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Patients with adenomatous polyposis syndromes such as familial adenomatous polyposis are at higher risk of colorectal cancer, hence continuous management is necessary. However, little is known about the etiology of patients with numerous laterally spreading tumors (LSTs), or how genetic alterations uniquely influence LSTs in colorectal carcinogenesis. The present case report investigated a woman with >150 non-granular type LSTs (LST-NG) and one sigmoid colon cancer. After subtotal colectomy via ileorectal anastomosis, genetic and epigenetic analyses were conducted by comparing the profiles of the patient's normal colonic mucosa, four LST-NG lesions and a cancer lesion. Using customized multigene panel testing, no pathogenic germline mutations were detected, including APC regulator of WNT signaling pathway, but identified a somatic pathogenic variant of APC in one LST-NG lesion, and both TP53 and F-box and WD repeat domain containing 7 somatic mutations in the cancer. Comprehensive genome-wide methylation analysis showed that CpG island promoters at zinc finger protein 625, LON peptidase N-terminal domain and ring finger 2, WD repeat domain 17 and syndecan 2 were methylated in both LST-NG and cancer, which may contribute to colorectal tumorigenesis as early as the LST-NG phase. [ABSTRACT FROM AUTHOR]

Abstract: Background: To investigate relationships between phenotypes and genotypes is not simple. We propose a phenotype-to-genotype screening strategy and pooled DNA system. As a pilot study of this strategy, we used arbitrarily primed polymerase chain reaction (AP-PCR) in combination with single-stranded DNA conformation polymorphism (SSCP) to screen for genetic polymorphisms associated with longevity. Methods: Study subjects were separated into 3 age groups, individuals aged >100 years, 90–99 years and 60–69 years. Genomic DNAs were prepared from each individual, pooled to represent the 5 study groups, and then the pooled genomic DNAs were subjected to AP-PCR-SSCP analysis. Results: We found 1 SNP more frequently in senior citizens with longevity. The genotype frequency of the 82133G>A polymorphism of human chromosome 3 clone RP11-61K12 (AC011199) differed significantly (P=0.0189, Fisher''s exact test) between older subjects (>90 years) and younger subjects (<70 years). It is noteworthy that the strategy we describe herein was useful for identifying an SNP that showed statistically significant differences in its distribution across the subject groups. Conclusions: The pooled DNA strategy and quantitative genotype discrimination can also be applied to screening for the relationship between phenotype and genotype more effectively. [Copyright &y& Elsevier]

SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert ® System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents.

Aims: In recent years, aberrant DNA methylation of specific CpG sites has been detected in many types of malignant tumors, and the epigenetic regulation of promoter CpG sites is considered an important mechanism underlying carcinogenesis. This study aimed to establish the epigenetics of the malignant transformation of malignant pheochromocytoma (PCC) and paraganglioma (PGL) by performing a methylation analysis., Materials and Methods: Based on the results of the Infinium HumanMethylation450 BeadChip array using DNA samples of PCC/PGL patients, candidate CpG sites that were hyper/hypo-methylated in metastatic tumors relative to those in the primary tumors of 2 patients with malignant PCC/PGL were selected. The methylation levels of the chosen candidate CpG sites were evaluated quantitatively., Results: Twelve CpG sites were selected as hypermethylated candidates, and 16 CpG sites were selected as hypomethylated candidates. Using two quantitative methylation analysis methods, one hypermethylated site (cg02119938) and one hypomethylated site (cg26870725) remained as candidates. These sites were related to ACSBG1 (acyl-CoA synthetase bubblegum family member 1) and MAST1 (microtubule-associated serine-threonine kinase 1), respectively. Immunohistochemical studies of ACSBG1 and MAST1 revealed that epigenetic changes in the malignant transformation of PCC/PGL might be associated with ACSBG1 silencing or MAST1 overexpression., Conclusions: Here, we report two noteworthy genes, ACSBG1 and MAST1 ; the aberrant promoter methylation/demethylation of these genes might be involved in their silencing/expression in malignant PCC/PGL. Further investigations are necessary to determine the role of ACSBG1 and/or MAST1 expression in malignant transformation and to establish pathological markers that can evaluate the malignant potential of PCC/PGL.

A next-generation DNA microarray system, FD10 has been developed. It is based around the PamChip, a custom-made microarray, which consists of a solid three-dimensional structure that facilitated the incorporation of probe molecules. We applied this microarray system on a detection of K-ras mutation at codon 12 in some cancer cell lines. The PCR products amplified by use of FITC labeled primers were applied onto probe-absorbed microarray. After hybridization, the signal was imaged by CCD camera and analyzed by the exclusive software. We confirmed the microarray results by PCR-SSCP and sequencing analyses. Ten, two and three out of 15 cell lines were homozygous for wild type allele, heterozygous for wild and mutant allele, and homozygous for mutant alleles, respectively. Signals hybridized with antisense probes were stronger than those with sense probes, without PSN1 cell line. The system had a good reproducibility. Essentially, the microarray results were consistent with PCR-SSCP and sequencing results. In conclusion, the FD10 microarray system was easy to operate and short to get results. It might be useful for a focused array applicable for specific purposes. The K-ras mutation detection system worked well and will be applied to clinical specimens soon.