Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population

This study aimed to estimate A-STR mutation rates in 2,317 Korean parent-child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39-1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38-1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.

Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10^-3 per generation, with an average mutation rate of 2.17 × 10^-3 (95% CI, 1.5-3.1 × 10^-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10^-3 (95% CI, 2.3-3.7 × 10^-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.

Identification of novel SNP markers for kinship analysis in the Korean population

Kinship testing using genetic markers such as short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is crucial for forensic analysis. Although STR markers have superior discriminatory power due to their highly polymorphic properties, they have several weak points in determining extended distant or complex relationships because of high mutation rates and low success rates in degraded samples. Therefore, SNPs are regarded as promising tools in forensic science because they have low mutation rates and small amplicon sizes. Herein, we propose an SNP panel consisting of 1400 autosomal SNPs obtained from the Korean National Standard Reference Variome (KoVariome) database. To evaluate its performance, in-silico analysis was performed using whole-genome sequencing (WGS) data from 21 Korean families. Subsequently, to estimate pairwise relatedness, kinship coefficients were calculated using PLINK, and Welch's one-way ANOVA test with Games-Howell's pairwise comparison test was performed. As a result, the average kinship coefficients of first- (parent-offspring and full siblings), second- (grandparent-grandchildren and aunt/uncle-niece/nephew), and third- (first cousin and grandniece/grandnephew) degree relatives, and unrelated were 0.24, 0.11, - 0.054, and - 0.0082, respectively. Consequently, relatives (first and second degree) were distinguished from non-relatives; however, further studies are required to investigate more effective SNP markers for discriminating extended kinship. Nevertheless, the results of this study go beyond the scope of screening using the discovered 1400 SNPs in Korean families and suggest the applicability of kinship analysis in the Korean population.

Validation and assessment of the Investigator® 24plex QS kit for forensic casework application: Comparison with the PowerPlex® fusion system and GlobalFiler™ PCR amplification kits

Casework evidence samples are likely to be placed under diverse and harsh environments as compared to quantified DNA samples including serial-diluted standard DNA samples. Internal validation of a novel STR kit using casework evidence sample, which is conducted according to various conditions such as DNA contamination and degradation, is crucial before being used as a forensic application. Therefore, this study aimed to elucidate the reliability of the Investigator® 24plex QS kit through DNA derived from casework evidence and to assess whether it is applicable to STR analysis together with PowerPlex® Fusion System and GlobalFiler™ PCR Amplification Kit. DNA was extracted from 189 casework evidence samples in a total of 77 cases. The mismatch of the allelic size of this kit through allelic sizing precision test, was suitable according to ENFSI guidelines. All heterozygous balance of the three kits were above 0.6 recommended value of ENFSI guideline. The number of allele drop-in was most frequent in the GlobalFiler™ PCR Amplification Kit. In addition, the number of allele drop-out was most frequent in the Investigator® 24plex QS kit. The cutoff concentration of DNA detected in three kits of one complete STR was approximately 45 pg/μL on average. Despite of several limitations, the Investigator® 24plex QS kit is considered to have the capability to be used for STR analysis of casework evidence samples.

Exosomal miR-193a and let-7g accelerate cancer progression on primary colorectal cancer and paired peritoneal metastatic cancer

A metastasis of colorectal cancer is difficult to diagnose, and has a poor prognosis. Therefore, we tried to elucidate the possibility of a diagnostic and prognostic marker. Exosomal miR-193a and let-7g were sorted by miRNA microarray. The expression of miR-193a in the PTM group was lower than that of the primary CRC group, and the expression of let-7g was higher than that of the primary CRC. MMP16 and CDKN1A expression was confirmed respectively for target genes of two miRNAs. When the mimics of these miRNAs were treated with cell lines, both MMP16 and CDKN1A decreased intracellular expression. Cell invasiveness and proliferation were decreased by miR-193a and increased by let-7g. The differences in expression of exosomal miR-193a and let-7g extracted from the plasma of patients were classified as cancer progression indicators. Furthermore, the survival rate decreased in the group with low miR-193a expression and high let-7g expression. Our study confirmed the possibility of using this as a diagnostic and prognostic marker for colorectal cancer by measuring the expression levels of exosomal miR-193a and let-7g in blood.

