Role of m5C RNA methylation regulators in colorectal cancer prognosis and immune microenvironment

BackgroundRNA modification has become one of the hot topics of research as it can be used for tumor prognosis. However, its role in various biological processes is still poorly understood. The aim of this study was to investigate the role of m⁵C and m¹A regulators on colorectal cancer prognosis using bioinformatics tools. The association between these regulators and differences in patient survival as well as the clinicopathological characteristics and tumor immune microenvironment in colorectal cancer tissues were assessed.MethodsWe selected publicly available colorectal cancer data sets from The Cancer Genome Atlas and used the “limma” package in R to identify differentially expressed genes. The least absolute shrinkage and selection operator regression model was used to calculate the prognostic risk, and a risk prediction model was constructed, to help assess the prognostic values of the differentially expressed genes. Finally, using TISCH and TIMER, we assessed the extent of cellular infiltration in colorectal cancer.ResultsWe explored NSUN6 and DNMT3A expression using UALCAN and HPA and found that their expression is significantly increased in colorectal cancer tissues and correlated with sex and TP53 mutation status. Moreover, we found NSUN6 and DNMT3A were related to the infiltration of six major immune cells, with DNMT3A being closely related to dendritic cells, CD4⁺ T cells, and B cells, whereas NSUN6 to B cells and CD8⁺ T cells.ConclusionOur findings suggest that m⁵C regulators can predict the clinical prognostic risk and regulate the tumor immune microenvironment in colorectal cancer.     

Drug metabolism‐related eight‐gene signature can predict the prognosis of gastric adenocarcinoma

BackgroundMetabolic abnormalities in patients with gastric adenocarcinoma lead to drug resistance and poor prognosis. Therefore, this study aimed to explore biomarkers that can predict the prognostic risk of gastric adenocarcinoma by analyzing drug metabolism‐related genes.MethodsThe RNA‐seq and clinical information on gastric adenocarcinoma were downloaded from the UCSC and gene expression omnibus databases. Univariate and least absolute shrinkage and selection operator regression analyses were used to identify the prognostic gene signature of gastric adenocarcinoma. The relationships between gastric adenocarcinoma prognostic risk and tumor microenvironment were assessed using CIBERSORT, EPIC, QUANTISEQ, MCPCounter, xCell, and TIMER algorithms. The potential drugs that could target the gene signatures were predicted in WebGestalt, and molecular docking analysis verified their binding stabilities.ResultsCombined with clinical information, an eight‐gene signature, including GPX3, ABCA1, NNMT, NOS3, SLCO4A1, ADH4, DHRS7, and TAP1, was identified from the drug metabolism‐related gene set. Based on their expressions, risk scores were calculated, and patients were divided into high‐ and low‐risk groups, which had significant differences in survival status and immune infiltrations. Risk group was also identified as an independent prognostic factor of gastric adenocarcinoma, and the established prognostic and nomogram models exhibited excellent capacities for predicting prognosis. Finally, miconazole and niacin were predicted as potential therapeutic drugs for gastric adenocarcinoma that bond stably with NOS3 and NNMT through hydrogen interactions.ConclusionsThis study proposed a drug metabolism‐related eight‐gene signature as a potential biomarker to predict the gastric adenocarcinoma prognosis risks.     

Novel intergenic KIF5B-MET fusion variant in a patient with gastric cancer: A case report

BACKGROUND MET fusion is a key driver mutation, but it is rare in gastric cancer (GC). Several MET (hepatocyte growth factor receptor) inhibitors have been approved for the treatment of MET-positive patients, but the tumor response is heterogeneous. With the development of next-generation sequencing, diverse MET fusion partner genes have been identified. We herein report a fusion variant involving KIF5B-MET in GC.CASE SUMMARYAfter thoracoscopic inferior lobectomy plus lymph node dissection under general anesthesia, a “tumor within a tumor” was found in the lung tumor tissue of a 64-year-old non-smoking male patient. Combining the medical history and the results of enzyme labeling, the focal area was considered to be GC. To seek potential therapeutic regimens, an intergenic region between KIF5B and MET fusion was identified. This fusion contains a MET kinase domain and coil-coiled domains encoded by KIF5B exons 1-25, which might drive the oncogenesis. CONCLUSIONOur finding could extend the spectrum and genomic landscape of MET fusions in GC and favor the development of personalized therapy.     

