Changes In Cancer Tissues Research Articles

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.

Contribution of Raman Spectroscopy to Diagnosis and Grading of Chondrogenic Tumors

In the last decade, Raman Spectroscopy has demonstrated to be a label-free and non-destructive optical spectroscopy able to improve diagnostic accuracy in cancer diagnosis. This is because Raman spectroscopic measurements can reveal a deep molecular understanding of the biochemical changes in cancer tissues in comparison with non-cancer tissues. In this pilot study, we apply Raman spectroscopy imaging to the diagnosis and grading of chondrogenic tumors, including enchondroma and chondrosarcomas of increasing histologic grades. The investigation included the analysis of areas of 50×50 μm2 to approximately 200×200 μm2, respectively. Multivariate statistical analysis, based on unsupervised (Principal Analysis Components) and supervised (Linear Discriminant Analysis) methods, differentiated between the various tumor samples, between cells and extracellular matrix, and between collagen and non-collagenous components. The results dealt out basic biochemical information on tumor progression giving the possibility to grade with certainty the malignant cartilaginous tumors under investigation. The basic processes revealed by Raman Spectroscopy are the progressive degrading of collagen type-II components, the formation of calcifications and the cell proliferation in tissues ranging from enchondroma to chondrosarcomas. This study highlights that Raman spectroscopy is particularly effective when cartilaginous tumors need to be subjected to histopathological analysis.

5'-Methylthioadenosine and Cancer: old molecules, new understanding.

While the metabolic changes in cancer tissues were first observed by Warburg Otto almost a century ago, altered metabolism has recently returned as a focus of cancer research. 5'-Methylthioadenosine (MTA) is a naturally occurring sulfur-containing nucleoside found in numerous species. While MTA was first isolated several decades ago, a lack of sensitive and specific analytical methodologies designed for its direct quantification has hampered the study of its physiological and pathophysiological features. Many studies indicate that MTA suppresses tumors by inhibiting tumor cell proliferation, invasion, and the induction of apoptosis while controlling the inflammatory micro-environments of tumor tissue. In this review, we assessed the effects of MTA and of related materials on the growth and functions of normal and malignant cells.

Specific N-linked glycosylation patterns in areas of necrosis in tumor tissues

Tissue necrosis is a form of cell death common in advanced and aggressive solid tumors, and is associated with areas of intratumoral chronic ischemia. The histopathology of necrotic regions appear as a scaffold of cellular membrane remnants, reflective of the hypoxia and cell degradation events associated with this cellular death pathway. Changes in the glycosylation of cell surface proteins is another common feature of cancer progression. Using a recently developed mass spectrometry imaging approach to evaluate N-linked glycan distributions in human formalin-fixed clinical cancer tissues, differences in the glycan structures of regions of tumor, stroma and necrosis were evaluated. While the structural glycan classes detected in the tumor and stromal regions are typically classified as high mannose or branched glycans, the glycans found in necrotic regions displayed limited branching, contained sialic acid modifications and lack fucose modifications. While this phenomenon was initially classified in breast cancer tissues, it has been also seen in cervical, thyroid and liver cancer samples. These changes in glycosylation within the necrotic regions could provide further mechanistic insight to necrotic changes in cancer tissue and provide new research directions for identifying prognostic markers of necrosis.

Quantitative Analysis of Exosomes From Murine Lung Cancer Cells by Flow Cytometry.

In vivo studies regarding biochemical, molecular biological, and histopathological changes in cancer tissues have been widely performed by the administration of carcinogens in rodents. In these established methods, dissection of the animal following sacrifice must be carried out. Exosomes are cell-derived vesicles that are present in all body fluids and these vesicles have specific roles within cells. Thus, much attention is given to the clinical application of exosomes that can possibly be used for prediction and therapy and as biomarkers related to cancer. To develop a new tool for monitoring in vivo genetic alterations, as a result of carcinogenesis, without the need for frequent euthanasia, we performed quantitative measurement of exosomes in Mlg2908 murine lung fibroblasts and LA-4 and KLN 205 murine lung cancer cells using fluorescence-activated cell sorting. We detected an increase in CD63-specific exosomes in LA-4 lung cancer cells. This result is able to be applied to the classification of cancer-specific proteins and miRNA as diagnostic markers.