The role of novel fusion genes in human GIST cell lines derived from imatinib-resistant GIST patients: A therapeutic potential of fusion gene

Gastrointestinal stromal tumor (GIST) is the most common sarcoma in the gastrointestinal (GI) tract. Approximately 85% of the GIST is associated with a c-KIT mutation. A few GISTs show mutations in the gene encoding platelet-derived growth factor receptor alpha (PDGFR α or PDGFRA) without c-KIT gene mutation. GIST without c-KIT or PDGFRA mutations, which called wild type GIST, is about 5-10% of the total GIST. Fusion genes were also reported as one of the factors associated with carcinogenesis and drug resistance. With five cell lines derived from imatinib-resistant patients, novel fusion genes were identified from RNA sequencing and both physiological role and therapeutic potential were elucidated. Next-generation sequencing (NGS) analysis and lentiviral transduction were used to effect of fusion gene on GISTs. All the GIST cell lines carried c-KIT-positivity. Three different fusion gene analysis methods were used to find candidate fusion genes, including EIF3K-ACTN4, SYNCRIP-SNX14 and EXOC2-AK7. A novel interchromosomal fusion gene of the candidates, especially EXOC2-AK7, was confirmed in both tissue and cell line. The transduction of fusion gene increased the proliferation compared with the control group. Additionally, the fusion gene increased wound coverage capability. The fusion gene-transduced cell lines were more sensitive than the control group in the treatment of imatinib. In conclusion, five different imatinib-resistant GIST cell lines including the EXOC2-AK7 fusion gene derived from GIST-R5 represent important research tools for the investigation of cancer cell mechanisms underlying drug resistance and genetic variation. Furthermore, our study may facilitate pre-clinical studies of new therapeutic strategies.

Detection of the mesenchymal-to-epithelial transition of invasive non-small cell lung cancer cells by their membrane undulation spectra

A cancer cell changes its state from being epithelial- to mesenchymal-like in a dynamic manner during tumor progression. For example, it is well known that mesenchymal-to-epithelial transition (MET) is essential for cancer cells to regain the capability of seeding on and then invading secondary/tertiary regions. However, there is no fast yet reliable method for detecting this transition. Here, we showed that membrane undulation of invasive cancer cells could be used as a novel marker for MET detection, both in invasive model cell lines and repopulated circulating tumor cells (rCTCs) from non-small cell lung cancer (NSCLC) patients. Specifically, using atomic force microscopy (AFM), it was found that the surface oscillation spectra of different cancer cells, after undergoing MET, all exhibited two distinct peaks from 0.001 to 0.007 Hz that are absent in the spectra before MET. In addition, by adopting the long short-term memory (LSTM) based recurrent neural network learning algorithm, we showed that the positions of recorded membrane undulation peaks can be used to predict the occurrence of MET in invasive NSCLC cells with high accuracy (>90% for model cell lines and >80% for rCTCs when benchmarking against the conventional bio-marker vimentin). These findings demonstrate the potential of our approach in achieving rapid MET detection with a much reduced cell sample size as well as quantifying changes in the mesenchymal level of tumor cells.

SORBS1 serves a metastatic role via suppression of AHNAK in colorectal cancer cell lines

Cbl-associated protein (CAP) is encoded by the sorbin and SH3 domain-containing 1 (SORBS1) gene. CAP has been reported to be associated with the actin cytoskeleton, receptor tyrosine kinase signaling and cell adhesion through interactions with various proteins. It may be hypothesized that SORBS1 has numerous unknown functions, which may include providing a favorable condition for metastasis. Although CAP has been demonstrated to possess a number of functions, the role of this protein has only been reported in metabolic signaling pathways and its function in cancer remains to be elucidated. In the present study, SORBS1 expression was detected in colorectal cancer cell lines divided into the primary group and the metastatic group by reverse transcription-quantitative PCR and western blot analysis. In addition, SORBS1 expression was manipulated by vector transfection and lentivirus transduction. The metastatic role of SORBS1, as determined by assessing its effects on cell proliferation and migration, was determined by colony formation assay, cell cycle analysis and Boyden chamber assay. To elucidate the SORBS1-binding protein, immunoprecipitation was performed. Co-localization of SORBS1 and AHNAK nucleoprotein (AHNAK) was identified by confocal microscopy. Notably, the protein expression levels of CAP were higher in SNU-769A and SW480 cells than in SNU-769B and SW620 cells. In addition, the number of colonies in the SORBS1-overexpressing group was significantly increased compared with that of the control group, as determined using the colony formation assay; the SORBS1 overexpression group formed >8-fold more colonies than the control group. The proliferative ability of the SORBS1 overexpression group was also significantly increased compared with the control group over the entire incubation period. Cell migration assays revealed that the number of migrated SORBS1-knockdown cells was reduced compared with the control in both HCT-116 and SNU-C4 cell lines; migration area was decreased to 31 and 26% in HCT-116 and SNU-C4 cell lines, respectively. Consequently, it was confirmed that SORBS1 could form a complex with AHNAK, which functions as a tumor suppressor through inhibition of phosphorylated-ERK and Rho-associated coiled-coil containing protein kinase 1. In conclusion, SORBS1 may serve a crucial role in cancer growth and migration via inhibition of AHNAK expression.

