Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.

A lanthanide-rich kilonova in the aftermath of a long gamma-ray burst.

Observationally, kilonovae are astrophysical transients powered by the radioactive decay of nuclei heavier than iron, thought to be synthesized in the merger of two compact objects1-4. Over the first few days, the kilonova evolution is dominated by a large number of radioactive isotopes contributing to the heating rate2,5. On timescales of weeks to months, its behaviour is predicted to differ depending on the ejecta composition and the merger remnant6-8. Previous work has shown that the kilonova associated with gamma-ray burst 230307A is similar to kilonova AT2017gfo (ref. 9), and mid-infrared spectra revealed an emission line at 2.15 micrometres that was attributed to tellurium. Here we report a multi-wavelength analysis, including publicly available James Webb Space Telescope data9 and our own Hubble Space Telescope data, for the same gamma-ray burst. We model its evolution up to two months after the burst and show that, at these late times, the recession of the photospheric radius and the rapidly decaying bolometric luminosity (Lbol ∝ t-2.7±0.4, where t is time) support the recombination of lanthanide-rich ejecta as they cool.

Fundamental immune-oncogenicity trade-offs define driver mutation fitness.

Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3-6 and immunoediting of neoantigens7,8; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations. Focusing on TP53, the most mutated gene in cancer1, we present an inference of mutant p53 concentration and demonstrate that TP53 hotspot mutations optimally solve an evolutionary trade-off between oncogenic potential and neoantigen immunogenicity. Our model anticipates patient survival in The Cancer Genome Atlas and patients with lung cancer treated with immunotherapy as well as the age of tumour onset in germline carriers of TP53 variants. The predicted differential immunogenicity between hotspot mutations was validated experimentally in patients with cancer and in a unique large dataset of healthy individuals. Our data indicate that immune selective pressure on TP53 mutations has a smaller role in non-cancerous lesions than in tumours, suggesting that targeted immunotherapy may offer an early prophylactic opportunity for the former. Determining the relative contribution of immunogenicity and oncogenic function to the selective advantage of hotspot mutations thus has important implications for both precision immunotherapies and our understanding of tumour evolution.

Ovarian cancer mutational processes drive site-specific immune evasion.

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1-4 patterned by distinct mutational processes5,6, tumour heterogeneity7-9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11-13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFß signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

Single-cell genomic variation induced by mutational processes in cancer.

How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

The evolutionary history of 2,658 cancers.

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.

Low-oxidation-state Ru sites stabilized in carbon-doped RuO2 with low-temperature CO2 activation to yield methane.

The generation of methane fuel using surplus renewable energy with CO2 as the carbon source enables both the decarbonization and substitution of fossil fuel feedstocks. However, high temperatures are usually required for the efficient activation of CO2. Here we present a solid catalyst synthesized using a mild, green hydrothermal synthesis that involves interstitial carbon doped into ruthenium oxide, which enables the stabilization of Ru cations in a low oxidation state and a ruthenium oxycarbonate phase to form. The catalyst shows an activity and selectivity for the conversion of CO2 into methane at lower temperatures than those of conventional catalysts, with an excellent long-term stability. Furthermore, this catalyst is able to operate under intermittent power supply conditions, which couples very well with electricity production systems based on renewable energies. The structure of the catalyst and the nature of the ruthenium species were acutely characterized by combining advanced imaging and spectroscopic tools at the macro and atomic scales, which highlighted the low-oxidation-state Ru sites (Run+, 0 < n < 4) as responsible for the high catalytic activity. This catalyst suggests alternative perspectives for materials design using interstitial dopants.

Design and content validation of a checklist about infection-prevention performance of intensive care nurses in simulation-based scenarios.

