scholarly journals Telomere Length Dynamics and Chromosomal Instability for Predicting Individual Radiosensitivity and Risk via Machine Learning

2021 ◽  
Vol 11 (3) ◽  
pp. 188
Author(s):  
Jared J. Luxton ◽  
Miles J. McKenna ◽  
Aidan M. Lewis ◽  
Lynn E. Taylor ◽  
Sameer G. Jhavar ◽  
...  

The ability to predict a cancer patient’s response to radiotherapy and risk of developing adverse late health effects would greatly improve personalized treatment regimens and individual outcomes. Telomeres represent a compelling biomarker of individual radiosensitivity and risk, as exposure can result in dysfunctional telomere pathologies that coincidentally overlap with many radiation-induced late effects, ranging from degenerative conditions like fibrosis and cardiovascular disease to proliferative pathologies like cancer. Here, telomere length was longitudinally assessed in a cohort of fifteen prostate cancer patients undergoing Intensity Modulated Radiation Therapy (IMRT) utilizing Telomere Fluorescence in situ Hybridization (Telo-FISH). To evaluate genome instability and enhance predictions for individual patient risk of secondary malignancy, chromosome aberrations were assessed utilizing directional Genomic Hybridization (dGH) for high-resolution inversion detection. We present the first implementation of individual telomere length data in a machine learning model, XGBoost, trained on pre-radiotherapy (baseline) and in vitro exposed (4 Gy γ-rays) telomere length measurements, to predict post radiotherapy telomeric outcomes, which together with chromosomal instability provide insight into individual radiosensitivity and risk for radiation-induced late effects.

2020 ◽  
Author(s):  
Jared J. Luxton ◽  
Miles J. McKenna ◽  
Aidan M. Lewis ◽  
Lynn E. Taylor ◽  
Sameer G. Jhavar ◽  
...  

AbstractThe ability to predict a cancer patient’s response to radiotherapy and risk of developing adverse late health effects would greatly improve personalized treatment regimens and individual outcomes. Telomeres represent a compelling biomarker of individual radiosensitivity and risk, as exposure can result in dysfunctional telomere pathologies that coincidentally overlap with many radiation-induced late effects, ranging from degenerative conditions like fibrosis and cardiovascular disease to proliferative pathologies like cancer. Here, telomere length was longitudinally assessed in a cohort of fifteen prostate cancer patients undergoing Intensity Modulated Radiation Therapy (IMRT) utilizing Telomere Fluorescence in situ Hybridization (Telo-FISH). To evaluate genome instability and enhance predictions for individual patient risk of secondary malignancy, chromosome aberrations were also assessed utilizing directional Genomic Hybridization (dGH) for high-resolution inversion detection. We present the first implementation of individual telomere length data in a machine learning model, XGBoost, trained on pre-radiotherapy (baseline) and in vitro exposed (4 Gy γ-rays) telomere length measures, to predict post-radiotherapy telomeric outcomes, which together with chromosomal instability provide insight into individual radiosensitivity and risk for radiation-induced late effects.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3208-3208
Author(s):  
Rodrigo T. Calado ◽  
James N Cooper ◽  
Phillip Scheinberg ◽  
Colin Wu ◽  
Marco A Zago ◽  
...  