Abstract 4862: SORBS1-AHNAK complex regulates metastatic properties of cancer

Purpose: CAP encoded by SORBS1, Vinexin and ArgBP2 is participated in the SoHo family of proteins. The SoHo protein interacts with different signaling molecules and involves with cell migration, and has been implicated in a variety of cellular processes including insulin-stimulated glucose transport. CAP has specific role in the stabilization of adhesion complexes and the consequent effect of cell migration. It is possible that CAP or complex between CAP and other proteins induces change of cancer cell characters. We assumed that SORBS1 has substantial role of cell proliferation, migration and interaction with other subcellular proteins.

Methods and materials: To elucidate endogenous role of SORBS1, colorectal cancer cell lines were manipulated by pcDNA, siRNA and shRNA in some colorectal cancer cell lines. Function of SORBS1 as regulator of cancer proliferation was demonstrated by cell cycle assay. And several methods including western blotting, cell migration assay and immunoprecipitation assay were performed for determining role of SORBS1 related other metastatic properties.

Conclusion: Colony formation ability and proliferation were induced by SORBS1-overexpression in HT29 cell line. In contrast, transient suppression of SORBS1 inhibits cell proliferation. Moreover, when SORBS1 was constantly suppressed in HCT-116 and SNU-C4 cell line, cell migration was impeded. According to immunoprecipitation data, we chose the AHNAK protein as the convincing candidate protein related with SORBS1. An interaction of SORBS1 and AHNAK was observed in both cytoplasm and nucleus. Expression level of SORBS1 and AHNAK was also negative correlation in extraction of cytoplasm and nucleus.

SORBS1 and AHNAK bind each other as form of protein complex, however, AHNAK known as nucleoprotein is abundant in both cytoplasm and nucleus when SORBS1 is suppressed. Consequently, these results indicate that SORBS1 has a key role of cancer cell growth and invasiveness through regulation of AHNAK expression and degradation.

Note: This abstract was not presented at the meeting.

Citation Format: Woo-Cheol Cho, Ji-Eun Jang, Ja-Lok Ku. SORBS1-AHNAK complex regulates metastatic properties of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4862. doi:10.1158/1538-7445.AM2017-4862

Cadherin- and Rigidity-Dependent Growth of Lung Cancer Cells in a Partially Confined Microenvironment

During tumor development, cancer cells constantly confront different types of extracellular barriers. However, fundamental questions like whether tumor cells will continue to grow against confinement or away from it and what key factors govern this process remain poorly understood. To address these issues, here we examined the growth dynamics of human lung epithelial carcinoma A549 cells partially confined in micrometer-sized cylindrical pores with precisely controlled wall stiffness. It was found that, after reaching confluency, the cell monolayer enclosed by a compliant wall was able to keep growing and pushing the boundary, eventually leading to a markedly enlarged pore. In contrast, a much reduced in-plane growth and elevated strain level among cells were observed when the confining wall becomes stiff. Furthermore, under such circumstance, cells switched their growth from within the monolayer to along the out-of-plane direction, resulting in cell stacking. We showed that these observations can be well explained by a simple model taking into account the deformability of the wall and the threshold stress for inhibiting cell growth. Interestingly, cadherins were found to play an important role in the proliferation and stress buildup within the cell monolayer by aggregating at cell-cell junctions. The stiff confinement led to an elevated expression level of cadherins. Furthermore, inhibition of N-cadherin resulted in a significantly suppressed cell growth under the same confining conditions.

Abstract 1640: SORBS1-related multiprotein complex regulates metastasis of cancer

Purpose: CAP (Cbl-associated protein), also known as Sorbin and SH3 domain-containing protein 1 is encoded by the SORBS1 gene. These proteins contain a conserved sorbin homology (SOHO) domain and three SH3 domains. CAP is an adaptor protein that has been associated with the actin cytoskeleton, signaling through receptor tyrosine kinases and cell adhesion. Although, CAP is proven to have many known functions, this protein is only reported in specific field of signaling pathway. Cell adhesion and actin dynamics which have been supposed to participate in CAP are crucial factors of cancer metastasis. The role of CAP has been described in the literature, although their specific roles remain to be clarified in cancer.

Methods and materials: Colorectal cancer cell lines were transduced by lentivirus containing shRNA plasmid (shSORBS1 plasmid). To elucidate function of SORBS1 as regulator of cancer metastasis, western blotting, cell migration assay and immunoprecipitation assays were performed.

