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Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.

The dynamics of hydrogen bond formation and breakage for water in the vicinity of water/hydrocarbon liquid interfaces is studied using molecular dynamics simulations. Several liquid alkanes are considered as the hydrocarbon phase in order to determine the effects of their chain length and extent of branching on the properties of the adjacent water phase. In addition to defining the interface location in terms of the laboratory-frame density profiles, the effects of interfacial fluctuations are considered by locating the interface in terms of the proximity of the molecules of the other phase. We find that the hydrogen bond dynamics of interfacial water is weakly influenced by the identity of the hydrocarbon phase and by capillary waves. In addition to calculating hydrogen bond time correlations, we examine how the hydrogen bond dynamics depend on local coordination and determine the extent of cooperativity in the population relaxation of the hydrogen bonds that a given molecule participates in. The contributions of translational diffusion and reorientation of molecular O−H bonds to the mechanism of hydrogen bond breakage and reformation are investigated. In previous work, we have shown that rotation of the principal axes of water is anisotropic at the interface and depends on the initial orientation of the molecule relative to the interface. Here, we extend this analysis to the reorientation of the O−H vector and to hydrogen bond time correlation. We find that hydrogen bond dynamics are also sensitive to the initial orientation of the molecules participating in the hydrogen bond. [ABSTRACT FROM AUTHOR]

Water/hydrocarbon interfaces are studied using molecular dynamics simulations in order to understand the effect of hydrocarbon branching on the dynamics of the system at and away from the interface. A recently proposed procedure for studying the intrinsic structure of the interface in such systems is utilized, and dynamics are probed in the usual laboratory frame as well as the intrinsic frame. The use of these two frames of reference leads to insight into the effect of capillary waves at the interface on dynamics. The systems were partitioned into zones with a width of 5 Å, and a number of quantities of dynamical relevance, namely, the residence times, mean squared displacements, the velocity auto correlation functions, and orientational time correlations for molecules of both phases, were calculated in the laboratory and intrinsic frames at and away from the interface. For the aqueous phase, translational motion is found to be (a) diffusive at long times and not anomalous as in proteins or micelles, (b) faster at the interface than in the bulk, and (c) faster upon reduction of the effect of capillary waves. The rotational motion of water is (a) more anisotropic at the interface than in the bulk and (b) dependent on the orientation of the covalent O−H bond with respect to the plane of the interface. The effect of hydrocarbon branching on aqueous dynamics was found to be small, a result similar to the effect on the interfacial water structure. The hydrocarbon phase shows a larger variation for all dynamical probes, a trend consistent with their interfacial structure. [ABSTRACT FROM AUTHOR]

The collective polarizability anisotropy dynamics in a set of three aromatic liquids, benzene (Bz), hexafluorobenzene (HFB), and 1,3,5-trifluorobenzene (TFB), has been studied by molecular dynamics simulation. These liquids have very similar shapes, but different electrostatic interactions due to opposite polarities of C−H and C−F bonds, giving rise to different local intermolecular structures in the liquid phase. We have investigated how these structural arrangements affect polarizability anisotropy dynamics observed in optical Kerr-effect (OKE) spectroscopy. We have modeled the interaction-induced polarizability with the first-order dipole-induced dipole approximation, with the molecular polarizability distributed over the carbon sites. Local contributions to the librational OKE spectrum were computed separately for molecules participating in parallel or perpendicular relative orientations within the first coordination shell. We found that the relative locations of parallel and perpendicular librational bands of the OKE spectra are closely related to the corresponding pair energy distributions of the closest four neighbors of a given molecule, corresponding to a model of a harmonic oscillator in a cage of nearest neighbors. This model predicts higher librational frequencies for more attractive intermolecular interactions, which in all three liquids correspond to parallel local arrangements. On the diffusive orientational time scale, all three liquids exhibit slower relaxation of molecules in parallel arrangements, although the difference in relaxation rates is substantial only in TFB, which has the strongest tendency toward parallel stacking. The analysis of the collective polarizability relaxation was performed using two different approaches, the projection scheme (J. Chem. Phys.1980, 72, 2801) and the theory developed by Steele (Mol. Phys.1987, 61, 1031) for the second time derivatives applied to collective time correlations. Both approaches allow the decomposition of the OKE response into contributions from orientational relaxation and other dynamical processes. We find that they lead to different predictions on how the response depends on collective reorientation and processes arising from fluctuations in the interaction-induced polarizability. We discuss the reasons for these differences and the advantages and disadvantages of the two analysis schemes. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation are performed for the water/hydrocarbon system to study the effect of hydrocarbon branching on interfacial properties. The following two series of hydrocarbons are considered:  (1) n-pentane, 2-methyl pentane, and 2,2,4-trimethyl pentane (constant chain length) and (2) n-octane, 2-methyl heptane, and 2,2,4-trimethyl pentane (constant molecular mass). With a simple algorithm for identification of surface sites and mapping nonsurface sites to these surface sites, intrinsic profiles were constructed with respect to the surface layer. Intrinsic density profiles for water and hydrocarbons with respect to the hydrocarbon and water surface, respectively, resemble density profiles of liquids in the presence of a wall. Order parameters were used to study orientation of molecules with respect to the surface normal and the hydrogen bond network was characterized in terms of the number of hydrogen bonds per water molecule and percentage of hydrogen bonded molecules in the first coordination shell. The corresponding intrinsic profiles were obtained. The O−H bond for surface water was found to have two preferential orientations, pointing toward the hydrocarbon phase and parallel to the interface. Hydrocarbon molecules in series 1 orient along the interface with the more branched molecule better aligned. For molecules in series 2, the larger molecular length reduces the alignment of molecules along the interface. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations of a probe solute (coumarin C153) in supercritical fluoroform are used to study time-dependent solute−solvent interactions. We study the dynamics of solvent reorganization in response to electronic excitation of C153 at a temperature of 1.03 Tc(the critical temperature) and a series of densities above and below the critical density. Simulations of a two-site and five-site models of fluoroform are presented and compared. The time-dependent solvation response after solute electronic excitation is studied in the two cases, and the five-site results present an earlier onset of exponential decay that is closer to what is expected to be the experimental response. This is confirmed by comparison to experiment. In addition to obtaining the solvation response from nonequilibrium MD trajectories, approximate solvation responses were obtained from equilibrium time correlations of the fluctuations in the solvation energy change in the presence of ground- and excited-state solutes. For the five-site model, the equilibrium excited-state response shows stronger density dependence than the ground-state one. The nonequilibrium response appears to have an intermediate decay rate between the two equilibrium functions. The solute-partial-charge-solvent-induced-dipole interaction was also taken into account by means of a perturbative approach, which improved the agreement with experimental measurements available at densities corresponding to 1.4−1.6 c(where cthe critical density). From the comparison between the two models, it is possible to conclude that an atomistic description is necessary for correctly representing the portion of solvation dynamics that is related to reorientation. This consideration is supported by providing results for orientational time correlation functions and by comparing the correlation times with the experimental ones. [ABSTRACT FROM AUTHOR]