Immune‐related lncRNA signature delineates an immune‐excluded subtype of liver cancer with unfavorable clinical outcomes

BackgroundLong non‐coding RNAs (lncRNAs) play crucial roles in immune regulation and, therefore, may be closely related to the tumor microenvironment (TME). However, there are few studies regarding the relationship between the lncRNAs and the TME in liver cancer.MethodsFirstly, we constructed a lncRNA signature based on the top 10 immune‐inversely related lncRNAs obtained from the ImmLnc database and performed disease‐free survival (DFS) and overall survival (OS) analyses for the patients included in the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA‐LIHC) stratified by the lncRNA signature. Then, we explored the relationship between the lncRNA signature with distinct mutation profiles and the tumor microenvironment (TME).ResultsThe lncRNA signature was successfully constructed and verified by survival analysis. The high lncRNA signature was correlated with a decreased DFS and OS in liver cancer and other two gastrointestinal cancers. The mutation profiles showed that the Lnc_high group had a higher number of mutations on many genes, mostly enriched in p53 and WNT pathways. The TME results showed that the Lnc_high group had the highest proportion (51%) of lymphocyte depletion‐characterized immune subtype, and a higher expression of immune checkpoint molecules such as LAG3, PD‐L1, CTLA4. On the contrary, in the Lnc_low group, infiltrating immune‐cell proportions were significantly higher, and a significant enhancement of four axes of the cancer immunity cycle immunogram was observed in this group.ConclusionsThe lncRNA signature we constructed identified an immune‐excluded subtype of liver cancer with unfavorable clinic outcomes, which could be tested as a biomarker for immunotherapy in the future.     

Mutation scanning of exon 20 of the BRCA1 gene by high-resolution melting curve analysis

Objectives5382insC frameshift mutation along with 5331G>A (G1738R) missense mutation, both found in exon 20 of the BRCA1 gene, are relatively frequent among the Greek breast and ovarian cancer population (46%). Our goal was to develop a novel, reliable and rapid genotyping/scanning method for mutation detection of the exon 20 of the BRCA1 gene, using high-resolution melting curve analysis.Design and methodsThe developed methodology was based on real-time PCR and high-resolution melting curve analysis in the presence of LCGreen I dye. Two amplicons on the exon 20 of BRCA1 gene were designed (157 bp and 100 bp), one flanking the exon's boundaries, and one embracing the 5382insC mutation. Our methodology was first optimized and validated by using genomic DNA samples with the 5382insC and 5331G>A (G1738R) mutations and wild-type. In total, the developed methodology was applied on 90 peripheral blood and 127 formalin-fixed paraffin-embedded breast tissue samples.ResultsSensitivity studies with gDNA isolated from peripheral blood showed that mutated DNA could be reliably detected in the presence of wild-type DNA at 5% and 0.5% ratio with the larger and the smaller amplicon, respectively. By using the developed methodology we successfully identified 5382insC, 5331G>A and 5370C>T (R1751X) mutations, in genomic DNA isolated from peripheral blood samples and 5382insC mutation in two breast tumors, as verified by DNA sequencing.ConclusionsThe combination of real-time PCR and high-resolution melting curve analysis provides a cost-efficient, simple and rapid approach to successfully scan exon 20 of BRCA1 gene for these clinically important and frequent mutations.     

Chemotherapy-associated clonal hematopoiesis mutations should be taken seriously in plasma cell-free DNA KRAS/NRAS/BRAF genotyping for metastatic colorectal cancer

