Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.

Summary: Neoplastic tumors originate from a single cell, and their evolution can be traced through lineages characterized by mutations, copy number alterations, and structural variants. These lineages are reconstructed and mapped onto evolutionary trees with algorithmic approaches. However, without ground truth benchmark sets, the validity of an algorithm remains uncertain, limiting potential clinical applicability. With a growing number of algorithms available, there is urgent need for standardized benchmark sets to evaluate their merits. Benchmark sets rely on in silico simulations of tumor sequence, but there are no accepted standards for simulation tools, presenting a major obstacle to progress in this field. Availability and implementation: All analysis done in the paper was based on publicly available data from the publication of each accessed tool.

3D genomic mapping reveals multifocality of human pancreatic precancers.

Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.

Chemical Constituents and Bioactivities of the Plant-Derived Fungus Aspergillus fumigatus.

A new bergamotane sesquiterpenoid, named xylariterpenoid H (1), along with fourteen known compounds (2-15), were isolated from the crude extract of Aspergillus fumigatus, an endophytic fungus isolated from Delphinium grandiflorum L. Their structures were elucidated mainly by extensive analyses of NMR and MS spectroscopic data. In addition, the screening results of antibacterial and cytotoxic activities of compounds 1-15 showed that compound 4 displayed antibacterial activities against Staphylococcus aureus and MRSA (methicillin-resistant S. aureus) with an MIC value of 3.12 µg/mL.

Sesquiterpenes and α-pyrones from an endophytic fungus Xylaria curta YSJ-5.

Chemical investigation of the culture extract of an endophyte Xylaria curta YSJ-5 from Alpinia zerumbet (Pers.) Burtt. et Smith resulted in the isolation of eight previously undescribed compounds including five eremophilane sesquiterpenes xylarcurenes A-E, one norsesquiterpene xylarcurene F, and two α-pyrone derivatives xylarpyrones A-B together with eight known related derivatives. Their chemical structures were extensively established based on the 1D- and 2D-NMR spectroscopic analysis, modified Mosher's method, electronic circular dichroism calculations, single-crystal X-ray diffraction experiments, and the comparison with previous literature data. All these compounds were tested for in vitro cytotoxic, anti-inflammatory, α-glucosidase inhibitory, and antibacterial activities. As a result, 6-pentyl-4-methoxy-pyran-2-one was disclosed to display significant antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus with minimal inhibitory concentration value of 6.3 µg/mL.

Islands of genomic stability in the face of genetically unstable metastatic cancer.

Introduction: Metastatic cancer affects millions of people worldwide annually and is the leading cause of cancer-related deaths. Most patients with metastatic disease are not eligible for surgical resection, and current therapeutic regimens have varying success rates, some with 5-year survival rates below 5%. Here we test the hypothesis that metastatic cancer can be genetically targeted by exploiting single base substitution mutations unique to individual cells that occur as part of normal aging prior to transformation. These mutations are targetable because ~10% of them form novel tumor-specific "NGG" protospacer adjacent motif (PAM) sites targetable by CRISPR-Cas9. Methods: Whole genome sequencing was performed on five rapid autopsy cases of patient-matched primary tumor, normal and metastatic tissue from pancreatic ductal adenocarcinoma decedents. CRISPR-Cas9 PAM targets were determined by bioinformatic tumor-normal subtraction for each patient and verified in metastatic samples by high-depth capture-based sequencing. Results: We found that 90% of PAM targets were maintained between primary carcinomas and metastases overall. We identified rules that predict PAM loss or retention, where PAMs located in heterozygous regions in the primary tumor can be lost in metastases (private LOH), but PAMs occurring in regions of loss of heterozygosity (LOH) in the primary tumor were universally conserved in metastases. Conclusions: Regions of truncal LOH are strongly retained in the presence of genetic instability, and therefore represent genetic vulnerabilities in pancreatic adenocarcinomas. A CRISPR-based gene therapy approach targeting these regions may be a novel way to genetically target metastatic cancer.

Evaluation of simulation methods for tumor subclonal reconstruction.

Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most tumors and the errors introduced by sequencing protocols and calling algorithms, tumor subclonal reconstruction algorithms are necessary to recapitulate the DNA sequence composition and tumor evolution in silico. With a growing number of these algorithms available, there is a pressing need for consistent and comprehensive benchmarking, which relies on realistic tumor sequencing generated by simulation tools. Here, we examine the current simulation methods, identifying their strengths and weaknesses, and provide recommendations for their improvement. Our review also explores potential new directions for research in this area. This work aims to serve as a resource for understanding and enhancing tumor genomic simulations, contributing to the advancement of the field.

Xylarcurcosides A-C, three novel isopimarane-type diterpene glycosides from Xylaria curta YSJ-5.

Three previously undescribed isopimarane-type diterpene glycosides named as xylarcurcosides A-C (1-3) along with two known ones 16-α-d-mannopyranosyloxyisopimar-7-en-19-oic acid (4) and hypoxylonoid A (5) were successfully isolated from an ethyl acetate extract of the endophytic fungus Xylaria curta YSJ-5 growing in leaves of Alpinia zerumbet. The spectroscopic methods, electronic circular dichroism (ECD) calculations, and X-ray diffraction experiments were conducted to identify their absolute chemical structures. All these compounds were tested for in vitro cytotoxic, anti-inflammatory, α-glucosidase inhibitory, and antibacterial activities. As a result, these novel compounds demonstrated no obvious cytotoxic and antibacterial activity.

LYRUS: a machine learning model for predicting the pathogenicity of missense variants.

SUMMARY: Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information. This study presents 〈Lai Yang Rubenstein Uzun Sarkar〉 (LYRUS), a machine learning method that uses an XGBoost classifier to predict the pathogenicity of SAVs. LYRUS incorporates five sequence-based, six structure-based and four dynamics-based features. Uniquely, LYRUS includes a newly proposed sequence co-evolution feature called the variation number. LYRUS was trained using a dataset that contains 4363 protein structures corresponding to 22 639 SAVs from the ClinVar database, and tested using the VariBench testing dataset. Performance analysis showed that LYRUS achieved comparable performance to current variant effect predictors. LYRUS's performance was also benchmarked against six Deep Mutational Scanning datasets for PTEN and TP53. AVAILABILITY AND IMPLEMENTATION: LYRUS is freely available and the source code can be found at https://github.com/jiaying2508/LYRUS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

A Phylogenetic Approach to Analyze the Conservativeness of BRCA1 and BRCA2 Mutations.

Identifying pathogenic mutations in BRCA1 and BRCA2 is a critical step for breast cancer prediction. Genome-wide association studies (GWAS) are the most commonly used method for inferring pathogenic mutations. However, identifying pathogenic mutations using GWAS can be difficult. The hypothesis of this study is that the pathogenic mutations in human BRCA1/BRCA2, which are present in many species, are more likely to be located in the evolutionarily conserved sites. This study defines the evolutionary conservativeness based on the previously developed Characteristic Attribute Organization System (CAOS) software. ClinVar is used to identify human pathogenic mutations in BRCA1 and BRCA2. Statistical tests suggest that compared to the non-pathogenic mutations, human pathogenic mutations were more likely to locate at the evolutionary conserved positions. The approach presented in this study shows promise in identifying pathogenic mutations in humans, suggesting that the methodology may be applied to other disease-related genes to identify putative pathogenic mutations.

Predictive factors for the benefit of triple-drug transarterial chemoembolization for patients with unresectable hepatocellular carcinoma.

