Targeted LC-MS/MS for the evaluation of proteomics biomarkers in the blood of neonates with necrotizing enterocolitis and late-onset sepsis

The Interaction between Stress and Inflammatory Bowel Disease in Pediatric and Adult Patients

Background: Inflammatory bowel diseases (IBDs) have seen an exponential increase in incidence, particularly among pediatric patients. Psychological stress is a significant risk factor influencing the disease course. This review assesses the interaction between stress and disease progression, focusing on articles that quantified inflammatory markers in IBD patients exposed to varying degrees of psychological stress. Methods: A systematic narrative literature review was conducted, focusing on the interaction between IBD and stress among adult and pediatric patients, as well as animal subjects. The research involved searching PubMed, Scopus, Medline, and Cochrane Library databases from 2000 to December 2023. Results: The interplay between the intestinal immunity response, the nervous system, and psychological disorders, known as the gut-brain axis, plays a major role in IBD pathophysiology. Various types of stressors alter gut mucosal integrity through different pathways, increasing gut mucosa permeability and promoting bacterial translocation. A denser microbial load in the gut wall emphasizes cytokine production, worsening the disease course. The risk of developing depression and anxiety is higher in IBD patients compared with the general population, and stress is a significant trigger for inducing acute flares of the disease. Conclusions: Further large studies should be conducted to assess the relationship between stressors, psychological disorders, and their impact on the course of IBD. Clinicians involved in the medical care of IBD patients should aim to implement stress reduction practices in addition to pharmacological therapies.

Necrotizing enterocolitis: current understanding of the prevention and management

Necrotizing enterocolitis (NEC) is one of the diseases in neonates, with a high morbidity and mortality rate, especially in preterm infants. This review aimed to briefly introduce the latest epidemiology, susceptibility factors, and clinical diagnosis and presentation of NEC. We also organized new prevention strategies by risk factors according to different pathogeneses and then discussed new treatment methods based on Bell's staging and complications, and the classification of mild to high severity based on clinical and imaging manifestations. Such a generalization will help clinicians and researchers to gain a deeper understanding of the disease and to conduct more targeted classification, grading prevention, and exploration. We focused on prevention and treatment of the early and suspected stages of NEC, including the discovery of novel biomarkers and drugs to control disease progression. At the same time, we discussed its clinical application, future development, and shortcomings.

Data-driven decision-making for precision diagnosis of digestive diseases

Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.

Association of anemia and platelet activation with necrotizing enterocolitis with or without sepsis among low birth weight neonates: a case-control study

Background

This study aims to evaluate the value of the proportion of large platelets (PLCR) and platelet crit (PCT) in predicting necrotizing enterocolitis (NEC) in low birth weight (LBW) neonates.

Methods

A total of 155 LBW (<2,500 g) neonates with NEC, who were admitted to the neonatal intensive care unit (NICU) of the hospital from January 1, 2017, to November 30, 2019, were included in the case group. According to the 1:3 case-control study design, a total of 465 LBW neonates without NEC (three for each LBW neonate with NEC), who were admitted to the NICU and born ≤24 h before or after the birth of the subjects, were included in the control group.

Results

During the study period, a total of 6,946 LBW neonates were born, of which 155 had NEC, including 92 who also had sepsis. Neonatal sepsis was the most important risk factor and confounding factor for NEC in LBW neonates. Further stratified analysis showed that in LBW neonates without sepsis, anemia [P = 0.001, odds ratio (OR) = 4.367, 95% confidence interval (CI): 1.853-10.291], high PLCR (P < 0.001, OR = 2.222, 95% CI: 1.633-3.023), and high PCT (P = 0.024, OR = 1.368, 95% CI: 1.042-1.795) increased the risk of NEC and the receiver operating characteristic curve area of PLCR, sensitivity, specificity, and cutoff value were 0.739, 0.770, 0.610, and 33.55, respectively.

Conclusions

The results showed that 2/100 LBW neonates were at risk for NEC, and the stratified analysis of the confounding factors of sepsis identified the risk factors of NEC in LBW neonates. This study first reported the significance of PLCR in the early prediction of NEC occurrence in LBW neonates without sepsis.