OBJECTIVE: To design, develop and validate a new tool, called NEUMOBACT, to evaluate critical care nurses' knowledge and skills in ventilator-associated pneumonia (VAP) and catheter-related bacteraemia (CRB) prevention through simulation scenarios involving central venous catheter (CVC), endotracheal suctioning (ETS) and mechanically ventilated patient care (PC) stations. BACKGROUND: Simulation-based training is an excellent way for nurses to learn prevention measures in VAP and CRB. DESIGN: Descriptive metric study to develop NEUMOBACT and analyse its content and face validity that followed the COSMIN Study Design checklist for patient-reported outcome measurement instruments. METHODS: The first version was developed with the content of training modules in use at the time (NEUMOBACT-1). Delphi rounds were used to assess item relevance with experts in VAP and CRB prevention measures, resulting in NEUMOBACT-2. Experts in simulation methods then assessed feasibility, resulting in NEUMOBACT-3. Finally, a pilot test was conducted among 30 intensive care unit (ICU) nurses to assess the applicability of the evaluation tool in clinical practice. RESULTS: Seven national experts in VAP and CRB prevention and seven national simulation experts participated in the analysis to assess the relevance and feasibility of each item, respectively. After two Delphi rounds with infection experts, four Delphi rounds with simulation experts, and pilot testing with 30 ICU nurses, the NEUMOBACT-FINAL tool consisted of 17, 26 and 21 items, respectively, for CVC, ETS and PC. CONCLUSION: NEUMOBACT-FINAL is useful and valid for assessing ICU nurses' knowledge and skills in VAP and CRB prevention, acquired through simulation. RELEVANCE FOR CLINICAL PRACTICE: Our validated and clinically tested tool could facilitate the transfer of ICU nurses' knowledge and skills learning in VAP and CRB prevention to critically ill patients, decreasing infection rates and, therefore, improving patient safety. PATIENT OR PUBLIC CONTRIBUTION: Experts participated in the Delphi rounds and nurses in the pilot test.

Percutaneous radiofrequency ablation is an effective treatment option for small renal masses, comparable to partial nephrectomy.

OBJECTIVES: The standard therapy for small renal masses (SRMs) remains partial nephrectomy (PN), which is associated with relatively high morbidity and complication rate. Therefore, percutaneous radiofrequency ablation (PRFA) emerges as an alternative therapy. This study aimed to compare the efficacy, safety, and oncological outcomes of PRFA versus PN. METHODS: A multicenter non-inferiority study with retrospective analysis of 291 patients with SRMs (N0M0), who underwent PN or PRFA (2:1), recruited prospectively from two hospitals in the Andalusian Public Health System, Spain, between 2014 and 2021. Comparisons of treatment features were evaluated using the t test, Wilcoxon-Mann-Whitney U test, chi-square test, Fisher test, and Cochran-Armitage trend test. Kaplan-Meier curves depicted overall survival (OS), local recurrence-free survival (LRFS), and metastasis-free survival (MFS) rates in the overall study population. RESULTS: A total of 291 consecutive patients were identified; 111 and 180 patients underwent PRFA and PN, respectively. Median follow-up time was 38 and 48 months, and mean hospitalization days were 1.04 and 3.57 days, respectively. The variables underpinned with high surgical risk were significantly increased in PRFA compared to those in PN (mean age was 64.56 and 57.47 years, the solitary kidney presence was 12.6% and 5.6%, ASA score ≥ 3 was 36% and 14.5%, respectively). The rest of oncological outcomes were comparable amongst PRFA and PN. Patients undergoing PRFA did not improve OS, LRFS, and MFS compared to those undergoing PN. Limitations comprise retrospective design and limited statistical power. CONCLUSION: PRFA for SMRs in high-risk patients is non-inferior in terms of oncological outcomes and safety compared to PN. CLINICAL RELEVANCE STATEMENT: Our study has a direct clinical application as it proves that radiofrequency ablation is an effective and uncomplicated therapeutic option for patients with small renal masses. KEY POINTS: •There are non-inferiority results in overall survival, local recurrence-free survival, and metastasis-free survival between PRFA and PN. •Our two-center study showed that PRFA is non-inferior to PN in oncological outcomes. •Contrast-enhanced power ultrasound-guided PRFA provides an effective therapy for T1 renal tumors.

