Copy Number Alterations in Hepatoblastoma: Literature Review and a Brazilian Cohort Analysis Highlight New Biological Pathways

Hepatoblastoma (HB) is a rare embryonal tumor, although it is the most common pediatric liver cancer. The aim of this study was to provide an accurate cytogenomic profile of this type of cancer, for which information in cancer databases is lacking. We performed an extensive literature review of cytogenetic studies on HBs disclosing that the most frequent copy number alterations (CNAs) are gains of 1q, 2/2q, 8/8q, and 20; and losses at 1p and 4q. Furthermore, the CNA profile of a Brazilian cohort of 26 HBs was obtained by array-CGH; the most recurrent CNAs were the same as shown in the literature review. Importantly, HBs from female patients, high-risk stratification tumors, tumors who developed in older patients (> 3 years at diagnosis) or from patients with metastasis and/or deceased carried a higher diversity of chromosomal alterations, specifically chromosomal losses at 1p, 4, 11q and 18q. In addition, we distinguished three major CNA profiles: no detectable CNA, few CNAs and tumors with complex genomes. Tumors with simpler genomes exhibited a significant association with the epithelial fetal subtype of HBs; in contrast, the complex genome group included three cases with epithelial embryonal histology, as well as the only HB with HCC features. A significant association of complex HB genomes was observed with older patients who developed high-risk tumors, metastasis, and deceased. Moreover, two patients with HBs exhibiting complex genomes were born with congenital anomalies. Together, these findings suggest that a high load of CNAs, mainly chromosomal losses, particularly losses at 1p and 18, increases the tendency to HB aggressiveness. Additionally, we identified six hot-spot chromosome regions most frequently affected in the entire group: 1q31.3q42.3, 2q23.3q37.3, and 20p13p11.1 gains, besides a 5,3 Mb amplification at 2q24.2q24.3, and losses at 1p36.33p35.1, 4p14 and 4q21.22q25. An in-silico analysis using the genes mapped to these six regions revealed several enriched biological pathways such as ERK Signaling, MicroRNAs in Cancer, and the PI3K-Akt Signaling, in addition to the WNT Signaling pathway; further investigation is required to evaluate if disturbances of these pathways can contribute to HB tumorigenesis. The analyzed gene set was found to be associated with neoplasms, abnormalities of metabolism/homeostasis and liver morphology, as well as abnormal embryonic development and cytokine secretion. In conclusion, we have provided a comprehensive characterization of the spectrum of chromosomal alterations reported in HBs and identified specific genomic regions recurrently altered in a Brazilian HB group, pointing to new biological pathways, and relevant clinical associations.

Hematopoietic mosaic chromosomal alterations in the New England Centenarian Study

Mosaic chromosomal alterations (mCAs) are structural alterations that include deletions, duplications, or copy-neutral loss of heterozygosity. mCAs are reported to be associated with survival, age, cancer, and cardiovascular disease. Previous studies of mCAs in large population-based cohorts (UK Biobank, MGBB, BioBank Japan, and FinnGen) have demonstrated a steady increase of mCAs as people age. The distribution of mCAs in centenarians and their offspring is not well characterized. We applied MOsaic CHromosomal Alteration (MoChA) caller on 2298 genome-wide genotype samples of 1582 centenarians, 443 centenarians’ offspring, and 273 unrelated controls from the New England Centenarian Study (NECS). Integrating Log R ratio and B-allele frequency (BAF) intensities with genotype phase information, MoChA employs a Hidden Markov Model to detect mCA-induced deviations in allelic balance at heterozygous sites consistent with genotype phase in the DNA microarray data. We analyzed mCAs spanning over 100 k base pairs, with an estimated cell fraction less than 50%, within samples with genome-wide BAF phase concordance across phased heterozygous sites less than 0.51, and with LOD score of more than 10 for the model based on BAF and genotype phase. Our analysis showed that somatic mCAs increase with older age up to approximately 102 years, but the prevalence of the subjects with mCAs tend to decrease after that age, thus suggesting that accumulation of mCAs is less prevalent in long-lived individuals. We also used Poisson regression to show that centenarians and their offspring tend to accumulate less mCA (RR = 0.63, p=0.045) compared to the controls.