Recent advances in our understanding of NEC diagnosis, prognosis and surgical approach

Necrotising enterocolitis (NEC) remains a devasting condition that has seen limited improvement in outcomes in recent years. The incidence of the disease is increasing as more extremely premature infants survive. NEC is responsible for 1 in 10 neonatal deaths and up to 61% of survivors have significant neurodevelopmental delay. The aim of this review is to highlight recent advances in diagnosis, prognosis and surgical approach in this condition. Many recent studies have reported novel methods of diagnosis of NEC with the aim of earlier and more accurate identification. These include imaging and machine learning techniques. Prognostication of NEC is particularly important to allow earlier escalation of therapy. Around 25% of infants with NEC will require surgery and recent data has shown that time from disease onset to surgery is greater in infants whose indication for surgery is failed medical management, rather than pneumoperitoneum. This indication was also associated with worse outcomes compared to pneumoperitoneum. Ongoing research has highlighted several new methods of disease prognostication which includes differentiating surgical from medical NEC. Finally, recent randomised controlled trials in surgical technique are discussed along with the implications of these for practice. Further, high quality research utilising multi-centre collaborations and high fidelity data from electronic patient records is needed to address the issues discussed and ultimately improve outcomes in NEC.

Biomarkers of necrotizing enterocolitis in the era of machine learning and omics

Necrotizing enterocolitis (NEC) continues to be a major cause of morbidity and mortality in preterm infants. Despite decades of research in NEC, no reliable biomarkers can accurately diagnose NEC or predict patient prognosis. The recent emergence of multi-omics could potentially shift NEC biomarker discovery, particularly when evaluated using systems biology techniques. Furthermore, the use of machine learning and artificial intelligence in analyzing this 'big data' could enable novel interpretations of NEC subtypes, disease progression, and potential therapeutic targets, allowing for integration with personalized medicine approaches. In this review, we evaluate studies using omics technologies and machine learning in the diagnosis of NEC. Future implications and challenges inherent to the field are also discussed.

Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a life-threatening condition for premature infants in neonatal intensive care units. Finding indicators that can predict NEC development before symptoms appear would provide more time to apply targeted interventions. In this study, stools from 132 very-low-birth-weight (VLBW) infants were collected daily in the context of a multi-center prospective study aimed at investigating the potential of fecal biomarkers for NEC prediction using proteomics technology. Eight of the VLBW infants received a stage-3 NEC diagnosis. Stools collected from the NEC infants up to 10 days before their diagnosis were available for seven of them. Their samples were matched with those from seven pairs of non-NEC controls. The samples were processed for liquid chromatography-tandem mass spectrometry analysis using SWATH/DIA acquisition and cross-compatible proteomic software to perform label-free quantification. ROC curve and principal component analyses were used to explore discriminating information and to evaluate candidate protein markers. A series of 36 proteins showed the most efficient capacity with a signature that predicted all seven NEC infants at least a week in advance. Overall, our study demonstrates that multiplexed proteomic signature detection constitutes a promising approach for the early detection of NEC development in premature infants.

Fecal amine metabolite analysis before onset of severe necrotizing enterocolitis in preterm infants: a prospective case-control study

Infants developing necrotizing enterocolitis (NEC) have a different metabolomic profile compared to controls. The potential of specific metabolomics, i.e. amino acids and amino alcohols (AAA), as early diagnostic biomarkers for NEC is largely unexplored. In this multicenter prospective case-control study, longitudinally collected fecal samples from preterm infants (born <30 weeks of gestation) from 1-3 days before diagnosis of severe NEC (Bell's stage IIIA/IIIB), were analyzed by targeted high-performance liquid chromatography (HPLC). Control samples were collected from gestational and postnatal age-matched infants. Thirty-one NEC cases (15 NEC IIIA;16 NEC IIIB) with 1:1 matched controls were included. Preclinical samples of infants with NEC were characterized by five increased essential amino acids-isoleucine, leucine, methionine, phenylalanine and valine. Lysine and ethanolamine ratios were lower prior to NEC, compared to control samples. A multivariate model was rendered based on isoleucine, lysine, ethanolamine, tryptophan and ornithine, modestly discriminating cases from controls (AUC 0.67; p < 0.001). Targeted HPLC pointed to several specific AAA alterations in samples collected 1-3 days before NEC onset, compared to controls. Whether this reflects metabolic alterations and has a role in early biomarker development for NEC, has yet to be elucidated.

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.

Biomarkers of Necrotizing Enterocolitis: The Search Continues

Necrotizing enterocolitis (NEC) is the most common gastrointestinal (GI) emergency in the neonatal intensive care unit. Despite advances in medical care, mortality and morbidity from NEC have not changed. This is likely due to the lack of a clear understanding of this multifactorial disease, and reliable biomarkers for accurate diagnosis of NEC. Currently, the diagnosis of NEC is made by a combination of nonspecific clinical signs, symptoms, and radiological findings. Though biomarkers have been studied extensively, none offer an acceptable sensitivity or specificity to be used. This review will focus on the available literature on biomarkers for preterm NEC, acknowledging the limitations in studies including the variability of inclusion criteria, and most importantly, the lack of gold standard case definition for NEC.