We present a study of local density augmentation around an attractive solute (i.e., giving rise to more attractive interaction with the solvent than solvent−solvent interactions) in supercritical fluoroform. This work is based on molecular dynamics simulations of coumarin 153 in supercritical fluoroform at densities both above and below the critical density, ranging from dilute gaslike to liquidlike, at a reduced temperature (T/Tc) of 1.03. We focused on studying the structure of the solvation shell and the variation of the solute electronic absorption and emission shifts with density. Quantum calculations at the density functional theory (DFT) level were run on the solute in the ground state, and time-dependent DFT calculations were performed in the solute excited state in order to determine the solute−solvent potential parameters. The results obtained for the Stokes shift are in agreement with the experimental measurements. To evaluate local density augmentation from simulations, we used two different definitions, one based on the solvation number and the other derived from solvatochromic shifts. In the former case, the agreement with experimental results is good, while, in the latter case, better agreement is achieved by perturbatively including the induced-dipole contribution to the solvation energy. [ABSTRACT FROM AUTHOR]

Hungary lies near the northern border of the apricot growing area, so frost hardiness is a decisive factor for the reliability of production. Both the development and loss of frost hardiness take place gradually in the overwintering organs, depending on the hereditary traits of the cultivars and the prevailing environmental conditions. Among the overwintering organs the flower buds are the most sensitive to frost. The frost hardiness of the flower buds of three Hungarian cultivars (Ceglédi bíborkajszi, Gönci magyar kajszi and Rózsakajszi C. 1406) was determined using artificial freezing tests during the dormancy period in 11 years. Mathematical models were developed to describe changes in frost hardiness of the flower buds in each cultivar. Ambient temperatures have a significant effect on the hardening and dehardening of flower buds, so it is important to study this trait as many years as possible. Based on the 11 years data characteristic features of frost hardiness of 3 apricot cultivars could be described accurately. Based on the results obtained the hardening process in the flower buds of apricot cultivars can be divided into two distinct phases. Tendencies in the changing of frost hardiness of 3 studied cultivars were similar, but significant differences were detected between them.

Biological active compounds and valuable characteristics of some apple varieties and candidates were measured in our trials. Fruits of ’Rosmerta’, ’Hesztia’, ’Cordelia’ and ’Artemisz’ are recommended to enrich the Hungarian assortments for fresh consumption and choice of new tastes. Based on examined parameters it can be assumed that novel Hungarian resistant varieties are suitable for juice and fruit concentrate production, and due to high pectin content of their remaining pomace these varieties can be raw material of pectin production as well as they are also suitable for jam production mixed with other fruit species. Furthermore, functional food industrial product having high quality can be produced by using novel resistant varieties because of their high pectin and polyphenol content. Beside of their high market value their suitability for growing among orchard conditions is confi rmed by lower costs of production because of less plant protection treatments.

Sour cherry production in the world is increasing gradually. Profitable production, i.e. yield, depends largely on weather conditions. If Hungary wishes to keep up with the most successful countries, attention should be paid to the weather during the dormancy period, being definitely decisive from the points of view of quality as well as quantity. In order to predict the expected risk factors, characterisation of the most important weather parameters is necessary. For that purpose, the database of the Institute of Research and Extension Service for Fruit Growing at Újfehértó Ltd. has been utilised. Records of weather conditions were collected throughout the period 1984-2005, i.e. daily minimum, maximum and mean temperatures (°C), and phenological diary of sour cherry varieties ’Újfehértói fürtös’, ’Kántorjánosi’ and ’Debreceni bôtermô’. For the future expectations study we have used the RegCM3.1 regional climate model with 10 km resolution. Data of 4 indicators have been traced: Average temperatures, Number of days without frost, Maximum length of periods without frost, Maximum length of frosty period. On the one hand, we surveyed the changes; on the other hand, estimates have been attempted for the future changes expected during the following decades.

There are three main pear production regions in Hungary. The most relevant is theWest-Transdanubian (Zala, Vas and Gyôr-Moson-Sopron counties), where up to 30% of total pear production occurs. The second most productive region is Pest County, where pear is grown mostly in gardens and garden plots, resulting in 15-20% of Hungarian production. In the northern Hungarian region (Bodrog valley in Borsod-Abaúj-Zemplén, Heves and Nógrád counties), the microclimate is perfect for optimal pear production. In our analysis, we focused on four plantations that are dominant in pear production in Hungary. Two of them are situated in south-western Hungary, one of them is in South Transdanubia and one is in North Hungary. Considering the personal attitude of the decision maker towards risk, the best alternative is ‘Williams’ in Alsóberecki, as the yield risk is the lowest with this variety, while the second best alternative is ‘Bosc Beurre,’ also produced in Alsóberecki. This is an irrigated area, and this fact evidently decreases the yield risk. The highest risk is in Bánfapuszta and in Zalasárszeg, for the non-irrigated ‘Williams’ variety. The highest yield with the lowest risk can be obtained with irrigation. Nevertheless, in the case that relevant data are available, and by incorporating cost and expected profit data, the stochastic dominance method is suitable for financial risk assessment, as well.

Grapevine bloom happens between end of May and the middle of June in Hungary. However, climate change in the past decades and the occurring weather anomalies can modi fy this date to a diverse degree. Among the weather factors, the bloom starting dates of grapevine depend mostly on temperature and relative humidity of air. There can be significant differences between North American and East Asian grapevine varieties, and of course, the early and late ripening varieties. ln this approach we investigated the starting dates of bloom between 2000 and 2004 for grapevine varieties grown in Helvecia, as well as the effectiveness of a temperature sum model. The model is based on the widely accepted cumulated heat sum concept, and the optimization was made for the least standard deviation in days as well as on the least average absolute deviation in days and on the least maximum deviation in days. The model is connected directly to a similar model for the budburst date of the same plantings (Hlaszny & ladanyi, 2009). We set the optimum lower base temperature to I 0.45 °C and the upper base temperature to 26 °C. The absolute values of the differences between the observations and the model estimations move between one and six days with an average of 1.81 days

This paper summarizes the main effects of extreme weather events on agricultural production and demonstrates their economic consequences. For cost-benefit analysis of economic impacts and for determination of risk levels simulation models are needed that contains the relationship between product line levels and elements. WIN-SIM model is developed for this goal, specialized for wine production. The model is suitable to analyze the market share, the cost and income relations as well as the relation structure of the product lines. The four levels of the model (site, vine growing, wine production and wine market levels) have individual values added from the aspect of end product, where the product line sets out from the site level and gets through the levels up to the consumer segments. Theoretically, all elements can be connected to any element of the next level and sublevel, but there are “prohibited contacts” because of professional, regulation or production practice reasons.

