Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

<p>Abstract</p> <p>Background</p> <p>It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of <it>HER2 </it>and <it>C-MYC </it>oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH).</p> <p>Methods</p> <p>Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested.</p> <p>Results</p> <p>The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for <it>HER2 </it>gene amplification was 88%. The incidence of <it>HER2 </it>amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers.</p> <p>Conclusions</p> <p>Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A-bomb radiation may affect the increased amount of CNA as a hallmark of GIN and, subsequently, be associated with a higher histologic grade in breast cancer found in A-bomb survivors.</p

Evidence for Association of the rs17822931-A Allele in ABCC11 with a Decreased Risk of Estrogen Receptor-negative Breast Cancer

The rs17822931 SNP of the human ABCC11 gene determines earwax types, and is also associated with some functions of apocrine glands, including the mammary gland. Nevertheless, whether the ABCC11 polymorphism is correlated with estrogen receptor (ER) status of breast cancer (BC) remains unclear. To investigate the correlation between rs17822931 and BC, we screened the genotypes in a total of 276 and 295 histological BC samples collected from Japanese and Ukrainian BC patients, and 269 and 264 ethnically-matched healthy individuals, respectively, using TaqManTM PCR. Genotype frequencies at rs178229131 in Japanese and Ukrainian BC patients were not significantly different from those in their respective control populations. Consistently, no correlation between rs178229131 and the susceptibility to BC was found. The AA genotype, which corresponds to dry earwax, occurred less frequently in ER -negative BC in Japanese [odds ratio, 0.48; 95% confidential interval, 0.29-0.80] but not in Ukrainian patients although a similar correlation was weakly observed. Our results indicate that the rs178229131-A allele may be important in reducing the risk of ER -negative BC development

Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

忘れられた作物「えどどころ」の起原 --ゲノム解析が明らかにする青森県三八上北地域に残る栽培イモの歴史--. 京都大学プレスリリース. 2022-08-10.A rhizomatous Dioscorea crop “Edo-dokoro” was described in old records of Japan, but its botanical identify has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of Aomori Prefecture, Japan. Rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, D. tokoro and D. tenuipes. Genome analysis revealed that Edo-dokoro is likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten from the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information

A Novel Diagnostic Method for Thyroid Follicular Tumors Based on Immunofluorescence Analysis of p53-Binding Protein 1 Expression: Detection of Genomic Instability

The preoperative diagnosis of thyroid follicular carcinomas (FCs) by fine-needle aspiration cytology is almost impossible. It was previously demonstrated that p53-binding protein 1 (53BP1) expression, based on immunofluorescence (IF),can serve as a valuable biomarker to estimate the malignant potential of various cancers. 53BP1 belongs to a class of DNA damage response molecules that rapidly localize to the site of DNA double-strand breaks,forming nuclear foci (NF). This study aimed to elucidate the utility of 53BP1 NF expression as a biomarker to differentiate follicular tumors (FTs). Methods: Associations between 53BP1 expression based on IF and histological types of FTs were analyzed using 27 follicular adenomas (FAs), 28 minimally invasive FCs, and 14 widely invasive FCs. Furthermore, the study clarified the relationship between 53BP1 NF and copy number aberrations (CNAs) based on array comparative genomic hybridization, a hallmark of genomic instability (GIN). Results: This study demonstrates differences in 53BP1 NF expression between FA and FC. The incidence of 53BP1 at NF significantly increased with FT progression in the following order: normal follicle < FA < minimally invasive FCs< widely invasive FCs. In contrast, no significant differences were observed in CNAs among the FT samples. Furthermore, there was no significant correlation between CNAs and 53BP1 at NF in FTs. Thus, based on a comparison of these two indicators of GIN, 53BP1 NF (by IF) was better able to estimate the malignancy of FTs compared to CNA (by array comparative genomic hybridization). Interestingly, IF revealed a heterogenous distribution of 53BP1 NF,which occurred more frequently in the invasive or subcapsular area than in the center of the tumor, suggesting intratumoral heterogeneity of GIN in FTs. Conclusions: It is proposed that IF analysis of 53BP1 expression could be a novel diagnostic method to estimate the malignant potential of FTs. Because 53BP1 NF reflect DNA double-strand breaks, it is hypothesized that the incidence of 53BP1 at NF can represent the level of GIN in tumor cells. IF analysis of 53BP1 expression will not only be　an auxiliary histologic technique to diagnose FTs accurately, but also a novel technique for preoperative diagnosis　using fine-needle aspiration cytology

Intracystic Papillary Carcinoma of Breast Harbors Significant Genomic Alteration Compared with Intracystic Papilloma: Genome-wide Copy Number and LOH Analysis Using High-Density Single-Nucleotide Polymorphism Microarrays.

Purpose: Intracystic papillary breast tumors consist of benign papilloma, carcinoma in situ and carcinoma with invasion. Using high-density single-nucleotide polymorphism arrays, this study aimed to determine the profile of genomic alterations in these lesions and to identify novel diagnostic criteria. Methods: Ten samples of intracystic papillary tumor, which included five papillomas (Pap), three papillary carcinomas in situ (PurePC) and two papillary carcinomas with invasion (PCinv), were studied. DNA was extracted from tumor and normal tissues that were microdissected from the same formalin-fixed paraffin embedded blocks. Using probe intensity and genotype data from high-density oligonucleotide SNP microarrays (AffymetrixR GeneChip Genome-wide Human 5.0), paired copy number and LOH analysis was performed using Partek Genomic Suite Software. Results: Quality control (QC) call rate, which is an index measuring the quality of a SNP microarray experiment, ranged from 70.75% to 91.93%, mean 80.72%. The mean total genomic alteration rate (sum of amplifications, deletions and copy-neutral loss of heterogeneity) with respect to the whole genome was 2.87%, 15.4% and 35.3% in Pap, PC and IDC, respectively, and was significantly different between samples (Kruskal-Wallis chi-squared test, p = 0.043). The most commonly altered regions (. 4/5) in papillary carcinoma were copy-neutral loss of heterogeneity at 3p21.31 and 3p14.2 and amplification at 20q13.13. Genes altered only in invasive carcinoma included genes concerned with transcription. Conclusions: Among intracystic papillary breast tumors, malignant tumors, including non-invasive tumors, which are difficult to diagnose histopathologically, harbor significant genomic alteration. Our findings may aid clinical management of these tumors and may provide insight into their carcinogenesis

