Alterations In Normal Tissues Research Articles

Methylation of PCDH17 and NEFH as prognostic biomarker for nonmetastatic RCC: A cohort study.

DNA methylation makes up a main part of the molecular mechanism of cancer evolution and has shown promising results in the prognosis of renal cell cancer (RCC). In this study, we investigated the possible association of promoter methylation of PCDH17, NEFH, RASSF1A, and FHIT, genes with the prognosis of nonmetastatic RCC patients. Cancerous and normal adjacent tissues from surgical specimens of 41 patients with long follow-up were treated for DNA isolation and bisulfite conversion. The gene promoter methylation was determined with quantitative methylation-specific PCR (qMSP). Wilcoxon signed-rank test was used for paired methylation comparisons, while univariate linear regression and Mann-Whitney test were applied for associating methylation status with clinical and disease characteristics. Cox regression proportional hazards models and Kaplan-Meier plots were used for survival analyses in reference to methylation status. Paired comparisons showed tissue-specific hypermethylation for PCDH17 (P < .001), NEFH (P < .001), RASSF1A (P = .032), while a positive association of methylation in normal tissues with age was demonstrated for PCDH17 (P < .001), RASSF1A (P < .001), FHIT (P < .001). PCDH17 was more methylated in cases with clear cell RCC (P = .015) and high-grade tumor (P = .013), while NEFH methylation was higher in locally advanced cases (P = .032). PCDH17 hypermethylation in cancerous and normal tissues was linked to shorter disease-specific survival (DSS, P = .026, P = .004), disease-free survival (DFS, P = .004, P = .019) while NEFH hypermethylation in cancerous tissues was related to shorter DSS (P = .032). Increased methylation difference of NEFH was also associated with shorter DSS (P = .041) and DFS (P = .020), while the corresponding parameter for PCDH17 was associated with poor DFS (P = .014). Kaplan-Meier curves for hypermethylation in cancer tissues demonstrated different clinical courses for PCDH17 (P = .017), NEFH (P = .023) regarding DSS, and PCDH17 (P = .001) regarding DFS. Our study not only highlights the prognostic value of promoter methylation of PCDH17 and NEFH in cancer tissues but also is the first report of the prognostic value of methylation alterations in normal tissues. Our findings are the first report of the prognostic value of methylation alterations in normal tissues, which can contribute to improved assessment of recurrence risk.

DNA Methylation in Ovarian Cancer Susceptibility.

Simple SummaryIt is well established that ovarian cancer “runs in families”, where ovarian and other cancers (commonly breast cancer) occur at early ages at onset and in multiple generations. After decades of genetic studies, rare high-risk genetic mutations in cancer susceptibility genes and over 40 common genetic variants with much smaller risks have been identified. However, based on familial studies, we know that additional heritable genetic risk factors exist. It is possible that epigenetic variation—differences in how DNA is read, and which genes are actively expressed (or not) —also contributes to ovarian cancer susceptibility. This review summarizes the current collection of epidemiological studies that have investigated the role of DNA methylation—one type of epigenetic mechanism—in the risk of ovarian cancer.Epigenetic alterations are somatically acquired over the lifetime and during neoplastic transformation but may also be inherited as widespread ‘constitutional’ alterations in normal tissues that can cause cancer predisposition. Epithelial ovarian cancer (EOC) has an established genetic susceptibility and mounting epidemiological evidence demonstrates that DNA methylation (DNAm) intermediates as well as independently contributes to risk. Targeted studies of known EOC susceptibility genes (CSGs) indicate rare, constitutional BRCA1 promoter methylation increases familial and sporadic EOC risk. Blood-based epigenome-wide association studies (EWAS) for EOC have detected a total of 2846 differentially methylated probes (DMPs) with 71 genes replicated across studies despite significant heterogeneity. While EWAS detect both symptomatic and etiologic DMPs, adjustments and analytic techniques may enrich risk associations, as evidenced by the detection of dysregulated methylation of BNC2—a known CSG identified by genome-wide associations studies (GWAS). Integrative genetic–epigenetic approaches have mapped methylation quantitative trait loci (meQTL) to EOC risk, revealing DNAm variations that are associated with nine GWAS loci and, further, one novel risk locus. Increasing efforts to mapping epigenome variation across populations and cell types will be key to decoding both the genomic and epigenomic causal pathways to EOC.

