Single-cell and spatial sequencing application in pathology

Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-seq) is one of the strategies that may help tackle the heterogeneous cells in a disease, but it does not usually provide histologic information. Spatial sequencing is designed to assign cell types, subtypes, or states according to the mRNA expression on a histological section by RNA sequencing. It can provide mRNA expressions not only of diseased cells, such as cancer cells but also of stromal cells, such as immune cells, fibroblasts, and vascular cells. In this review, we studied current methods of spatial transcriptome sequencing based on their technical backgrounds, tissue preparation, and analytic procedures. With the pathology examples, useful recommendations for pathologists who are just getting started to use spatial sequencing analysis in research are provided here. In addition, leveraging spatial sequencing by integration with scRNA-seq is reviewed. With the advantages of simultaneous histologic and single-cell information, spatial sequencing may give a molecular basis for pathological diagnosis, improve our understanding of diseases, and have potential clinical applications in prognostics and diagnostic pathology.

Clinical Implications of Circulating Tumor DNA from Ascites and Serial Plasma in Ovarian Cancer / Journal of the Korean Cancer Association, 대한암학회지

Purpose@#The purpose of this study was to identify the clinical utility of circulating tumor DNA (ctDNA) from ascites and serial plasma samples from epithelial ovarian cancer (EOC) patients. @*Materials and Methods@#Using targeted next-generation sequencing, we analyzed a total of 55 EOC samples including ctDNA from ascites and serial plasma and gDNA from tumor tissues. Tumor tissues and ascites were collected during debulking surgeries and plasma samples were collected before and after the surgeries. Because one EOC patient underwent secondary debulking surgery, a total of 11 tumor tissues, 33 plasma samples, and 11 ascites samples were obtained from the 10 patients. @*Results@#Of the 10 patients, nine (90%) contained somatic mutations in both tumor tissues and ascites ctDNA. This mutational concordance was confirmed through correlation analysis. The mutational concordance between ascites and tumor tissues was valid in recurrent/progressive ovarian cancer. TP53 was the most frequently detected gene with mutations. ctDNA from serial plasma samples identified EOC progression/recurrence at a similar time or even more rapidly than cancer antigen 125, an established serum protein tumor marker for EOC. @*Conclusion@#Our data suggest that ascites ctDNA can be used to identify the mutational landscape of ovarian cancer for therapeutic strategy planning.

Mutational signatures and chromosome alteration profiles of squamous cell carcinomas of the vulva

Vulvar squamous cell carcinoma (SCC) consists of two different etiologic categories: human papilloma virus (HPV)-associated (HPV (+)) and HPV-non-associated (HPV (−)). There have been no genome-wide studies on the genetic alterations of vulvar SCCs or on the differences between HPV (+) and HPV (−) vulvar SCCs. In this study, we performed whole-exome sequencing and copy number profiling of 6 HPV (+) and 9 HPV (−) vulvar SCCs and found known mutations (TP53, CDKN2A and HRAS) and copy number alterations (CNAs) (7p and 8q gains and 2q loss) in HPV (−) SCCs. In HPV (+), we found novel mutations in PIK3CA, BRCA2 and FBXW7 that had not been reported in vulvar SCCs. HPV (−) SCCs exhibited more mutational loads (numbers of nonsilent mutations and driver mutations) than HPV (+) SCCs, but the CNA loads and mutation signatures between HPV (+) and HPV (−) SCCs did not differ. Of note, 40% and 40% of the 15 vulvar SCCs harbored PIK3CA and FAT1 alterations, respectively. In addition, we found that the SCCs harbored kataegis (a localized hypermutation) in 2 HPV (+) SCCs and copy-neutral losses of heterozygosity in 4 (one HPV (+) and 3 HPV (−)) SCCs. Our data indicate that HPV (+) and HPV (−) vulvar SCCs may have different mutation and CNA profiles but that there are genomic features common to SCCs. Our data provide useful information for both HPV (+) and HPV (−) vulvar SCCs and may aid in the development of clinical treatment strategies.

Circulating Tumor DNA in a Breast Cancer Patient's Plasma Represents Driver Alterations in the Tumor Tissue

Tumor tissues from biopsies or surgery are major sources for the next generation sequencing (NGS) study, but these procedures are invasive and have limitation to overcome intratumor heterogeneity. Recent studies have shown that driver alterations in tumor tissues can be detected by liquid biopsy which is a less invasive technique capable of both capturing the tumor heterogeneity and overcoming the difficulty in tissue sampling. However, it is still unclear whether the driver alterations in liquid biopsy can be detected by targeted NGS and how those related to the tissue biopsy. In this study, we performed whole-exome sequencing for a breast cancer tissue and identified PTEN p.H259fs*7 frameshift mutation. In the plasma DNA (liquid biopsy) analysis by targeted NGS, the same variant initially identified in the tumor tissue was also detected with low variant allele frequency. This mutation was subsequently validated by digital polymerase chain reaction in liquid biopsy. Our result confirm that driver alterations identified in the tumor tissue were detected in liquid biopsy by targeted NGS as well, and suggest that a higher depth of sequencing coverage is needed for detection of genomic alterations in a liquid biopsy.

