Proteomic and Metabolomic Characterization of COVID-19 Patient Sera.

Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model was validated using 10 independent patients, 7 of which were correctly classified. Targeted proteomics and metabolomics assays were employed to further validate this molecular classifier in a second test cohort of 19 COVID-19 patients, leading to 16 correct assignments. We identified molecular changes in the sera of COVID-19 patients compared to other groups implicating dysregulation of macrophage, platelet degranulation, complement system pathways, and massive metabolic suppression. This study revealed characteristic protein and metabolite changes in the sera of severe COVID-19 patients, which might be used in selection of potential blood biomarkers for severity evaluation.

Proteomic and metabolomic investigation of serum lactate dehydrogenase elevation in COVID-19 patients.

Serum lactate dehydrogenase (LDH) has been established as a prognostic indicator given its differential expression in COVID-19 patients. However, the molecular mechanisms underneath remain poorly understood. In this study, 144 COVID-19 patients were enrolled to monitor the clinical and laboratory parameters over 3 weeks. Serum LDH was shown elevated in the COVID-19 patients on admission and declined throughout disease course, and its ability to classify patient severity outperformed other biochemical indicators. A threshold of 247 U/L serum LDH on admission was determined for severity prognosis. Next, we classified a subset of 14 patients into high- and low-risk groups based on serum LDH expression and compared their quantitative serum proteomic and metabolomic differences. The results showed that COVID-19 patients with high serum LDH exhibited differentially expressed blood coagulation and immune responses including acute inflammatory responses, platelet degranulation, complement cascade, as well as multiple different metabolic responses including lipid metabolism, protein ubiquitination and pyruvate fermentation. Specifically, activation of hypoxia responses was highlighted in patients with high LDH expressions. Taken together, our data showed that serum LDH levels are associated with COVID-19 severity, and that elevated serum LDH might be consequences of hypoxia and tissue injuries induced by inflammation.

Prediction of severe illness due to COVID-19 based on an analysis of initial Fibrinogen to Albumin Ratio and Platelet count.

Concomitant coagulation disorder can occur in severe patients withCOVID-19, but in-depth studies are limited. This study aimed to describe the parameters of coagulation function of patients with COVID-19 and reveal the risk factors of developing severe disease. This study retrospectively analyzed 113patients with SARS-CoV-2 infection in Taizhou Public Health Center. Clinical characteristics and indexes of coagulation function were collected. A multivariate Cox analysis was performed to identify potential biomarkers for predicting disease progression. Based on the results of multivariate Cox analysis, a Nomogram was built and the predictive accuracy was evaluated through the calibration curve, decision curve, clinical impact curve, and Kaplan-Meier analysis. Sensitivity, specificity, predictive values were calculated to assess the clinical value. The data showed that Fibrinogen, FAR, and D-dimer were higher in the severe patients, while PLTcount, Alb were much lower. Multivariate Cox analysis revealed that FAR and PLT count were independent risk factors for disease progression. The optimal cutoff values for FAR and PLT count were 0.0883 and 135*109/L, respectively. The C-index [0.712 (95% CI = 0.610-0.814)], decision curve, clinical impact curve showed that Nomogram could be used to predict the disease progression. In addition, the Kaplan-Meier analysis revealed that potential risk decreased in patients with FAR<0.0883 and PLT count>135*109/L.The model showed a good negative predictive value [(0.9474 (95%CI = 0.845-0.986)].This study revealed that FAR and PLT count were independent risk factors for severe illness and the severity of COVID-19 might be excluded when FAR<0.0883 and PLT count>135*109/L.

The history of chromosomal instability in genome doubled tumors.

Tumors frequently display high chromosomal instability and contain multiple copies of genomic regions. Here, we describe GRITIC, a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 6,091 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-doubled tumors. We measured chromosomal instability before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains often accumulate as punctuated bursts, commonly after genome doubling. We infer that genome duplications typically affect the landscape of copy number losses, while only minimally impacting copy number gains. In summary, GRITIC is a novel copy number gain timing framework that permits the analysis of copy number evolution in chromosomally unstable tumors.

Preoperative prealbumin-to-fibrinogen ratio to predict survival outcomes in hepatocellular carcinoma patients after hepatic resection.