County Szabolcs-Szatmár-Bereg produces more than the half of the total sour cherry grown in Hungary. Successful production, i.e. yield, depends largely on weather conditions. Most attention should be paid to the weather during the blooming period, being most decisive from the points of view of quality as well as quantity. In order to predict yields expected, the characterisation of the most important weather parameters is necessary. For that purpose, the database of the Institute of Research and Extension Service for Fruit Growing at Újfehértó Ltd. has been utilised. Records of weather conditions were collected throughout the period 1984-2005, i.e. daily minimum, maximum and mean temperatures (°C), precipitation (mm), and phonological diary of sour cherry varieties ’Újfehértói fürtös’, ’Kántorjánosi’ and ’Debreceni bôtermô’. Data of 7 indicators have been traced: number of frosty days, the absolute minimum temperatures, means of minimum temperatures, number of days when daily means were above 10°C, means of maximum temperatures, number of days without precipitation, and number of days when precipitation was more than 5 mm. On the one hand, we surveyed the changes; on the other hand, estimates have been attempted for the future changes expected during the following decades. The indicators being associated with certain risky events may serve for the prediction of the future recommendations to prevent damages.

Experiences of the last decades showed univocally that the climatic changes, especially the warming up, influenced clearly the phenology, i.e. speed of growth and development of plants. To check the effects, the phenological studies became a topic of special interest. Our research has been performed at Újfehértó, the Research Institute of Fruit Growing and Extension, where the respective database accumulated observations during the period 1984–2005, where the meteorological data as well as the parallel phenological diary referring to the varieties ’Újfehértói fürtös’, ’Kántorjánosi’ and ’Debreceni bôtermô’ during the period 1984–1991 have been utilised. The method of calculating the sum of daily mean temperatures, “degree days”, is based on the observation that the plants are able to utilise cumulatively – in growth and development – the temperature above a set basic temperature. Our phenology model examined the correlation between the sum of degree days and the date of sprouting (budburst). The basic temperature has been determined by optimization, above which (threshold temperature) the accumulation of daily means was most active, or alternatively, below which the daily means are most sensitively expressed in the phenology. The model has been extended to the calculation of the end of rest period (endodormancy) – by optimization as well. Our phenology model will be suitable for two main purposes: for estimating the time of budburst for the Hungarian region during the next decades calculated on the basis of regionally downscaled climate models; on the other hand, by applying our model, the risk of damage caused by spring frosts could be estimated more exactly than earlier.

Long term data of hail events of three meteorological stations (Budapest, Debrecen and Szeged) were investigated. The hail event frequencies show significant differences in the time period 1901–2000 when the first and the second half of the century are compared. The frequencies of hail events are higher in the first half of the century in case of Debrecen and Szeged while it is higher in the second 50 years for Budapest. None of the frequencies of hail events in between 2001–2008 are significantly higher, though the average of precipitation fell during these events is higher except for Szeged. We have found that the results about the monthly distribution of hail events differ from the ones in the literature; the ratio of hail events is significantly less in the vegetation period.

Importance: Although differences in the prevalence of key cancer-specific somatic mutations as a function of genetic ancestry among patients with cancer has been well-established, few studies have addressed the practical clinical implications of these differences for the growing number of biomarker-driven treatments., Objective: To determine if the approval of precision oncology therapies has benefited patients with cancer from various ancestral backgrounds equally over time., Design, Setting, and Participants: A retrospective analysis of samples from patients with solid cancers who underwent clinical sequencing using the integrated mutation profiling of actionable cancer targets (MSK-IMPACT) assay between January 2014 and December 2022 was carried out. The annual fraction of patients per ancestral group with at least 1 level 1 biomarker was calculated for FDA drug approvals from January 1998 to December 2023. Analysis began in January 2024., Main Outcomes and Measures: For each patient, genetic ancestry was quantitatively inferred, and patients were grouped based on predominant reference ancestry. OncoKB was used to identify all Food and Drug Administration (FDA)-recognized somatic biomarkers associated with FDA-approved therapies (level 1 biomarkers) in each tumor sample., Results: Overall, the study included 59 433 patients. The approval of the EGFR-tyrosine kinase inhibitor erlotinib for patients with EGFR-mutant lung cancers in 2013 disproportionately benefited patients of East Asian and South Asian ancestries, leading to higher patient fractions with level 1 biomarkers in these ancestral groups compared with other populations. Although the increase in precision oncology drug approvals from 2019 to 2020 had a notable positive impact on clinical actionability for patients of European ancestry, patients of African ancestry had the lowest fraction of level 1 biomarkers compared with other groups from 2019 onward., Conclusion and Relevance: This study systematically assessed and compared temporal changes in genomic biomarker-based eligibility for precision oncology therapies as a function of inferred genetic ancestry derived from DNA sequencing data. Despite the accelerated rate of FDA approvals for precision oncology therapies over the past decade, measurable differences in biomarker-based drug eligibility among patient ancestral groups exist. These differences may exacerbate the systemic disparities in clinical outcomes in patients of African ancestry due to existing deficiencies in their access to cancer care.

Histologic features, including architectural patterns, cytologic features, and 2021 World Health Organization nuclear grade have been shown to have prognostic significance in epithelioid diffuse pleural mesothelioma (DPM). Biphasic and sarcomatoid DPM, regardless of morphology, have worse outcomes. These prognostic findings are well-established but correlation of architectural patterns, cytologic features, and nuclear grade with genetic alterations has not been well studied. To investigate relationships between histologic findings and genomic alterations, 128 treatment-naïve DPM specimens (70% epithelioid, 23% biphasic and 6.3% sarcomatoid) with next generation sequencing data were retrospectively reviewed. Alterations in BAP1 were the most common genomic alteration (n=62, 48%), followed by CDKN2A (n=49, 38%) and NF2 (n=38, 30%). NF2 alterations were significantly more frequent in biphasic DPM (53% in biphasic versus 25% in sarcomatoid and 22% in epithelioid; p=0.005). In epithelioid DPM, TP53 alterations were associated with presence of prognostically unfavorable histology, including micropapillary or solid architecture, pleomorphic features and high nuclear grade. Tumors with low tumor infiltrating lymphocytes had a higher rate of BAP1 alterations compared to tumors with higher levels of tumor infiltrating lymphocytes (67% versus 30%; p=0.002). The findings of this study enhance our understanding of the relationships among prognostically significant histologic and molecular features of DPM and provide preliminary data to support increased integration of these findings in clinical diagnosis of pleural mesothelioma., (Copyright © 2025. Published by Elsevier Inc.)

