| Literature DB >> 32354167 |
Pedro Martínez-Paz1,2, Marta Aragón-Camino2,3, Esther Gómez-Sánchez1,2,3, Mario Lorenzo-López1,2,3, Estefanía Gómez-Pesquera1,2,3, Rocío López-Herrero2,3, Belén Sánchez-Quirós2,3, Olga de la Varga2,3, Álvaro Tamayo-Velasco2,4, Christian Ortega-Loubon2,5, Emilio García-Morán2,6, Hugo Gonzalo-Benito2,7, María Heredia-Rodríguez1,2,8, Eduardo Tamayo1,2,3.
Abstract
Nowadays, mortality rates in intensive care units are the highest of all hospital units. However, there is not a reliable prognostic system to predict the likelihood of death in patients with postsurgical shock. Thus, the aim of the present work is to obtain a gene expression signature to distinguish the low and high risk of death in postsurgical shock patients. In this sense, mRNA levels were evaluated by microarray on a discovery cohort to select the most differentially expressed genes between surviving and non-surviving groups 30 days after the operation. Selected genes were evaluated by quantitative real-time polymerase chain reaction (qPCR) in a validation cohort to validate the reliability of data. A receiver-operating characteristic analysis with the area under the curve was performed to quantify the sensitivity and specificity for gene expression levels, which were compared with predictions by established risk scales, such as acute physiology and chronic health evaluation (APACHE) and sequential organ failure assessment (SOFA). IL1R2, CD177, RETN, and OLFM4 genes were upregulated in the non-surviving group of the discovery cohort, and their predictive power was confirmed in the validation cohort. This work offers new biomarkers based on transcriptional patterns to classify the postsurgical shock patients according to low and high risk of death. The results present more accuracy than other mortality risk scores.Entities:
Keywords: biomarker; microarray; mortality; postsurgical shock; sepsis; transcriptomic profile
Year: 2020 PMID: 32354167 PMCID: PMC7287660 DOI: 10.3390/jcm9051276
Source DB: PubMed Journal: J Clin Med ISSN: 2077-0383 Impact factor: 4.241
Primers used for qPCR of genes from human.
| Gene | Forward (5′-3′) | Reverse (5′-3′) | Efficiency |
|---|---|---|---|
|
| CCTTGCACATGCCGGAG | ACAGAGCCTCGCCTTTG | 87.2% |
|
| GCATCTGTATTCTCAAAAACTCTGA | GGTGCTCTGTGGCTTCTG | 96.9% |
|
| AAGAGATTACCAGCCACAGAC | GCTGAACTGTCCCAAACTG | 90.0% |
|
| GCCGGATTTGGTTAGCTGA | CATGGAGCACAGGGTCTTG | 99.7% |
|
| TGCTGATGTTCACCACACC | CTGAAGACCAAGCTGAAAGAGT | 92.2% |
qPCR: quantitative real-time polymerase chain reaction.
Characteristics of postsurgical patients.
| Discovery Cohort | Validation Cohort | |||||
|---|---|---|---|---|---|---|
| Surviving ( | Non-Surviving ( |
| Surviving ( | Non-Surviving ( |
| |
|
| ||||||
| Age | 69.15 | 71.86 | 0.297 | 69.06 | 72.70 | 0.108 |
| Male ( | 55 (63) | 18 (62) | 0.967 | 50 (63) | 23 (70) | 0.517 |
|
| ||||||
| High blood pressure | 64 (73) | 19 (66) | 0.458 | 46 (58) | 23 (70) | 0.255 |
| Chronic cardiovascular disease | 53 (60) | 14 (48) | 0.259 | 20 (25) | 10 (30) | 0.587 |
| Chronic respiratory disease | 14 (16) | 5 (17) | 0.866 | 14 (18) | 8 (24) | 0.428 |
| Chronic renal failure | 10 (11) | 6 (21) | 0.205 | 5 (6) | 3 (9) | 0.605 |
| Chronic hepatic failure | 3 (3) | 0 (0) | 0.314 | 1 (1) | 0 (0) | 0.516 |
| Diabetes mellitus | 25 (28) | 7 (24) | 0.655 | 16 (20) | 6 (18) | 0.801 |
| Cancer | 23 (26) | 5 (17) | 0.330 | 17 (22) | 9 (27) | 0.511 |
| Immunosuppression | 4 (5) | 1 (3) | 0.800 | 4 (5) | 0 (0) | 0.188 |
|
| ||||||
| Length of hospital stay | 30.51 | 18.31 | 0.011 | 37.22 | 12.21 | 0.000 |
| Length of ICU stay | 8.26 | 7.03 | 0.525 | 10.58 | 6.61 | 0.021 |
| Mortality (% (7 days)) | 0 (0) | 14 (48) | 0.000 | 0 (0) | 15 (45) | 0.000 |
| Mortality (% (15 days)) | 0 (0) | 21 (72) | 0.000 | 0 (0) | 28 (85) | 0.000 |
|
| ||||||
| Cardiac surgery | 54 (61) | 14 (48) | 0.215 | 34 (43) | 15 (45) | 0.814 |
| General surgery | 26 (30) | 12 (41) | 0.238 | 35 (44) | 15 (45) | 0.911 |
| Others | 8 (9) | 3 (11) | 1.000 | 10 (13) | 3 (10) | 0.755 |
|
| ||||||
| Respiratory tract | 19 (22) | 9 (31) | 0.301 | 20 (25) | 8 (24) | 0.905 |
| Abdomen | 15 (17) | 5 (17) | 0.981 | 17 (22) | 8 (24) | 0.752 |
| Urinary tract | 12 (14) | 4 (14) | 0.983 | 13 (16) | 2 (6) | 0.141 |
| Surgical site | 22 (25) | 5 (17) | 0.390 | 21 (27) | 7 (21) | 0.550 |