Dispersive magnetic solid-phase extraction for capsaicinoid compounds in human serum using LC-HRMS: targeted and non-targeted approaches.

A new analytical method based on the use of dispersive magnetic solid-phase extraction (DMSPE) is described for the preconcentration of capsaicin (CAP), dihydrocapsaicin (DCAP), and N-vanillylnonanamide (PCAP) from human serum samples. The influence of several experimental factors affecting the adsorption (nature and amount of magnetic material, adsorption time, and pH) and desorption (nature of solvent, its volume and desorption time) steps was studied. Among seven different nanomaterials studied, the best results were obtained using magnetic multiwalled carbon nanotubes, which were characterized by means of spectrometry- and microscopy-based techniques. Analyses were performed by ultra-high-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry using electrospray ionization in positive mode (UHPLC-ESI-Q-TOF-MS). The developed method was validated by obtaining several parameters, including linearity (0.3-300 µg L-1 range), and limits of detection which were 0.1, 0.15, and 0.17 µg L-1 for CAP, DCAP, and PCAP, respectively. The repeatability of the method, expressed as relative standard deviation (RSD, n = 7), varied from 3.4 to 11%. The serum samples were also studied through a non-targeted approach in a search for capsaicinoid metabolites and related compounds. With this objective, the fragmentation pathway of this family of compounds was initially studied and a strategy was established for the identification of novel or less studied capsaicinoid-derived compounds.

Marine Puupehenone and Puupehedione: Synthesis and Future Perspectives.

Puupehenone and puupehedione are natural products isolated from marine organisms. These compounds display a broad spectrum of biological activities, the in vitro antitubercular activity of puupehenone being a stand out, and are equipped with an interesting structural complexity. These products have served to stimulate the continual interest of the synthetic community. The first part of this article is a review of their total synthesis, using natural compounds which have the potential to be transformed into these marine compounds as starting materials; the synthetic routes employed to generate the basic skeleton; and the advances made to synthesize the pyran C ring with the required diastereoselectivity to obtain the natural products. Finally, this perspective shows a personal reflection of the authors on a possible unified and efficient retrosynthetic route that could allow easy access to these natural products, as well as their epimers at the C8 carbon and which could be used to address future biological issues in the production of pharmacologically active compounds.

Unifying the Synthesis of a Whole Family of Marine Meroterpenoids through a Biosynthetically Inspired Sequence of 1,2-Hydride and Methyl Shifts as Key Step.

Marine meroterpenoids have attracted a great deal of attention from synthetic research groups due to their attractive and varied biological activities and their unique and diverse structures. In most cases, however, further biological studies have been severely limited mainly to the scarcity of natural supply and because almost none of the reported syntheses methods has enabled unified access for a large number of marine meroterpenoids with aureane and avarane skeletons. Based on our previous publications and the study of recent manuscripts on marine meroterpenoids, we have conceived a unified strategy for these fascinating marine compounds with aureane or avarane skeletons using available drimane compounds as starting materials. The key step is a biosynthetic sequence of 1,2-hydride and methyl shifts. This strategy is of great synthetic value to access marine meroterpenoids through easy chemical synthetic procedures. Finally, several retrosynthetic proposals are made for the future synthesis of several members of this class of meroterpenoids, focused on consolidating these 1,2-rearrangements as a versatile and unified strategy that could be widely used in the preparation of these marine meroterpenoids.

A Concise Diastereoselective Total Synthesis of α-Ambrinol.

(-)-cis-α-Ambrinol is a natural product present in ambergris, a substance of marine origin that has been highly valued by perfumers. In this paper, we present a new approach to its total synthesis. The starting material is commercially available α-ionone and the key step is an intramolecular Barbier-type cyclization induced by CpTiCl2, an organometallic compound prepared in situ by a CpTiCl3 reduction with Mn.