Abstract Abstract 3208 Poster Board III-145 In murine models, telomere erosion promotes chromosomal instability via breakage-fusion-bridge cycles, contributing to the early stages of tumorigenesis. However, direct evidence that short telomeres predispose to cancer development in humans is lacking. In acquired aplastic anemia, evolution to malignant clonal disorders is a major complication after immunosuppressive therapy, affecting up to 15 percent of patients at 10 years. We investigated whether telomere length measured at diagnosis predicted clonal evolution in these patients. Telomere length was measured from DNA extracted from peripheral blood leukocytes collected at disease presentation in 183 consecutive patients enrolled in successive clinical trials for immunosuppressive regimen as first line therapy for severe aplastic anemia at the Clinical Research Center, National Institutes of Health (ClinicalTrials.gov identifier numbers, NCT00001964, NCT00260689, and NCT00061360) and 164 healthy volunteers. Leukocyte telomere length of aplastic anemia patients at diagnosis was in the normal range and was not shorter than in healthy controls (ANOVA-F test). Telomere length was corrected for age and patients were separated into two groups: patients with short telomeres (in the lowest quartile) and long telomeres (other quartiles). Telomere length was a critical and independent predictive biomarker for evolution to myelodysplastic syndrome, especially monosomy 7, and acute myeloid leukemia (AML) in patients with acquired aplastic anemia (Multivariate Cox Proportional Hazard Model, P=0.006). Patients with short telomeres had six-fold higher probability to develop clonal malignant disease than did patients with longer telomeres. Bone marrow cells of aplastic patients were cultured in vitro for short term in the presence of cytokines and high-dose granulocyte-colony stimulating factor (G-CSF) and cells of patients with short telomeres (n=5) showed increased telomere-free chromosomal ends in comparison to cells of patients with long telomeres (n=6), by fluorescence in situ hybridization (FISH; P<0.0001). Spectral karyotyping (SKY) revealed that cultured bone marrow cells of patients with short telomeres exhibited aneuploidy and translocations, including Robertsonian translocations, which were not found in cells of patients with long telomeres. Bone marrow cells at diagnosis were further evaluated for the presence of monosomy 7 cells using interphase FISH in 73 patients. Telomere length inversely correlated with the frequency of monosomy 7 cells: the shortest the telomeres, the highest the percentage of aneuploid cells at diagnosis (Pearson r=-0.5110; P=0.0009). We further employed bone marrow cells of clinically healthy individuals carrying loss-of-function telomerase mutations and with extremely short telomeres (n=5) as a model for telomere dysfunction in hematopoietic cells in the absence of human disease. In vitro culture of these cells yielded aberrant karyotypes by SKY, including translocations and aneuploidy, and end-to-end chromosomal fusions by FISH. These results indicate that telomere length at diagnosis predicts evolution to myelodysplasia and leukemia in patients with acquired aplastic anemia treated with immunosuppression. Our findings support the hypothesis that short and dysfunctional telomeres restrain stem cell proliferation and predispose for malignant transformation by selecting stem cells that are prone to chromosomal instability. This is the first prospective study to demonstrate that short telomeres in human hematopoietic cells promote chromosomal instability in vitro and predispose to malignant transformation in humans. Disclosures Cooper: NIH-Pfizer: Research Funding.


2016 ◽  
Vol 38 (4) ◽  
pp. 276-279 ◽  
Author(s):  
M A Pilinska ◽  
G M Shemetun ◽  
O V Shemetun ◽  
S S Dybsky ◽  
O B Dybska ◽  
...  

In the lecture we have generalized and analyzed the data of cytogenetic laboratory of National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine on 30-year selective cytogenetic monitoring among the priority contingents of different ages exposed to radiation after Chornobyl accident in Ukraine. It is highlighted that not only targeted but also untargeted radiation-induced cytogenetic effects should be explored, especially in delayed terms following radiation exposure. The new methodical approaches for studying “bystander effect”, individual radiosensitivity, and various forms of radiation-induced chromosomal instability (delayed, hidden, transmissible) have been proposed. These approaches proved to be advantageous for analyzing cytogenetic patterns of induction and persistence of chromosomal instability in human somatic cells because of “bystander effect” and “bystander type effect”. The phenomenon of positive “reverse” bystander effect has been found. The possibility of modifying the inherited individual human susceptibility to mutagenic exposure by ionizing radiation has been estimated. Finally, the association between hypersensitivity to radiation exposure and realization of oncopathology in exposed individuals has been revealed. The increased intensity of human somatic chromosomal mutagenesis was confirmed not only in the nearest but in the delayed terms following Chornobyl accident as a result of radiation-induced both targeted and untargeted cytogenetic effects. Such effects can be considered as risk factors for malignant transformation of cells, hereditary diseases, birth defects, and multifactorial somatic pathology. This article is a part of a Special Issue entitled “The Chornobyl Nuclear Accident: Thirty Years After”.


