FT-Raman spectra in combination with machine learning and multivariate analyses as a diagnostic tool in brain tumors.

Brain tumors are one of the most dangerous, because the position of these are in the organ that governs all life processes. Moreover, a lot of brain tumor types were observed, but only one main diagnostic method was used - histopathology, for which preparation of sample was long. Consequently, a new, quicker diagnostic method is needed. In this paper, FT-Raman spectra of brain tissues were analyzed by Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), four different machine learning (ML) algorithms to show possibility of differentiating between glioblastoma G4 and meningiomas, as well as two different types of meningiomas (atypical and angiomatous). Obtained results showed that in meningiomas additional peak around 1503 cm-1 and higher level of amides was noticed in comparison with glioblastoma G4. In the case of meningiomas differentiation, in angiomatous meningiomas tissues lower level of lipids and polysaccharides were visible than in atypical meningiomas. Moreover, PCA analyses showed higher distinction between glioblastoma G4 and meningiomas in the FT-Raman range between 800 cm-1 and 1800 cm-1 and between two types of meningiomas in the range between 2700 cm-1 and 3000 cm-1. Decision trees showed, that the most important peaks to differentiate glioblastoma and meningiomas were at 1151 cm-1 and 2836 cm-1 while for angiomatous and atypical meningiomas - 1514 cm-1 and 2875 cm-1. Furthermore, the accuracy of obtained results for glioblastoma G4 and meningiomas was 88 %, while for meningiomas - 92 %. Consequently, obtained data showed possibility of using FT-Raman spectroscopy in diagnosis of different types of brain tumors.

Infrared Spectroscopy as a Potential Diagnostic Tool for Medulloblastoma.

INTRODUCTION: Medulloblastoma (MB) is the most common malignant tumor of the central nervous system in childhood. FTIR spectroscopy provides a holistic view of the chemical composition of biological samples, including the detection of molecules such as nucleic acids, proteins, and lipids. This study evaluated the applicability of FTIR spectroscopy as a potential diagnostic tool for MB. MATERIALS AND METHODS: FTIR spectra of MB samples from 40 children (boys/girls: 31/9; age: median 7.8 years, range 1.5-21.5 years) treated in the Oncology Department of the Children's Memorial Health Institute in Warsaw between 2010 and 2019 were analyzed. The control group consisted of normal brain tissue taken from four children diagnosed with causes other than cancer. Formalin-fixed and paraffin-embedded tissues were sectioned and used for FTIR spectroscopic analysis. The sections were examined in the mid-infrared range (800-3500 cm-1) by ATR-FTIR. Spectra were analysed using a combination of principal component analysis, hierarchical cluster analysis, and absorbance dynamics. RESULTS: FTIR spectra in MB were significantly different from those of normal brain tissue. The most significant differences related to the range of nucleic acids and proteins in the region 800-1800 cm-1. Some major differences were also revealed in the quantification of protein conformations (α-helices, ß-sheets, and others) in the amide I band, as well as in the absorbance dynamics in the 1714-1716 cm-1 range (nucleic acids). It was not, however, possible to clearly distinguish between the various histological subtypes of MB using FTIR spectroscopy. CONCLUSIONS: MB and normal brain tissue can be distinguished from one another to some extent using FTIR spectroscopy. As a result, it may be used as a further tool to hasten and enhance histological diagnosis.

MicroRNA gene methylation landscape in pediatric B-cell precursor acute lymphoblastic leukemia.

BACKGROUND: Aberrant DNA methylation is an important mechanism by which the normal patterns of microRNA expression are disrupted in human cancers including B-cell precursor acute lymphoblastic leukemia (BCP ALL), the most common pediatric malignancy. OBJECTIVES: To characterize the methylation profile landscape of microRNA genes in BCP ALL patients. MATERIAL AND METHODS: We employed Infinium® MethylationEPIC BeadChip Arrays to measure the methylation of microRNA genes from bone marrow samples of children with BCP ALL (n = 38) and controls without neoplasms (n = 4). RESULTS: This analysis revealed differential methylation of the microRNA genes in the pediatric BCP ALL when compared to the control. A subcluster amongst BCP ALL patients with TCF3-PBX1 genetic subtype was also observed. No other differences were observed in association with age, gender or risk group. Several interesting leukemia-related phenotypes are enriched by the genes with hyperand hypomethylated sites located in promoters as well as gene bodies. The top 3 miRNA genes, promoters of which were the most statistically significantly hypermethylated in BCP ALL were MIR1273G, MIR1304 and MIR663, and the top 3 hypomethylated were MIR4442, MIR155 and MIR3909. CONCLUSIONS: In this study, a different microRNA genes methylation landscape was shown in pediatric BCP ALL compared to children without neoplasms. A visible subcluster among BCP ALL samples consisted of individuals with TCF3-PBX1 genetic subtype. No other differences were observed in association with age, gender or risk group. Several interesting leukemia-connected phenotypes were found, associated with genes with hyperand hypomethylated sites located on promoters as well as gene bodies.