BackgroundGenotyping of plasma cell-free DNA (cfDNA) is an increasingly important method to assess the tumor mutation status in colorectal cancer (CRC) patients. Clonal hematopoiesis (CH) releases non-tumor somatic mutations into blood, causing false positive results in cfDNA-based tumor genotyping. It is still not clear if CH should be examined in all CRC patients undergoing cfDNA analysis.MethodsWe analyzed cfDNA KRAS, NRAS and BRAF genotypes in 236 metastatic CRC patients, who had matched tissue genotyping results, by next-generation sequencing using plasma cfDNA. The cfDNA-only mutations with allele frequencies (AFs) < 5% were highly suspicious for being CH-derived mutations. The origins of cfDNA mutations were confirmed by droplet digital polymerase chain reaction (ddPCR) using paired peripheral blood cells (PBCs) and CH-derived mutations were finally determined. One patient with a CH-derived mutation was followed up and the subpopulation of blood cells, in which CH was present, was investigated.ResultsThree CH-derived mutations, KRAS Q61H, KRAS G12D and KRAS G12V, were identified in the patient cohort. All three patients harboring corresponding CH-derived mutations had a prior chemotherapy history. The CH-derived KRAS G12V mutation in a patient was found only present in lymphocytes and persisting under treatment. For all cfDNA mutations, the CH-derived ones were clustered in the patients with < 5% mutation AF and prior chemotherapy.ConclusionThe prevalence of CH in CRC patients was limited, and prior chemotherapy was a contributing factor of CH. It is recommended for patients with < 5% mutation AF and prior chemotherapy to have genotyping analysis of their PBCs following plasma cfDNA genotyping.     

内镜活检胃癌组织中MUC3A,MUC13表达及与病理参数和预后的关系

目的:探讨内镜活检胃癌组织中黏蛋白3A(MUC3A)、黏蛋白13(MUC13)表达及与病理参数和预后的关系。方法:选取2013年1月至2014年12月南阳市中心医院肿瘤科收治的接受内镜活检的116例患者胃癌组织和癌旁正常组织进行分析,采用免疫组织化学法检测所有组织样本中MUC3A,MUC13表达,观察二者表达情况,并分析二者与临床病理参数及预后的关系。结果:胃癌患者组织MUC3A,MUC13阳性率分别为68.97%和66.38%,高于正常组织的32.76%和7.76%(P<0.05);胃癌组织中MUC3A,MUC13表达与年龄、性别、肿瘤大小无关(P>0.05),与组织分化、浸润深度、TNM分期、淋巴结转移有关(P<0.05);随访5年结果显示:胃癌组织中MUC3A阳性患者中位生存时间为(40.50±1.95)个月,低于阴性患者的(48.67±2.51)个月(P<0.05),MUC3A阳性患者预后5年生存率为32.50%,低于阴性患者的55.56%(P<0.05);MUC13阳性患者中位生存时间为(38.52±1.92)个月,低于阴性患者的(49.06±2.71)个月(P<0.05),MUC13阳性患者预后5年生存率为30.00%,低于阴性患者的61.11%(P<0.05);COX多因素回归分析显示:TNM分期,淋巴结转移,MUC3A,MUC13是影响胃癌预后的独立危险因素(P<0.05)。结论:MUC3A,MUC13在胃癌组织中呈高表达,且与临床病理参数及预后密切相关,二者均有望作为判定胃癌发生发展及预后评估的参考指标。     

Detection of Low-Level KRAS Mutations Using PNA-Mediated Asymmetric PCR Clamping and Melting Curve Analysis with Unlabeled Probes