Background: This study aimed to evaluate the clinical application of the preoperative prealbumin-to-fibrinogen ratio (PFR) in the clinical diagnosis of hepatocellular carcinoma (HCC) patients and its prognostic value. Methods: The clinical and laboratory data of 269 HCC patients undergoing surgical treatment from January 2012 to January 2017 in Taizhou Hospital were retrospectively analysed. The Cox regression model was used to analyse the correlation between the PFR and other clinicopathological factors in overall survival (OS) and disease-free survival (DFS). Results: Cox regression analysis showed that the PFR (hazard ratio (HR)=2.123; 95% confidence interval (95% CI), 1.271-3.547; P=0.004) was an independent risk factor affecting the OS of HCC patients. Furthermore, a nomogram was built based on these risk factors. The C-index for the OS nomogram was 0.715. Conclusions: Nomograms based on the PFR can be recommended as the correct and actual model to evaluate the prognosis of patients with HCC.

NFIL3 and its immunoregulatory role in rheumatoid arthritis patients.

Nuclear-factor, interleukin 3 regulated (NFIL3) is an immune regulator that plays an essential role in autoimmune diseases. However, the relationship between rheumatoid arthritis (RA) and NFIL3 remains largely unknown. In this study, we examined NFIL3 expression in RA patients and its potential molecular mechanisms in RA. Increased NFIL3 expression levels were identified in peripheral blood mononuclear cells (PBMCs) from 62 initially diagnosed RA patients and 75 healthy controls (HCs) by quantitative real-time PCR (qRT-PCR). No correlation between NFIL3 and disease activity was observed. In addition, NFIL3 expression was significantly upregulated in RA synovial tissues analyzed in the Gene Expression Omnibus (GEO) dataset (GSE89408). Then, we classified synovial tissues into NFIL3-high (≥75%) and NFIL3-low (≤25%) groups according to NFIL3 expression levels. Four hundred five differentially expressed genes (DEGs) between the NFIL3-high and NFIL3-low groups were screened out using the "limma" R package. Enrichment analysis showed that most of the enriched genes were primarily involved in the TNF signaling pathway via NFκB, IL-17 signaling pathway, and rheumatoid arthritis pathways. Then, 10 genes (IL6, IL1ß, CXCL8, CCL2, PTGS2, MMP3, MMP1, FOS, SPP1, and ADIPOQ) were identified as hub genes, and most of them play a key role in RA. Positive correlations between the hub genes and NFIL3 were revealed by qRT-PCR in RA PBMCs. An NFIL3-related protein-protein interaction (PPI) network was constructed using the STRING database, and four clusters (mainly participating in the inflammatory response, lipid metabolism process, extracellular matrix organization, and circadian rhythm) were constructed with MCODE in Cytoscape. Furthermore, 29 DEGs overlapped with RA-related genes from the RADB database and were mainly enriched in IL-17 signaling pathways. Thus, our study revealed the elevated expression of NFIL3 in both RA peripheral blood and synovial tissues, and the high expression of NFIL3 correlated with the abnormal inflammatory cytokines and inflammatory responses, which potentially contributed to RA progression.

DeCiFering the subclonal composition of tumors.

Accurately identifying the subclones that make up tumors is critical for understanding cancer biology. In an article in this issue of Cell Systems, Satas et al. examine mutations with an evolutionary perspective to decipher the composition of tumors.

Preoperative lymphocyte-to-monocyte ratio versus platelet-to-lymphocyte ratio as a prognostic predictor for non-small cell lung cancer patients.

BACKGROUND: We investigated the prognostic value of the preoperative lymphocyte-to-mononuclear ratio (LMR) and platelet-to-lymphocyte ratio (PLR) in a large cohort of patients with non-small cell lung cancer (NSCLC). METHODS: Clinical-pathological data from 507 NSCLC patients at Taizhou Hospital of Zhejiang Province between 2010 and 2016 were retrospectively evaluated. X-tile software was used to assess the optimal cutoff levels for LMR and PLR. Univariate and multivariate Cox regression models were used to assess the prognostic factors. RESULTS: The median follow-up duration after surgical resection was 34.5 months. Patients were stratified into 2 groups by LMR (2.6 and > 2.6) and PLR (179.6 and > 179.6). Our results revealed that lower LMR (HR = 3.163 (1.821-5.493), P = 0.000), age (HR = 2.252 (1.412-3.592), P = 0.001), T stage (HR = 3.749 (2.275-6.179), P = 0.000), N stage (HR = 3.106 (1.967-4.902), P = 0.000), and cut edge (HR = 3.830 (1.077-13.618), P = 0.038) were considered to be independent indicators for overall survival (OS) of NSCLC patients. For disease-free survival (DFS), age, sex, T stage, N stage, LMR and cut edge were verified to be independent prognostic factors in patients with NSCLC. CONCLUSIONS: In the study cohort, reduced LMR was a robust independent predictor for both OS and DFS in patients with NSCLC who underwent surgical resection.