Comprehensive molecular profiling by next-generation sequencing has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT TM . Special emphasis is given to the use of residual supernatant cell-free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples are similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples have excellent performance overall, low-level cross-contamination is identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples have negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy, delivered successful results in 71% of cases where tumor tissue from CB was depleted., Competing Interests: Competing interests: C.V. reports intellectual property rights and equity interest in Paige.AI, Inc. A.R.B. has ownership/equity interests in Johnson and Johnson. M.B. has received advisory or consulting fees from AstraZeneca, Eli Lilly and Company, and PetDx, Inc. M.L. has received advisory or consulting fees from Takeda Oncology, Janssen Pharmaceuticals, AstraZeneca, ADC Therapeutics, Paige.AI, Merck, Bayer, and Lilly Oncology and has received research funding from Loxo Oncology, Helsinn Therapeutics, Merus NV, Elevation Oncology, and Rain Therapeutics. O.L. has received advisory or consulting fees from Hologic and Janssen Research & Development, LLC. M.A. has received advisory or consulting fees from Axis Medical Education, Clinical Education Alliance, LLC, Merck Sharp & Dohme, PeerView Institute for Medical Education (PVI), Physicians’ Education Resource, RMEI Medical Education, LLC, and Roche. The following Authors declare no competing interests: D.K., S.Y., S.N., K.N., R.F., N.R., I.R., J.C., and A.Y., (© 2024. The Author(s).)

Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. Previous work has demonstrated that next-generation sequencing data can be used to identify samples with MSI-high phenotype. However, low tumor purity, as frequently observed in routine clinical samples, poses a challenge to the sensitivity of existing algorithms. To overcome this critical issue, we developed MiMSI, an MSI classifier based on deep neural networks and trained using a dataset that included low tumor purity MSI cases in a multiple instance learning framework. On a challenging yet representative set of cases, MiMSI showed higher sensitivity (0.895) and auROC (0.971) than MSISensor (sensitivity: 0.67; auROC: 0.907), an open-source software previously validated for clinical use at our institution using MSK-IMPACT large panel targeted NGS data. In a separate, prospective cohort, MiMSI confirmed that it outperforms MSISensor in low purity cases (P = 8.244e-07)., Competing Interests: Competing interests: John Ziegler is an employee of MongoDB, New York. Jaclyn F. Hechtman is an employee of Caris Life Sciences and has received consulting fees from Pfizer. Ryan N. Ptashkin is an employee of Natera. Gowtham Jayakumaran is an employee of Guardant Health. Sumit Middha is an employee of Adaptimmune. Shweta S. Chavan is an employee of Repertoire Immune Medicines, Cambridge, MA. Chad Vanderbilt has equity, Intellectual Property Rights, Professional Services and Activities (uncompensated) for Paige.AI. Deborah DeLair is an employee of Northwell Health, Greenvale, NY. Jinru Shia has been engaged in Professional Services and Activities (uncompensated) for Paige.AI. Nicole DeGroat is an employee of Regeneron Pharmaceuticals, Tarrytown, NY. Ryma Benayed is an employee of AstraZeneca, New York. Marc Ladanyi received advisory board compensation from Merck, Bristol-Myers Squibb, Takeda, Bayer, Lilly Oncology, and Paige.AI, and research support from LOXO Oncology and Helsinn Healthcare. Michael F. Berger received consulting fees from Eli Lilly, AstraZeneca, and Paige.AI, grant support from Boundless Bio, and has intellectual property rights in SOPHiA Genetics. Thomas J. Fuchs is the founder, chief scientist, and shareholder of Paige.AI and is an employee of Elli Lilly and Company. A. Rose Brannon has intellectual property rights in SOPHiA Genetics. Ahmet Zehir is an employee of Natera and received honoraria from Illumina. The remaining authors declare no competing interests., (© 2024. The Author(s).)

The canonical model of tumor suppressor gene (TSG)-mediated oncogenesis posits that loss of both alleles is necessary for inactivation. Here, through allele-specific analysis of sequencing data from 48,179 cancer patients, we define the prevalence, selective pressure for, and functional consequences of biallelic inactivation across TSGs. TSGs largely assort into distinct classes associated with either pan-cancer (Class 1) or lineage-specific (Class 2) patterns of selection for biallelic loss, although some TSGs are predominantly monoallelically inactivated (Class 3/4). We demonstrate that selection for biallelic inactivation can be utilized to identify driver genes in non-canonical contexts, including among variants of unknown significance (VUSs) of several TSGs such as KEAP1. Genomic, functional, and clinical data collectively indicate that KEAP1 VUSs phenocopy established KEAP1 oncogenic alleles and that zygosity, rather than variant classification, is predictive of therapeutic response. TSG zygosity is therefore a fundamental determinant of disease etiology and therapeutic sensitivity., Competing Interests: Declaration of interests M.A.P. reports stock ownership in Amgen. Y.R.M.-G. reports travel, accommodation, and expenses from AstraZeneca and Loxo Oncology/Eli Lilly. She acknowledges honoraria from Virology Education and Projects in Knowledge (for a CME program funded by an educational grant from Amgen). She acknowledges associated research funding to the institution from Mirati Therapeutics, Loxo Oncology at Eli Lilly, Elucida Oncology, Taiho Oncology, Hengrui USA, Ltd/Jiangsu Hengrui Pharmaceuticals, Luzsana Biotechnology, Endeavor Biomedicines, and AbbVie. She is an employee of Memorial Sloan Kettering Cancer Center, which has an institutional interest in Elucida. She acknowledges royalties from Rutgers University Press and Wolters Kluwer. She acknowledges food/beverages from Endeavor Biomedicines. D.B.S. reports personal fees from Pfizer, Scorpion Therapeutics, FORE Therapeutics, Function Oncology, Fog Pharma, Elsie Biotechnologies, Rain Oncology, and BridgeBio outside the submitted work. M.F.B. declares consulting activity from Astrazeneca, Eli Lilly, and Paige AI. A.J.S. reports grants and personal fees from BMS, Merck, Iovance Biotherapeutics, and Amgen; personal fees from Johnson & Johnson, KSQ Therapeutics, Enara Bio, Perceptive Advisors, Oppenheimer and Co, Umoja Biopharma, Legend Biotech, Prelude Therapeutics, Immunocore, Lyell Immunopharma, and Heat Biologics; and grants from GSK, PACTpharma, Achilles Therapeutics, and Harpoon Therapeutics outside of the submitted work., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Aims: Although molecular tests developed for a growing list of oncogenic alterations have significantly aided in the classification of head and neck carcinomas, tumours in which prototypical histologic and immunophenotypic features are lacking or only partially developed continue to pose diagnostic challenges. Searching for known diagnostic and therapeutic targets by clinical next-generation sequencing (NGS) assays can often lead to new discoveries., Methods and Results: We present our institutional experience in applying targeted RNA NGS in 36 head and neck carcinomas that were morphologically difficult to classify between 2016 and 2023. The patients ranged in age from 5 to 83 years (median, 64), with the majority of tumors occurring in the major salivary glands and the sinonasal tract. Overall, seven (19%) cases showed unusual gene rearrangements, including five novel alterations: MON2::STAT6 in a hard palate adenocarcinoma with mucinous features, POC5::RAF1 in apocrine intraductal carcinoma of the lacrimal gland, EWSR1::CDADC1 fusion in a basaloid carcinoma of the submandibular gland, NFATC2::NUTM2B in myoepithelial carcinoma, and NSD3::NCOA2 fusion in a peculiar high-grade carcinoma with a peritheliomatous growth pattern, and focal myogenic differentiation. Potential therapeutic actionability was identified in three cases (RAF1 and FGFR2 fusions)., Conclusion: These findings broaden the current spectrum of gene rearrangements in head and neck carcinomas and support the utility of clinical NGS in identifying unusual, actionable alterations in diagnostically challenging cases., (© 2024 John Wiley & Sons Ltd.)

