Nanopore single-molecule analysis of biomarkers: Providing possible clues to disease diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic COVID-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.Copyright © 2023 Elsevier B.V.

Carcinoembryonic antigen (CEA) and other surrogate inflammatory biomarkers in COVID-19

It has been two years since the global outbreak of the highly contagious and deadly corona virus disease (COVID-19) caused by SARS-CoV-2 first emerged in China. Since then, various diagnostic, prognostic and treatment strategies undertaken to address the pandemic have been dynamically evolving. Predictive and prognostic role of various biomarkers in COVID-19 has been a subject of intense exploration. We aimed to determine the association of Carcinoembryonic antigen (CEA) and various surrogate inflammatory biomarkers with the severity of COVID-19 disease. This retrospective cohort study was carried out on 98 patients admitted in Jaypee Hospital, Noida with COVID-19 disease. Information regarding demographics, laboratory parameters and clinical history was collected from Hospital Information System. Serum levels of CEA and other biomarkers such as Neutrophil-lymphocyte ratio (NLR), C-reactive protein (CRP), Interleukin-6 (IL-6), Ferritin, and Procalcitonin (PCT) were assessed. Correlation analyses were performed between the parameters and acute respiratory distress syndrome (ARDS) stages. Logistic regression and ROC curve analysis were performed to assess the various parameters for distinguishing COVID-19 patients requiring ICU admission. Mean hospital stay, NLR, CEA, IL-6, CRP, Ferritin (P < 0.0001) and PCT (P = 0.01) were significantly higher in ICU patients when compared to general ward patients. NLR, median serum CEA, IL-6, and CRP levels were significantly higher in non-survivor compared to the survivors (P < 0.0001, 0.0341 and 0.0092). CEA correlated well with disease severity based upon ARDS classification and was a better marker to differentiate patient according to ARDS stages (ARDS 0 vs 2 P = 0.0006;0 vs 3 P < 0.0001;ARDS 1 vs 2 P = 0.0183;1 vs 3 P = 0.0006). The area under the Receiver operating characteristic (ROC) curve for CEA was 0.7467 (95% CI- 0.64885- 0.84459) which revealed the potential of CEA as a biomarker to distinguish COVID-19 patients requiring ICU admission. CEA can be used to predict the severity of COVID-19 associated ARDS as well as patients requiring ICU admission. Along with routine inflammatory biomarkers (NLR, CRP, IL-6, PCT, and ferritin), CEA should be used for early identification of critical COVID-19 positive patients and for assessing prognosis.

Immune phenotypes correlate with the outcome of severe Covid-19 infection

Despite the tremendous impact of the Sars-CoV-2 global pandemic and becoming focus of scientific research[1], many aspects of the disease and its pathophysiology, especially concerning prognostic parameters and treatments remain uncertain. The aim of our study is to assess and link immune profiles of the dysregulated cellular immune response in patients hospitalized with severe Covid-19 to their outcomes. Therefore, we immune phenotyped severly ill Sars-CoV-2 patients on our ICU and to surviving to non-surviving patients and healthy controls. Methods Using flow cytometry (BD-Fortessa), we created a 14-parameter immunoprofile of 25 Covid-19 patients from our ICU and 11 of healthy control individuals. The analysis was based on live/dead control, CD3, CD4, CD8, CD19, CD66b, CD14, CD16, IL-10, TNF-α, IL-1β, HLA-DR and IL-6 antibodies. Both clusters (survivors, n=16;non-survivors, n=9) and healthy controls (n=11) were compared with each other by Kruskal-Wallis test with Dunns-Ls post-test correction for multiple testing (Prism V.9.0). The patients in both groups had a similar age and at the time of analysis (Fig. 1A), the treatment was insignificantly more invasive in non-survivors than in survivors (7-point WHO ordinal scale means 5.8 vs. 5.3, p = 0.43) (Fig.1 D). Similarly, the blood tests and the viral loads were comparable in both groups. Study has permission from the ethic commission (AZ-249/20 S-EB). Results The study showed that cell specific cytokine expressions are distinct in survivors compared to non-survivors even at an early stage of the critical disease. Surviving Covid patients showed increased TFNá levels throughout all cell populations, which met significance in CD4+ T (Fig.2 A) Cells and CD135+ DC. (Fig. 4 C). IL-6 levels, however, were significantly lower in CD4+ T cells of survivors (Fig. 2 B). Similarly, proinflammatory, classical CD16+ monocytes of non-survivors exhibited an increase in IL-6 and IL-1â. Moreover, dendritic cells of non-survivors seemed to be exhausted revealing less TNFá and IL-6 and IL-1â (Fig 4) Conclusion: Taken together, a disability of monocyte activation and exhaustion of dendritic cell reaction was associated with a worsened outcome of severely ill Covid-19 patients [2,3]. On the contrary a sufficient TNFá response, especially of CD4 and dendritic cells might be required to overcome the infection. Therefore, our findings suggest that measuring cell specific levels of cytokines and cell population shifts might be of high clinical relevance to predict the outcome of the disease and offer new therapeutical options for these patients.