Prognostic value of combined preoperative fibrinogen-albumin ratio and platelet-lymphocyte ratio score in patients with breast cancer: A prognostic nomogram study.

OBJECTIVE: The purpose of this study was to evaluate the prognostic value of combined preoperative fibrinogen-albumin ratio and platelet-lymphocyte ratio score (FAR-PLR score) in breast cancer, and to establish a nomogram based on the score as well as clinicopathological factors to predict the prognosis of breast cancer. METHODS: The study cohort included 707 breast cancer patients who underwent curative resection in Taizhou Hospital of Zhejiang Province, China from January 2010 to April 2016. FAR and PLR increased by 2 at the same time, only one index increased by 1, and none increased by 0. The relationship of preoperative FAR-PLR score with overall survival time (OS) and disease free survival time (DFS) in breast cancer was analyzed by log-rank test and COX proportional risk regression model, and a nomogram was established based on the results of multivariate analysis. RESULTS: The average patient follow-up time was 61.2 months. The FAR-PLR score was conversely correlated with OS and DFS (P < 0.001). In the stage I-II group and III group, the FAR-PLR scores were significantly different among high, medium and low groups of OS and DFS (P < 0.01). FAR-PLR score was also found to be a powerful predictor of prognosis in Luminal B-like subtype, Her-2 overexpression subtype, and triple-negative subtype breast cancers; the higher the FAR-PLR score, the worse the prognosis. Forest charts and multivariate COX proportional risk regression model analysis showed that preoperative FAR-PLR score was an independent risk factor of OS (HR = 1.759, 95%CI = 1.410-2.210, P = 0.000) and DFS (HR = 1.729, 95%CI = 1.385-2.158, P = 0.000) in breast cancer. Based on the COX regression analysis of multiple factors, a nomogram prediction model for the survival of breast cancer was established. The calibration curve analysis indicated that the nomogram results were highly consistent between predicted and actual outcomes. Compared to stage (C-index of OS and DFS were 0.583 and 0.588 respectively), PR (C-index of OS and DFS were 0.592 and 0.592 respectively) and FAR-PLR score (C-index of OS and DFS were 0.592 and 0.591 respectively), the nomogram showed better predictive accuracy (C-index of OS and DFS were 0.652 and 0.651 respectively). CONCLUSIONS: The results of this study suggest that preoperative FAR-PLR score may be a potential new biomarker for predicting survival and prognosis of breast cancer. A prognostic nomogram model based on preoperative FAR-PLR score and clinicopathological factors may help doctors make better clinical decisions for breast cancer treatment.

The prognostic relevance and expression of progranulin in adult patients with acute myeloid leukemia.

Progranulin (PGRN) is a secreted protein that can regulate cell cycle progression, cell motility, and tumorigenesis. The PGRN expression in hematological malignancies is limited to multiple myeloma, but its expression and survival prognostic role in acute myeloid leukemia (AML) is still controversial.To evaluate the PGRN expression and estimate its survival prognostic role in AML patients.In this study, all patients were divided into three groups, which included 38 newly diagnosed adult AML patients, 33 complete remissions (CR-AML) patients, and 60 healthy control (HC) patients. The endpoints were relapse-free survival (RFS) and overall survival (OS). We investigated plasma PGRN levels by using enzyme-linked immunosorbent assay.Plasma PGRN levels in AML patients were higher than that in CR-AML and HC groups. After two chemo cycles, 16 patients had complete remission (CR). The level of plasma PGRN in non-CR patients compared to CR patients was obviously different (median 44.19 vs 21.10 ng/mL) (P = .025). In non-M3 (French-American-British classification) patients, 70% (21/30) patients relapsed in 1 year and 80% (24/80) patients died in the observed time. Using the value (median 19.95) as a "cut-off" value, we have divided non-M3 patients into low- and high-PGRN expression groups. High-PGRN expression patients had a poorer RFS with a median of 5.4 months (95% CI 3.7-7.1) and low-PGRN expression patients had a good RFS with a median of 8.9 months (95% CI 6.3-11.5; P = .027). In the survival analyses, high-PGRN expression of AML patients had shorter OS than low-PGRN expression of AML patients (6.2 vs 20.5 months, P = .008).PGRN is overexpressed in AML, which is a convenient and independent prognostic marker that is measured easily in AML patients.