Detection of somatic mutations in clinical cancer specimens is often hampered by excess wild-type DNA. The aim of this study was to develop a simple and economical protocol without using fluorescent probes to detect low-level mutations. In this study, we combined peptide nucleic acid (PNA)-clamping PCR with asymmetric primers and a melting curve analysis using an unlabeled detection probe. PNA-clamping PCR, which suppressed amplification of the wild-type allele, was more sensitive for KRAS codon 12 mutation detection than nonclamping PCR in 5 different mutant cell lines. Three detection probes were tested (a perfectly matched antisense, a mismatched antisense, and a mismatched sense), and the mismatched sense detection probe showed the highest sensitivity (0.1% mutant detection) under clamping conditions. With this probe, we were able to detect not only the perfectly matched KRAS mutation, but also 4 other mismatched mutations of KRAS. We then applied this protocol to 10 human colon cancer tissues with KRAS codon 12 mutations, successfully detecting the mutations in all of them. Our data indicate that the combination of perfectly matched antisense PNA and a mismatched sense detection probe can detect KRAS mutations with a high sensitivity in both cell lines and human tissues. Moreover, this study might prove an easily applicable protocol for the detection of low-level mutations in other cancer genes.The need to detect somatic mutations in the presence of excess wild-type sequences (low-level mutation detection) is frequently encountered in cancer genetics. Cancer biopsies often consist of inhomogeneous mixtures of stromal cells and cancer cells, and thus “pure” tumor biopsies are, themselves, genetically heterogeneous. Also, early detection of mutant DNA in body fluids, including blood and urine, requires a “needle in a haystack” approach to mutation detection.¹Excess wild-type DNA exhausts essential reagents during polymerase chain reaction (PCR) and tends to mask mutation sequence signals during the detection process. To date, a general strategy to overcome this difficulty has been to suppress wild-type amplification or enrich the mutant allele, followed by a detection procedure that provides a sufficient resolution to disclose mutant signals.^2,3,4,5,6,7 However, most of the methods currently used are not convenient for use in clinical laboratories because of multiple procedural manipulations that are both time-consuming and cost-ineffective. Most importantly, the risk of contamination during multiple transfers is high. Therefore, it is necessary to develop more convenient and simpler methods for clinical application of low-level mutant detection.Recently, peptide nucleic acid (PNA) has been used to improve mutation detection in clinical specimens by suppressing wild-type allele amplification.^8,9,10 There are two crucial features of PNA that make it a PCR clamp for specific alleles: PNA cannot function as a primer for DNA polymerase or serve as a substrate for the exonuclease activities of Taq polymerase. Melting curve analysis is a technique for identifying single nucleotide polymorphisms or mutations.^8,9,10 Recently, a high-saturation intercalating dye called LCGreen was introduced for the melting curve analysis, and this dye has been used in genotyping for monitoring the melting of small amplicons by unlabeled probes instead of fluorescence probes.^11,12 In the present study, we combined PNA clamping–based asymmetric PCR with a melting curve analysis using unlabeled probe in a single step and detected different types of KRAS mutant templates in a ratio of 1:1000 wild-type alleles.     

Estimation of the occurrence rates of IDH1 and IDH2 mutations in gliomas and the reconsideration of IDH-wildtype anaplastic astrocytomas: an institutional experience

ObjectivesMost diffuse gliomas are reported to harbor isocitrate dehydrogenase (IDH) mutations. However, when these mutations are tested in clinical practice, the results are often negative.MethodsThis study examined the frequency of IDH1 and IDH2 mutations in gliomas classified according to the revised 2016 World Health Organization classification, and investigated their prognostic relevance. We tested 87 gliomas for IDH1 and IDH2 mutations using the peptide nucleic acid clamp method.ResultsIDH1 mutations were observed in 42% of diffuse astrocytomas, 23% of anaplastic astrocytomas, all oligodendrogliomas and anaplastic oligodendrogliomas, and 17% of glioblastomas. An IDH2 mutation was identified in one case of diffuse astrocytoma. In the survival analysis of diffuse astrocytic tumors, patients with IDH1/2-wildtype anaplastic astrocytomas tended to have a poor prognosis, similar to that of glioblastomas.ConclusionsIDH2 mutations were infrequent in gliomas. In anaplastic astrocytomas, the frequency of IDH1/2-wildtype was relatively high, and the prognosis of patients with this type of tumor was very similar to that of those with glioblastomas. It may therefore be necessary to reconsider the classification and treatment strategies for IDH1/2-wildtype anaplastic astrocytomas.     

A novel WT1 gene mutation in a chinese girl with denys‐drash syndrome

ObjectiveDenys‐Drash syndrome (DDS) is defined by the triad of Wilms tumor, nephrotic syndrome, and/or ambiguous genitalia. Genetic testing may help identify new gene mutation sites and play an important role in clinical decision‐making.MethodsWe present a patient with an XY karyotype and female appearance, nephropathy, and Wilms tumor in the right kidney. Genomic DNA was extracted from peripheral blood cells according to standard protocols. “Next‐generation” sequencing (NGS) was performed to identify novel variants. The variant was analyzed with Mutation Taster, and its function was explored by a cell growth inhibition assay.ResultsWe found the first case of Denys‐Drash syndrome with the uncommon missense mutation (c.1420C>T, p.His474 Tyr) in the WT1 gene. In silico analysis, the variant was predicted “disease‐causing” by Mutation Taster. The mutated variant showed a weaker effect in inhibiting tumor cells than wild‐type WT1.ConclusionsThe uncommon missense mutation (c.1420C>T, p.His474 Tyr) in the WT1 gene may be a crucial marker in DDS.     