Dose-Response ◽  
2007 ◽  
Vol 5 (4) ◽  
pp. dose-response.0 ◽  
Author(s):  
Kara Schnarr ◽  
Ian Dayes ◽  
Jinka Sathya ◽  
Douglas Boreham

Radiation protection regulations have been established to reduce exposure of individuals to acceptable safe levels. These limits assume that people have similar responses to ionizing radiation and that there is no variation in individual radiation risk. The purpose of this research was to determine if apoptosis in lymphocytes can be used to assess individual sensitivity to ionizing radiation. Blood samples were taken from 54 males ranging in age from 19–85 years. Apoptosis was measured using modified flow cytometry based Annexin-FITC/7AAD and DiOC6/7AAD assays in different populations of lymphocytes (total mixed lymphocyte population, subset CD4+ or CD8+ lymphocytes) after exposure to in vitro doses of 0, 2, 4 or 8Gy (dose rate 0.1Gy/min). The variation in individual responses to radiation was large. The variation was the largest in the CD4+ lymphocyte subpopulation. Radiation-induced apoptosis decreased with age of donor demonstrating that as people age their lymphocytes may become relatively more resistant to radiation. This research shows that individuals have marked differences in their sensitivity to radiation and protection policies may someday need to be tailored for some individuals.


2020 ◽  
Vol 17 (3) ◽  
pp. 365-375
Author(s):  
Vasyl Kovalishyn ◽  
Diana Hodyna ◽  
Vitaliy O. Sinenko ◽  
Volodymyr Blagodatny ◽  
Ivan Semenyuta ◽  
...  

Background: Tuberculosis (TB) is an infection disease caused by Mycobacterium tuberculosis (Mtb) bacteria. One of the main causes of mortality from TB is the problem of Mtb resistance to known drugs. Objective: The goal of this work is to identify potent small molecule anti-TB agents by machine learning, synthesis and biological evaluation. Methods: The On-line Chemical Database and Modeling Environment (OCHEM) was used to build predictive machine learning models. Seven compounds were synthesized and tested in vitro for their antitubercular activity against H37Rv and resistant Mtb strains. Results: A set of predictive models was built with OCHEM based on a set of previously synthesized isoniazid (INH) derivatives containing a thiazole core and tested against Mtb. The predictive ability of the models was tested by a 5-fold cross-validation, and resulted in balanced accuracies (BA) of 61–78% for the binary classifiers. Test set validation showed that the models could be instrumental in predicting anti- TB activity with a reasonable accuracy (with BA = 67–79 %) within the applicability domain. Seven designed compounds were synthesized and demonstrated activity against both the H37Rv and multidrugresistant (MDR) Mtb strains resistant to rifampicin and isoniazid. According to the acute toxicity evaluation in Daphnia magna neonates, six compounds were classified as moderately toxic (LD50 in the range of 10−100 mg/L) and one as practically harmless (LD50 in the range of 100−1000 mg/L). Conclusion: The newly identified compounds may represent a starting point for further development of therapies against Mtb. The developed models are available online at OCHEM http://ochem.eu/article/11 1066 and can be used to virtually screen for potential compounds with anti-TB activity.


2021 ◽  
pp. 096032712110361
Author(s):  
Hayal Cobanoglu ◽  
Akin Cayir

Tetrachlorvinphos is an organophosphate that is classified as a carcinogen in humans by several authorities. Due to very limited data regarding the genotoxic potential, we aimed to comprehensively investigate in vitro genotoxic potential of tetrachlorvinphos. We performed our study by applying the cytokinesis-block micronucleus cytome and sister chromatid exchange (SCE) assays to human peripheral blood lymphocytes. We evaluated micronucleus (MN) and SCE frequencies and cytokinesis-block proliferation index in both exposed and non-exposed lymphocytes. We also calculated the chromosomal instability level in response to exposure by combining the results of MN and SCE. We found that MN frequency did not increase with exposure to tetrachlorvinphos (0–50 µg/ml). In contrast, we observed that SCE frequencies significantly increased with exposure to ≥5 µg/ml tetrachlorvinphos. Furthermore, exposure to tetrachlorvinphos at concentrations of 50 µg/ml induced a significant increase in chromosomal instability level ( p < 0.05). Cytokinesis-block proliferation index level did not significantly decrease in response to tetrachlorvinphos exposure. Our findings reveal that tetrachlorvinphos resulted in different DNA damages that were measured by two assays. Furthermore, our findings suggested that exposure to tetrachlorvinphos increased chromosomal instability that is a hallmark of many malignancies. We conclude that although tetrachlorvinphos does not significantly increase the MN level, the significant increase of both SCE and CIN frequencies indicates the genotoxic potential of tetrachlorvinphos in human peripheral lymphocytes. Additionally, tetrachlorvinphos is not cytotoxic in the range of tested concentrations.


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