Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization.

Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.

Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer.

Introduction: Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes. Methods: Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects. Results: We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity. Discussion: Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.

Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinoma.

BACKGROUND: Late detection of hepatocellular carcinoma (HCC) results in an overall 5-year survival rate of less than 16%. Liquid biopsy (LB) assays based on detecting circulating tumor DNA (ctDNA) might provide an opportunity to detect HCC early noninvasively. Increasing evidence indicates that ctDNA detection using mutation-based assays is significantly challenged by the abundance of white blood cell-derived mutations, non-tumor tissue-derived somatic mutations in plasma, and the mutational tumor heterogeneity. METHODS: Here, we employed concurrent analysis of cancer-related mutations, and their fragment length profiles to differentiate mutations from different sources. To distinguish persons with HCC (PwHCC) from healthy participants, we built a classification model using three fragmentomic features of ctDNA through deep sequencing of thirteen genes associated with HCC. RESULTS: Our model achieved an area under the curve (AUC) of 0.88, a sensitivity of 89%, and a specificity of 82% in the discovery cohort consisting of 55 PwHCC and 55 healthy participants. In an independent validation cohort of 54 PwHCC and 53 healthy participants, the established model achieved comparable classification performance with an AUC of 0.86 and yielded a sensitivity and specificity of 81%. CONCLUSIONS: Our study provides a rationale for subsequent clinical evaluation of our assay performance in a large-scale prospective study.

Clinical validation of a ctDNA-Based Assay for Multi-Cancer Detection: An Interim Report from a Vietnamese Longitudinal Prospective Cohort Study of 2795 Participants.

The SPOT-MAS assay "Screening for the Presence Of Tumor by Methylation And Size" detects the five most common cancers in Vietnam by evaluating circulating tumor DNA in the blood. Here, we validated its performance in a prospective multi-center clinical trial, K-DETEK. Our analysis of 2795 participants from 14 sites across Vietnam demonstrates its ability to detect cancers in asymptomatic individuals with a positive predictive value of 60%, with 83.3% accuracy in detecting tumor location. We present a case report to support further using SPOT-MAS as a complementary method to achieve early cancer detection and provide the opportunity for early treatment.

Exposure to Electronic Cigarette Advertisements and Use of Electronic Cigarettes: A Meta-analysis of Prospective Studies.

INTRODUCTION: Electronic cigarette (EC) advertisements remain unregulated and approach consumers in TV commercials, print ads, radio, and other forms of digital marketing. AIMS AND METHODS: This study aimed to assess whether exposure to EC advertisements is associated with the use of EC by using a meta-analysis of prospective studies. We searched PubMed, EMBASE, and Web of Science to locate eligible studies in November 2021. Pooled adjusted odds ratios (aORs) with 95% confidence intervals (CIs) were calculated using a random-effects meta-analysis. RESULTS: Out of 1635 articles searched from databases, we included seven prospective studies that met inclusion criteria in the final analysis. Four out of seven studies involved participants under 18 years of age. In the meta-analysis of all studies, exposure to EC advertisements was significantly associated with the increased use of ECs (aOR = 1.53, 95% CI 1.22 to 1.92; I2 = 60.1%). In the subgroup meta-analyses by source of advertisements, there was no significant association between exposure to EC advertisements on TV, radio, or billboards and the use of EC, while exposure to EC advertisements in retail stores and on Internet or social media significantly increased the use of EC. CONCLUSIONS: Exposure to EC advertisements was associated with the increased use of ECs, specifically in retail stores and on Internet or social media among adolescents and young adults. Because EC use could serve as a gateway to cigarette smoking in adolescents and young adults, more strict regulations and restrictions on EC advertisements are needed. IMPLICATIONS: Concurrent with the rise in electronic cigarette (EC) sales, advertising expenditures for ECs have been increased in the past decade, and there is controversy over the association between exposure to EC advertisements and the use of ECs. This meta-analysis of seven prospective studies showed that exposure to EC advertisements was significantly associated with the increased use of ECs, specifically in retail stores and on Internet or social media among adolescents and young adults. Because, EC use could serve as a gateway to cigarette smoking in adolescents and young adults, more strict regulations and restrictions on EC advertisements are needed.

Circulating DNA methylation profile improves the accuracy of serum biomarkers for the detection of nonmetastatic hepatocellular carcinoma.

Aim: This study exploited hepatocellular carcinoma (HCC)-specific circulating DNA methylation profiles to improve the accuracy of a current screening assay for HCC patients in high-risk populations. Methods: Differentially methylated regions in cell-free DNA between 58 nonmetastatic HCC and 121 high-risk patients with liver cirrhosis or chronic hepatitis were identified and used to train machine learning classifiers. Results: The model could distinguish HCC from high-risk non-HCC patients in a validation cohort, with an area under the curve of 0.84. Combining these markers with the three serum biomarkers (AFP, lectin-reactive AFP, des-γ-carboxy prothrombin) in a commercial test, µTASWako®, achieved an area under the curve of 0.87 and sensitivity of 68.8% at 95.8% specificity. Conclusion: HCC-specific circulating DNA methylation markers may be added to the available assay to improve the early detection of HCC.

The early detection of liver cancer in high-risk populations can help people with the disease have a higher chance of survival and better quality of life. However, this is still a healthcare challenge. Current commercial blood tests measuring protein signatures in the blood have low accuracy due to increased levels of these proteins being detected in both liver cancer patients and patients with chronic liver diseases. In this study, we identified a set of signatures in DNA released by cancer cells into the bloodstream and used them as biomarkers to distinguish liver cancer patients from high-risk patients. We also demonstrated that adding those signatures to a commercial blood test currently used in clinics could improve the accuracy in detecting liver cancer patients.