Alteration of p62/SQSTM1 Expression Is Uncommon in Gastrointestinal and Prostate Cancer Tissues

No abstract available.

Mutational and Expressional Analysis of DOK2 Gene in Non-small Cell Lung Cancers

PURPOSE: Mounting evidence indicates that perturbation of tyrosine phosphorylation is implicated in the development of many human diseases, including cancers. Docking proteins (DOKs) are tyrosine-phosphorylated proteins that negatively regulate tyrosine kinase signaling and they are considered to be tumor suppressors. Deletion and the altered expression of the DOK2 gene have been studied in leukemias and lung cancers. However, the somatic mutation status of the DOK2 gene has not been studied in lung cancers. The aim of this study was to see whether alterations of DOK2 protein expression and somatic mutation of the DOK2 gene are present in human non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: We analyzed DOK2 somatic mutation in 45 NSCLCs (23 adenocarcinomas (AD) and 22 squamous cell carcinomas (SCC) by single-strand conformation polymorphism (SSCP). We examined the DOK2 protein expression in 45 NSCLCs by immunohistochemistry. RESULTS: SSCP analysis revealed no evidence of somatic mutation in the DNA sequences encoding the DOK2 gene in the 45 NSCLCs. Among the informative cases, 27% and 21% of the ADs and SCCs showed allelic loss in the DOK2 locus, respectively. On the immunohistochemistry, DOK2 protein was expressed in the normal bronchial epithelial cells, while it was lost in 10 (22%) of the NSCLCs. CONCLUSION: Our data indicates that DOK2 is altered in NSCLC at the expressional level, but not at the mutational level. The data also suggests that loss of the expression of DOK2 might play roles in NSCLC development by possibly altering tyrosine kinase signaling.

Copy Number Alterations of BCAS1 in Squamous Cell Carcinomas

BACKGROUND: Breast carcinoma amplified sequence 1 (BCAS1), located in 20q13, is amplified and overexpressed in breast cancers. Even though BCAS1 is expected to be an oncogene candidate, its contribution to tumorigenesis and copy number status in other malignancies is not reported. To elucidate the role of BCAS1 in squamous cell carcinomas, we investigated the copy number status and expression level of BCAS1 in several squamous cell carcinoma cell lines, normal keratinocytes and primary tumors. METHODS: We quantitated BCAS1 gene by real-time polymerase chain reaction (PCR). Expression level of BCAS1 was measured by real-time reverse transcription-PCR and immunoblot. RESULTS: Seven (88%) of 8 squamous cell carcinoma cell lines showed copy number gain of BCAS1 with various degrees. BCAS1 gene in primary tumors (73%) also showed copy number gain. However, expression level did not show a linear correlation with copy number changes. CONCLUSIONS: We identified copy number gain of BCAS1 in squamous cell carcinomas. Due to lack of linear correlation between copy numbers of BCAS1 and its expression level, we could not confirm that the overexpression of BCAS1 is a common finding in squamous cell carcinoma cell lines. However, this study shows that the copy number gain of BCAS1 is a common finding in squamous cell carcinomas.

A Frameshift Mutation of the Pro-Apoptotic VDAC1 Gene in Cancers with Microsatellite Instability

No abstract available.

Frameshift Mutation of MARS Gene Encoding an Aminoacyl-tRNA Synthetase in Gastric and Colorectal Carcinomas with Microsatellite Instability

No abstract available.

Mutational Analysis of ASPP1 and ASPP2 Genes, a p53-related Gene, in Gastric and Cololorectal Cancers with Microsatellite Instability

No abstract available.

Mutational Analysis of MITOSTATIN, a Candidate Tumor-Suppressor Gene, at a Mononucleotide Repeat in Gastric and Colorectal Carcinoma

No abstract available.

