Stratification of HPV-associated and HPV-negative oropharyngeal squamous cell carcinomas based on DNA methylation epigenotypes

While the incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing in these two decades, primarily due to human papillomavirus (HPV), stratification of OPSCC into molecular subgroups showing different clinicopathological features has not been fully investigated. We performed DNA methylome analysis using Infinium 450k for 170 OPSCC cases, including 89 cases in our cohort and 81 cases reported by The Cancer Genome Atlas, together with targeted exon sequencing analysis. We stratified OPSCC by hierarchical clustering analysis using methylome data. Methylation levels of classifier markers were validated quantitatively using pyrosequencing, and area under the curve (AUC) values of receiver operating characteristics (ROC) curves were calculated. OPSCC was stratified into four epigenotypes: HPV(+) high-methylation (OP1), HPV(+) intermediate-methylation (OP2), HPV(−) intermediate-methylation (OP3) and HPV(−) low-methylation (OP4). Ten methylation marker genes were generated: five to classify HPV(+) cases into OP1 and OP2, and five to classify HPV(−) cases into OP3 and OP4. AUC values of ROC curves were 0.969 and 0.952 for the two marker panels, respectively. While significantly higher TP53 mutation and CCND1 copy number gains were observed in HPV(−) than in HPV(+) groups (p < 0.01), no significant difference of genomic aberrations was observed between OP1 and OP2, or OP3 and OP4. The four epigenotypes showed significantly different prognosis (p = 0.0006), distinguishing the most favorable OPSCC subgroup (OP1) among generally favorable HPV(+) cases, and the most unfavorable OPSCC subgroup (OP3) among generally unfavorable HPV(−) cases. HPV(+) and HPV(−) OPSCC are further divided into distinct DNA methylation epigenotypes, showing significantly different prognosis.     

Tracking myeloma tumor DNA in peripheral blood

Over the past years, the emergence of liquid biopsy technologies has dramatically expanded our ability to assess multiple myeloma without the need for invasive sampling. Interrogation of cell-free DNA from the peripheral blood recapitulates the mutational landscape at excellent concordance with matching bone marrow aspirates. It can quantify disease burden and identify previously undetected resistance mechanisms which may inform clinical management in real-time. The convenience of sample acquisition and storage provides strong procedural benefits over currently available testing. Further investigations will have to define the role of cell-free DNA as a diagnostic measure by determining clinically relevant tumor thresholds in comparison to existing routine parameters. This review presents an overview of currently available assays and discusses the clinical value, potential and limitations of cell-free DNA technologies for the assessment of this challenging disease.     

慢性HBV感染者HBsAg血清学清除后为什么还发生肝细胞癌?

本文综述了慢性HBV感染者HBsAg血清学清除后发生肝细胞癌的风险、机制及启示。     

The circulating tumor DNA (ctDNA) alteration level predicts therapeutic response in metastatic breast cancer: Novel prognostic indexes based on ctDNA

PurposeCirculating tumor DNA (ctDNA) has good clinical guiding value for metastatic breast cancer (MBC) patients. This study aimed to apply a novel genetic analysis approach for therapeutic prediction based on ctDNA alterations.MethodThis nonrandomized, multicenter study recruited 223 MBC patients (NCT05079074). Plasma samples were collected for target-capture deep sequencing of ctDNA at baseline, after the 2nd cycle of treatment, and when progressive disease (PD) was evaluated. Samples were categorized into four levels according to the number of ctDNA alterations: level 1 (no alterations), level 2 (1–2 alterations), level 3 (3–4 alterations) and level 4 (≥5 alterations). According to ctDNA alteration level and variant allele frequency (VAF), a novel ctDNA-level Response Evaluation Criterion in Solid Tumors (ctle-RECIST) was established to assess treatment response and predict progression-free survival (PFS).ResultsThe median PFS in level 1 (6.63 months) patients was significantly longer than that in level 2–4 patients (level 2: 5.70 months; level 3–4: 4.90 months, p < 0.05). After 2 cycles of treatment, based on ctle-RECIST, the median PFS of level-based disease control rate (lev-DCR) patients was significantly longer than that of level-based PD (lev-PD) patients [HR 2.42 (1.52–3.85), p < 0.001]. In addition, we found that ctDNA level assessment could be a good supplement to radiologic assessment. The median PFS in the dual-DCR group tended to be longer than that in the single-DCR group [HR 1.41 (0.93–2.13), p = 0.107].ConclusionThe ctDNA alteration level and ctle-RECIST could be novel biomarkers of prognosis and could complement radiologic assessment in MBC.     