Genetic and epigenetic alterations in normal tissues have differential impacts on cancer risk among tissues

Genetic and epigenetic alterations are both involved in carcinogenesis, and their low-level accumulation in normal tissues constitutes cancer risk. However, their relative importance has never been examined, as measurement of low-level mutations has been difficult. Here, we measured low-level accumulations of genetic and epigenetic alterations in normal tissues with low, intermediate, and high cancer risk and analyzed their relative effects on cancer risk in the esophagus and stomach. Accumulation of genetic alterations, estimated as a frequency of rare base substitution mutations, significantly increased according to cancer risk in esophageal mucosae, but not in gastric mucosae. The mutation patterns reflected the exposure to lifestyle risk factors. In contrast, the accumulation of epigenetic alterations, measured as DNA methylation levels of marker genes, significantly increased according to cancer risk in both tissues. Patients with cancer (high-risk individuals) were precisely discriminated from healthy individuals with exposure to risk factors (intermediate-risk individuals) by a combination of alterations in the esophagus (odds ratio, 18.2; 95% confidence interval, 3.69-89.9) and by only epigenetic alterations in the stomach (odds ratio, 7.67; 95% confidence interval, 2.52-23.3). The relative importance of epigenetic alterations upon genetic alterations was 1.04 in the esophagus and 2.31 in the stomach. The differential impacts among tissues will be critically important for effective cancer prevention and precision cancer risk diagnosis.

Genomic features of normal tissues from prophylactic surgery in BRCA1/2 mutation carriers.

e13055 Background: Genomic alterations in normal tissues from pathogenic germline BRCA1/2 mutation (mut) carriers are as yet poorly described. We investigated the genomic status of normal breast (NB) and hystero-salpingo-oophorectomy (GYN) tissues removed upon prophylactic surgery in a real-life cohort of BRCA1/2 carriers. Methods: By using targeted NGS we examined the mut status of 220 samples (39 peripheral blood and 181 paraffin tissue) from 53 BRCA1/2 carriers who underwent prophylactic surgery, 42 with and 11 without prior cancer manifestation (PCM). We compared germline BRCA1/2 mut status with tumor, NB and GYN mut status. Results: Eight patients carried germline BRCA2 and 45 BRCA1 mut. Somatic mut were most frequent in BRCA2 (28%), BRCA1 (17%), TP53 (7%) among 136 NB and GYN samples; and, in TP53 (49%; p &lt; 0.001) and BRCA1 (38%; p = 0.039) among 45 tumor samples. Among all tissue types, the 85 NB had the lowest mut load (p = 0.001). In NB and GYN, mut load was higher in BRCA1 vs. BRCA2 carriers (p = 0.027) and in those with BRCA1 substitutions/indels vs. exon deleting and skipping mut (p &lt; 0.001). In tumors, only germline BRCA1 substitutions/indels were associated with higher mut load (p = 0.014). Preservation of germline mut in tissues was assessable in 84 samples from 26 patients. The germline mut was lost in 8 tumor and NB samples from 6 patients (23%) with PCM. Somatic deleterious mut in the BRCA1 BRCT-domain emerged in two such cases; the rest had combinations of TP53, MRE11A and NF1 mut. GYN samples from these patients retained the germline mut and presented the highest mut load among all examined samples (p &lt; 0.001). Conclusions: Somatic mut in normal tissues from BRCA1/2 carriers are affected by the inherited mutated gene and by the type of the germline mut concerning BRCA1. Germline BRCA1 mut may be substituted by somatic mut in tumor and normal tissues, in an organ specific manner. Mutagenesis in tumors and normal tissues appear to be driven by different pathways. Our findings shed new light on the biological impact of BRCA1/2 mut in tissues.

Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing

We present the bottleneck sequencing system (BotSeqS), a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. We use BotSeqS to show age- and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal human tissues can vary by several orders of magnitude, depending on biologic and environmental factors. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues.

Abstract NG01: Accumulation of somatic mutations in normal and cancerous tissues with age

Abstract Fundamental theories in carcinogenesis and aging evoke the accumulation of rare somatic mutations in normal tissues over time. However, absence of a simple and systematic method to characterize somatic mutations in normal tissues precludes the understanding of their functional consequences. We present Bottleneck Sequencing System (BotSeqS), a next-generation sequencing method that quantitates rare somatic point mutations simultaneously across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. Using BotSeqS, we determine the mutation frequencies and spectra in normal brain, kidney, and colon from a total of 34 individuals ranging from &amp;lt; 1 to 98 years old. We show an age and tissue-dependent accumulation of rare point mutations and demonstrate that the somatic mutational burden in normal tissues can vary by several orders of magnitude depending on biological and environmental factors. For example, individuals with defects in the mismatch repair machinery or exposure to environmental carcinogens (smoking, aristolochic acid) show significant increases in mutational frequencies and altered mutational spectra compared to controls. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, we find that the mutational spectra of normal tissues were different from each other but similar to cancers from the same tissue type, suggesting that the differential mutational spectra observed in cancers are tissue-specific rather than cancer-specific. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues. Citation Format: Margaret L. Hoang, Isaac Kinde, Cristian Tomasetti, Thomas Rosenquist, Arthur P. Grollman, Kenneth W. Kinzler, Bert Vogelstein, Nickolas Papadopoulos. Accumulation of somatic mutations in normal and cancerous tissues with age. [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 NG01.