Mutation spectrum associated with metastasis of advanced cholangiocarcinoma

BackgroundThe mutations associated with metastasis in advanced-stage cholangiocarcinoma (CCA) have not been investigated.ObjectiveTo explore mutations in patients with advanced CCA and independent factors related to metastasis.MethodsThis retrospective study performed next-generation sequencing of tumor specimens from patients with advanced CCA treated between January 2017 and December 2019. Tumor mutational burden (TMB), microsatellite instability, and programmed cell death ligand (PD-L)1 positivity were determined. Factors independently associated with metastasis were explored via logistic regression.ResultsNinety-one patients were included in this study. TP53 mutation frequencies were significantly higher in extrahepatic than intrahepatic CCA, while ARID1A mutations were significantly more frequent in intrahepatic CCA. Mutation frequencies in six selected genes did not differ according to patient age or sex. SMAD4 mutations were significantly less frequent in stage IV cancer; ARID1A and PBRM1 mutation frequencies were significantly higher in TMB >10 tumors. PBRM1 mutation frequencies were significantly higher in PD-L1-positive tumors, but lower in patients with metastasis. Multivariable analysis showed that a history of biliary surgery, SMAD4 mutations, and PBRM1 mutations were independently associated with CCA metastasis.ConclusionsA history of biliary surgery and mutations in SMAD4 and PBRM1 are independent protective factors for metastasis in patients with advanced CCA.     

Ultrasensitive profiling of UV-induced mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex

BackgroundTuberous sclerosis complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed.MethodsA multiplex high-sensitivity PCR assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAFs).ResultsMHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second-hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2-mm biopsy at median VAF 0.08%, generating more than 150,000 incipient facial tumors (subclinical “micro-FAFs”) in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single-nucleotide or dinucleotide variant and a 1- to 9-nucleotide deletion, in cis.ConclusionTSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAFs) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures.FundingThis work was supported by the TSC Alliance; the Engles Family Fund for Research in TSC and LAM; and the NIH, National Heart, Lung, and Blood Institute (U01HL131022-04 and Intramural Research Program).     

Enhanced Ratio of Signals Enables Digital Mutation Scanning for Rare Allele Detection

The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence.In the era of personalized medicine, mutation detection methods that target mutations known to influence therapy response or clinical outcome are of great interest. Although real-time PCR methodologies have been described and are widely used for detecting mutations in clinical samples,^1–4 interest in digital PCR⁵ is rising in view of the unique aspects of the technology and the emergence of commercial droplet digital PCR (ddPCR) platforms.^5–8 ddPCR has been implemented in a variety of fields such as cancer biomarker and viral load detection, fetal screening, or library quantification for next-generation sequencing.⁹ One of the most common ddPCR applications is in the detection of known DNA variants present within a large excess of wild-type DNA, for instance in DNA from heterogeneous samples that harbor subclonal populations of mutated tumor cells.¹⁰In ddPCR, the amplification reaction is compartmentalized into microscopic emulsion-based droplets containing at most a few target molecules per droplet. By segregating the interrogated sample, the effect of in-droplet target competition is reduced, which translates into increased assay discrimination and facile determination of wild-type versus mutant status.¹¹ However, as currently applied, ddPCR can only be used to detect mutations at known sequence positions. ddPCR incorporates two reporter probes, one mutant-specific and one wild-type, because of the requirement to account for PCR-amplification variability among droplets. This approach, by design, allows only the detection of previously known mutations. In cancer, tumor suppressor genes such as TP53 harbor mutations that are scattered throughout the gene as opposed to oncogenes that usually carry mutations located in specific hotspots.¹² Although mutation scanning methods based on amplicon fluorescent melting analysis following real-time PCR have been developed,^13–16 monitoring fluorescent melting within individual droplets during ddPCR is not available at this time. Accordingly, a ddPCR approach that could be implemented in a mutation scanning format is desirable.Here, we demonstrate that incorporation of coamplification at lower denaturation temperature PCR (COLD-PCR),^17–21 within the ddPCR workflow in conjunction with two fluorescently labeled probes matching the wild-type amplicon, provides a simple and robust method for mutation scanning of target amplicons. COLD-PCR suppresses wild-type sequences and enables preferential amplification of mutation-containing droplets, for any mutation along the amplicon.^21,22 Detecting changes to the ratio of COLD-PCR–enhanced signals caused by mutations anywhere within the probed region enables mutation scanning with high selectivity. This novel enhanced ratio of signal-based mutation scanning COLD-ddPCR enables a rapid method for the detection of mutations during ddPCR without prior knowledge of the specific DNA variant present in the target sequence. We demonstrate in this paper the application of COLD-ddPCR to the detection of multiple mutations present in TP53 exon 8, as well as for the T790M resistance mutation in EGFR exon 20 in DNA from mutated cell lines and cell-free circulating DNA (cfDNA) from clinical cancer samples.     