Familial brain arteriovenous malformation maps to 5p13-q14, 15q11-q13 or 18p11: linkage analysis with clipped fingernail DNA on high-density SNP array.

Familial arteriovenous malformations (AVM) in the brain is a very rare disease. It is defined as its occurrence in two or more relatives (up to third-degree relatives) in a family without any associated disorders, such as hereditary hemorrhagic telangiectasia. We encountered a Japanese family with brain AVM in which four affected members in four successive generations were observed. One DNA sample extracted from leukocytes of the proband and ten DNA samples from clipped finger nails of other members were available. A genome-wide linkage analysis was performed on this pedigree using Affymetrix GeneCip 10K 2.0 Xba Array and MERLIN software. We obtained sufficient performance of SNP genotyping in the fingernail samples with the mean SNP call rate of 92.49%, and identified 18 regions with positive LOD scores. Haplotype and linkage analyses with microsatellite markers at these regions confirmed three possible disease-responsible regions, i.e., 5p13.2-q14.1, 15q11.2-q13.1 and 18p11.32-p11.22. Sequence analysis was conducted for ten selected candidate genes at 5p13.2-q14.1, such as MAP3K1, DAB2, OCLN, FGF10, ESM1, ITGA1, ITGA2, EGFLAM, ERBB2IP, and PIK3R1, but no causative genetic alteration was detected. This is the first experience of adoption of fingernail DNA to genome-wide, high-density SNP microarray analysis, showing candidate brain AVM susceptible regions

A Predictive Factor of the Quality of Microarray Comparative Genomic Hybridization Analysis for Formalin-fixed Paraffin-embedded Archival Tissue

Utilizing formalin-fixed paraffin-embedded (FFPE) archival tissue, the most common form of tissue preservation in routine practice, for cytogenetic analysis using microarray comparative genomic hybridization (aCGH) remains challenging. We searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types (31 breast cancers, 24 lung cancers, and 8 thyroid tumors), followed by aCGH analysis using high-density oligonucleotide microarrays. Tumor DNA from matched frozen samples and from FFPE samples after whole-genome amplification were also analyzed in 2 and 4 case, respectively. The derivative log ratio spread (DLRSpread) was used to assess the overall quality of each aCGH result. The DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5 (P<0.0001; correlation coefficients=-0.796, 0.551, -0.481, respectively). Stepwise multiple linear regression analysis revealed that the double-stranded DNA ratio of tumor DNA is the most significant predictive factor of DLRSpread (regression coefficient=-0.4798; P=<0.0001). The cytogenetic profiles of FFPE and matched frozen samples showed good concordance. Although the double-stranded DNA ratios were increased after whole-genome amplification, the DLRSpread was not improved. The double-stranded DNA ratio can be used to predict the performance of aCGH analysis for DNA from FFPE samples. Using this quality metric, valuable FFPE archival tissue samples can be utilized for aCGH analysis

Vascular transection using endovascular stapling in hepatic resection

In anatomical resection of the liver, transection of the hepatic vein or Glisson\u27s pedicle is necessary. We examined the surgical records and outcome of 25 patients who underwent hepatectomy. An endovascular stapler with 36 and 60 mm staples was used for transection of the hepatic vein or Glisson\u27s pedicle, and hepatic parenchyma including vessels. Surgery included also left lateral sectorectomy in 6 patients, right lateral sectorectomy in one, right hepatectomy in 12, left hepatectomy in two and trisegraenteetomy in 4. Endovascular stapling was used for transection of hepatic veins (n=25) in all patients and Glisson\u27s pedicle (n=8). No failure of firing occurred during cutting. Injury of an aberrant bile duct occurred in one patient, but none suffered bleeding or bile leakage from the transected parts. Vascular transection using vascular stapler could be performed safely and rapidly during anatomical hepatic resection

Successful Colectomy for Hemorrhagic Colitis with Hemolytic Uremic Syndrome and Acute Encephalopathy due to Escherichia coli O157 Infection

An 81-year-old man was admitted to a primary care hospital due to bloody diarrhea. The findings of abdominal computed tomography indicated ischemic colitis, so conservative therapy was started. On the 4th hospital day, the patient was transferred to our hospital because of renal dysfunction. Physical examination showed clouding of consciousness and abdominal distention. Abdominal computed tomography revealed massive ascites and thickening of the whole colonic wall. With a diagnosis of acute abdomen, an emergent laparotomy was performed. Extended right hemicolectomy was performed because of severe ischemic change and necrosis of the right side of the colon. In the stool culture before the operation, Escherichia coli O157 and verotoxin were found, so this case was diagnosed as hemorrhagic colitis with hemolytic uremic syndrome and acute encephalopathy due to Escherichia coli O157 infection. Postoperatively, the hemolytic uremic syndrome and acute encephalopathy were prolonged. However, with intensive care, the patient recovered and was discharged on the 33rd postoperative day