Abstract 3171: Powerful target capture/NGS approach reveals extensive genetic changes including SNVs, CNVs and gross chromosomal rearrangements in colorectal cancers

Abstract Introduction: Accurate and comprehensive molecular analyses of genetic changes in cancer tissues are critical for cancer management, treatment, and genetic counseling. Study of the complete molecular profiles in patient's blood, cacinoma tissue and surrounding pathological normal tissues will help us understand the etiology of colorectal cancers (CRC) as either hereditary or sporadic. In addition, this study will also reveal somatic changes and possible targets for therapy. Multigene target capture followed by deep next generation sequencing (NGS) provides a powerful approach to simultaneously detect both single nucleotide variants (SNVs) and exonic copy number variants (CNVs) in a time and cost effective fashion. Method: DNA samples were prepared from blood, freshly frozen normal surrounding and carcinoma or polyp tissues from 20 patients with CRC and 10 patients with colorectal polyps. A custom probe library containing 183 cancer related genes was used to capture the target sequences followed by NGS with deep coverage (average depth per base is ∼1000X). Both SNVs and CNVs were analyzed based on in-house developed analytical algorithm and bioinformatics pipeline. Results: This study revealed extensive genetic changes in colon carcinoma tissues. At least 40% of the colon carcinoma samples harbor loss-of-function pathogenic germline mutations in cancer related genes. However, loss of function germline mutations were not found in the polyps. Germline missense variants of unknown significance were identified in 60% of the polyps. Multiple deleterious somatic mutations are identified in all carcinoma tissues but only 1-2 somatic mutations per sample are found in the polyps. Almost every carcinoma tissue harbor gross chromosomal rearrangement, which is only found in about 50% of the polyp tissues.. NGS based CNV analysis revealed 2 germline events (FANCD2 E15-16 del; whole ALK gene dup). Somatic CNV events are more frequently observed in carcinoma tissues. Gross changes at chromosomal levels were also detected by using the NGS CNV analytical algorithm. Recurrent somatic pathogenic variants in genes associated with CRC, such as APC, TP53, and KRAS were identified while novel likely pathogenic variants in novel genes possibly linked to CRC were also discovered for further investigation. Heterogeneity of carcinoma tissues within the same individual was suggested by comparing allele frequency of different somatic mutations. Numerous loss of heterozygosity was observed in both carcinoma and polyp tissues. Conclusion: Target capture/NGS approach allows simultaneous analyses of SNVs and CNVs with quantitative data to distinguish between germline and somatic mutations. These analyses reveal abundant and valuable molecular information for target therapy, patient management, genetic counseling, and new insights of possible pathogenic mechanism Citation Format: Hongzheng Dai, Xia Tian, Stella Chen, Yue Wang, Tzu-Wei Yang, Chun-Che Lin, Ming-Chang Tsai, Chih-Hong Wang, Chi-Chou Huang, Chin-Ying Shih, Guang-Yuh Chiou, Yuh-Jyh Jong, Lee-Jun Wong. Powerful target capture/NGS approach reveals extensive genetic changes including SNVs, CNVs and gross chromosomal rearrangements in colorectal cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3171.

Highlights 2014 on glycoscience; glycosyltransferases and glycobiomarkers.

The field of glycobiology has continued to grow and mature, establishing the role of glycans in a myriad of biological processes. Many new functions of glycans have emerged from studies on different eukaryotic and prokaryotic organisms. The development of new analytical tools and techniques have fuelled the generation of a lot of information on the structure of glycans, factors determining their structure and their derangement in several pathological conditions. One of the major themes of the recently held International Symposium on Carbohydrates in Bangalore, India was glycoconjugates and glycobiology, in which scientists working at the forefront of research in these areas reported their findings on different aspects of glycans in physiology and pathology. Selected contributions from these sessions are presented in this special issue of the journal. These contributions comprise short critical reviews or original research papers focusing on (a) glycosyl transferases in physiology and pathology (b) glycobiomarkers and (c) structural analysis of glycans. Critical information embedded within the oligosaccharides on the glycoconjugates as represented by the structural features of the glycans are important in specific biological processes however alterations in glycan structures occur during development of diseases such as cancer. Glycosyl transferases, which constitute a large family of enzymes displaying exquisite specificity for both glycosyl donor and the acceptor, are largely responsible for glycosyl transfer reactions that generate a diversity of glycan structures on glycoconjugates. Many substances including natural compounds are known to affect the activity of these enzymes, making them potential drug targets. At least six articles in the ensuing pages describe the biological importance and features of glycosyl transferases. These include data relating to (a) resiliency to mutagenicity of glycosyltransferases involved in bloodgroup antigen synthesis (b) role of O-linked glycans and protein –O-glycosylation in protein folding (c) microbial cell wall biosynthesis as well as formation of GPI anchors (d) characterisation of glycosyltransferases from new sources (e) glycosyl transferasebased assays to demonstrate glycan changes in cancer tissues. A number of changes can occur in glycan expression during the development of pathological conditions. Identification and validation of these glycan changes in disease conditions make them useful surrogate markers for the disease or drug response. A strategy for developing glycobiomarkers for disease has been described in one of the contributions while another paper reports the potential of 9-O-acylated sialic acids in differentiating normal haematopoietic stem cells from leukemic stem cells. Further, changes in cell surface proteoglycans in tumor cells and the potential of cell surface molecules such as receptor for advanced glycation end-products in recognising such molecules and development of glycomimetics based on these, have been discussed. P. R. Sudhakaran (*) Department of Computational Biology and Bioinformatics, University of Kerala, Karyavattom, Trivandrum, Kerala, India e-mail: prslab@gmail.com