Background: Approximately 10% of lung adenocarcinomas (LUAD) have mucinous histology (LUADMuc), which is associated to a light/absent smoking history and a high prevalence of KRAS mutations. We sought to characterize LUADMuc by comparing it to LUAD without mucinous histology (LUADnon-muc) and determine the relative benefit of current treatments., Patients and Methods: Patients with LUAD from five institutions and TCGA PanCancer Atlas classified as LUADMuc or LUADnon-muc were included. Clinicopathologic, genomic, immunophenotypic, transcriptional features, and treatment outcomes were compared between LUADMuc and LUADnon-muc., Results: Of 4,082 patients with LUAD, 9.9% had LUAD Muc . Compared to LUAD non-muc , patients with LUAD Muc had a lighter smoking history (median: 15 vs 20 pack-years, P=0.008), lower PD-L1 TPS (median: 0% vs 5%, P<0.0001), and lower tumor mutation burden (median: 6.8 vs 8.5 mutations/megabase, P<0.0001). Mutations in KRAS, NKX2-1 (TTF-1), STK11, SMARCA4, GNAS, and ALK rearrangements were enriched in LUAD Muc , while TP53, EGFR, BRAF, and MET mutations were enriched in LUAD non-muc . At stage IV diagnosis, LUAD Muc was more likely to have contralateral lung metastasis (55.2% vs 36.9%, P<0.0001) and less likely to have brain metastases (23.3% vs 41.9%, P<0.0001). Compared to LUAD non-muc , LUAD Muc cases showed lower intratumor CD8 + , PD-1 + , CD8 + PD-1 + , and FOXP3 + cells. Among metastatic cases receiving ICIs, compared to LUAD non-muc (N=1,511), LUAD Muc (N=112) had lower objective response rate (ORR, 8.4% vs 25.9%, P<0.0001), and shorter median progression-free survival (mPFS, 2.6 vs 3.9 months, P<0.0001) and overall survival (mOS, 9.9 vs 17.2 months, P<0.0001). Similarly, patients with LUAD Muc had worse outcomes to chemo-immunotherapy. LUAD Muc (N=18) and LUAD non-muc (N=150) had similar ORR (16.7% vs 34.9%, P=0.12) and mPFS (4.6 vs 5.6 months, P=0.17) to treatment with KRAS G12C inhibitors, but LUAD Muc had shorter mOS (6.8 vs 10.8 months, P=0.018)., Conclusion: LUAD Muc represents a distinct LUAD subpopulation with unique clinicopathologic, genomic, immunophenotypic, and transcriptional features, achieving worse outcomes to standard immunotherapy-based treatments., (Copyright © 2024. Published by Elsevier Ltd.)

The digitization of health records and growing availability of tumour DNA sequencing provide an opportunity to study the determinants of cancer outcomes with unprecedented richness. Patient data are often stored in unstructured text and siloed datasets. Here we combine natural language processing annotations 1,2 with structured medication, patient-reported demographic, tumour registry and tumour genomic data from 24,950 patients at Memorial Sloan Kettering Cancer Center to generate a clinicogenomic, harmonized oncologic real-world dataset (MSK-CHORD). MSK-CHORD includes data for non-small-cell lung (n = 7,809), breast (n = 5,368), colorectal (n = 5,543), prostate (n = 3,211) and pancreatic (n = 3,109) cancers and enables discovery of clinicogenomic relationships not apparent in smaller datasets. Leveraging MSK-CHORD to train machine learning models to predict overall survival, we find that models including features derived from natural language processing, such as sites of disease, outperform those based on genomic data or stage alone as tested by cross-validation and an external, multi-institution dataset. By annotating 705,241 radiology reports, MSK-CHORD also uncovers predictors of metastasis to specific organ sites, including a relationship between SETD2 mutation and lower metastatic potential in immunotherapy-treated lung adenocarcinoma corroborated in independent datasets. We demonstrate the feasibility of automated annotation from unstructured notes and its utility in predicting patient outcomes. The resulting data are provided as a public resource for real-world oncologic research., Competing Interests: Competing interests: S.B.M. declares professional services and activities for Amgen, Clinical Care Options, Daiichi Sankyo, Elevation Oncology, MedPage Today, Novartis, Physicians’ Education Resource, Pinetree Therapeutics, Purple Biotech and Vindico Medical Education; and equity in McKesson. L.B. declares professional services and activities for the Cancer Prevention & Research Institute of Texas. M.R. declares professional services and activities (uncompensated) for Artios Pharma, AstraZeneca, Foundation Medicine, Pfizer and Tempus Labs; and professional services and activities for Change Healthcare, Clinical Education Alliance, Genome Quebec, MJH Associates and myMedEd. M.L. declares equity in and professional services and activities (uncompensated) for Paige.AI. D.B.S. declares professional services and activities for American Association for Cancer Research, BridgeBio, Fog Pharmaceuticals, Paige.AI, Pfizer, Rain Therapeutics; and equity in and professional services and activities for Elsie Biotechnologies, Fore Biotherapeutics, Function Oncology, Pyramid Biosciences and Scorpion Therapeutics. D.R.J. declares professional services and activities for AstraZeneca, Dava Oncology and MORE Health; and professional services and activities (uncompensated) for Merck & Co. D.G. declares professional services and activities for AstraZeneca, Grail, Johnson & Johnson, Med Learning Group, Medtronic and Varian Medical Systems. H.Y. declares professional services and activities for AbbVie, AstraZeneca, Black Diamond Therapeutics, Blueprint Medicines, C4 Therapeutics, Daiichi Sankyo, Ipsen Pharma, Janssen Pharmaceuticals, Taiho and Takeda Pharmaceuticals. R.Y. declares professional services and activities for Mirati Therapeutics and Zai Lab. W.A. declares professional services and activities for AstraZeneca, Clinical Education Alliance, Janssen Oncology and Touch Independent Medical Education. W.P. declares professional services and activities for Astellas. J.G.-A. declares professional services and activities for Ethicon; and equity in and professional services and activities for Intuitive Surgical. P.D.S. declares professional services and activities for the National Comprehensive Cancer Network and the National Institutes of Health. R. Levine declares equity, a fiduciary role or position and intellectual property rights in and professional services and activities (uncompensated) for Ajax Therapeutics; equity in Anovia Biosciences, Bakx Therapeutics, Epiphanes, Imago Biosciences and Syndax; professional services and activities for AstraZeneca, Genome Quebec, Goldman Sachs, Incyte, Janssen Pharmaceuticals and Jubilant Therapeutics; equity in and professional services and activities (uncompensated) for Auron Therapeutics and the Isoplexis Corporation; equity in and professional services and activities for C4 Therapeutics, Kurome Therapeutics, Mana Therapeutics, Mission Bio, Prelude Therapeutics, Scorpion Therapeutics, Zentalis Pharmaceuticals; intellectual property rights in the Cure Breast Cancer Foundation and Epizyme; professional services and activities (uncompensated) for the ECOG-ACRIN Cancer Research Group; equity and a fiduciary role or position in and professional services and activities (uncompensated) for Qiagen; and a fiduciary role or position in and professional services and activities for The Mark Foundation. C.M.R. declares professional services and activities for Amgen, AstraZeneca, Bridge Medicines, D2G Oncology, Harpoon Therapeutics and Jazz Pharmaceuticals; intellectual property rights in Daiichi Sankyo; and equity in Earli. M.F.B. declares professional services and activities for AstraZeneca and Paige.AI; professional services and activities (uncompensated) for JCO Precision Oncology and the Journal of Molecular Diagnostics; and intellectual property rights in SOPHiA GENETICS. P.R. declares professional services and activities for Biovica, Inivata, Novartis, Prelude Therapeutics and SAGA Diagnostics; professional services and activities (uncompensated) for Guardant Health, Paige.AI and Tempus Labs; and equity, a fiduciary role or position and intellectual property rights in Odyssey Biosciences. B.T.L. declares professional services and activities (uncompensated) for Amgen, the Asia Society, AstraZeneca, Bolt Biotherapeutics and Daiichi Sankyo; and intellectual property rights in Karger Publishers and Shanghai Jiao Tong University Press. G.J.R. declares professional services and activities (uncompensated) for the American Association for Cancer Research, the American Society of Clinical Oncology, Mirati Therapeutics, Pfizer, Takeda Pharmaceuticals and Verastem; and professional services and activities for Harborside Press, MJH Associates, the National Comprehensive Cancer Network, Phillips Gilmore Oncology Communications, Research to Practice and Triptych Health Partners. H.S. declares professional services and activities for Bayer, Pfizer, Regeneron Pharmaceuticals, Sanofi and WCG Oncology; and intellectual property rights in Elucida Oncology. J.S.R.-F. is an employee of AstraZeneca, has served as a consultant for Goldman Sachs, Paige.AI and REPARE Therapeutics; and has served as an adviser for Roche, Genentech, Roche Tissue Diagnostics, Ventana, Novartis, InVicro, GRAIL, Goldman Sachs, Paige.AI and Volition RX. J. Gao and M.C. are employees of Caris., (© 2024. The Author(s).)