Prognostic significance of pre-resection albumin/fibrinogen ratio in patients with non-small cell lung cancer: A propensity score matching analysis.

BACKGROUND: Nutrition and coagulation play important roles in cancer progression. This study was aimed to investigate the value of the albumin/fibrinogen ratio (AFR) in non-small cell lung cancer (NSCLC) patients, through a propensity score matching (PSM) method. METHODS: We retrospectively analyzed 529 NSCLC patients underwent surgical resection from 2010 to 2015. PSM was used to eliminate possible biases. A Cox proportional hazards regression model was performed to evaluate the prognostic value of AFR in NSCLC. RESULTS: The optimal value was 9.67 for the AFR by ROC (receiver operating characteristic) curve. The AFR was statistically significantly associated with age, sex, smoking history, histological subtype, tumor size, pathological stage and adjuvant therapy (p < 0.05). Multivariate analysis indicated that the pathological stage and pre-resection AFR were independent prognostic factors for patients with NSCLC. Additionally, elevated AFR indicated a better outcome, and patients with higher AFR had lower risk for overall death (OS) (HR 0.512, 95% CI 0.316-0.829, p = 0.006) as well as disease-free death (DFS) (HR 0.561, 95% CI 0.399-0.787, p = 0.001). The propensity score model identified 120 patients from each group that were balanced for age, sex, smoking history, histological subtype, tumor size, stage distribution and adjuvant therapy. In multivariable regression analysis of PSM groups, the result indicated that the AFR was predictive for OS (HR 0.392, 95% CI 0.225-0.683, p < 0.001) and DFS (HR 0.526, 95% CI 0.344-0.805, p = 0.003). CONCLUSIONS: Pre-resection AFR can be considered as an independent prognostic factor in NSCLC patients, and higher AFR may enhance OS and DFS of NSCLC patients.

Cross-sectional and longitudinal analysis of cancer vaccination trials registered on the US Clinical Trials Database demonstrates paucity of immunological trial endpoints and decline in registration since 2008.

INTRODUCTION: Cancer vaccination has been researched as a means of treating and preventing cancer, but successful translational efforts yielding clinical therapeutics have been limited. Numerous reasons have been offered in explanation, pertaining both to the vaccine formulation, and the clinical trial methodology used. This study aims to characterize the tumor vaccine clinical trial landscape quantitatively, and explore the possible validity of the offered explanations including the translational obstacles posed by the current common endpoints. METHODS: We performed a detailed cross-sectional and longitudinal analysis of tumor vaccine trials (n=955) registered in the US Clinical Trials database. RESULTS: The number of tumor vaccine trials initiated per annum has declined 30% since a peak in 2008. In terms of vaccine formulation, 25% of trials use tumor cell/lysate preparations; whereas, 73% of trials vaccinate subjects against defined protein/peptide antigens. Also, 68% of trials do not use vectors for antigen delivery. Both these characteristics of tumor vaccines have remained unchanged since 1996. The top five types of cancer studied are: melanoma (22.6%); cervical cancer (13.0%); breast cancer (11.3%); lung cancer (9.5%); and prostate cancer (9.4%). In addition, 86% of the trials are performed where there is established disease rather than prophylactically, of which 67% are performed exclusively in the adjuvant setting. Also, 42% of Phase II trials do not measure any survival-related endpoint, and only 23% of Phase III trials assess the immune response to vaccination. CONCLUSION: The clinical trial effort in tumor vaccination is declining, necessitating a greater urgency in identifying and removing the obstacles to clinical translation. These obstacles may include: 1) vaccination against a small range of antigens; 2) naked delivery of antigen; 3) investigation of less immunogenic cancer types; and 4) investigation in the setting of established disease. In addition, the prevalence of late phase failure may be due to inadequate assessment of survival-related endpoints in Phase II trials. The clinical trial development of tumor vaccines should include mechanism-based translational endpoints, as well as the discovery of immune biomarkers with which to stratify, monitor, and prognosticate patients.