Tissue invasion and metastasis: Molecular, biological and clinical perspectives

Cancer is a key health issue across the world, causing substantial patient morbidity and mortality. Patient prognosis is tightly linked with metastatic dissemination of the disease to distant sites, with metastatic diseases accounting for a vast percentage of cancer patient mortality. While advances in this area have been made, the process of cancer metastasis and the factors governing cancer spread and establishment at secondary locations is still poorly understood. The current article summarizes recent progress in this area of research, both in the understanding of the underlying biological processes and in the therapeutic strategies for the management of metastasis. This review lists the disruption of E-cadherin and tight junctions, key signaling pathways, including urokinase type plasminogen activator (uPA), phosphatidylinositol 3-kinase/v-akt murine thymoma viral oncogene (PI3K/AKT), focal adhesion kinase (FAK), β-catenin/zinc finger E-box binding homeobox 1 (ZEB-1) and transforming growth factor beta (TGF-β), together with inactivation of activator protein-1 (AP-1) and suppression of matrix metalloproteinase-9 (MMP-9) activity as key targets and the use of phytochemicals, or natural products, such as those from Agaricus blazei, Albatrellus confluens, Cordyceps militaris, Ganoderma lucidum, Poria cocos and Silybum marianum, together with diet derived fatty acids gamma linolenic acid (GLA) and eicosapentanoic acid (EPA) and inhibitory compounds as useful approaches to target tissue invasion and metastasis as well as other hallmark areas of cancer. Together, these strategies could represent new, inexpensive, low toxicity strategies to aid in the management of cancer metastasis as well as having holistic effects against other cancer hallmarks

Designing a broad-spectrum integrative approach for cancer prevention and treatment

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notablesuccesses in some cancers; however, significant problems remain with this approach. Many targetedtherapies are highly toxic, costs are extremely high, and most patients experience relapse after a fewdisease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistantimmortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are notreliant upon the same mechanisms as those which have been targeted). To address these limitations, aninternational task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspectsof relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a widerange of high-priority targets (74 in total) that could be modified to improve patient outcomes. For thesetargets, corresponding low-toxicity therapeutic approaches were then suggested, many of which werephytochemicals. Proposed actions on each target and all of the approaches were further reviewed forknown effects on other hallmark areas and the tumor microenvironment. Potential contrary or procar-cinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixedevidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of therelationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. Thisnovel approach has potential to be relatively inexpensive, it should help us address stages and types ofcancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for futureresearch is offered

Identifying pri-miRNA transcription start sites

MicroRNAs (miRNAs) are small non-coding RNAs that can regulate gene expression playing vital role in nearly all biological pathways. Even though miRNAs have been intensely studied for more than two decades, information regarding miRNA transcription regulation remains limited. The rapid cleavage of primary miRNA transcripts (pri-miRNAs) by Drosha in the nucleus hinders their identification with conventional RNA-seq approaches. Identifying the transcription start site (TSS) of miRNAs will enable genome-wide identification of their expression regulators, including transcription factors (TFs), other non-coding RNAs (ncRNAs) and epigenetic modifiers, providing significant breakthroughs in understanding the mechanisms underlying miRNA expression in development and disease. Here we present a protocol that utilizes microTSS, a versatile computational framework for accurate and single-nucleotide resolution miRNA TSS predictions as well as miRGen, a database of miRNA gene TSSs coupled with genome-wide maps of TF binding sites. © 2018, Springer Science+Business Media, LLC, part of Springer Nature

Molecular determinants of radiosensitivity in normal and tumor tissue: A bioinformatic approach

Although radiation therapy is a treatment of choice for cancer, a high percentage of patients develop adverse effects in normal tissue following radiotherapy, mainly, due to genetic factors. Notably, although it is established that a lower dose of ionizing radiation can minimize the tumor cell population in radiosensitive cancer patients, the sensitivity of tumor cells to radiation has not gained enough attention. In this mini-review, the molecular pathways/mechanisms and the related molecules involved in clinically relevant radiotoxicity, as well as normal and tumor cell radiosensitivity, were investigated for various types of cancers employing bioinformatics approaches. A total of 255 genes/gene products were retrieved and investigated in this study, which are implicated in pathways related mainly to DNA damage repair, oxidative stress, apoptosis and fibrosis. Furthermore, a novel molecular gene signature of normal tissue radiotoxicity was identified. The findings of our study could be utilized by healthcare professionals in personalized clinical decision-making, in order to efficiently sensitize tumor cells to radiation and yet minimize adverse effects in the adjacent normal tissues as well as to improve the quality of life in cancer patients undergoing radiotherapy. © 2017 Elsevier B.V

A guide for using transmission electron microscopy for studying the radiosensitizing effects of gold nanoparticles in vitro

The combined effects of ionizing radiation (IR) with high-z metallic nanoparticles (NPs) such as gold has developed a growing interest over the recent years. It is currently accepted that radiosensitization is not only attributed to physical effects but also to underlying chemical and biological mechanisms’ contributions. Low-and high-linear energy transfer (LET) IRs produce DNA damage of different structural types. The combination of IR with gold nanoparticles may increase the clustering of energy deposition events in the vicinity of the NPs due to the production mainly of photoelectrons and Auger electrons. Biological lesions of such origin for example on DNA are more difficult to be repaired compared to isolated lesions and can augment IR’s detrimental effects as shown by numerous studies. Transmission electron microscopy (TEM) offers a unique opportunity to study the complexity of these effects on a very detailed cellular level, in terms of structure, including nanoparticle uptake and damage. Cellular uptake and nanoparticle distribution inside the cell are crucial in order to contribute to an optimal dose enhancement effect. TEM is mostly used to observe the cellular localization of nanoparticles. However, it can also provide valuable insights on the NPs’ radiosensitization pathways, by studying the biochemical mechanisms through immunogold-labelling of antigenic sites at ultrastructural level under high resolution and magnification. Here, our goal is to describe the possibilities, methodologies and proper use of TEM in the interest of studying NPs-based radiosensitization mechanisms. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

