, Laura Whitall Garcia, Arenn Jauhal, Zahi Touma
{"title":"Lupus nephritis: Biomarkers.","authors":"Chrisanna Dobrowolski, Shu Min Lao, Fadi Kharouf, Paula Parnizari Croci, Joan Wither, Dafna D Gladman, Laura Whitall Garcia, Arenn Jauhal, Zahi Touma","doi":"10.1016/bs.acc.2024.10.002","DOIUrl":"10.1016/bs.acc.2024.10.002","url":null,"abstract":"<p><p>Lupus nephritis (LN) or renal involvement of systemic lupus erythematosus (SLE), is a common manifestation occurring in at least 50 % of SLE patients. LN remains a significant source of morbidity, often leading to progressive renal dysfunction and is a major cause of death in SLE. Despite these challenges, advances in the understanding of the pathogenesis and genetic underpinnings of LN have led to a commendable expansion in available treatments over the past decade. This chapter provides a foundation for the understanding LN pathogenesis, diagnosis, and epidemiology, and guides the reader through recent advances in biomarkers, genetic susceptibility of this intricate condition.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"124 ","pages":"87-122"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evangelos Kalogirou, Spyridon Voulgaris, George A Alexiou
{"title":"Coagulopathy prediction in traumatic brain injury.","authors":"Evangelos Kalogirou, Spyridon Voulgaris, George A Alexiou","doi":"10.1016/bs.acc.2025.01.003","DOIUrl":"10.1016/bs.acc.2025.01.003","url":null,"abstract":"<p><p>Traumatic brain injury (TBI) represents a significant public health concern. Besides the initial primary injury, a defining point of TBI is causing secondary, delayed damage through inflammatory biochemical processes. Among the complications arising from this inflammatory response, coagulopathy emerges as a critical concern. With an overall prevalence of 32.7 %, TBI-induced coagulopathy significantly contributes to increased mortality rates and unfavorable patient outcomes, through its clinical manifestations, such as progressive hemorrhagic injury (PHI). This chapter investigates biomarkers capable of accurately detecting coagulopathy and PHI in TBI, evaluating their potential utility based on statistical evidence from various studies and exploring their possible association in the biochemical processes guiding or following TBI-induced coagulopathy. Notably, glucose emerges as a standout candidate, exhibiting a sensitivity of 91.5 % and specificity of 87.5 % for predicting coagulopathy. Furthermore, interleukin-33, with a sensitivity of 93.3 % and specificity of 66.7 %, and galectin-3, with a sensitivity of 67.7 % and specificity of 85.5 %, are promising for PHI. Despite these encouraging findings, significant efforts remain necessary to translate biomarker diagnostic utility into clinical practice effectively. Further research and validation studies are imperative to elucidate the intricate biochemical processes underlying TBI-induced coagulopathy and to refine the clinical application of biomarkers for improved patient management and outcomes in real-world settings.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"126 ","pages":"199-231"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"MDDB: A public databank of host microRNAs in Tuberculosis diagnosis.","authors":"Piyush Agrawal, Aditya Upadhyay, Ravindra Kumar Chauhan, Awanish Kumar","doi":"10.1016/bs.acc.2025.04.006","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.04.006","url":null,"abstract":"<p><p>Tuberculosis (TB) remains a major global health challenge due to its high mortality rate. Several factors contribute significantly including delayed diagnosis, emergence of drug resistance, and biofilm formation. Although various diagnostic methods are available for TB, such as sputum smear microscopy, culture techniques, and real-time polymerase chain reaction (PCR). They have notable limitations, including false positives and negatives, timeliness, and high cost. Therefore, there is an urgent need for an early and accurate diagnostic approach to control the infection. MicroRNA (miRNA)-based diagnostics have emerged as a promising alternative, offering the potential for earlier detection and reduced false-positivity. However, this field is still in development and requires specialized tools to accelerate miRNA research, streamline the process, and facilitate the creation of innovative diagnostic methods. To address this need, the MicroRNA Disease Databank (MDDB) was developed as a centralized platform providing extensive miRNA-related information. Freely accessible at https://mddb.nitrr.ac.in/., MDDB offers comprehensive details on miRNA locations, associated disease characteristics, probe sequences, and molecular mechanisms. This resource aims to support the development of novel miRNA-based diagnostic biomarkers. This article provides an in-depth overview of the MDDB tool, highlighting its construction, features, and accessibility. Currently, MDDB focuses on host miRNAs relevant to TB, allowing researchers to quickly access critical miRNA data. By leveraging this resource, researchers will potentially accelerate the development of effective diagnostic biomarkers for TB and other chronic diseases in the future.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"127 ","pages":"221-253"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Emerging markers in celiac disease.","authors":"Sajjad Bakhtiari, Mohammad Rostami-Nejad","doi":"10.1016/bs.acc.2025.06.010","DOIUrl":"https://doi.org/10.1016/bs.acc.2025.06.010","url":null,"abstract":"<p><p>Celiac disease (CD) is a chronic autoimmune disorder triggered by gluten ingestion in genetically predisposed individuals. Current diagnostic methods rely on serological markers, histological examination of duodenal biopsies, and HLA genotyping. However, these approaches have limitations. Advancements in serology have introduced novel autoantibodies beyond tissue transglutaminase (tTG) and endomysial antibodies (EMA), such as neo-epitope tTG and transglutaminase isoforms. Genetic and epigenetic markers, including non-HLA risk alleles, DNA methylation patterns, and non-coding RNAs, provide deeper insights into CD susceptibility. Additionally, cytokine profiling and immune response markers, such as pro-inflammatory and anti-inflammatory cytokines, chemokines, and adhesion molecules, reflect disease pathophysiology and may serve as diagnostic and prognostic tools. Gut microbiota alterations and metabolomic signatures further highlight immune dysregulation and metabolic changes in CD, offering potential biomarkers for diagnosis and disease monitoring. Protein and peptide biomarkers, including intestinal fatty acid-binding protein (I-FABP), plasma citrulline, and regenerating gene Ia (REG Ia), provide insights into intestinal damage and mucosal healing. Furthermore, emerging technologies such as point-of-care testing (POCT) and nanoparticle-based assays enhance diagnostic precision. The objective of this chapter is to provide a comprehensive review of emerging biomarkers and novel technologies that can improve the diagnosis and monitoring of CD. Emphasis is placed on advances in serology, genetic and epigenetic profiling, immune and cytokine markers, metabolomics, and gut microbiota analysis. The chapter also discusses the integration of multi-omics approaches and artificial intelligence-driven analysis as future directions for refining diagnostic accuracy and enabling personalized disease management.</p>","PeriodicalId":101297,"journal":{"name":"Advances in clinical chemistry","volume":"129 ","pages":"123-189"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}