Mutation and Expression of DNA2 Gene in Gastric and Colorectal Carcinomas

BACKGROUND: Deregulation of DNA repair and replication are involved in cancer development. DNA2 is a nuclease/helicase that plays roles in DNA repair and replication. The aim of this study was to explore DNA2 mutation and DNA2 protein expression in gastric cancers (GCs) and colorectal cancers (CRCs). METHODS: We analyzed two mononucleotide repeats in DNA2 in 27 GCs with high microsatellite instability (MSI-H), 34 GCs with stable MSI (MSS), 29 CRCs with MSI-H and 35 CRCs with MSS by single-strand conformation polymorphism. We also analyzed DNA2 expression in GCs and CRCs either with MSI-H or MSS. RESULTS: We found DNA2 mutations in two GCs (7.1%) and two CRCs with MSI-H (6.9%), but not in cancers with MSS. The mutations consisted of three cases of a c.2593delT and one of a c.2592_2593delTT, which would result in premature stopping of amino acid synthesis (p.Ser865Hisfsx6 and p.Ser865Thrfsx20, respectively). DNA2 expression was observed in 16 (80%) of the GCs and 15 (75%) of the CRCs with MSI-H, but all of the cancers with DNA2 frameshift mutations were weak or negative for DNA2. CONCLUSIONS: Our data indicate that DNA2 mutation and loss of DNA2 expression occur in GCs and CRCs, and suggest that these alterations may contribute to cancer pathogenesis by deregulating DNA repair and replication.

Mutational and Expressional Analysis of ATG5 Gene in Non-Small Cell Lung Cancers

PURPOSE: Several lines of evidence have indicated that perturbations of autophagy are involved in the development of many human diseases, including cancer. The autophagy-related genes (ATG) encode proteins that play important roles in autophagic processes. The aim of this study was to see whether alterations of the ATG5 protein expression and somatic mutations of the ATG5 gene are present in human non-small cell lung cancers (NSCLCs). MATERIALS AND METHODS: We analyzed the ATG5 somatic mutations in 45 NSCLCs by performing single-strand conformation polymorphism (SSCP). We examined the ATG5 protein expression in 45 NSCLCs by performing immunohistochemistry. RESULTS: The SSCP analysis revealed no evidence of somatic mutation in the DNA sequences encoding the ATG5 gene in the 45 NSCLCs. On the immunohistochemistry, ATG5 protein was expressed in the normal bronchial epithelial cells, while it was lost in 9 (20%) of the NSCLCs. CONCLUSION: Our data indicates that ATG5 is altered in NSCLC at the expressional level, but not at the mutational level. The data also suggests that the loss of expression of ATG5 might play a role in the pathogenesis of NSCLC by altering autophagic and apoptotic cell death.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Mutational Analysis of TTK Gene in Gastric and Colorectal Cancers with Microsatellite Instability / Journal of the Korean Cancer Association, 대한암학회지

PURPOSE: The TTK gene plays a crucial role in regulation of the mitotic checkpoint. The TTK gene has an A9 mononucleotide repeat in the coding sequences, which harbors mutations in gastric (GC) and colorectal cancers (CRC) with microsatellite instability (MSI). However, there are three more repeats (the A7s) in the coding sequences that have not been analyzed. The aim of this study was to explore whether the three A7s as well as the A9 are altered in GC and CRC, and to find any association of TTK mutation with clinocopathologic characteristics of GC and CRC. MATERIALS AND METHODS: We analyzed exon 5 (A7 and A7) and exon 22 (A9 and A7) which have repeat sequences in 30 GC with high MSI (MSI-H), 15 GC with low MSI (MSI-L), 35 CRC with MSI-H, and 15 CRC with MSI-L, by single-strand conformation polymorphism (SSCP) and DNA sequencing assays. RESULTS: Overall, we detected 23 frameshift mutations in the repeat sequences of TTK in the GC with MSI-H (11/30; 36.7%) and the CRC with MSI-H (12/35; 34.3%), but not in the cancers with MSI-L. The mutations were observed in both A9 and A7 of exon 22, but in neither of the two A7s of exon 5. The mutations consisted of c.2560delA, c.2560dupA, c.2571delA and c.[2560delA(+)2571delA]. All of the mutations were frameshift mutations and would result in premature stops of TTK protein synthesis. There was no significant difference in clinopathologic parameters of the cancers with the mutations. CONCLUSION: Our data indicate that frameshift mutations of TTK are common in both GC and CRC with MSI-H, and that the mutations occur not only in the A9 repeat but also in the A7 repeat. The data suggest that frameshift mutations of TTK might alter cell cycle control in the affected cells and contribute to pathogenesis of cancers with MSI-H.

