Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma

A Case Study on PPM1D and 9 Other Shared Germline Alterations in a Family

BACKGROUND

The use of high-throughput genotyping techniques has enabled us to identify the rare germline genetic variants with different pathogenicity and penetrance, and understand their role in cancer predisposition. We report here a familial cancer case, a study from Western Indian.

METHODS

NGS-WES was carried out in a lung cancer patient who has a family history of multiple cancers across generations, including tongue, lung, brain, cervical, urothelial, and esophageal cancer. The results were validated by data mining from available data bases. I-TASSER, RasMol and PyMol were used for protein structure modelling.

RESULTS

The sequencing by NGS-WES revealed PPM1D c.1654C>T (p.Arg552Ter) mutation in hotspot region exon 6 leading to sudden protein truncation and loss of the C-terminal, due to the substitution of C>T. This mutation was classified as a variant of uncertain significance (VUS), due to limited data on lung cancer, The three unaffected siblings of proband did not show any pathogenic variants and comparative analysis of the four siblings indicate 9 shared genetic variants, classified as benign as per ClinVar.

CONCLUSION

PPM1D constitutional genetic alterations are rare and uncommon in different ethnic populations. This gene encodes a phosphatase playing role in regulating the P53 tumor suppressor pathway and DNA damage response. Genetic alterations in the PPM1D gene maybe linked to history of gliomas, breast cancer, and ovarian cancer onset in the proband's family.
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Nadir paranazal sinüs kanserlerinde yeni tanımlanan reseptör tirozin kinaz mutasyonları ve potansiyel fonksiyonel etkileri

Amaç: Paranazal sinüs kanserleri oldukça nadir görülen heterojen bir hastalık grubudur. Maksiler sinüs skuamoz hücreli karsinomu, paranazal sinüs kanserlerinin anatomik ve histolojik olarak en yaygın alt tipidir. Bu kanserin genetik profiline dair bilginin sınırlı olması, hastaların hedefli tedavi seçeneklerinden yararlanamamasına neden olmaktadır. Çalışmamızda bu nadir kanserdeki reseptör tirozin kinaz mutasyonlarının tanımlanması ve mutasyonların olası fonksiyonel etkilerinin tahmin edilmesi amaçlanmıştır. Gereç ve Yöntem: Bu amaçla 30 olgunun tümörüne ait FFPE dokulardan DNA izolasyonu gerçekleştirildi, olguların mutasyon profili yeni nesil sekanslama yöntemi ve biyoinformatik değerlendirme ile belirlendi. Belirlenen patojenik/ olası patojenik varyantların fonksiyonel etkileri farklı in silico araçlar yardımıyla tahminlendi. Bulgular: Olgularının tamamında en az bir adet patojenik/olası patojenik KIT, PDFGRA ve RETmutasyonu belirlendi. KIT geninin katalitik bölgesindeki mutasyonların kinaz aktivitesini arttıracağı tahmin edildi. PDFGRA genindeki p.P567P ve p.D1074D mutasyonları, 30 olgunun tamamında ve SRA veritabanından elde edilen normal dokulara ait okumaların tümünde belirlendi. Sonuç: Reseptör tirozin kinaz mutasyonlarının paranazal sinüs kanserlerinde de önemli rol oynayabileceğinin belirlenmiş olması özellikle artmış kinaz aktivitesini hedefleyen tedavi yaklaşımlarını bu olguların erişimine sunma potansiyeli taşıması bakımından oldukça önemlidir.

p21-activated kinase 2 binds to transcription factor SOX2 and up-regulates DEK to promote the progression of lung squamous cell carcinoma

Lung squamous cell carcinoma (LSCC) is a prevalent and progressive subtype of lung cancer. This study aimed to substantiate the regulatory effect of the PAK2/SOX2/DEK axis on the LSCC development. LSCC tissues (n = 83) and adjacent normal tissues were collected and SOX2 expression was determined by qRT-PCR and Western blotting. Correlation between SOX2 expression and the prognosis of LSCC patients was then explored utilizing Kaplan-Meier analysis. Co-immunoprecipitation and glutathione-S-transferase pull-down assays were conducted to validate the binding of SOX2 to DEK. Gain- and loss- of function assays were then performed on LSCC cells, with CCK-8 and Transwell assays applied to detect the malignant behaviors of cells. A mouse xenograft model of LSCC was further established for in vivo validation. The expression levels of SOX2, PAK2 and DEK were up-regulated in LSCC tissues and cells. SOX2 overexpression was correlated with poor prognosis of LSCC patients. Knockdown of SOX2 weakened the viability and the migratory and invasive potential of LSCC cells. Further, PAK2 directly interacted with SOX2. PAK2 overexpression accelerated the malignant phenotypes of LSCC cells through interplay with SOX2. Moreover, SOX2 activated the expression of DEK, and silencing DEK attenuated the malignant behaviors of LSCC cells. In conclusion, PAK2 could bind to the transcription factor SOX2 and thus activate the expression of DEK, thereby driving the malignant phenotypes of LSCC cells both in vivo and in vitro.