Serum amyloid A, ferritin and carcinoembryonic antigen as biomarkers of severity in patients with COVID-19.

In view of the rapid spread of COVID-19 and the high mortality rate of severe cases, reliable risk stratifying indicators of prognosis are necessary to decrease morbidity and mortality. The aim of the present study was to evaluate the value of serum amyloid A (SAA) and carcinoembryonic antigen (CEA) as prognostic biomarkers in comparison to other predictors, including C-reactive protein (CRP) and ferritin levels. This study included 124 patients diagnosed with COVID-19, and they were assigned to one of two groups: Mild and severe, based on the severity of the infection. Radiological and laboratory investigations were performed, including evaluation of CRP, ferritin, D-Dimer, SAA and CEA levels. Significantly higher levels of CRP, ferritin, D-Dimer, SAA and CEA were observed in severe cases. SAA was significantly correlated with CRP (r=0.422, P<0.001), ferritin (r=0.574, P<0.001), CEA (r=0.514, P<0.001) and computed tomography severity score (CT-SS; r=0.691, P<0.001). CEA was correlated with CRP (r=0.441, P<0.001), ferritin (r=0.349, P<0.001) and CT-SS (r=0.374, P<0.001). Receiver operator characteristic (ROC) curves for performance of SAA, CEA, ferritin, CRP and SAA showed the highest AUC value of 0.928, with a specificity of 93.1%, and a sensitivity of 98.5% at a cut-off of 16 mg/l. The multi-ROC curve for SAA and ferritin showed 100% specificity, 100% sensitivity and 100% efficiency, with an AUC of 1.000. Thus, combining SAA and ferritin may have guiding significance for predicting COVID-19 severity. SAA alone showed the highest prognostic significance. Both SAA and CEA were positively correlated with the CT-SS. Early monitoring of these laboratory markers may thus provide significant input for halting disease progression and reducing mortality rates.

Carcinoembryonic Antigen Elevation in a Patient with SARS-CoV-2 and a History of Colon Cancer.

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic continues to affect millions of people and impact health-care delivery worldwide. New data and insights into the diagnosis and treatment of SARS-CoV-2 are emerging rapidly. Several prognostic biomarkers have been studied in patients with SARS-CoV-2. Among those biomarkers is the carcinoembryonic antigen (CEA). We report the case of a 46-year-old male with a history of colon cancer who was found to have an elevated CEA level during routine surveillance. Further workup confirmed a diagnosis of SARS-CoV-2 infection. The CEA level normalized with the resolution of the infection.

The predicting roles of carcinoembryonic antigen and its underlying mechanism in the progression of coronavirus disease 2019.