A comprehensive regulatory and industry review of modeling and simulation practices in oncology clinical drug development.

Exposure-response (E-R) analyses are an integral component in the development of oncology products. Characterizing the relationship between drug exposure metrics and response allows the sponsor to use modeling and simulation to address both internal and external drug development questions (e.g., optimal dose, frequency of administration, dose adjustments for special populations). This white paper is the output of an industry-government collaboration among scientists with broad experience in E-R modeling as part of regulatory submissions. The goal of this white paper is to provide guidance on what the preferred methods for E-R analysis in oncology clinical drug development are and what metrics of exposure should be considered.

Early life supplementation with a natural blend containing turmeric, thymol, and yeast cell wall components to optimize rumen anatomical and microbiological development and productivity in dairy goats.

Ruminants are born with an anatomically, microbiologically, and metabolically immature rumen. Optimizing the rearing of young ruminants represent an important challenge in intensive dairy farms. Therefore, the objective of this study was to evaluate the effects of dietary supplementation of young ruminants with a plant extract blend containing turmeric, thymol, and yeast cell wall components such as mannan oligosaccharides and ß-glucans. One hundred newborn female goat kids were randomly allocated to 2 experimental treatments, which were unsupplemented (CTL) or supplemented with the blend containing plant extracts and yeast cell wall components (PEY). All animas were fed with milk replacer, concentrate feed, and oat hay, and were weaned at 8 wk of age. Dietary treatments lasted from wk 1 to 22 and 10 animals from each treatment were randomly selected to monitor feed intake, digestibility, and health-related indicators. These latter animals were euthanized at wk 22 of age to study the rumen anatomical, papillary, and microbiological development, whereas the remaining animals were monitored for reproductive performance and milk yield during the first lactation. Results indicated that PEY supplementation did not lead to feed intake or health issues because PEY animals tended to have a higher concentrate intake and lower diarrheal incidence than CTL animals. No differences between treatments were noted in terms of feed digestibility, rumen microbial protein synthesis, health-related metabolites, or blood cell counts. Supplementation with PEY promoted a higher rumen empty weight, and rumen relative proportion to the total digestive tract weight, than CTL animals. This was accompanied with a higher rumen papillary development in terms of papillae length and surface area in the cranial ventral and caudal ventral sacs, respectively. The PEY animals also had higher expression of the MCT1 gene, which is related to volatile fatty acid absorption by the rumen epithelium, than CTL animals. The antimicrobial effects of the turmeric and thymol could explain the decreased the rumen absolute abundance of protozoa and anaerobic fungi. This antimicrobial modulation led to a change in the bacterial community structure, a decrease in the bacteria richness, and to the disappearance (i.e., Prevotellaceae_UCG-004, Bacteroidetes_BD2-2, Papillibacter, Schwartzia, and Absconditabacteriales_SR1) or decline of certain bacterial taxa (i.e., Prevotellaceae_NK3B31_group, and Clostridia_UCG-014). Supplementation with PEY also decreased the relative abundance of fibrolytic (i.e., Fibrobacter succinogenes and Eubacterium ruminantium) and increased amylolytic bacteria (Selenomonas ruminantium). Although these microbial changes were not accompanied with significant differences in the rumen fermentation, this supplementation led to increased body weight gain during the preweaning period, higher body weight during the postweaning period, and higher fertility rate during the first gestation. On the contrary, no residual effects of this nutritional intervention were noted on the milk yield and milk components during the first lactation. In conclusion, supplementation with this blend of plant extracts and yeast cell wall component in early life could be considered as a sustainable nutritional strategy to increase body weight gain and optimize the rumen anatomical and microbiological development in young ruminants, despite having minor productive implications later in life.

Hydrogen Sensing Mechanism of WS2 Gas Sensors Analyzed with DFT and NAP-XPS.