Cytotoxic and genotoxic effects of the ethanolic extract from the rind of the fruit of Sterculia striata St. Hil. & Naudin / Efeitos citotóxicos e genotóxicos do extrato etanólico da casca do fruto de Sterculia striata St. Hil. & Naudin

The species Sterculia striata A. St. Hil. Naudin has been used by the population in food and in the treatment of skin conditions, mainly for the treatment of boils. Recently, for this species has also been attributed an antioxidant, anti-inflammatory and antibacterial action. However, little is known about its cytogenotoxic potential. The present work aimed to evaluate the cytotoxic and genotoxic effects of the ethanolic extract from the rind of the fruit of Sterculia striata A. St. Hil. Naudin. Phytochemical analysis of the ethanolic extract was performed to determine the presence of secondary metabolites. Concentrations ranging from 0.1 to 1000 µg/ml of the ethanolic extract from the rind of the fruit Sterculia striata were tested for toxicity and cytotoxicity, by the Artemia salina bioassay and the MTT test, respectively. For the genotoxicity analysis, the Allium cepa test was used, at concentrations from 9 to 1000 µg/ml of the extract. All data were analyzed and compared to controls. The statistical test of analysis of variance (ANOVA with a fixed factor) was used, followed by Tukey's multiple comparisons test, for p0.05. Phytochemical screening revealed the presence of tannins, flavonones, flavonols, saponins, alkaloids, steroids and triterpenes. The results showed a decline in the survival rate at high concentrations, in the Artemia salina and MTT tests, the latter being more sensitive for presenting a significant reduction from the concentration of 81 µg/mL. As for the results obtained for the genotoxicity parameter, an increase in the number of chromosomal alterations in root cells exposed to concentrations was observed, also from 81 µg/ml, through the Allium cepa test. The main chromosomal alterations verified were delays, bridges and breaks, in metaphase and anaphase. Taken together, it can be concluded that the ethanolic extract of the rind of the fruit of Sterculia striata A. St. Hil. Naudin exhibits cytotoxic and genotoxic effects mainly at higher concentrations.

CINmetrics: An R package for chromosomal instability analysis

Genomic instability has been an important hallmark in cancer and more recently in neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple Chromosomal Instability Scores developed across many studies in the literature; however, these scores have not been compared because of a lack of single tool available to calculate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also show how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). Availability: The package is available on CRAN at https://cran.r-project.org/package=CINmetrics and on github at https://github.com/lasseignelab/CINmetrics

Incident disease associations with mosaic chromosomal alterations on autosomes, X and Y chromosomes: insights from a phenome-wide association study in the UK Biobank

Background Mosaic chromosomal alterations (mCAs) are large chromosomal gains, losses and copy-neutral losses of heterozygosity (LOH) in peripheral leukocytes. While many individuals with detectable mCAs have no notable adverse outcomes, mCA-associated gene dosage alterations as well as clonal expansion of mutated leukocyte clones could increase susceptibility to disease. Results We performed a phenome-wide association study (PheWAS) using existing data from 482,396 UK Biobank (UKBB) participants to investigate potential associations between mCAs and incident disease. Of the 1290 ICD codes we examined, our adjusted analysis identified a total of 50 incident disease outcomes associated with mCAs at PheWAS significance levels. We observed striking differences in the diseases associated with each type of alteration, with autosomal mCAs most associated with increased hematologic malignancies, incident infections and possibly cancer therapy-related conditions. Alterations of chromosome X were associated with increased lymphoid leukemia risk and, mCAs of chromosome Y were linked to potential reduced metabolic disease risk. Conclusions Our findings demonstrate that a wide range of diseases are potential sequelae of mCAs and highlight the critical importance of careful covariate adjustment in mCA disease association studies.