Purpose: Well-differentiated papillary peritoneal mesothelial tumors (WDPMTs) are understudied and discrete from peritoneal mesotheliomas (PMs). We report clinicopathologic characteristics and outcomes of a large prospective WDPMT cohort., Methods: Patients with WDPMT identified between August 2007 and December 2020 were followed through January 2023. Clinical characteristics and outcomes were annotated. Overall survival (OS) was assessed from pathologic diagnosis. Germline variants were analyzed, and targeted next-generation sequencing (NGS; MSK-IMPACT) data were compared to PMs and diffuse pleural mesotheliomas (DPMs)., Results: Among 54 patients, median age at diagnosis was 55 (range 20-76), 50% were female (n = 27), and 46% were smokers (n = 25; median 8 pack/years). Most (94%, n = 51) WDPMTs were found during surgical explorations for other indications, primarily other malignancies. Two patients underwent surgical resection for WDPMT; none received systemic therapy for WDPMT. Median OS was not reached (19/54; median follow up 4.5 years). Somatic NGS was available for 35% (19/54) of patients. TRAF7 alterations were enriched in WDPMT (89%; 17/19) compared with PM (0%; 0/50; p < 0.0001) and DPM (0%; 0/74; p < 0.0001). In WDPMT compared with PM and DPM, there were less BAP1 (0% [0/0] vs. 4% [8/50] vs. 46% [34/74]; p = 0.001 and p < 0.0001, respectively) and NF2 (0% [0/0] vs. 24% [12/50] vs. 31% [23/74]; p = 0.03 and p = 0.001 respectively) alterations. Pathogenic germline variants were present in 23% (4/17) of WDPMTs., Conclusions: Well-differentiated papillary peritoneal mesothelial tumors were primarily incidental findings. There was no WDPMT-related mortality, so there was no distinct role for routine cytoreductive surgery or systemic therapy. Genomic profiles can help to differentiate WDPMT from DPM and PM., (© 2024. The Author(s).)

Purpose: Desmoplastic small round cell tumor (DSRCT) is a rare but highly aggressive soft tissue sarcoma that arises in the abdominopelvic cavity of young males. Since the discovery of EWSR1::WT1 fusion as the driver of DSRCT, no actionable genomic alterations have been identified, limiting disease management to a combination of surgery, chemotherapy, and radiation, with very poor outcomes. Herein, we evaluated ERBB2/HER2 expression in DSRCT as a therapeutic target., Experimental Design: ERBB2/HER2 expression was assessed in clinical samples and patient-derived xenografts (PDX) using RNA sequencing, RT-qPCR, and a newly developed HER2 IHC assay (clone 29D8). Responses to HER2 antibody-drug conjugates (ADC)-trastuzumab deruxtecan (T-DXd) and trastuzumab emtansine-were evaluated in DSRCT PDX, cell line, and organoid models. Drug internalization was demonstrated by live microscopy. Apoptosis was evaluated by Western blotting and caspase activity assays., Results: ERBB2/HER2 was detectable in DSRCT samples from patients and PDXs, with higher sensitivity RNA assays and improved IHC detectability using clone 29D8. Treatment of ERBB2/HER2-expressing DSRCT PDX, cell line, and organoid models with T-DXd or trastuzumab emtansine resulted in tumor regression. This therapeutic response was long-lasting in T-DXd-treated xenografts and was mediated by rapid HER2 ADC complex internalization and cytotoxicity, triggering p53-mediated apoptosis and growth arrest. Xenograft regression was associated with bystander payload effects triggering global tumor niche responses proportional to HER2 status., Conclusions: ERBB2/HER2 is a therapeutic target in DSRCT. HER2 ADCs may represent novel options for managing this exceptionally aggressive sarcoma, possibly fulfilling an urgent and historically unmet need for more effective clinical therapy., (©2024 American Association for Cancer Research.)

