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Skalska-Bugala A, Starczak M, Szukalski Ł, Gawronski M, Siomek-Gorecka A, Szpotan J, Labejszo A, Zarakowska E, Szpila A, Jachalska A, Szukalska A, Kruszewski M, Sadowska A, Wasilow A, Baginska P, Czyz J, Olinski R, Rozalski R, Gackowski D. Diagnostic and Prognostic Power of Active DNA Demethylation Pathway Intermediates in Acute Myelogenous Leukemia and Myelodysplastic Syndromes. Cells 2022; 11:cells11050888. [PMID: 35269510 PMCID: PMC8909098 DOI: 10.3390/cells11050888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
Acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are characterized by genomic instability, which may arise from the global hypomethylation of the DNA. The active DNA demethylation process may be linked with aberrant methylation and can be involved in leukemogenesis. The levels of 5-methylcytosine oxidation products were analyzed in minimally invasive material: the cellular DNA from peripheral blood cells and urine of patients with AML and MDS along with the control group, using isotope-dilution two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. The receiver operating characteristic curve analysis was used for the assessment of the ability to discriminate patients’ groups from the control group, and AML from MDS. The most diagnostically useful for discriminating AML patients from the control group was the urinary excretion of 5-hydroxymethylcytosine (AUC = 0.918, sensitivity: 85%, and specificity: 97%), and 5-(hydroxymethyl)-2′-deoxyuridine (0.873, 74%, and 92%), while for MDS patients 5-(hydroxymethyl)-2′-deoxycytidine in DNA (0.905, 82%, and 98%) and urinary 5-hydroxymethylcytosine (0.746, 66%, and 92%). Multi-factor models of classification trees allowed the correct classification of patients with AML and MDS in 95.7% and 94.7% of cases. The highest prognostic value of the analyzed parameters in predicting the transformation of MDS into AML was observed for 5-carboxy-2′-deoxycytidine (0.823, 80%, and 97%) and 5-(hydroxymethyl)-2′-deoxyuridine (0.872, 100%, and 75%) in DNA. The presented research proves that the intermediates of the active DNA demethylation pathway determined in the completely non-invasive (urine) or minimally invasive (blood) material can be useful in supporting the diagnostic process of patients with MDS and AML. The possibility of an early identification of a group of MDS patients with an increased risk of transformation into AML is of particular importance.
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Affiliation(s)
- Aleksandra Skalska-Bugala
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Łukasz Szukalski
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Maciej Gawronski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Agnieszka Siomek-Gorecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Justyna Szpotan
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Anna Labejszo
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Anna Jachalska
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Adriana Szukalska
- Clinic of Hematology, University Hospital No. 2—Jan Biziel Memorial Hospital, 85-168 Bydgoszcz, Poland; (A.S.); (M.K.)
| | - Marcin Kruszewski
- Clinic of Hematology, University Hospital No. 2—Jan Biziel Memorial Hospital, 85-168 Bydgoszcz, Poland; (A.S.); (M.K.)
| | - Anna Sadowska
- Department of Hematology, Nicolaus Copernicus Hospital, 87-100 Toruń, Poland;
| | - Aleksandra Wasilow
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Patrycja Baginska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Jaroslaw Czyz
- Department of Hematology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (Ł.S.); (A.J.); (J.C.)
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
| | - Rafal Rozalski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Correspondence: (R.R.); (D.G.); Tel.: +48-525-853-749 (D.G & R.R)
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-092 Bydgoszcz, Poland; (A.S.-B.); (M.S.); (M.G.); (A.S.-G.); (J.S.); (A.L.); (E.Z.); (A.S.); (A.W.); (P.B.); (R.O.)
- Correspondence: (R.R.); (D.G.); Tel.: +48-525-853-749 (D.G & R.R)
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Mandair GS, Akhter MP, Esmonde-White FWL, Lappe JM, Bare SP, Lloyd WR, Long JP, Lopez J, Kozloff KM, Recker RR, Morris MD. Altered collagen chemical compositional structure in osteopenic women with past fractures: A case-control Raman spectroscopic study. Bone 2021; 148:115962. [PMID: 33862262 PMCID: PMC8259347 DOI: 10.1016/j.bone.2021.115962] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022]
Abstract
Incidences of low-trauma fractures among osteopenic women may be related to changes in bone quality. In this blinded, prospective-controlled study, compositional and heterogeneity contributors of bone quality to fracture risk were examined. We hypothesize that Raman spectroscopy can differentiate between osteopenic women with one or more fractures (cases) from women without fractures (controls). This study involved the Raman spectroscopic analysis of cortical and cancellous bone composition using iliac crest biopsies obtained from 59-cases and 59-controls, matched for age (62.0 ± 7.5 and 61.7 ± 7.3 years, respectively, p = 0.38) and hip bone mineral density (BMD, 0.827 ± 0.083 and 0.823 ± 0.072 g/cm3, respectively, p = 0.57). Based on aggregate univariate case-control and odds ratio based logistic regression analyses, we discovered two Raman ratiometric parameters that were predictive of past fracture risk. Specifically, 1244/1268 and 1044/959 cm-1 ratios, were identified as the most differential aspects of bone quality in cortical cases with odds ratios of 0.617 (0.406-0.938 95% CI, p = 0.024) and 1.656 (1.083-2.534 95% CI, p = 0.020), respectively. Both 1244/1268 and 1044/959 cm-1 ratios exhibited moderate sensitivity (59.3-64.4%) but low specificity (49.2-52.5%). These results suggest that the organization of mineralized collagen fibrils were significantly altered in cortical cases compared to controls. In contrast, compositional and heterogeneity parameters related to mineral/matrix ratios, B-type carbonate substitutions, and mineral crystallinity, were not significantly different between cases and controls. In conclusion, a key outcome of this study is the significant odds ratios obtained for two Raman parameters (1244/1268 and 1044/959 cm-1 ratios), which from a diagnostic perspective, may assist in the screening of osteopenic women with suspected low-trauma fractures. One important implication of these findings includes considering the possibility that changes in the organization of collagen compositional structure plays a far greater role in postmenopausal women with osteopenic fractures.
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Affiliation(s)
- Gurjit S Mandair
- School of Dentistry, Departments of Biologic and Materials, University of Michigan, Ann Arbor, MI, USA.
| | | | | | - Joan M Lappe
- Osteoporosis Research Center, Creighton University, Omaha, NE, USA
| | - Susan P Bare
- Osteoporosis Research Center, Creighton University, Omaha, NE, USA
| | - William R Lloyd
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jason P Long
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Lopez
- School of Dentistry, Departments of Biologic and Materials, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M Kozloff
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Robert R Recker
- Osteoporosis Research Center, Creighton University, Omaha, NE, USA
| | - Michael D Morris
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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Modeling Road Accident Severity with Comparisons of Logistic Regression, Decision Tree and Random Forest. INFORMATION 2020. [DOI: 10.3390/info11050270] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To reduce the damage caused by road accidents, researchers have applied different techniques to explore correlated factors and develop efficient prediction models. The main purpose of this study is to use one statistical and two nonparametric data mining techniques, namely, logistic regression (LR), classification and regression tree (CART), and random forest (RF), to compare their prediction capability, identify the significant variables (identified by LR) and important variables (identified by CART or RF) that are strongly correlated with road accident severity, and distinguish the variables that have significant positive influence on prediction performance. In this study, three prediction performance evaluation measures, accuracy, sensitivity and specificity, are used to find the best integrated method which consists of the most effective prediction model and the input variables that have higher positive influence on accuracy, sensitivity and specificity.
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