The challenge of drug resistance in cancer treatment: a current overview

It is generally accepted that recent advances in anticancer agents have contributed significantly to the improvement of both the disease-free survival and quality of life in cancer patients. However, in many instances, a favorable initial response to treatment changes afterwards, thereby leading to cancer relapse and recurrence. This phenomenon of acquired resistance to therapy, it is a major problem for totally efficient anticancer therapy. The failure to obtain an initial response reflects a form of intrinsic resistance. Specific cell membrane transporter proteins are implicated in intrinsic drug resistance by altering drug transport and pumping drugs out of the tumor cells. Moreover, the gradual acquisition of specific genetic and epigenetic abnormalities in cancer cells could contribute greatly to acquired drug resistance. A critical issue in the clinical setting, is that the problem of drug resistance appears to have a negative effect on also the new molecularly-targeted anticancer drugs. Several ongoing efforts are being made by the medical community aimed to the identification of such resistance mechanisms and the development of novel drugs that could overcome them. In this review, the major drug resistance mechanisms and strategies to overcome them are critically discussed, and also possible future directions are suggested. © 2018, Springer Science+Business Media B.V., part of Springer Nature

DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data

Background: The widespread usage of Cap Analysis of Gene Expression (CAGE) has led to numerous breakthroughs in understanding the transcription mechanisms. Recent evidence in the literature, however, suggests that CAGE suffers from transcriptional and technical noise. Regardless of the sample quality, there is a significant number of CAGE peaks that are not associated with transcription initiation events. This type of signal is typically attributed to technical noise and more frequently to random five-prime capping or transcription bioproducts. Thus, the need for computational methods emerges, that can accurately increase the signal-to-noise ratio in CAGE data, resulting in error-free transcription start site (TSS) annotation and quantification of regulatory region usage. In this study, we present DeepTSS, a novel computational method for processing CAGE samples, that combines genomic signal processing (GSP), structural DNA features, evolutionary conservation evidence and raw DNA sequence with Deep Learning (DL) to provide single-nucleotide TSS predictions with unprecedented levels of performance. Results: To evaluate DeepTSS, we utilized experimental data, protein-coding gene annotations and computationally-derived genome segmentations by chromatin states. DeepTSS was found to outperform existing algorithms on all benchmarks, achieving 98% precision and 96% sensitivity (accuracy 95.4%) on the protein-coding gene strategy, with 96.66% of its positive predictions overlapping active chromatin, 98.27% and 92.04% co-localized with at least one transcription factor and H3K4me3 peak. Conclusions: CAGE is a key protocol in deciphering the language of transcription, however, as every experimental protocol, it suffers from biological and technical noise that can severely affect downstream analyses. DeepTSS is a novel DL-based method for effectively removing noisy CAGE signal. In contrast to existing software, DeepTSS does not require feature selection since the embedded convolutional layers can readily identify patterns and only utilize the important ones for the classification task. This study highlights the key role that DL can play in Molecular Biology, by removing the inherent flaws of experimental protocols, that form the backbone of contemporary research. Here, we show how DeepTSS can unleash the full potential of an already popular and mature method such as CAGE, and push the boundaries of coding and non-coding gene expression regulator research even further. © 2022, The Author(s)

Dielectric and UV spectrophotometric study of physicochemical effects of ionizing radiation on mammalian macromolecular DNA

The purpose of this work was the comparative investigation of physicochemical effects induced by γ and α radiation on the thermal denaturation dynamics of native macromolecular calf thymus DNA, combining dielectric relaxation spectroscopy (DRS) and UV thermal transition spectrophotometry (TTS), while the apparent molecular weight (MW) distribution of the DNA macromolecules was measured by pulse field gel electrophoresis (PFGE). A DNA thermal stability enhancement over the non-irradiated samples was observed at radiation doses <10 Gy for γ rays and 32 Gy for α particles, attributed to the development of intra and/or intermolecular DNA-DNA interactions, whereas at higher irradiation doses, the expected decrease of thermal stability was observed. Moreover, in all studied cases, the recorded conductivity changes were found to precede by 2 to 3°(2 those of UV TTS absorbance changes, a fact indicative of a multi-stage process for DNA thermal transition. Finally, the displacement of the low dose region limit towards higher doses in the case of α particles, confirm earlier results attesting higher yields of DNA strand breaks induced by γ rays compared to α particles

Low doses of α- and γ-radiation enhance DNA thermal stability

Isolated calf thymus DNA in buffered solutions has been exposed to 0-150 Gy of α- and γ-radiation. The effects of α- and γ-radiation on the thermal stability and electrophoretic mobility of the DNA molecules have been studied by UV spectroscopic 'melting' and Pulsed Field Gel Electrophoresis (PFGE), respectively. The observed thermal denaturation parameters were fitted to the energy propagation descriptive model. The experimental results for the samples exposed to relatively low (low) doses indicate an increased thermal stability and a reduced mobility over that of the controls. The expected overall degradation of the DNA molecules was confirmed for the samples exposed to high doses. Our results are in good agreement with the predictions of the energy propagation model, which now is also tested in the low dose region and for an additional type of ionising radiation (α-particles). Our findings are consistent with conformational changes at low doses resulting in a DNA form characterised by localised alterations, which affect the energy flow along the DNA molecule. Copyright (C) 1999 Elsevier Science B.V