Spectroscopic evaluation of carcinogenesis in endometrial cancer.

Carcinogenesis is a multifaceted process of cancer formation. The transformation of normal cells into cancerous ones may be difficult to determine at a very early stage. Therefore, methods enabling identification of initial changes caused by cancer require novel approaches. Although physical spectroscopic methods such as FT-Raman and Fourier Transform InfraRed (FTIR) are used to detect chemical changes in cancer tissues, their potential has not been investigated with respect to carcinogenesis. The study aimed to evaluate the usefulness of FT-Raman and FTIR spectroscopy as diagnostic methods of endometrial cancer carcinogenesis. The results indicated development of endometrial cancer was accompanied with chemical changes in nucleic acid, amide I and lipids in Raman spectra. FTIR spectra showed that tissues with development of carcinogenesis were characterized by changes in carbohydrates and amides vibrations. Principal component analysis and hierarchical cluster analysis of Raman spectra demonstrated similarity of tissues with cancer cells and lesions considered precursor of cancer (complex atypical hyperplasia), however they differed from the control samples. Pearson correlation test showed correlation between cancer and complex atypical hyperplasia tissues and between non-cancerous tissue samples. The results of the study indicate that Raman spectroscopy is more effective in assessing the development of carcinogenesis in endometrial cancer than FTIR.

A Preliminary Study of FTIR Spectroscopy as a Potential Non-Invasive Screening Tool for Pediatric Precursor B Lymphoblastic Leukemia.

Early detection of the most common pediatric neoplasm, B-cell precursor lymphoblastic leukemia (BCP-ALL), is challenging and requires invasive bone marrow biopsies. The purpose of this study was to establish new biomarkers for early screening to detect pediatric leukemia. In this small cohort study, Fourier transform infrared (FTIR) spectra were obtained from blood sera of 10 patients with BCP-ALL and were compared with the control samples from 10 children with some conditions other than neoplasm. Using various analytical approaches, including a new physical model, some significant differences were observable. The most important include: the different peak area ratio 2965/1645 cm-1 (p = 0.002); the lower average percentage of both ß-sheet and ß-turn protein structures in the sera of BCP-ALL patients (p = 0.03); an AdaBoost-based predictive model for classifying healthy vs. BCP-ALL patients with 85% accuracy; and the phase shift of the first derivative in the spectral range 1050-1042 cm-1 correlating with white blood cell (WBC) and blast cell count in BCP-ALL patients contrary to the samples obtained from healthy controls. Although verification in larger groups of patients will be necessary, these promising results suggest that FTIR spectroscopy may have future potential for the early screening of BCP-ALL.

First Identification of the Effects of Low Frequency Electromagnetic Field on the Micromolecular Changes in Adipose Tissue-Derived Mesenchymal Stem Cells by Fourier Transform Infrared Spectroscopy.

Purpose: In this study, we hypothesize that exposure of adipose tissue-mesenchymal stem cells (AT-MSCs) to electromagnetic field (EMF) may impact adipose stem cells' micromolecular structure (analyzed using Fourier transform infrared spectroscopy [FTIR]). Materials and Methods: The AT-MSCs were exposed to continuous vertically applied sinusoidal EMF with a frequency of 50 Hz and a flux density of 1.5 mT for 24, 48, and 72 h. After an appropriate time (24, 48, 72 h) cells were washed with PBS, scrubbed, and immediately taken into FTIR analyses. Results: EMFs affect AT-MSCs. The greatest differences were in the range of nucleic acids and proteins in the fingerprint region which occurred after 24 and 48 h of EMF exposure. However, in the case of 72 h of EMF exposure, no significant differences were noticed in the FTIR spectra towards the control. Conclusions: FTIR spectra show differences between samples under the influence of EMF before they will be manifested at the morphological level. The largest differences in the range of nucleic acids and proteins in the fingerprint region occurred at 24 and 48 h of EMF exposure. That means it was during the first 48 h after EMF exposure a great number of dynamic changes occurred. However, in the case of AT-MSCs in 72 h EMF and 72 h control, no significant differences were noted in the FTIR spectra, which means that the chemical composition in these two cases is similar. EMF is not neutral for stem cells, especially in the in the first hours of interaction (24 h, 48 h).