Pathogenic Variant Profile of Hereditary Cancer Syndromes in a Vietnamese Cohort.

BACKGROUND: Hereditary cancer syndromes (HCS) are responsible for 5-10% of cancer cases. Genetic testing to identify pathogenic variants associated with cancer predisposition has not been routinely available in Vietnam. Consequently, the prevalence and genetic landscape of HCS remain unknown. METHODS: 1165 Vietnamese individuals enrolled in genetic testing at our laboratory in 2020. We performed analysis of germline mutations in 17 high- and moderate- penetrance genes associated with HCS by next generation sequencing. RESULTS: A total of 41 pathogenic variants in 11 genes were detected in 3.2% individuals. The carrier frequency was 4.2% in people with family or personal history of cancer and 2.6% in those without history. The percentage of mutation carriers for hereditary colorectal cancer syndromes was 1.3% and for hereditary breast and ovarian cancer syndrome was 1.6%. BRCA1 and BRCA2 mutations were the most prevalent with the positive rate of 1.3% in the general cohort and 5.1% in breast or ovarian cancer patients. Most of BRCA1 mutations located at the BRCA C-terminus domains and the top recurrent mutation was NM_007294.3:c.5251C>T (p.Arg1751Ter). One novel variant NM_000038.6(APC):c.6665C>A (p.Pro2222His) was found in a breast cancer patient with a strong family history of cancer. A case study of hereditary cancer syndrome was illustrated to highlight the importance of genetic testing. CONCLUSION: This is the first largest analysis of carrier frequency and mutation spectrum of HCS in Vietnam. The findings demonstrate the clinical significance of multigene panel testing to identify carriers and their at-risk relatives for better cancer surveillance and management strategies.

Liquid Nickel Salts: Synthesis, Crystal Structure Determination, and Electrochemical Synthesis of Nickel Nanoparticles.

New nickel-containing ionic liquids were synthesized, characterized and their electrochemistry was investigated. In addition, a mechanism for the electrochemical synthesis of nanoparticles from these compounds is proposed. In these so-called liquid metal salts, the nickel(II) cation is octahedrally coordinated by six N-alkylimidazole ligands. The different counter anions that were used are bis(trifluoromethanesulfonyl)imide (Tf2 N(-) ), trifluoromethanesulfonate (OTf(-) ) and methanesulfonate (OMs(-) ). Several different N-alkylimidazoles were considered, with the alkyl sidechain ranging in length from methyl to dodecyl. The newly synthesized liquid metal salts were characterized by CHN analysis, FTIR, DSC, TGA and viscosity measurements. An odd-even effect was observed for the melting temperatures and viscosities of the ionic liquids, with the complexes with an even number of carbon atoms in the alkyl chain of the imidazole having a higher melting temperature and a lower viscosity than the complexes with an odd number of carbons. The crystal structures of several of the nickel(II) complexes that are not liquid at room temperature were determined. The electrochemistry of the compounds with the lowest viscosities was investigated. The nickel(II) cation could be reduced but surprisingly no nickel deposits were obtained on the electrode. Instead, nickel nanoparticles were formed at 100 % selectivity, as confirmed by TEM. The magnetic properties of these nanoparticles were investigated by SQUID measurements.

Redox-activity and self-organization of iron-porphyrin monolayers at a copper/electrolyte interface.

The electrochemical behaviour and molecular structure of a layer of water-soluble 5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)-porphyrin-Fe(III) pentatosylate, abbreviated as FeTMPyP, on a chloride modified Cu(100) electrode surface were investigated by means of cyclic voltammetry (CV) and in-situ electrochemical scanning tunneling microscopy. Voltammetric results of HOPG in an electrolyte containing FeTMPyP molecules indicate three distinguishable redox steps involving both the central iron metal and the π-conjugated ring system. However, only the first two reduction steps are observable within the narrow potential window of CVs of Cu(100) measured in the same electrolyte. In the potential range below the first reduction peak, at which the [Fe(III)TMPyP](5+) molecules are reduced to the corresponding [Fe(II)TMPyP](4+) species, in-situ scanning tunneling microscopy (STM) images revealed, for the first time, a highly ordered adlayer of this reduced porphyrin species on the chloride terminated Cu(100) surface. The ordered adlayer exhibits a (quasi)square unit cell with the lattice vectors |a→2|=|b→2|=1.53±0.1 nm and an angle of 93° ± 2° between them. A model is proposed based on the STM observation illustrating the arrangement of the [Fe(II)TMPyP](4+) molecules at the electrolyte/copper interface.

Lymphangioma of the vagina.

BACKGROUND: Vaginal lymphangioma is an extremely rare lesion. Lymphangioma in other areas is usually asymptomatic, and bleeding is a common complication and presentation. CASE: We describe the identification of a vaginal lymphangioma in a 47-year-old woman and discuss the histopathology, diagnosis, and management, based on colposcopy and histology results. CONCLUSION: Vaginal lymphangioma should be identified by histopathology to exclude other malignant tumours in the vagina and to plan appropriate therapy.

Contexte : Le lymphangiome vaginal est une lésion extrêmement rare. Lorsqu'il affecte d'autres parties du corps, le lymphangiome est habituellement asymptomatique; les saignements en constituent une complication et une présentation courantes. Cas : Nous décrivons l'identification d'un lymphangiome vaginal chez une femme de 47 ans et nous discutons de son histopathologie, de son diagnostic et de sa prise en charge, en fonction des résultats de la colposcopie et de l'histologie. Conclusion : Le lymphangiome vaginal devrait être identifié par histopathologie afin d'écarter la présence possible d'autres tumeurs malignes dans le vagin et de planifier un traitement adéquat.