The prognostic effect of PNN in digestive tract cancers and its correlation with the tumor immune landscape in colon adenocarcinoma

BackgroundThe present study investigated the expression, mutation, and methylation profile of PNN and its prognostic value in digestive tract cancers. The disparities in signaling pathways and the immune landscape in colon adenocarcinoma (COAD) based on PNN expression were specifically explored.MethodsThe expression, mutation, methylation levels of PNN, and survival data in esophageal cancer, gastric adenocarcinoma, COAD, and rectal adenocarcinoma were evaluated using several bioinformatic databases. Gene Ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) were performed to investigate the enriched biological functions and pathways in COAD. Several acknowledged bioinformatic algorithms were employed to assess the correlation between PNN expression and the tumor immune landscape in COAD.ResultsPNN was upregulated and remarkably related to tumor stage in digestive tract cancers. High expression of PNN was positively associated with poor progression‐free survival and overall survival time, specifically in COAD. PNN expression was identified as an independent prognostic factor in COAD. GO and GSEA analyses revealed that PNN participates in multiple biological processes underlying carcinogenicity in COAD. Further investigation showed that PNN expression was significantly associated with tumor‐infiltrating immune cells, immune cell functions, and several immune checkpoints in COAD. The PNN low expression group had a lower tumor immune dysfunction and exclusion (TIDE) score and a higher immunophenoscore (IPS), indicating a better response to immunotherapy.ConclusionPNN was highly expressed in digestive tract cancers and could act as an independent prognostic factor and a response predictor for immunotherapy in COAD.     

Concomitant PIK3CA amplification and RASSF1A or PAX6 hypermethylation predict worse survival in gastric cancer

ObjectivesA large number of genetic and epigenetic alterations have been found in gastric cancer, but there is remarkably little consensus on the value of individual biomarker in diagnosis and prognosis of this cancer. This study was designed to illustrate the value of PIK3CA amplification in combination with promoter methylation of RASSF1A and PAX6 genes in early diagnosis and prognosis of gastric cancer.Design and methodsUsing real-time quantitative PCR, quantitative methylation-specific PCR (Q-MSP), and methylation-specific PCR (MSP) assays, we examined PIK3CA amplification and promoter methylation of RASSF1A and PAX6 genes in a cohort of gastric cancers, and explored the association of various (epi)genotypes with clinical outcomes of gastric cancer patients.ResultsWe demonstrated that PIK3CA gene was specifically amplified in gastric cancers, but not in normal gastric tissues. Moreover, frequent methylation of RASSF1A and PAX6 was also found in gastric cancers. Given the patients harboring diverse (epi)genotypes, we thus investigated the effect of various (epi)genotypes on poor prognosis in gastric cancer. The data showed that concomitant PIK3CA amplification and RASSF1A or PAX6 methylation were closely associated with poor clinical outcomes, particularly survival, as compared to other (epi)genotypes in gastric cancer.ConclusionsWe found frequent PIK3CA amplification and promoter methylation of RASSF1A and PAX6 genes in gastric cancers, and demonstrated that concomitant PIK3CA amplification and promoter methylation in any one of these two genes were significantly associated with worse survival in gastric cancer. Collectively, such (epi)genotypes may be strong and independent poor prognostic factors for gastric cancer patients.     