Crizotinib successfully overcomes MET amplification in ROS1-rearranged NSCLC after entrectinib failure.

PURPOSEThe impact of the intratumoral microbiome on immune checkpoint inhibitor (ICI) efficacy in patients with non-small-cell lung cancer (NSCLC) is unknown. Preclinically, intratumoral Escherichia is associated with a proinflammatory tumor microenvironment and decreased metastases. We sought to determine whether intratumoral Escherichia is associated with outcome to ICI in patients with NSCLC.PATIENTS AND METHODSWe examined the intratumoral microbiome in 958 patients with advanced NSCLC treated with ICI by querying unmapped next-generation sequencing reads against a bacterial genome database. Putative environmental contaminants were filtered using no-template controls (n = 2,378). The impact of intratumoral Escherichia detection on overall survival (OS) was assessed using univariable and multivariable analyses. The findings were further validated in an external independent cohort of 772 patients. Escherichia fluorescence in situ hybridization (FISH) and transcriptomic profiling were performed.RESULTSIn the discovery cohort, read mapping to intratumoral Escherichia was associated with significantly longer OS (16 v 11 months; hazard ratio, 0.73 [95% CI, 0.59 to 0.92]; P = .0065) in patients treated with single-agent ICI, but not combination chemoimmunotherapy. The association with OS in the single-agent ICI cohort remained statistically significant in multivariable analysis adjusting for prognostic features including PD-L1 expression ( P = .023). Analysis of an external validation cohort confirmed the association with improved OS in univariable and multivariable analyses of patients treated with single-agent ICI, and not in patients treated with chemoimmunotherapy. Escherichia localization within tumor cells was supported by coregistration of FISH staining and serial hematoxylin and eosin sections. Transcriptomic analysis correlated Escherichia-positive samples with expression signatures of immune cell infiltration.CONCLUSIONRead mapping to potential intratumoral Escherichia was associated with survival to single-agent ICI in two independent cohorts of patients with NSCLC.

Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patients' management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs of samples. In contrast to solid tumors, in hematologic malignancies conventional sources of normal control material (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell-free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control material, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we found that nail cfDNA is a robust germline control for paired genomic studies. In a subset of patients, nail DNA may be contaminated by tumor DNA, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1,482) than among those with lymphoid diseases (5.4%; 61/1,128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. Donor DNA was identified in 22% (11/50) of nails collected after allogeneic stem-cell transplantation. In this cohort, an association with a recent history of graft-versus-host disease was identified. These findings should be considered as a potential limitation to the use of nails as a source of normal control DNA but could also provide important diagnostic information regarding the disease process.

The characterization of genetic alterations in tumor samples has become standard practice for many human cancers to achieve more precise disease classification and guide the selection of targeted therapies. Cerebrospinal fluid (CSF) can serve as a source of tumor DNA in patients with central nervous system (CNS) cancer. We performed comprehensive profiling of CSF circulating tumor DNA (ctDNA) in 711 patients using an FDA-authorized platform (MSK-IMPACT™) in a hospital laboratory. We identified genetic alterations in 489/922 (53.0%) CSF samples with clinically documented CNS tumors. None of 85 CSF samples from patients without CNS tumors had detectable ctDNA. The distribution of clinically actionable somatic alterations was consistent with tumor-type specific alterations across the AACR GENIE cohort. Repeated CSF ctDNA examinations from the same patients identified clonal evolution and emergence of resistance mechanisms. ctDNA detection was associated with shortened overall survival following CSF collection. Next-generation sequencing of CSF, collected through a minimally invasive lumbar puncture in a routine hospital setting, provides clinically actionable cancer genotype information in a large fraction of patients with CNS tumors., (© 2024. The Author(s).)

Purpose: Even though BRAF fusions are increasingly detected in standard multigene next-generation sequencing panels, few reports have explored their structure and impact on clinical course., Experimental Design: We collected data from patients with BRAF fusion-positive cancers identified through a genotyping protocol of 97,024 samples. Fusions were characterized and reviewed for oncogenic potential (in-frame status, non-BRAF partner gene, and intact BRAF kinase domain)., Results: We found 241 BRAF fusion-positive tumors from 212 patients with 82 unique 5' fusion partners spanning 52 histologies. Thirty-nine fusion partners were not previously reported, and 61 were identified once. BRAF fusion incidence was enriched in pilocytic astrocytomas, gangliogliomas, low-grade neuroepithelial tumors, and acinar cell carcinoma of the pancreas. Twenty-four patients spanning multiple histologies were treated with MAPK-directed therapies, of which 20 were evaluable for RECIST. Best response was partial response (N = 2), stable disease (N = 11), and progressive disease (N = 7). The median time on therapy was 1 month with MEK plus BRAF inhibitors [(N = 11), range 0-18 months] and 8 months for MEK inhibitors [(N = 14), range 1-26 months]. Nine patients remained on treatment for longer than 6 months [pilocytic astrocytomas (N = 6), Erdheim-Chester disease (N = 1), extraventricular neurocytoma (N = 1), and melanoma (N = 1)]. Fifteen patients had acquired BRAF fusions., Conclusions: BRAF fusions are found across histologies and represent an emerging actionable target. BRAF fusions have a diverse set of fusion partners. Durable responses to MAPK therapies were seen, particularly in pilocytic astrocytomas. Acquired BRAF fusions were identified after targeted therapy, underscoring the importance of postprogression biopsies to optimize treatment at relapse in these patients., (©2024 American Association for Cancer Research.)

Purpose: MDM2, a negative regulator of the TP53 tumor suppressor, is oncogenic when amplified. MDM2 amplification (MDM2amp) is mutually exclusive with TP53 mutation and is seen in 6% of patients with lung adenocarcinoma (LUAD), with significant enrichment in subsets with receptor tyrosine kinase (RTK) driver alterations. Recent studies have shown synergistic activity of MDM2 and MEK inhibition in patient-derived LUAD models with MDM2amp and RTK driver alterations. However, the combination of MDM2 and RTK inhibitors in LUAD has not been studied., Methods: We evaluated the combination of MDM2 and RTK inhibition in patient-derived models of LUAD., Results: In a RET-fusion LUAD patient-derived model with MDM2amp, MDM2 inhibition with either milademetan or AMG232 combined with selpercatinib resulted in long-term in vivo tumor control markedly superior to either agent alone. Similarly, in an EGFR-mutated model with MDM2amp, combining either milademetan or AMG232 with osimertinib resulted in long-term in vivo tumor control, which was strikingly superior to either agent alone., Conclusion: These preclinical in vivo data provide a rationale for further clinical development of this combinatorial targeted therapy approach.