Simultaneous FTIR and Raman Spectroscopy in Endometrial Atypical Hyperplasia and Cancer.

Currently, endometrial carcinoma (EC) is the most common genital cancer in high-income countries. Some types of endometrial hyperplasia (EH) may be progressing to this malignancy. The diagnosis of EC and EH is based on time consuming histopathology evaluation, which is subjective and causes discrepancies in reassessment. Therefore, there is a need to create methods of objective evaluation allowing the diagnosis of early changes. The study aimed to simultaneously asses Fourier Transform Infrared (FTIR) and Raman spectroscopy combined with multidimensional analysis to identify the tissues of endometrial cancer, atypical hyperplasia and the normal control group, and differentiate them. The results of FTIR and Raman spectroscopy revealed quantitative and qualitative changes in the nucleic acid and protein in the groups of cancer and atypical hyperplasia, in comparison with the control group. Changes in the lipid region were also observed in Raman spectra. Pearson correlation coefficient demonstrated a statistically significant correlation between Raman spectra for the cancer and atypical hyperplasia groups (0.747, p < 0.05) and for atypical hyperplasia and the controls (0.507, p < 0.05), while FTIR spectra demonstrated a statistically significant positive correlation for the same group as in Raman data and for the control and cancer groups (0.966, p < 0.05). To summarize, the method of spectroscopy enables differentiation of atypical hyperplasia and endometrial cancer tissues from the physiological endometrial tissue.

Hounsfield units and fractal dimension (test HUFRA) for determining PET positive/negative lymph nodes in pediatric Hodgkin's lymphoma patients.

OBJECTIVES: We had developed a method that can help detect and identify lymph nodes affected by the neoplastic process. Our group evaluated the fractal dimension (FD) and X-ray attenuation (XRA) of lymph nodes in HL and compared to their metabolic activity as measured by 18F-FDG-PET examination. METHODS: The training set included 72 lymph nodes from 31 consecutive patients, and the tested set of 71 lymph nodes from next 19 patients. The measurement of FD of each lymph node was performed before the start of therapy using original software. X-ray attenuation (XRA) expressed in HU (Hounsfield Units) from CT scans was compared with the metabolic activity of the lymphatic nodes, measured by 18F-FDG-PET examination. RESULTS: Significant differences were observed between XRAmax and FDmax values in assessing the PET(+) and PET(-) nodes. All nodes were scored from 0 to 2. The HUFRA test properly qualified 95% with a score of 2 and 0 points as PET(+) or PET(-). CONCLUSION: The HUFRA test can differentiate about 70-80% of lymph nodes as PET(+) or PET(-) based solely on the CT examination. It can be useful in patients who were not subjected to 18FFDG-PET/CT examination before the treatment, or who had an unreliable result of 18F-FDG-PET/CT with further research requirements.

In vitro study of effects of ELF-EMF on testicular tissues of roe deer (Capreolus capreolus) - FTIR and FT-Raman spectroscopic investigation.

Electromagnetic fields (EMF) are classified as an environmental factor affecting living organisms. The aim of the study was to evaluate the effect of EMF at different frequencies (50 and 120 Hz), durations of treatment (2 and 4 h) and with the magnetic induction of 8 m T on testicular tissues of roe deer (Capreolus capreolus) in vitro by comparison with the control samples. Fourier Transform Raman Spectroscopy (FT-Raman) and Fourier Transform Infrared Spectroscopy (FTIR) were utilized in this study to identify the chemical changes in the testicular tissues. The FTIR and FT-Raman spectroscopy methods were used to evaluate differences in spectra of the treated tissues compared to the control group. The results from the analysis of the spectra indicated there were characteristic differences in the testicular tissue compared with the control samples. There was identification of peaks attributed to different biochemical components. Comparing the spectra for different frequencies and treatment times, there was a greater intensity of peaks originating from most of the functional groups in the tissues evaluated. With the FTIR spectra, there were five of 15 peaks, while with the FT-Raman spectra, there were six of ten peaks that were shifted. For FTIR and FT-Raman analyzed spectral ranges, results from the PCA analysis indicate there was no similarity between control groups (2 and 4 h) and samples treated with EMF at a frequency of 120 Hz for 2 and 4 h. In conclusion, therefore, EMF is an environmental factor affecting the testis of roe deer.

Predicting Ewing Sarcoma Treatment Outcome Using Infrared Spectroscopy and Machine Learning.

BACKGROUND: Improved outcome prediction is vital for the delivery of risk-adjusted, appropriate and effective care to paediatric patients with Ewing sarcoma-the second most common paediatric malignant bone tumour. Fourier transform infrared (FTIR) spectroscopy of tissues allows the bulk biochemical content of a biological sample to be probed and makes possible the study and diagnosis of disease. METHODS: In this retrospective study, FTIR spectra of sections of biopsy-obtained bone tissue were recorded. Twenty-seven patients (between 5 and 20 years of age) with newly diagnosed Ewing sarcoma of bone were included in this study. The prognostic value of FTIR spectra obtained from Ewing sarcoma (ES) tumours before and after neoadjuvant chemotherapy were analysed in combination with various data-reduction and machine learning approaches. RESULTS: Random forest and linear discriminant analysis supervised learning models were able to correctly predict patient mortality in 92% of cases using leave-one-out cross-validation. The best performing model for predicting patient relapse was a linear Support Vector Machine trained on the observed spectral changes as a result of chemotherapy treatment, which achieved 92% accuracy. CONCLUSION: FTIR spectra of tumour biopsy samples may predict treatment outcome in paediatric Ewing sarcoma patients with greater than 92% accuracy.

FTIR Spectroscopy of Cerebrospinal Fluid Reveals Variations in the Lipid: Protein Ratio at Different Stages of Alzheimer's Disease.

Alzheimer's disease (AD) is a disease of advanced civilization and a common form of dementia in people over 65 years of age. We used Fourier transform infrared (FTIR) spectroscopy combined with principal component analysis (PCA) to determine changes in the quantity and quality of the cerebrospinal fluid from AD patients at three different stages of the disease (ADI, ADII, and ADIII), as well as from patients with mild cognitive impairment (MCI). Moreover, based on the FTIR spectra, we calculated the ratio of α-helix and ß-sheet secondary protein structures as well as the lipid-protein balance as potential AD markers. The FTIR spectra of cerebrospinal fluid obtained from MCI, ADI, ADII, and ADIII patients showed that peaks corresponding to protein and deoxyribonucleic acid (DNA), and phospholipid and lipid vibrations were shifted in comparison with those of control subjects. Furthermore, the levels of these chemical compounds were lower in the patients than in the control subjects. The ß-sheet secondary protein structure levels were increased in the MCI and AD patients compared with the control subjects. In addition, significant changes in the lipid-protein balance were observed. Interestingly, as the disease progressed, the lipid-protein balance became further disrupted, that is, the lipid amount decreased with disease progression. PCA analysis of lipid-protein FTIR regions revealed that the spectra could be used to distinguish between controls and patients with MCI, ADI, ADII, and ADIII.

Body Mass Index (BMI) and Infectious/Febrile Episodes in Children with Intermediate Risk Acute Lymphoblastic Leukemia (IR ALL).

The incidence of treatment related mortality in children with acute lymphoblastic leukemia (ALL) is reported to be between 2% and 4% with infections being the leading cause. AIM: To establish a relationship between body mass index at diagnosis (BMI 0), after protocol I therapy completion (BMI I) and the incidence rate ratio (IRR) of infectious/febrile episodes in children with ALL intermediate risk. METHODS: Thirty one consecutive patients (2-18 years old, with a male to female ratio of 19/12) with newly diagnosed ALL that were treated uniformly according to ALL IC 2009 protocol were included in this analysis. RESULTS: A BMI decrease of at least 5% during protocol I therapy and BMI 1 under 15th percentile score corresponds significantly with higher IRR (with P-values 0.04 and 0.006 respectively) during the whole intensive therapy. CONCLUSION: Some relationships between BMI reduction and higher IRR in ALL patients were found, but their significance is limited by the size of the group analyzed.

The distinguishable DNA whole genome methylation profile of 2 cases of pediatric precursor B acute lymphoblastic leukaemia (BCP ALL) with prodromal, preleukemic phase: A case report.

RATIONALE: A prolonged, prodromal phase before definitive paediatric precursor B acute lymphoblastic leukaemia (BCP ALL) diagnosis is rarely observed. PATIENTS CONCERNS: In the first, the patient presented with an aplastic preleukemic phase, whilst the second presented with a rheumatic-like preliminary phase. DIAGNOSES: The case reports of two patients with BCP ALL with a prodromal phase lasting a few weeks are presented. INTERVENTIONS AND OUTCOMES: DNA whole genome profile methylation analysis of bone marrow cells obtained at diagnosis revealed a pattern of methylation that was readily distinguishable from both healthy and standard course BCP ALL bone marrow samples. LESSONS: The biological implication of this observation remains unclear, with many differentially methylated loci involved in many processes like neurogenesis, cell projection organization and adhesion along with leucocyte activation and apoptosis. The prevalence and clinical significance of these methylation changes is unknown but this data indicates that the epigenetic basis of BCP ALL with a prolonged, prodromal phase requires a more detailed assessment.

Distinguishing Ewing sarcoma and osteomyelitis using FTIR spectroscopy.

The differential diagnosis of Ewing sarcoma and osteomyelitis can be challenging and can lead to delays in treatment with possibly devastating results. In this retrospective, small-cohort study we demonstrate, that the Fourier Transformed Infrared (FTIR) spectra of osteomyelitis bone tissue can be differentiated from Ewing sarcoma and normal bone tissue sampled outside tumour area. Significant differences in osteomyelitis samples can be seen in lipid and protein composition. Supervised learning using a quadratic discriminant analysis classifier was able to differentiate the osteomyelitis samples with high accuracy. FTIR spectroscopy, alongside routine radiological and histopathological methods, may offer an additional tool for the differential diagnosis of osteomyelitis and ES.

Prediction of Ewing Sarcoma treatment outcome using attenuated tissue reflection FTIR tissue spectroscopy.

Ewing sarcoma is the second most common type of primary bone cancer and predominantly affects children and young people. Improved outcome prediction is key to delivering risk-adjusted, appropriate and effective care to cancer patients. Advances in the Fourier Transform Infrared (FTIR) spectroscopy of tissues enable it to be a non-invasive method to obtain information about the biochemical content of any biological sample. In this retrospective study, attenuated tissue reflection FTIR spectroscopy of biopsy samples from paediatric patients reveals spectral features that are diagnostic for Ewing Sarcoma. Furthermore, our results suggest that spectral features such as these may be of value for the prediction of treatment outcome independent to well-known, routinely used risk factors.

Hounsfield units from unenhanced 18F-FDG-PET/CT are useful in evaluating supradiaphragmatic lymph nodes in children and adolescents with classical Hodgkin's lymphoma.

BACKGROUND: The precise identification of the primarily-affected nodal regions in Hodgkin's lymphoma(HL) is essential in determining the stage of the disease and the intensity of chemotherapy and radiotherapy. OBJECTIVES: The aim of this study was to use the degree of X-ray attenuation (XRA) in Hounsfield units(HU) and the lymph node-to-muscle attenuation ratio (LN/M) in computed tomography (CT) unenhancedimaging, routinely performed with 18F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET),to distinguish HL-affected supradiaphragmatic lymph nodes. MATERIAL AND METHODS: The study included 52 patients with classical HL treated according to the EuroNet-PHL-C1 protocol. Patients received 2 chemotherapy cycles after 18F-FDG-PET/CT testing, followedby re-examination. The lymph nodes were evaluated according to the Society for Pediatric Oncology andHematology's GPOH-HD-2002 study and Lugano criteria as not-involved (NI-LN) and involved (I-LN). RESULTS: A significant difference (p < 0.001) was found in the XRA and LN/M values between NI-LN andI-LN before treatment and after the 2 chemotherapy cycles. The optimal cut-off point for XRA (44.7 HU) andLN/M (0.79) values distinguishing I-LN from NI-LN nodes was determined by receiver operating characteristic(ROC) analysis. After 2 cycles of chemotherapy, higher XRA (p = 0.002) and LN/M (p = 0.001) values in thegroup with inadequate early CTx response were found. CONCLUSIONS: The use of XRA in HU and LN/M, together with the existing standard, can improve the qualificationof supradiaphragmatic lymph nodes in HL.