SELE gene as a characteristic prognostic biomarker of colorectal cancer

ObjectiveTo investigate the expression and clinical value of the E-selectin gene (SELE) in colorectal cancer (CRC).MethodsUsing gene expression profiles and clinicopathological data for patients with CRC from The Cancer Genome Atlas, and tumor and adjacent normal tissues from 31 patients with CRC from Xianyang Central Hospital, we studied the correlation between SELE gene expression and clinical parameters using Kaplan–Meier and Cox proportional hazards regression analyses.ResultsHigher expression of SELE was significantly associated with a poorer prognosis and shorter survival in patients with CRC. The median expression level of SELE was significantly higher in CRC tissues compared with healthy adjacent tissue. Cox regression analysis showed that the prognosis of CRC was significantly correlated with the expression of SELE. Immunohistochemical analysis also showed that positive expression of E-selectin increased significantly in line with increasing TNM stage.Conclusion: This study confirmed that SELE gene expression is an independent prognostic factor in patients with CRC.     

双源双能CT个性化扫描评估胃癌术前分期

目的 探讨个性化调节双源双能CT（DSDECT）扫描对胃癌术前分期的价值。方法 收集经胃镜证实的60例胃癌患者,术前对30例采用常规方式（注射对比后40s及70s扫描,常规组）、30例采用小剂量团注测试（testbolus,TB）方法行增强CT扫描（TB组）。对TB组图像进行MIP和VR重建,观察胃周主要血管显示率及变异情况。将两组术前CT诊断结果分别与术后病理结果进行对照,比较二者对胃癌术前分期的准确性。随机选取30例于16排CT（16排CT组）和27例于64排CT（64排CT组）接受腹部双期增强扫描,比较TB组、16排组及64排CT组的容积CT剂量指数（CTDIvol）。结果 常规组术前T分期准确率为66.67%（20/30）,N分期准确率为76.67%（23/30）;TB组T分期准确率为63.33%（19/30）,N分期准确率为70.00%（21/30）,两组术前T分期、N分期准确率差异均无统计学意义（P均>0.05）。TB组中,胃左动脉、胃网膜左动脉、胃网膜右动脉显示率均为100%（30/30）,胃右动脉显示率为80.00%（24/30）,腹腔干及其主要分支血管变异率为13.33%（4/30）。TB组辐射剂量低于16排组及64排CT组（P均<0.001）。结论 采用TB技术行腹部CT扫描对胃癌术前分期具有较高准确率,并可清晰显示胃周血管。DSDECT具有低辐射剂量的优势,二者联合应用对胃癌术前分期具有较高价值。     

BRCA1/BRCA2 mutation spectrum analysis in South Asia: a systematic review

ObjectiveBreast cancer (BC) is the most common form of cancer among Asian females. Mutations in the BRCA1/BRCA2 genes are often observed in BC cases and largely increase the lifetime risk of having BC. Because of the paucity of high-quality data on the molecular spectrum of BRCA mutations in South Asian populations, we aimed to explore these mutations among South Asian countries.MethodsA systematic literature search was performed for the BRCA1 and BRCA2 gene mutation spectrum using electronic databases such as PubMed, EMBASE, and Google Scholar. Twenty studies were selected based on specific inclusion and exclusion criteria.ResultsThe 185delAG (c.68_69del) mutation in exon 2 of BRCA1 was the most common recurrent mutation and founder mutation found. Various intronic variants, variants of unknown significance, large genomic rearrangements, and polymorphisms were also described in some studies.ConclusionsThe South Asian population has a wide variety of genetic mutations of BRCA1 and BRCA2 that differ according to countries and ethnicities. A stronger knowledge of various population-specific mutations in these cancer susceptibility genes can help provide efficient strategies for genetic testing.