The Application Value of Syndecan-2 Gene Methylation for Colorectal Cancer Diagnosis: A Clinical Study and Meta-Analyses

Objective

Syndecan-2 (SDC2) methylation has been previously reported as a sensitive biomarker for the early detection of colorectal cancer (CRC). Droplet digital PCR (ddPCR) is the latest development of PCR technology. It can accurately detect and quantify the target sequence of nucleic acid. ddPCR is widely used in research and clinical diagnosis. In the present study, we aimed to develop a ddPCR method to detect SDC2 gene methylation and evaluate the diagnostic value of SDC2 gene methylation.

Methods

First, a ddPCR method was developed to measure SDC2 methylation in stool samples collected from 51 cases of normal, 23 cases of adenoma, and 86 cases of CRC. Subsequently, a meta-analysis of existing studies was conducted to judge the diagnostic value of SDC2 gene methylation in CRC. PUBMED, EMBASE, Web of Science, and Scopus databases were searched for relative studies. Meta-analysis was performed using Meta Disc 1.4 and STATA 15.0 software.

Results

The ddPCR showed that the linearity, sensitivity, and specificity for the detection of SDC2 gene methylation could be down to 0.1% methylation level and 5 ng of methylated DNA input. In 109 cases of CRC, 107 cases could be detected, and the sensitivity was 98.17%. The median value of the percentage of methylated reference (PMR) in colorectal adenoma and CRC patients was significantly higher compared with the normal individuals (p < 0.001). In addition, we found that the PMR value was associated with the clinical staging of CRC. The difference of PMR in stage II and stage IIIA was statistically significant (p < 0.05). Moreover, the meta-analysis showed that 11 out of 87 studies were identified to report the feasibility of SDC2 gene methylation as a method to diagnose early CRC. The pooled sensitivity and specificity of SDC2 gene methylation test for CRC were 0.80 [95% CI (0.68–0.88)] and 0.93 [95% CI (0.91–0.94)], respectively. The pooled diagnostic odds ratio (DOR) and area under curve (AUC) were 52.46 [95% CI (30.43–90.45)] and 0.94 [95% CI (0.92, 0.96)], respectively.

Conclusions

The ddPCR method was more sensitive and convenient to detect SDC2 gene methylation, and the pooled analysis showed that methylated SDC2 was a valuable biomarker for the non-invasive detection of CRC.

Insights of fibroblast growth factor receptor 3 aberrations in pan-cancer and their roles in potential clinical treatment

Fibroblast growth factor receptor 3 (FGFR3) alters frequently across various cancer types and is a common therapeutic target in bladder urothelial carcinoma (BLCA) with FGFR3 variants. Although emerging evidence supports the role of FGFR3 in individual cancer types, no pan-cancer analysis is available. In this work, we used the open comprehensive datasets, covering a total of 10,953 patients with 10,967 samples across 32 TCGA cancer types, to identify the full alteration spectrum of FGFR3. FGFR3 abnormal expression, methylation patterns, alteration frequency, mutation location distribution, functional impact, and prognostic implications differed greatly from cancer to cancer. The overall alteration frequency of FGFR3 was relatively low in all cancers. Targetable mutations were mainly detected in BLCA, and S249C, Y373C, G370C, and R248C were hotspot mutations that could be targeted by an FDA approved erdafitinib. Genetic fusions were mainly observed in glioma, followed by BLCA. FGFR3-TACC3 was the most common fusion type which was proposed as novel therapeutic targets in glioma and was targetable with erdafitinib in BLCA. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were two lung cancer subtypes, FGFR3 fusion and hotspot mutation like S249C were observed more commonly in LUSC but not in LUAD. DNA methylation was correlated with the expression of FGFR3 and its downstream genes in some tumors. FGFG3 abnormal expression and alterations exhibited clinical correlations with patient prognosis in several tumors. This work exhibited the full alteration spectrum of FGFR3 and indicated several new clues for their application as potential therapeutic targets and prognostic indicators.

Updates on Clinical Use of Liquid Biopsy in Colorectal Cancer Screening, Diagnosis, Follow-Up, and Treatment Guidance

Colorectal cancer (CRC) is one of the most common cancers worldwide, being the third most diagnosed in the world and the second deadliest. Solid biopsy provides an essential guide for the clinical management of patients with colorectal cancer; however, this method presents several limitations, in particular invasiveness, and cannot be used repeatedly. Recently, clinical research directed toward the use of liquid biopsy, as an alternative tool to solid biopsy, showed significant promise in several CRC clinical applications, as (1) detect CRC patients at early stage, (2) make treatment decision, (3) monitor treatment response, (4) predict relapses and metastases, (5) unravel tumor heterogeneity, and (6) detect minimal residual disease. The purpose of this short review is to describe the concept, the characteristics, the genetic components, and the technologies used in liquid biopsy in the context of the management of colorectal cancer, and finally we reviewed gene alterations, recently described in the literature, as promising potential biomarkers that may be specifically used in liquid biopsy tests.