Mutational Analysis of the Tumor Suppressor WTX Gene in Non-small Cell Lung Cancer

PURPOSE : In a recent study of Wilms' tumors, a new X chromosome gene, Wilms' tumor gene on the X chromosome (WTX), was discovered that was found to harbor small deletions and point mutations. The WTX protein negatively regulates Wnt/beta-catenin signaling, and is considered to be a tumor suppressor gene. One of the questions about the WTX gene is whether the genetic alterations of the WTX gene are specific only to Wilms' tumors. The aim of this study was to explore whether the WTX gene mutation is a characteristic of human non-small cell lung cancer (NSCLC). MATERIALS AND METHODS : In the current study, we analyzed the part of the WTX gene encoding the N-terminal of WTX, where most of the WTX point mutations have been detected in Wilms' tumors. Forty-eight NSCLC tissues were analyzed by a single-strand conformation polymorphism assay and DNA sequencing. RESULTS : SSCP analysis revealed no evidence of somatic mutations in the DNA sequences encoding the N-terminal of the WTX gene in the 48 NSCLC tissues. CONCLUSION : The data presented here indicate that the WTX gene may not be somatically-mutated in human NSCLCs, and suggest that NSCLCs may not utilize mutational events of the WTX gene in the process of pathogenesis

Alterations of the Apoptosis Genes and Their Products in Non-small Cell Lung Cancer Tissues

Apoptosis is a principal type of cell death, and it has a profound effect on the development of cancer. It is also well known that anti-cancer agents induce apoptosis, and defects in the apoptosis pathways reduce the treatment sensitivity. Of the many pathways that induce apoptosis, the mechanisms of the intrinsic and extrinsic apoptosis pathways are well established. Non-small cell lung cancer (NSCLC) is a leading cause of cancer death worldwide, yet the exact molecular mechanisms of its development remain unclear. Apoptosis deregulations may underlie the development and pathogenesis of NSCLC. This review discusses the general mechanisms of apoptosis, the constituents of the apoptosis machinery and the alterations of the apoptosis-related genes in NSCLC

Mutational Analysis of JAK1 Exons 10 and 13 in Non-small Cell Lung Cancers

PURPOSE : JAK kinases play important roles not only in normal cellular processes, but they are also important in tumor development. A recent study identified two somatic mutations of JAK1 in leukemia cells that were detected in exon 10 (p.T478S) and exon 13 (p.V623A). The aim of this study was to see whether the JAK1 mutations in these exons occur in non-small cell lung cancers (NSCLC). MATERIALS AND METHODS : We analyzed the exons 10 and 13 of JAK1 for detecting somatic mutations in NSCLC by performing polymerase chain reaction (PCR) and single-strand conformation polymorphism (SSCP) assay. RESULTS : The SSCP analysis revealed no evidence of somatic mutation in the DNA sequences of JAK1 exon 10 and exon 13 in the 47 NSCLCs. CONCLUSION : The data presented here indicate that the JAK1 exons 10 and 13 may not be somatically mutated in human NSCLCs, and this suggests that the JAK1 mutation in exons 10 and 13 may not play an important role in the tumorigenesis of NSCLCs

Mutational Analysis of Pro-apoptotic BNIP3 Gene in Non- Small Cell Lung Cancers

PURPOSE : Cell death deregulation is a hallmark of human cancers. BNIP3, which was initially identified as a pro-apoptotic member of the Bcl-2 family, plays an important role in apoptosis, necrosis and autophagy. This study was conducted to explore whether mutation of the BNIP3 gene is a characteristic of human non-small cell lung cancers (NSCLC). MATERIALS AND METHODS : In the current study, we used polymerase chain reaction (PCR), single-strand conformation polymorphism (SSCP), and DNA sequencing to detect somatic mutations in the DNA sequences encoding the BH3 (Bcl-2 homology3) and TM (transmembrane) domains that are important to the cell death function of BNIP3 in 48 NSCLCs. RESULTS : SSCP analysis revealed no evidence of somatic mutation in the DNA sequences encoding the BH3 and TM domains of the human BNIP3 gene in the 48 NSCLCs evaluated in this study. CONCLUSION : The data presented here indicate that the pro-apoptotic BNIP3 gene may not be somatically mutated in human NSCLCs, which suggests that mutational events of the BNIP3 gene may not be involved in the mechanisms by which NSCLCs evade cell death

Mutational Analysis of Pro-apoptotic BAD Gene in Nonsmall Cell Lung Cancer

PURPOSE : Evidence exists that deregulation of apoptosis is involved in the mechanisms of cancer development, and the somatic mutations of apoptosisrelated genes have been reported in human cancers. Bcl- XL/Bcl-2-associated death promoter (BAD), a pro-apoptotic member of Bcl-2 family, plays an important role in the intrinsic apoptosis pathway. MATERIALS AND METHODS : To explore the possibility that the genetic alterations of BAD might be involved in the development of human cancers, we analyzed the entire coding region and all splice sites of human BAD gene in 100 human non-small cell lung cancers (NSCLC) by polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP). RESULTS : The PCR-SSCP analysis detected no mutation in the entire coding regions and all splice sites of human BAD gene in the 100 NSCLCs. CONCLUSION : The data presented here suggested that BAD gene mutation may not contribute to the pathogenesis of human NSCLCs