Biomarkers for the Diagnosis of Neonatal Sepsis

Neonatal sepsis is a major cause of morbidity and mortality in neonates and is challenging to diagnose. Infants manifest nonspecific clinical signs in response to sepsis; these signs may be caused by noninfectious conditions. Time to antibiotics affects neonatal sepsis outcome, so clinicians need to identify and treat neonates with sepsis expeditiously. Clinicians use serum biomarkers to measure inflammation and infection and assess the infant's risk of sepsis. However, current biomarkers lack sufficient sensitivity or specificity to be consider useful diagnostic tools. Continued research to identify novel biomarkers as well as novel ways of measuring them is sorely needed.

Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside

Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.

Effects of an early life diet containing large phospholipid-coated lipid globules on hepatic lipid metabolism in mice

We recently reported that feeding mice in their early life a diet containing a lipid structure more similar to human milk (eIMF, Nuturis) results in lower body weights and fat mass gain upon high fat feeding in later life, compared to control (cIMF). To understand the underlying mechanisms, we now explored parameters possibly involved in this long-term effect. Male C57BL/6JOlaHsd mice, fed rodent diets containing eIMF or cIMF from postnatal (PN) day 16-42, were sacrificed at PN42. Hepatic proteins were measured using targeted proteomics. Lipids were assessed by LC-MS/MS (acylcarnitines) and GC-FID (fatty-acyl chain profiles). Early life growth and body composition, cytokines, and parameters of bile acid metabolism were similar between the groups. Hepatic concentrations of multiple proteins involved in β-oxidation (+ 17%) the TCA cycle (+ 15%) and mitochondrial antioxidative proteins (+ 28%) were significantly higher in eIMF versus cIMF-fed mice (p < 0.05). Hepatic L-carnitine levels, required for fatty acid uptake into the mitochondria, were higher (+ 33%, p < 0.01) in eIMF-fed mice. The present study indicates that eIMF-fed mice have higher hepatic levels of proteins involved in fatty acid metabolism and oxidation. We speculate that eIMF feeding programs the metabolic handling of dietary lipids.

Emerging Biomarkers for Prediction and Early Diagnosis of Necrotizing Enterocolitis in the Era of Metabolomics and Proteomics

Necrotizing Enterocolitis (NEC) is a catastrophic disease affecting predominantly premature infants and is characterized by high mortality and serious long-term consequences. Traditionally, diagnosis of NEC is based on clinical and radiological findings, which, however, are non-specific for NEC, thus confusing differential diagnosis of other conditions such as neonatal sepsis and spontaneous intestinal perforation. In addition, by the time clinical and radiological findings become apparent, NEC has already progressed to an advanced stage. During the last three decades, a lot of research has focused on the discovery of biomarkers, which could accurately predict and make an early diagnosis of NEC. Biomarkers used thus far in clinical practice include acute phase proteins, inflammation mediators, and molecules involved in the immune response. However, none has been proven accurate enough to predict and make an early diagnosis of NEC or discriminate clinical from surgical NEC or other non-NEC gastrointestinal diseases. Complexity of mechanisms involved in NEC pathogenesis, which remains largely poorly elucidated, could partly explain the unsatisfactory diagnostic performance of the existing NEC biomarkers. More recently applied technics can provide important insight into the pathophysiological mechanisms underlying NEC but can also aid the detection of potentially predictive, early diagnostic, and prognostic biomarkers. Progress in omics technology has allowed for the simultaneous measurement of a large number of proteins, metabolic products, lipids, and genes, using serum/plasma, urine, feces, tissues, and other biological specimens. This review is an update of current data on emerging NEC biomarkers detected using proteomics and metabolomics, further discussing limitations and future perspectives in prediction and early diagnosis of NEC.

Precision medicine in pediatric sepsis

PURPOSE OF REVIEW

Pediatric sepsis is a heterogeneous state associated with significant morbidity and mortality, but treatment strategies are limited. Clinical trials of immunomodulators in sepsis have shown no benefit, despite having a strong biological rationale. There is considerable interest in application of a precision medicine approach to pediatric sepsis to identify patients who are more likely to benefit from targeted therapeutic interventions.