Nanostructured tungsten disulfide (WS2) is one of the most promising candidates for being used as active nanomaterial in chemiresistive gas sensors, as it responds to hydrogen gas at room temperature. This study analyzes the hydrogen sensing mechanism of a nanostructured WS2 layer using near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and density functional theory (DFT). The W 4f and S 2p NAP-XPS spectra suggest that hydrogen makes physisorption on the WS2 active surface at room temperature and chemisorption on tungsten atoms at temperatures above 150 °C. DFT calculations show that a hydrogen molecule physically adsorbs on the defect-free WS2 monolayer, while it splits and makes chemical bonds with the nearest tungsten atoms on the sulfur point defect. The hydrogen adsorption on the sulfur defect causes a large charge transfer from the WS2 monolayer to the adsorbed hydrogen. In addition, it decreases the intensity of the in-gap state, which is generated by the sulfur point defect. Furthermore, the calculations explain the increase in the resistance of the gas sensor when hydrogen interacts with the WS2 active layer.

Pressure release technique versus placebo applied to cervical and masticatory muscles in patients with chronic painful myofascial temporomandibular disorder: A randomised clinical trial.

BACKGROUND: The therapeutic approach to myofascial TMD should focus on pain relief and rehabilitation of function. OBJECTIVE: This study investigated whether pressure release technique (PRT) is effective for reducing pain in people with chronic myofascial temporomandibular disorders (TMD). METHODS: A single-blinded randomised parallel-group trial, with 3 months follow-up was conducted. A total of 72 patients were randomly allocated to receive PRT or sham PRT. Primary outcome was pain assessed with a visual analogue scale (VAS). Secondary outcomes included pressure pain thresholds (PPTs), range of opening of the mouth (ROM), Neck Disability Index (NDI), Pain Catastrophizing Scale (PCS), Tampa Scale for Kinesiophobia (TSK-11), State-Trait Anxiety Index (STAI) and State-Trait Depression Index (ST-DEP). All parameters were assessed at baseline, at the end of the treatment and at 3 months follow-up. Statistical analysis was performed by ANOVA. RESULTS: There were significant main effects of time, group and interaction between time and group (F ≥ 21.92; p < .001) on VAS pain. Post hoc tests showed a significant reduction in VAS pain scores in the PRT group (≥31.9%; p < .001). Effect sizes were moderate in the PRT group at all follow-up periods (≥1.25 Cohen's d). Also, there were significant effects of time in secondary outcomes (F ≥ 9.65; p < .001), and there were also interactions between time and group (F ≥ 3.82; p < .002) with better effects in the PRT group. CONCLUSIONS: The inclusion of PRT to conventional management with occlusal splints and self-care management appears to be effective to improve self-reported levels of pain in patients with chronic myofascial TMD pain. Retrospectively registered (ClinicalTrials.gov: NCT03619889).

Parp Inhibitors and Radiotherapy: A New Combination for Prostate Cancer (Systematic Review).

PARPi, in combination with ionizing radiation, has demonstrated the ability to enhance cellular radiosensitivity in different tumors. The rationale is that the exposure to radiation leads to both physical and biochemical damage to DNA, prompting cells to initiate three primary mechanisms for DNA repair. Two double-stranded DNA breaks (DSB) repair pathways: (1) non-homologous end-joining (NHEJ) and (2) homologous recombination (HR); and (3) a single-stranded DNA break (SSB) repair pathway (base excision repair, BER). In this scenario, PARPi can serve as radiosensitizers by leveraging the BER pathway. This mechanism heightens the likelihood of replication forks collapsing, consequently leading to the formation of persistent DSBs. Together, the combination of PARPi and radiotherapy is a potent oncological strategy. This combination has proven its efficacy in different tumors. However, in prostate cancer, there are only preclinical studies to support it and, recently, an ongoing clinical trial. The objective of this paper is to perform a review of the current evidence regarding the use of PARPi and radiotherapy (RT) in PCa and to give future insight on this topic.