Whole‐exome sequencing and host cell reactivation assay lead to a diagnosis of xeroderma pigmentosum group D with mild ultraviolet radiation sensitivity

A case of xeroderma pigmentosum (XP) group D in a 39‐year‐old Japanese man is reported. The patient had suffered from moderate to severe solar sensitivity and freckle‐like pigmented macules in sun‐exposed areas since 6 years of age, and developed skin malignancies such as squamous cell carcinoma, actinic keratosis, Bowen’s disease and basal cell carcinoma. The minimal erythema dose for ultraviolet (UV) radiation was decreased with a delayed peak reaction. The level of unscheduled DNA synthesis of fibroblasts from the patient was 70% of normal, while they expressed POLH, a gene product responsible for the XP variant. Whole‐exome sequencing indicated that the patient harbored a homozygous mutation of c.1802G>T, p.Arg601Leu in ERCC2. A genetic complementation test was carried out by host cell reactivation assay, which showed that the patient’s fibroblasts recovered only when they were transfected with XPD cDNA, confirming the diagnosis of XP‐D. Arg601Leu mutation in ERCC2 may be related to mild UV radiation sensitivity and moderate skin lesions.     

A short review on DNA damage and repair effects in lip cancer

Increasing trend in oral cancer (0.6% per year) and its related mortality has been reported worldwide since 2010. The United States alone reports an increase of 57% within the past 10 years. This emphasizes the need not only for designing strategies of prevention and planning but also for an effective treatment regime for the various oral cancers. Cancers of the lips, tongue, cheeks, floor of the mouth, and hard palate have been primarily classified under the category of oral cancers. If left undiagnosed, these cancers can be life threatening. Amongst these, the most undesignated and understudied cancer type is the lip carcinoma, which is either categorized under oral cancer or/as well as skin cancer or head and neck cancer. However, lip cancer corresponds to 25–30% of all diagnosed oral cancers. Though the etiology of lip cancer is not yet fully understood, numerous risk factors involved in its development are now being studied. The cells in the lip region are continuously exposed to various DNA damaging agents from endogenous as well as exogenous sources. Flaws in DNA repair mechanisms involved in eliminating these damages may be linked to the origin of carcinogenesis. Accumulation of DNA damage and defect in repair mechanisms may play a role in lip carcinogenesis and progression. This literature review is an exhaustive compilation of the research work performed on the role of DNA damage and repair responses in lip carcinoma which will pave a path for researchers to identify predictive DNA repair biomarker/s for lip cancer, and its diagnosis, prevention, and treatment.     

孕妇外周血中无细胞胎儿DNA的研究进展及应用

孕妇外周血中无细胞胎儿DNA(cffDNA)是无创性产前诊断中重要的胎儿物质的检测来源.由于孕妇血中大部分是母体DNA,而游离胎儿DNA的量非常少,仅占3％～6％.因此从孕妇血中成功分离cffDNA,对后续的无创性产前诊断有着十分重要的意义.本文分别从孕妇外周血中cffDNA的发现来源,cffDNA的结构与稳定性,分离孕妇外周血中的cffDNA的实验方法,及在无创性产前诊断中的应用等方面进行介绍,并着重对该技术近年来的研究进展作一综述.旨在探寻较高效率分离孕妇外周血中cffDNA的实验方法,为无创性产前诊断提供较高浓度的检测物质,提高其准确率及成功率.