Patterns of Somatically Acquired Amplifications and Deletions in Apparently Normal Tissues of Ovarian Cancer Patients

Little is understood about the occurrence of somatic genomic alterations in normal tissues and their significance in the context of disease. Here, we identified potential somatic copy number alterations (pSCNAs) in apparently normal ovarian tissue and peripheral blood of 423 ovarian cancer patients. There were, on average, two to four pSCNAs per sample detectable at a tissue-level resolution, although some individuals had orders of magnitude more. Accordingly, we estimated the lower bound of the rate of pSCNAs per cell division. Older individuals and BRCA mutation carriers had more pSCNAs than others. pSCNAs significantly overlapped with Alu and G-quadruplexes, and the affected genes were enriched for signaling and regulation. Some of the amplification/deletion hotspots in pan-cancer genomes were hot spots of pSCNAs in normal tissues as well, suggesting that those regions might be inherently unstable. Prevalence of pSCNA in peripheral blood predicted survival, implying that mutations in normal tissues might have consequences for cancer patients.

Multiparametric MRI for localized prostate cancer: lesion detection and staging.

Multiparametric MRI of the prostate combines high-resolution anatomic imaging with functional imaging of alterations in normal tissue caused by neoplastic transformation for the identification and characterization of in situ prostate cancer. Lesion detection relies on a systematic approach to the analysis of both anatomic and functional imaging using established criteria for the delineation of suspicious areas. Staging includes visual and functional analysis of the prostate “capsule” to determine if in situ disease is, in fact, organ-confined, as well as the evaluation of pelvic structures including lymph nodes and bones for the detection of metastasis. Although intertwined, the protocol can be optimized depending on whether lesion detection or staging is of the highest priority.

Photodynamic therapy with m-tetrahydroxyphenylchlorin in vivo: optimization of the therapeutic index.

The therapeutic index of meta-tetrahydroxyphenylchlorin-mediated photodynamic therapy (mTHPC-PDT) was assessed in BALB/c nude mice bearing human malignant mesothelioma xenografts. Equal doses of 650 nm laser light were delivered to the tumour and to an equal-sized area of the hind leg (control site) after i.p. administration of mTHPC. Twenty-one groups of 6 animals each were treated under various drug-light conditions and at drug-light intervals ranging from 4 hr to 6 days. After light delivery the extent of tumour necrosis and the depth of alterations in normal tissue were assessed by light microscopy of standardized histological sections. A therapeutic index (TI) of mTHPC-PDT was defined as the cross-sectional area of tumour necrosis per depth of visible tissue injury at the control site. This TI was strongly related to the conditions of treatment. In particular, it was increased by prolonging the drug-light interval up to 5 days and by increasing the dose of light for any dose of drug. The most profound increase of TI was obtained by increasing the intensity of light administered at the chosen interval while reducing the dose of drug. Our findings suggest that threshold conditions operate in PDT and have important implications for clinical application of the treatment.

Magnetic resonance imaging of primary intracranial tumors: A review

The experience in magnetic resonance (MR) imaging of primary intracranial neoplasia at University of California, San Francisco is reviewed. Seventy patients have been evaluated by MR and computerized tomography (CT). MR scans were performed using a multi-slice spin echo technique with a long pulse repetition time (TR = 2000 msec), and long echo sampling delay (TE = 56 msec). This method was most sensitive in differentiating normal gray and white matter and in detecting both cerebral edema and abnormal tissue with prolonged T 2 characteristics. More sensitive to slight alterations in normal tissue, MR may detect a focal lesion in cases in which CT shows only mass effect. Moreover, MR may demonstrate more thoroughly the extent of tumor infiltration and broaden the characterization of abnormal tissue. Posterior fossa and brainstem anatomy are invariably better depicted by MR. The major limitations of MR include its inability to detect foci of tumor calcification, demonstrate the severity of bone destruction, or reliably distinguish tumor nidus from surrounding edema.

Thoracic effects of therapeutic irradiation for breast carcinoma

Therapeutic irradiation produces alterations in normal tissue which, when visible on diagnostic x-ray examinations, may be confused with recurrent tumor or other unrelated conditions. Therapeutic irradiation of breast carcinoma may produce gross effects in the lungs, bone, breast, heart and great vessels, esophagus, liver, and spinal cord. The radiographic appearance of such changes is presented and contrasted with changes secondary to the malignancy itself or benign inflammatory processes. Recognition is imperative for proper management.