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Motivation: High-throughput data is providing a comprehensive view of the molecular changes in cancer tissues. New technologies allow for the simultaneous genome-wide assay of the state of genome copy number variation, gene expression, DNA methylation and epigenetics of tumor samples and cancer cell lines.Analyses of current data sets find that genetic alterations between patients can differ but often involve common pathways. It is therefore critical to identify relevant pathways involved in cancer progression and detect how they are altered in different patients.Results: We present a novel method for inferring patient-specific genetic activities incorporating curated pathway interactions among genes. A gene is modeled by a factor graph as a set of interconnected variables encoding the expression and known activity of a gene and its products, allowing the incorporation of many types of omic data as evidence. The method predicts the degree to which a pathway's activities (e.g. internal gene states, interactions or high-level ‘outputs’) are altered in the patient using probabilistic inference.Compared with a competing pathway activity inference approach called SPIA, our method identifies altered activities in cancer-related pathways with fewer false-positives in both a glioblastoma multiform (GBM) and a breast cancer dataset. PARADIGM identified consistent pathway-level activities for subsets of the GBM patients that are overlooked when genes are considered in isolation. Further, grouping GBM patients based on their significant pathway perturbations divides them into clinically-relevant subgroups having significantly different survival outcomes. These findings suggest that therapeutics might be chosen that target genes at critical points in the commonly perturbed pathway(s) of a group of patients.Availability:Source code available at http://sbenz.github.com/ParadigmContact: jstuart@soe.ucsc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Changes in cancer tissue induced by treatment with bevacizumab in metastatic breast cancer.

1134 Background: Bevacizumab in combination with several cytotoxic chemotherapy option has recently emerged as a standard treatment of HER2-negative metastatic breast cancer. This study tries to identify molecular changes induced by treatment with bevacizumab. Methods: 19 patients with metastatic breast cancer were biopsied (only skin, lymph node, breast tumor biopsies were allowed) on day 0 and 15 days after a single administration of bevacizumab (10mg/kg intravenously infused over 90 minutes). RNA was extracted from the tissue and the expression of genes involved in notch signaling were examined with the use of superarray technology (commercially available through Bioscience Corporation). At the same time points blood samples were drawn from the patients and were tested for the presence of CEC (circulating endothelial cells) with FACS and angiogenic factors with ELISA. Patients enrolled had a PS of 0-1, adequate liver and kidney function and no contraindications for the use of bevacizumab. Results: Although expression of Notch receptors was not altered with a single dose of bevacizumab, increased expression of Notch target genes such as Hey1 and Hey2 was observed. Expression of Jag-2, ADAM-10, ADAM-17, and HOXB4 was also increased. The levels of VEGF increased but CEC and PDGF levels showed mixed responses. Analysis of the results is ongoing. Conclusions: Increased expression of Notch target genes may indicate activation of the Notch pathway in patients treated with bevacizumab. No significant financial relationships to disclose.

Alterations of O-glycan biosynthesis in human colon cancer tissues.

Human colon cancer is associated with antigenic and structural changes in mucin-type carbohydrate chains (O-glycans). To elucidate the control of the biosynthesis of these O-glycans is colon cancer, we have studied glycosyltransferase and sulphotransferase activities involved in the assembly of elongated O-glycan structures. We analysed homogenates prepared from cancer tissue, adjacent normal and distal normal tissue from 20 patients. Several transferase activities showed pronounced changes in cancer tissue. The changes correlate with previous findings of a loss of O-glycans in cancer mucins, but did not always correlate with levels of Tn, sialyl-Tn, T and Lex antigens in homogenates or with the differentiation status and Duke's stages of the cancer tissue or the patient's blood type, sex and age. UDP-GlcNAc: Gal NAc-R beta 3-N-acetylglucosaminyltransferase (where GlcNAc is N-acetyl-D-glucosamine and GalNAc is N-acetyl-D-galactosamine) synthesizing O-glycan core 3, GlcNAc beta 1-3GalNAc-, CMP-sialic acid: GalNAc-peptide alpha 6-sialyltransferase synthesizing the sialyl-Tn antigen and sulphotransferase activities towards O-glycan core 1, Gal beta 1-3GalNAc-, were found to be decreased in cancer. UDP-GlcNAc: Gal beta 1-3GalNAc beta 6-N-acetylglucosaminyltransferase was also decreased in cancer concomitant with a loss of the ability to synthesize the I antigen and core 4, GlcNAc beta 1-6(GlcNAc beta 1-3) GalNAc-, CMP-sialic acid: Gal beta 1-3GalNAc-R alpha 3-sialyltransferase and GDP-fucose: Gal beta-R alpha 2-fucosyltransferase, synthesizing the blood group H determinant, were found to be 4- and 3- to 8-fold increased, respectively, in cancer compared to normal tissue. The data suggest that the biosynthesis of antigens and mucin-bound O-glycan structures in colon cancer is subject to complex control mechanisms.