RECENT FINDINGS

Precision medicine requires a clear understanding of the molecular basis of disease. 'Omics data' and bioinformatics tools have enabled identification of endotypes of pediatric septic shock, with corresponding biological pathways. Further, using a multibiomarker-based approach, patients at highest risk of poor outcomes can be identified at disease onset. Enrichment strategies, both predictive and prognostic, may be used to optimize patient selection in clinical trials and identify a subpopulation in whom therapy of interest may be trialed. A bedside-to-bench-to-bedside model may offer clinicians pragmatic tools to aid in decision-making.

SUMMARY

Precision medicine approaches may be used to subclassify, risk-stratify, and select pediatric patients with sepsis who may benefit from new therapies. Application of precision medicine will require robust basic and translational research, rigorous clinical trials, and infrastructure to collect and analyze big data.

Simultaneous determination of metabolic and elemental markers in methamphetamine-induced hepatic injury to rats using LC-MS/MS and ICP-MS

Methamphetamine (METH) is one of the most highly addictive illicit drugs abused all over the world. Much evidence indicates that METH abuse leads to major toxicity, medical consequences, and even severe public health consequences. Existing studies usually focus on the pathomechanism of METH-induced toxicity; therefore, data on metabolites and elements correlating with particular toxicity remain scarce. The objective of the present study is to develop appropriate analytical procedures to identify the differential metabolic and elemental biomarkers on METH-induced hepatic injury to rats. The rats were administrated with METH (15 mg/mL/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The alanine aminotransferase and aspartate aminotransferase activity levels of in the rat serum of the METH group increase significantly compared with those of the control group, suggesting obvious hepatic injury. The results are further confirmed by the histopathological microscopic observation. A total of 18 small molecular metabolites and 19 elements are selected to perform the simultaneous quantification based on the combination of liquid chromatography coupled with tandem mass spectrometry and inductively coupled plasma mass spectrometry. Sample preparation was optimized to cover all the analytes. Both methods are optimized and validated according to developed guidelines such as limits of detection, limits of quantification, linearity, precision, and recovery. All the obtained data are within the satisfactory range. The normalized data were processed according to the partial least squares discrimination analysis (PLS-DA) model. Five differential metabolic and six elemental markers are identified in rat plasma based on the variable importance in projection (VIP) (> 1) and t test results. Overall, the results obtained in this study demonstrate the developed methods are suitable for simultaneous determination of metabolic and elemental markers in the hepatic injury to rats induced by METH. Graphical abstract.

Multiomics-based strategies for taming intestinal inflammation in the neonate

PURPOSE OF REVIEW

The purpose of this review is to discuss evolving research into intestinal inflammatory responses as they relate to the developing microbiome and to provide insights into developing multiomic tools that are being used to describe these relationships. Intestinal inflammatory conditions are common, and in the neonate present special challenges, especially in the form of necrotizing enterocolitis (NEC) and other conditions that involve damage or breakdown of the mucosal barrier, leading to systemic inflammation and damage to distal sites, such as the liver and brain.

RECENT FINDINGS

Recent studies show that when a dysbiosis (microbial imbalance or impaired microbiota) occurs, an inflammatory response that can affect the entire body is frequently the result. We are recognizing that not only the microbial diversity and relative abundance of certain taxa play a role in dysbiosis and inflammation, but their functional capabilities in terms of metabolite production and interaction with the immune system of the host afre critical in future health and disease.

SUMMARY

A multiomic approach to evaluate these microorgansims as well as their interaction with the host by using systems-based concepts is becoming possible and is likely to shed new light on various disease entities and how we can best prevent and treat them.

A pilot case-control study of urine metabolomics in preterm neonates with necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a leading cause of gastrointestinal morbidity and mortality in preterm neonates. The aim of this pilot study was to explore using metabolomics alternations in the urine metabolites related to NEC that could possibly serve as diagnostic biomarkers of the disease. Urine samples were prospectively collected at the day of initial evaluation for NEC from 15 diseased preterm neonates (five Bell's stage I and ten stage II/III) and an equal number of matched controls. Urine metabolic profiles were assessed using non-targeted nuclear magnetic resonance spectroscopy and targeted liquid chromatography-tandem mass spectrometry monitoring 108 metabolites. Multivariate statistical models with data from either analytical approach showed clear separation between the metabolic profiles of neonates with NEC and controls. Twenty-five discriminant metabolites were identified belonging to amino and organic acids, sugars and vitamins. A number of metabolite combinations were found to have an excellent diagnostic performance in detecting neonates developing NEC. Our results show that the metabolic profile of neonates with NEC differs significantly from that of controls, making possible their separation using urine metabolomic analysis. Nevertheless, whether the small set of significant metabolites detected in this investigation could be used as early diagnostic biomarkers of NEC should be validated in larger studies.