Conclusion: According to the several reports of SORBS1 function, phosphorylation of ERK and mTOR was identified. Although ERK phosphorylation were not changed in normal condition, there were different aspects between control group and SORBS1 knockdown group with insulin treatment. Moreover, mTOR phosphorylation of SORBS1 knockdown group was less in the control group than in the normal condition.

Immunoprecipitation of SORBS1 was performed to search for the binding compounds. We chose the AHNAK protein as the convincing candidate protein related with SORBS1. Several studies reported that AHNAK protein is related to proliferation and EMT by binding of specific signaling molecules. Indeed, there were remarkable differences of invasiveness ability between control group and knockdown group.

Citation Format: Woo-Cheol Cho, Ja-Lok Ku. SORBS1-related multiprotein complex regulates metastasis of cancer. [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 1640.

A future of cancer prevention and cures: highlights of the Centennial Meeting of the American Association for Cancer Research

The Centennial Meeting of the American Association for Cancer Research (AACR) was held from 14-18 April 2007 at the Los Angeles Convention Center. This meeting brought together a diverse group of over 18 000 researchers working in the fields of basic and applied cancer sciences, and explored how cancer research could be used most effectively to prevent and cure cancer at the earliest possible stage. The goal of the AACR Annual Meeting was to stimulate the dialog between basic and clinical researchers so that the translation of new discoveries might be speeded up for the benefit of cancer patients. Advances in the clinical application of genomics, epigenomics and proteomics to diagnose, monitor and prognosticate cancer development led to a dramatic increase in the number of presentations with a translational focus at this year's meeting. Several remarkable areas were particularly highlighted in this report, including The Cancer Genome Atlas, cancer stem cells, microRNA and siRNA, targeted therapy and individualized treatment. This article tries to bring attention to some hot topics in the program that are both new and noteworthy. For those who did not attend the meeting, this report may serve as a highlight of this important international cancer research meeting.

Remarkable application of serum EBV EBER-1 in monitoring response of nasopharyngeal cancer patients to salvage chemotherapy

Nineteen consecutive patients with metastatic or recurrent nasopharyngeal cancer (NPC) receiving combination chemotherapy were monitored for EBV DNA in their serum. EBV DNA (EBER-1) concentration in serum was measured before, during, and after chemotherapy. Thirteen patients had additional multiple prechemotherapy readings. There was a significant lead time from first detection of serum EBER-1 to clinical recurrence in 62% of patients by a mean of 17.4 weeks (range: 8-74.5 weeks; mean = 28.2 weeks if confined to the 8 patients with significant lead time). The median EBER-1 concentration was significantly higher in those with distant metastasis as compared to those with loco-regional recurrence only (17,468 vs. 684 pg/mL serum; p = 0.046, Mann-Whitney U test). Among the 13 patients who responded to chemotherapy, 4 exhibited clinical complete remission (CR) who were only found in the group with EBER-1 DNA drop to background level, while the magnitude of EBER-1 drop did not discriminate partial remission (PR) and stable disease (SD) patients clearly. Subsequent profile of EBER-1 DNA showed concordance with clinical course of either continuous remission or later progression. EBER-1 DNA in serum can become a useful adjunctive surrogate marker to monitor chemotherapeutic response in NPC patients with distant metastasis or advanced local recurrence.

Pilot fragile X screening in normal population of Taiwan

Fragile X syndrome (FXS) is the most common hereditary form of mental retardation. Molecular analysis of the FMR1 gene has now been applied to diagnosis and carrier detection. Because treatment is not feasible, prevention of FXS by prenatal diagnosis of carrier women early during pregnancy is important. The aim of this pilot study was to ascertain the prevalence of mutant FMR1 gene in normal population of Taiwan and to evaluate the efficacy of a betaine-based polymerase chain reaction (PCR) and nonradioactive Southern blot assays. The DNA was randomly and anonymously collected from 100 women and 100 men. The results showed 62% of the women were heterozygous for the CGG-repeat size in FMR1 gene. One of 300 X chromosomes in this study showed premutation, with 95 CGG repeats. All other chromosomes have CGG repeats ranging from 19 to 52, with eight chromosomes (3%) having more than 40 CGG repeats. The most prevalent allele has 29 repeats (48.1%), followed by 30 (24.0%) and 36 (9.5%), respectively. The results of this study reconfirmed previous reports that the prevalent FMR1 CGG repeat alleles in Chinese population are different from that of other populations. However, the prevalence of premutation gene seems to be comparable among them. The betaine-based PCR could minimize the intrinsic problem of preferential amplification and may reliably determine the different allele repeats in heterozygous females. This nonradioactive Southern blot protocol is safe, efficient, and inexpensive. However, further technical improvement may be needed to be more cost-effective for a wide screening of all pregnant women.