| Bacteremia | 23 (26) | 7 (24) | 0.831 | 28 (35) | 7 (21) | 0.139 |
|
| ||||||
| Gram + | 42 (48) | 9 (31) | 0.116 | 43 (54) | 10 (30) | 0.020 |
| Gram − | 46 (52) | 14 (48) | 0.709 | 40 (51) | 13 (39) | 0.277 |
| Fungi | 17 (19) | 5 (17) | 0.804 | 16 (20) | 7 (21) | 0.909 |
|
| ||||||
| SOFA score | 7 (7) | 10 (3) | 0.000 | 9 (3) | 10 (3) | 0.351 |
| APACHE score | 13 (6) | 16 (6.5) | 0.000 | 13 (5) | 16 (3) | 0.006 |
| Total bilirubin (mg/dL) | 0.72 (1.56) | 0.99 (1.08) | 0.324 | 0.98 (1.67) | 1.27 (1.10) | 0.662 |
| Glucose (mg/dL) | 157 (65) | 159 (97) | 0.142 | 169 (76) | 193 (145) | 0.258 |
| Platelet count (cell/mm3) | 131,000 (96,250) | 100,000 (131,500) | 0.415 | 149,000 (163,250) | 123,000 (137,500) | 0.565 |
| INR | 1.36 (0.37) | 1.31 (0.49) | 0.989 | 1.33 (0.33) | 1.31 (0.49) | 0.325 |
| ScvO2 (%) | 72.30 (11.9) | 66.70 (17.1) | 0.007 | 70.90 (18.00) | 67.00 (19.10) | 0.334 |
| C-reactive protein (mg/L) | 107.80 (208.4) | 186.00 (228.4) | 0.012 | 208.60 (213.50) | 184.40 (241.60) | 0.417 |
| Procalcitonin (ng/mL) | 0.99 (9.82) | 5.24 (19.49) | 0.276 | 3.72 (23.10) | 8.02 (20.46) | 0.775 |
| Lactate (mM) | 3.11 (1.86) | 4.33 (5.50) | 0.004 | 2.89 (2.11) | 5.00 (5.00) | 0.003 |
| White Blood cells (cells/mm3) | 13,370 (10,540) | 13,560 (10,490) | 0.639 | 15,470 (11,960) | 15,350 (10,605) | 0.193 |
| Neutrophils (cells/mm3) | 11,738 (9803) | 12,319 (10,623) | 0.585 | 13,614 (11,310) | 12,921 (10,420) | 0.192 |
ICU, intensive care units; SOFA, sequential organ failure assessment; APACHE, acute physiology and chronic health evaluation; INR, international normalized ratio; ScvO2, central venous oxygen saturation. Quantitative data are expressed as medians with interquartile range (IQR). Qualitative data are presented as percentages and absolute numbers. A p-value ≤ 0.05 was considered to indicate significant differences (bold values).
Figure 1Identification of biomarker genes from gene expression data. (a) Heat map plot of genes of interest. Rows represent the gene expression value and columns represent the samples. The scale bar represents the intensity of expression of transcripts, with red indicating overexpressed transcripts and green representing underexpressed transcripts. The top bar indicates surviving (yellow) and non-surviving patients (black); (b) Kaplan–Meier plot showing survival probability of two groups of patients clustered by risk mortality. The numbers below the graph indicate the number of patients at risk of death in each group; (c) volcano plot of the differentially expressed genes, with red coloring for fold changes >1.5 and p-value < 0.01; (d) protein–protein interaction network of differentially expressed genes.
Figure 2Relative mRNA levels of OLFM4, CD177, RETN, and IL1R2 in surviving patients and non-surviving patients as measured by qPCR. The primers and reference genes are given in the Methods section. Horizontal lines within the boxes represent the median, and the boundaries of the boxes indicate the 25th and 75th percentiles, while the whiskers indicate the highest and lowest values. The Y-axis represents the RNA expression levels in arbitrary units and logarithmic scale. qPCR, quantitative real-time polymerase chain reaction.
Figure 3Quantification of mortality prediction accuracy by ROC AUC. (a) ROC AUC analysis of gene expression; (b) ROC AUC analysis of multivariate regression model that includes gene expression, emergency, sex, and age data, as well as creatinine, bilirubin, lactate, and white blood cell levels, as adjusted variables. ROC, receiver operating characteristic; AUC, area under the curve.
AUC values for different biomarkers.
| Biomarker | Area | Asymptotic 95% Confidence Interval |
|---|---|---|
| SOFA score | 0.580 | 0.456–0.705 |
| APACHE score | 0.647 | 0.543–0.751 |
| Procalcitonin | 0.589 | 0.478–0.699 |
| C-reactive protein | 0.444 | 0.323–0.565 |
| White blood cells | 0.447 | 0.332–0.563 |
| Neutrophils | 0.446 | 0.332–0.560 |
AUC, area under the curve; SOFA, sequential organ failure assessment; APACHE, acute physiology and chronic health evaluation.
Figure 4Survival analysis based on regression model. (a) Risk mortality tree generated by classification and regression tree (CART) analysis; (b) Kaplan–Meier curve for overall survival based on CART analysis.