BACKGROUND: The coronavirus disease 2019 (COVID-19) has induced a worldwide epidemiological event with a high infectivity and mortality. However, the predicting biomarkers and their potential mechanism in the progression of COVID-19 are not well known. OBJECTIVE: The aim of this study is to identify the candidate predictors of COVID-19 and investigate their underlying mechanism. METHODS: The retrospective study was conducted to identify the potential laboratory indicators with prognostic values of COVID-19 disease. Then, the prognostic nomogram was constructed to predict the overall survival of COVID-19 patients. Additionally, the scRNA-seq data of BALF and PBMCs from COVID-19 patients were downloaded to investigate the underlying mechanism of the most important prognostic indicators in lungs and peripherals, respectively. RESULTS: In total, 304 hospitalized adult COVID-19 patients in Wuhan Jinyintan Hospital were included in the retrospective study. CEA was the only laboratory indicator with significant difference in the univariate (P < 0.001) and multivariate analysis (P = 0.020). The scRNA-seq data of BALF and PBMCs from COVID-19 patients were downloaded to investigate the underlying mechanism of CEA in lungs and peripherals, respectively. The results revealed the potential roles of CEA were significantly distributed in type II pneumocytes of BALF and developing neutrophils of PBMCs, participating in the progression of COVID-19 by regulating the cell-cell communication. CONCLUSION: This study identifies the prognostic roles of CEA in COVID-19 patients and implies the potential roles of CEACAM8-CEACAM6 in the progression of COVID-19 by regulating the cell-cell communication of developing neutrophils and type II pneumocyte.

Prognostic Value of a Clinical Biochemistry-Based Nomogram for Coronavirus Disease 2019.

Background: This study aimed to explore the predictive value of a clinical biochemistry-based nomogram in COVID-19. Methods: The plasma or serum concentrations/levels of carcinoembryonic antigen (CEA) and other biomarkers, e.g., C-reactive protein (CRP), white blood cell (WBC), interleukin-6 (IL-6), ferritin (Fer), procalcitonin (PCT), lymphocyte percentage (L%), D-dimer (D2), and neutrophils percentage (Neu%), were assessed in 314 hospitalized patients with confirmed COVID-19. The area under the curve was used to estimate the diagnostic and prognostic value for COVID-19. Cox and logistic regression analyses were used to estimate the independent prognostic risk factors for the survival of patients with COVID-19. Results: Receiver operating characteristic (ROC) curves were used to determine the area under the curve (AUC) values for CEA, IL-6, CRP, PCT, Fer, D-dimer levels and L%, Neu%, and WBC to assess disease classification. The critical values for these markers to predict severe disease type were then determined. The hazard ratio of prognosis for risk of COVID-19 identified CEA, WBC, CRP, PCT, Fer, D-dimer, Neu%, and L% as independent prognostic factors. For the nomogram of overall survival (OS), the C-index was 0.84, demonstrating a good discriminative performance. Conclusions: An OS nomogram for the clinical diagnosis and treatment of COVID-19 was constructed using biomarkers. These data will be useful for the diagnosis, management, and therapy of COVID-19.

Carcinoembryonic Antigen: A Potential Biomarker to Evaluate the Severity and Prognosis of COVID-19.

Background and Objectives: Corona Virus Disease 2019 (COVID-19) has become a serious pandemic disease worldwide. Identification of biomarkers to predict severity and prognosis is urgently needed for early medical intervention due to high mortality of critical cases with COVID-19. This retrospective study aimed to indicate the values of carcinoembryonic antigen (CEA) in evaluating the severity and prognosis of COVID-19. Methods: We included 46 death cases from intensive care unit and 68 discharged cases from ordinary units with confirmed COVID-19 of Wuhan Jin Yin-tan Hospital from January 1 to March 22, 2020. Laboratory and radiologic data were analyzed retrospectively. All patients were followed up until April 10, 2020. Results: COVID-19 patients in the death group had significantly higher CEA levels (ng/ml) than discharged group (14.80 ± 14.20 vs. 3.80 ± 2.43, P < 0.001). The risk of COVID-19 death increased 1.317 times for each additional 1 ng/ml CEA level (OR = 1.317, 95% CI: 1.099-1.579). The standardized and weighted receiver operating characteristic curve (ROC) analysis adjusted to age, sex, and ferritin levels suggested that the area under the curve (AUC) of the serum CEA levels was 0.808 in discrimination between death cases and discharged cases with COVID-19 (P < 0.001). We found mortality of COVID-19 is associated with elevated CEA levels increased (HR = 1.023, 95% CI: 1.005-1.042), as well as age (HR = 1.050, 95% CI: 1.016-1.086) and ferritin levels (HR = 1.001, 95% CI: 1.001-1.002) by survival analysis of Cox regression model. Among discharged patients, CEA levels were significant lower in moderate cases compared to the severe and critical cases (P = 0.005; OR = 0.488, 95% CI: 0.294-0.808) from binary logistic regression analysis. The AUC of CEA levels was 0.79 in distinguishing moderate cases from discharged COVID-19 patients by standardized and weighted ROC analysis (P < 0.001). A positive correlation between CEA levels and CT scores existed in discharged patients (Correlation Coefficient: 0.687; P < 0.001). Conclusions: Elevated CEA levels increased the risk of death from COVID-19 and CEA levels were related to CT scores of the discharged patients positively.