Cancer-associated venous thromboembolism (VTE) is a major source of oncologic cost, morbidity and mortality. Identifying high-risk patients for prophylactic anticoagulation is challenging and adds to clinician burden. Circulating tumor DNA (ctDNA) sequencing assays ('liquid biopsies') are widely implemented, but their utility for VTE prognostication is unknown. Here we analyzed three plasma sequencing cohorts: a pan-cancer discovery cohort of 4,141 patients with non-small cell lung cancer (NSCLC) or breast, pancreatic and other cancers; a prospective validation cohort consisting of 1,426 patients with the same cancer types; and an international generalizability cohort of 463 patients with advanced NSCLC. ctDNA detection was associated with VTE independent of clinical and radiographic features. A machine learning model trained on liquid biopsy data outperformed previous risk scores (discovery, validation and generalizability c-indices 0.74, 0.73 and 0.67, respectively, versus 0.57, 0.61 and 0.54 for the Khorana score). In real-world data, anticoagulation was associated with lower VTE rates if ctDNA was detected (n = 2,522, adjusted hazard ratio (HR) = 0.50, 95% confidence interval (CI): 0.30-0.81); ctDNA - patients (n = 1,619) did not benefit from anticoagulation (adjusted HR = 0.89, 95% CI: 0.40-2.0). These results provide preliminary evidence that liquid biopsies may improve VTE risk stratification in addition to clinical parameters. Interventional, randomized prospective studies are needed to confirm the clinical utility of liquid biopsies for guiding anticoagulation in patients with cancer., (© 2024. The Author(s).)

The co-occurrence of germline and somatic oncogenic alterations is frequently observed in breast cancer, but their combined biologic and clinical significance has not been evaluated. To assess the role of germline-somatic interactions on outcomes in routine practice, we developed an integrated clinicogenomic pipeline to analyze the genomes of over 4,500 patients with breast cancer. We find that germline (g) BRCA2 -associated tumors are enriched for RB1 loss-of-function mutations and manifest poor outcomes on standard-of-care, front-line CDK4/6 inhibitor (CDK4/6i) combinations. Amongst these tumors, g BRCA2 -related homologous recombination deficiency (HRD) as well as baseline RB1 LOH status promote acquisition of RB1 loss-of- function mutations under the selective pressure of CDK4/6i, causing therapy resistance. These findings suggest an alternative therapeutic strategy using sequential targeting of HRD in g BRCA- associated breast cancers through PARP inhibitors prior to CDK4/6i therapy to intercept deleterious RB1 -loss trajectories and thus suppress the emergence of CDK4/6 inhibitor resistance. More broadly, our findings demonstrate how germline-somatic driven genomic configurations shape response to systemic therapy and can be exploited therapeutically as part of biomarker-directed clinical strategies.

Small cell lung carcinoma (SCLC) is a highly aggressive malignancy that is typically associated with tobacco exposure and inactivation of RB1 and TP53 genes. Here we performed detailed clinicopathologic, genomic and transcriptomic profiling of an atypical subset of SCLC that lacked RB1 and TP53 co-inactivation and arose in never/light smokers. We found that most cases were associated with chromothripsis - massive, localized chromosome shattering - recurrently involving chromosomes 11 or 12, and resulting in extrachromosomal (ecDNA) amplification of CCND1 or co-amplification of CCND2/CDK4/MDM2, respectively. Uniquely, these clinically aggressive tumors exhibited genomic and pathologic links to pulmonary carcinoids, suggesting a previously uncharacterized mode of SCLC pathogenesis via transformation from lower-grade neuroendocrine tumors or their progenitors. Conversely, SCLC in never-smokers harboring inactivated RB1 and TP53 exhibited hallmarks of adenocarcinoma-to-SCLC derivation, supporting two distinct pathways of plasticity-mediated pathogenesis of SCLC in never-smokers.

Comprehensive molecular profiling by next generation sequencing (NGS) has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT ™ . Special emphasis is given to the use of residual supernatant cell free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples were similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples had excellent performance overall, low-level cross-contamination was identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples had negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy delivered successful results in 71% of cases where tumor tissue from CB was depleted.

Anti-PD(L)-1 inhibition combined with platinum doublet chemotherapy (Chemo-IO) has become the most frequently used standard of care regimen in patients with non-small cell lung cancer (NSCLC). The negative impact of antibiotics on clinical outcomes prior to anti-PD(L)-1 inhibition monotherapy (IO) has been demonstrated in multiple studies, but the impact of antibiotic exposure prior to initiation of Chemo-IO is controversial. We assessed antibiotic exposures at two time windows: within 60 days prior to therapy (-60 d window) and within 60 days prior to therapy and 42 days after therapy (-60 + 42d window) in 2028 patients with advanced NSCLC treated with Chemo-IO and IO monotherapy focusing on objective response rate (ORR: rate of partial response and complete response), progression-free survival (PFS), and overall survival (OS). We also assessed impact of antibiotic exposure in an independent cohort of 53 patients. Univariable and multivariable analyses were conducted along with a meta-analysis from similar studies. For the -60 d window, in the Chemo-IO group (N = 769), 183 (24%) patients received antibiotics. Antibiotic exposure was associated with worse ORR (27% vs 40%, p = 0.001), shorter PFS (3.9 months vs. 5.9 months, hazard ratio [HR] 1.35, 95%CI 1.1,1.6, p = 0.0012), as well as shorter OS (10 months vs. 15 months, HR 1.50, 95%CI 1.2,1.8, p = 0.00014). After adjusting for known prognostic factors in NSCLC, antibiotic exposure was independently associated with worse PFS (HR 1.39, 95%CI 1.35,1.7, p = 0.002) and OS (HR 1.61, 95%CI 1.28,2.03, p < 0.001). Similar results were obtained in the -60 + 42d window, and also in an independent cohort. In a meta-analysis of patients with NSCLC treated with Chemo-IO (N = 4) or IO monotherapy (N = 13 studies) antibiotic exposure before treatment was associated with worse OS among all patients (n = 11,351) (HR 1.93, 95% CI 1.52, 2.45) and Chemo-IO-treated patients (n = 1201) (HR 1.54, 95% CI 1.28, 1.84). Thus, antibiotics exposure prior to Chemo-IO is common and associated with worse outcomes, even after adjusting for other factors. These results highlight the need to implement antibiotic stewardship in routine oncology practice., (© 2024. The Author(s).)

Purpose: Diffuse pleural mesotheliomas (DPM) with genomic near-haploidization (GNH) represent a novel subtype first recognized by The Cancer Genome Atlas project; however, its clinicopathologic and molecular features remain poorly defined., Experimental Design: We analyzed clinical genomic profiling data from 290 patients with DPM using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay. Allele-specific copy number analysis was performed using the Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing (FACETS) algorithm., Results: A total of 210 patients were evaluable for loss of heterozygosity (LOH) analysis using FACETS from MSK-IMPACT tumor:normal sequencing data. In this cohort, GNH, defined as LOH across >80% of the genome, was detected in 10 cases (4.8%). Compared with non-GNH tumors, GNH DPMs were associated with younger age and less frequent self-reported history of occupational asbestos exposure. