Lima K.M.G.,Lancaster University |
Lima K.M.G.,Federal University of Rio Grande do Norte |
Gajjar K.B.,Lancaster University |
Gajjar K.B.,Central Lancashire Teaching Hospitals NHS Foundation Trust |
And 2 more authors.
Biotechnology Progress | Year: 2015
Ovarian cancer is a solid tumor and a leading cause of mortality. Diagnostic tools for the detection of early stage (stage I) ovarian cancer are urgently needed. For this purpose, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) coupled with variable selection methods, successive projection algorithm or genetic algorithm (GA) combined with linear discriminant analysis (LDA), were employed to identify spectral biomarkers in blood plasma or serum samples for accurate diagnosis of different stages of ovarian cancer, histological type and segregation based on age. Three spectral datasets (stage I vs. stage II-IV; serous vs. non-serous carcinoma; and, ≤60 years vs. >60 years) were processed: sensitivity and specificity required for real-world diagnosis of ovarian cancer was achieved. Toward segregating stage I vs. stage II-IV, sensitivity and specificity (plasma blood) of 100% was achieved using a GA-LDA model with 33 wavenumbers. For serous vs. non-serous category (plasma blood), the sensitivity and specificity levels, using 29 wavenumbers by GA-LDA, were remarkable (up to 94%). For ≤60 years and >60 years categories (plasma blood), the sensitivity and specificity, using 42 wavenumbers by GA-LDA, gave complete accuracy (100%). For serum samples, sensitivity and specificity results gave relatively high accuracy (up to 91.6% stage I vs. stage II-IV; up to 93.0% serous vs. non-serous; and, up to 96.0% ≤60 years vs. >60 years) using several wavenumbers. These findings justify a prospective population-based assessment of biomarkers signatures using ATR-FTIR spectroscopy as a screening tool for stage of ovarian cancer. © 2015 American Institute of Chemical Engineers.
Lima K.M.G.,Lancaster University |
Lima K.M.G.,Federal University of Rio Grande do Norte |
Gajjar K.,Lancaster University |
Gajjar K.,Central Lancashire Teaching Hospitals NHS Foundation Trust |
And 8 more authors.
Analytical Methods | Year: 2014
Cervical cancer is the second most common cancer in women worldwide. We set out to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy combined with principal component analysis-linear discriminant analysis (PCA-LDA) or, variable selection techniques employing successive projection algorithm or genetic algorithm (GA) could classify cervical cytology according to human papilloma virus (HPV) infection [high-risk (hr) vs. low-risk (lr)]. Histopathological categories for squamous intraepithelial lesion (SIL) were segregated into grades (low-grade vs. high-grade) of cervical intraepithelial neoplasia (CIN) expressing different HPV infection (16/18, 31/35 or HPV Others). Risk assessment for HPV infection was investigated using age (≤29 years vs. >30 years) as the distinguishing factor. Liquid-based cytology (LBC) samples (n = 350) were collected and interrogated employing ATR-FTIR spectroscopy. Accuracy test results including sensitivity and specificity were determined. Sensitivity in hrHPV category was high (≈87%) using a GA-LDA model with 28 wavenumbers. Sensitivity and specificity results for >30 years for HPV, using 28 wavenumbers by GA-LDA, were 70% and 67%, respectively. For normal cervical cytology, accuracy results for ≤29 years and >30 years were high (up to 81%) using a GA-LDA model with 27 variables. For the low-grade cervical cytology dataset, 83% specificity for ≤29 years was achieved using a GA-LDA model with 33 wavenumbers. HPV16/18 vs. HPV31/35 vs. HPV Others were segregated with 85% sensitivity employing a GA-LDA model with 33 wavenumbers. We show that ATR-FTIR spectroscopy of cervical cytology combined with variable selection techniques is a powerful tool for HPV classification, which would have important implications for the triaging of patients. © The Royal Society of Chemistry 2014.
Theophilou G.,Lancaster University |
Theophilou G.,Central Lancashire Teaching Hospitals NHS Foundation Trust |
Paraskevaidi M.,University of Ioannina |
Lima K.M.,Lancaster University |
And 5 more authors.
Expert Review of Molecular Diagnostics | Year: 2015
The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing 'omics' technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention. © Informa UK, Ltd.
PubMed | Lancaster University, Federal University of Rio Grande do Norte, LEC Tokyo Legal Mind University and Central Lancashire Teaching Hospitals NHS Foundation Trust
Type: Journal Article | Journal: The Analyst | Year: 2016
Surgical management of ovarian tumours largely depends on their histo-pathological diagnosis. Currently, screening for ovarian malignancy with tumour markers in conjunction with radiological investigations has a low specificity for discriminating benign from malignant tumours. Also, pre-operative biopsy of ovarian masses increases the risk of intra-peritoneal dissemination of malignancy. Intra-operative frozen section, although sufficiently accurate in differentiating tumours according to their histological type, increases operation times. This results in increased surgery-related risks to the patient and additional burden to resource allocation. We set out to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, combined with chemometric analysis can be applied to discriminate between normal, borderline and malignant ovarian tumours and classify ovarian carcinoma subtypes according to the unique spectral signatures of their molecular composition. Formalin-fixed, paraffin-embedded ovarian tissue blocks were de-waxed, mounted on Low-E slides and desiccated before being analysed using ATR-FTIR spectroscopy. Chemometric analysis in the form of principal component analysis (PCA), successive projection algorithm (SPA) and genetic algorithm (GA), followed by linear discriminant analysis (LDA) of the obtained spectra revealed clear segregation between benign versus borderline versus malignant tumours as well as segregation between different histological tumour subtypes, when these approaches are used in combination. ATR-FTIR spectroscopy coupled with chemometric analysis has the potential to provide a novel diagnostic approach in the accurate diagnosis of ovarian tumours assisting surgical decision making to avoid under-treatment or over-treatment, with minimal impact to the patient.
PubMed | Imperial College London, University of Central Lancashire and Central Lancashire Teaching Hospitals NHS Foundation Trust
Type: | Journal: Mutagenesis | Year: 2016
Mitochondrial diseases have been extensively investigated over the last three decades, but many questions regarding their underlying aetiologies remain unanswered. Mitochondrial dysfunction is not only responsible for a range of neurological and myopathy diseases but also considered pivotal in a broader spectrum of common diseases such as epilepsy, autism and bipolar disorder. These disorders are a challenge to diagnose and treat, as their aetiology might be multifactorial. In this review, the focus is placed on potential mechanisms capable of introducing defects in mitochondria resulting in disease. Special attention is given to the influence of xenobiotics on mitochondria; environmental factors inducing mutations or epigenetic changes in the mitochondrial genome can alter its expression and impair the whole cells functionality. Specifically, we suggest that environmental agents can cause damage in mitochondrial DNA and consequently lead to mutagenesis. Moreover, we describe current approaches for handling mitochondrial diseases, as well as available prenatal diagnostic tests, towards eliminating these maternally inherited diseases. Undoubtedly, more research is required, as current therapeutic approaches mostly employ palliative therapies rather than targeting primary mechanisms or prophylactic approaches. Much effort is needed into further unravelling the relationship between xenobiotics and mitochondria, as the extent of influence in mitochondrial pathogenesis is increasingly recognised.
PubMed | Lancaster University and Central Lancashire Teaching Hospitals NHS Foundation Trust
Type: | Journal: Scientific reports | Year: 2015
Prostate cancer is the most commonly-diagnosed malignancy in males worldwide; however, there is marked geographic variation in incidence that may be associated with a Westernised lifestyle. We set out to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy combined with principal component analysis-linear discriminant analysis or variable selection techniques employing genetic algorithm or successive projection algorithm could be utilised to explore differences between prostate tissues from differing years. In total, 156 prostate tissues from transurethral resection of the prostate procedures for benign prostatic hyperplasia from 1983 to 2013 were collected. These were distributed to form seven categories: 1983-1984 (n=20), 1988-1989 (n=25), 1993-1994 (n=21), 1998-1999 (n=21), 2003-2004 (n=21), 2008-2009 (n=20) and 2012-2013 (n=21). Ten-m-thick tissue sections were floated onto Low-E (IR-reflective) slides for ATR-FTIR or Raman spectroscopy. The prostate tissue spectral phenotype altered in a temporal fashion. Examination of the two categories that are at least one generation (30 years) apart indicated highly-significant segregation, especially in spectral regions containing DNA and RNA bands (1,000-1,490cm(-1)). This may point towards alterations that have occurred through genotoxicity or through epigenetic modifications. Immunohistochemical studies for global DNA methylation supported this. This study points to a trans-generational phenotypic change in human prostate.