Elevated carcinoembryonic antigen in patients with COVID-19 pneumonia.

PURPOSE: Coronavirus disease 2019 (COVID-19) tends to affect multiple organs and induce abnormal laboratory parameters. We designed this study to investigate the association between carcinoembryonic antigen (CEA) elevation and SARS-CoV-2 infection. METHODS: We retrospectively analyzed 177 patients with confirmed SARS-CoV-2 infection who received plasma CEA assays during hospitalization. Patients with other causes of CEA elevation were excluded. Data regarding epidemiological and demographical characteristics, clinical symptoms, laboratory tests, and outcomes were analyzed. Linear regression analysis was used to evaluate the correlation between CEA levels and inflammation severity. RESULTS: 171 patients were included in the final study and 32 patients (18.7%) had raised serum of CEA (> 5 ng/ml), with a median (range) age of 66 (53-86). The median [interquartile range (IQR)] CEA level was 11.4 ng/ml (8.1-21.6), which was significantly higher than the upper limit of reference range. CEA level between 5-10 ng/ml was in 11 patients, 10-15 ng/ml in 10 patients, and > 15 ng/ml in 11 patients. No correlation was found between CEA levels and lymphocyte (R2 = 0.055; P = 0.10) nor CRP (R2 = 0.026; P = 0.38). The median levels of CEA were 20.0 ng/ml (IQR, 14.7-23.0) in non-survivors and 10.9 ng/ml (IQR 7.5-16.1) in survivors, and the difference between two groups was statistically significant (P = 0.048). CONCLUSION: SARS-CoV-2 infection might be another cause of CEA elevation, with nearly 20% of patients experienced transient and marked CEA increment during COVID-19 pneumonia. The false-positive results of CEA elevation might have clinical significance for patients with colorectal cancer.

Elevations of serum cancer biomarkers correlate with severity of COVID-19.

In this retrospective study, we evaluated the levels of a series of serum biomarkers in coronavirus disease 2019 (COVID-19) patients (mild: 131; severe: 98; critical: 23). We found that there were significant increases in levels of human epididymis protein 4 (HE4) (73.6 ± 38.3 vs 46.5 ± 14.7 pmol/L; P < .001), cytokeratin-19 fragment (CYFRA21-1) (2.2 ± 0.9 vs 1.9 ± 0.8 µg/L; P < .001), carcinoembryonic antigen (CEA) (3.4 ± 2.2 vs 2.1 ± 1.2 µg/L; P < .001), carbohydrate antigens (CA) 125 (18.1 ± 13.5 vs 10.5 ± 4.6 µg/L; P < .001), and 153 (14.4 ± 8.9 vs 10.1 ± 4.4 µg/L; P < .001) in COVID-19 mild cases as compared to normal control subjects; their levels showed continuous and significant increases in severe and critical cases (HE4, CYFRA21-1, and CA125: P < .001; CEA and CA153: P < .01). Squamous cell carcinoma antigen (SCC) and CA199 increased significantly only in critical cases of COVID-19 as compared with mild and severe cases and normal controls (P < .01). There were positive associations between levels of C-reactive protein and levels of HE4 (R = .631; P < .001), CYFRA21-1 (R = .431; P < .001), CEA (R = .316; P < .001), SCC (R = .351; P < .001), CA153 (R = .359; P < .001) and CA125 (R = .223; P = .031). We concluded that elevations of serum cancer biomarkers positively correlated with the pathological progressions of COVID-19, demonstrating diffuse and acute pathophysiological injuries in COVID-19.