BACKGROUND: Compared with single-drug TACE, our previous phase III study demonstrated that triple-drug transarterial chemoembolization (TACE) prolonged overall survival (OS) in patients with unresectable hepatocellular carcinoma (HCC). The aim of this study was to find which patients can benefit from the triple drugs TACE compared with single-drug TACE. METHODS: Patients in the triple-drug TACE arm received sponge embolization and emulsions composed of 50 mg epirubicin, 50 mg lobaplatin, 6 mg mitomycin C, and lipiodol, while patients in the single-drug TACE arm received sponge embolization and emulsions composed of 50 mg epirubicin and lipiodol. From July 2007 to November 2009, 244 patients (224 men and 20 women; age ranged from 21 to 75 years) from our phase III study formed the initial cohort. From January 2010 to June 2015, external validation cohort was composed of 449 patients (411 men and 38 women; age ranged from 18 to 75 years) from another institution. The validation cohort after propensity score matching (PSM) (n = 374) was analyzed. Cox proportional hazard model was used to evaluate the interaction term between treatments for each subgroup. This retrospective study was approved by the institutional review board at each center. RESULTS: No difference was observed in the baseline characteristic of three cohorts. This exploratory analysis showed that triple-drug TACE brought a survival benefit in the initial cohort, validation cohort (before PSM), and validation cohort (after PSM) compared with single-drug TACE. The outcomes of three cohorts all showed that a significantly greater OS triple-drug chemotherapy benefit versus single-drug chemotherapy was seen in patients with large tumors (larger than 10 cm) while no survival difference was seen in patients with small tumors (10 cm or smaller). CONCLUSIONS: Triple-drug TACE seems to benefit patients with HCC larger than 10 cm in particular compared with single-drug TACE.

Sorafenib plus hepatic arterial infusion chemotherapy with oxaliplatin versus sorafenib alone for advanced hepatocellular carcinoma.

OBJECTIVE: To compare the efficacy of sorafenib plus hepatic arterial infusion chemotherapy (HAIC) with oxaliplatin to that of sorafenib alone in patients with advanced hepatocellular carcinoma (HCC). METHODS: This was a retrospective, single-center trial. Between April 3, 2017 and July 2, 2018, 104 patients with Child-Pugh A and advanced HCC received either 400 mg of sorafenib orally twice daily plus HAIC with oxaliplatin (oxaliplatin 85 mg/m2, every 3 weeks via repetitive catheterization) (n = 46, soraOXA group) or 400 mg of only sorafenib orally twice daily (n = 58, sorafenib group). Overall survival, progression-free survival, objective response rate, and treatment-related adverse events were compared. RESULTS: The median overall survival was 9.37 months (95% CI, 7.05-11.68) in the soraOXA group versus 4.8 months (95% CI, 2.98-6.62) in the sorafenib group (HR 0.46 [95% CI, 0.29-0.72]; P < 0.001). The soraOXA group also showed a higher objective response rate (16 [34.8%] vs 1 [1.7%]; P < 0.001) and a longer progression-free survival rate (5.5 months [95% CI, 2.32-8.68] vs 2.4 months [95% CI, 1.65-3.15], HR 0.54 [95% CI, 0.36-0.81], P = 0.003) than the sorafenib group. There was no significant difference in the overall incidence of any grade adverse events, grade 3/4 adverse events, serious adverse events, or incidence of treatment termination due to adverse events between the two groups. CONCLUSION: Compared with sorafenib alone, sorafenib plus HAIC with oxaliplatin showed favorable treatment outcomes in patients with advanced HCC. The merits of this approach need to be established with a prospective trial.

[Study on anti-HPV activity of Asarum heterotropoides].

OBJECTIVE: To screen anti-HPV effective fraction from Asarum heterotropoides. METHODS: Asarum heterotropoides was extracted with systematic solvents (petroleum benzine, ether, ethyl acetate, n-butanol, ethanol and distilled water) accordingly. The Polymerase Chain Reaction (FQ-PCR) was applied in the vitro pharmacodynamics for the extracts from Asarum heterotropoides. The amplification of HPV-DNA in the lesions of the isolated Condyloma acuminatum. RESULTS: After the water extracts of Asarum heterotropoides was used for HPV-DNA, the PCR amplification showed negative, with the minimum effective concentration 0.4 g/ml. But the other solvents extracts from Asarum heterotropoides appeared positive. CONCLUSION: The water extracts from Asarum heterotropoides are effective on anti-Human papillomavirus.