Chemical composition, phytotoxicity and cytogenotoxicity of essential oil from leaves of Psidium guajava L. cultivars

Natural products with biological activity, such as essential oils, can be used in the search for and development of ecological herbicides as an alternative to reduce the damage caused by synthetic herbicides. This work to aimed to determine the chemical composition and phytotoxic properties of the essential oils, at concentrations of 3000, 1500, 750, 375 and 187.5 µg/mL, of four cultivars of Psidium guajava (guava) evaluated on germination and root growth of plant models Lactuca sativa and Sorghum bicolor, as well as in the L. sativa cell cycle. Exposure to essential oils reduced germination and root growth in bioassays, especially at the highest concentration (3000 µg/mL). The essential oils interfered in the normal dynamics of the cell cycle of L. sativa at most concentrations, causing a decrease in the mitotic index and increasing of chromosomal alterations, evidencing aneugenic and clastogenic action. The biological activity of the oils was associated with the presence of sesquiterpenes and monoterpenes found here, such as caryophyllene oxide, (E) -caryophyllene, and limonene. Thus, the essential oils of cultivars of guava demonstrated the promising potential for use as natural herbicides.

Next Generation Cytogenetics in Myeloid Hematological Neoplasms: Detection of CNVs and Translocations

Conventional cytogenetics are the gold standard for the identification of chromosomal alterations recurrent in myeloid neoplasms. Some next-generation sequencing (NGS) panels are designed for the detection of copy number variations (CNV) or translocations; however, their use is far from being widespread. Here we report on the results of a commercial panel including frequent mutations, CNVs and translocations in myeloid neoplasms. Frequent chromosomal alterations were analyzed by NGS in 135 patients with myeloid neoplasms and three with acute lymphoblastic leukemia. NGS analysis was performed using the enrichment-capture Myeloid Neoplasm-GeneSGKit (Sistemas Genómicos, Spain) gene panel including 35 genes for mutational analysis and frequent CNVs and translocations. NGS results were validated with cytogenetics and/or MLPA when possible. A total of 66 frequent alterations included in NGS panel were detected, 48 of them detected by NGS and cytogenetics. Ten of them were observed only by cytogenetics (mainly trisomy 8), and another eight only by NGS (mainly deletion of 12p). Aside from this, 38 secondary CNVs were detected in any of the genes included mainly for mutational analysis. NGS represents a reliable complementary source of information for the analysis of CNVs and translocations. Moreover, NGS could be a useful tool for the detection of alterations not observed by conventional cytogenetics.

Genetic variant in SPDL1 reveals novel mechanism linking pulmonary fibrosis risk and cancer protection

Idiopathic Pulmonary Fibrosis (IPF) is a rare disease with poor prognosis. By contrast, cancer is common in any elderly population and a leading killer, but is now often curable. Of note, whereas IPF is driven by cellular senescence, cancer is characterized by uncontrolled cell division. Using data available from two large biobank-based studies (Finnish FinnGen study and UK biobank), we conducted a comprehensive analysis of the shared genetic background of IPF and cancer. In a population sample of 218,792 Finns with complete longitudinal health histories, we estimated the effect of individual genetic variants to the lifetime risk of IPF and cancer. We extend the analysis from IPF-GWAS to pan-cancer meta-analysis over FinnGen and UK Biobank and finally to the identification of genetic drivers of somatic chromosomal alterations. We detected six loci (SPDL1, MAD1L1, MAP2K1, RTEL1-STMN3, TERC-ACTRT3, OBFC1) associated with both IPF and cancer, all closely related to cellular division. However, each individual signal is found with opposite effects over the two diseases, termed as antagonistic pleiotropy. Several of these loci (TERC-ACTRT3, RTEL1-STMN3, OBFC1) are among the strongest inherited factors for constitutive telomere length variation and consistently indicate that shorter telomere length would increase the risk for IPF but protect from malignancy. However, a Finnish enriched SPDL1 missense variant and a common MAD1L1 intronic variant had no effect on telomere length but were shown to protect individuals from accumulation of somatic mutations. The decreased risk of cancer in SPDL1 and MAD1L1 variant carriers might result from a lower number of chromosomal alterations accumulated over time, conversely leading to fibrosis in the lung due to cellular senescence-induced inflammation. We hypothesize that the SPDL1 missense variant functions as gain-of-function mutation, leading to cellular senescence, a barrier to cancer and a driver of fibrosis in IPF. If translated to therapy, these findings might not only be able to offer relief to individuals with IPF, but also to protect from onset of cancer.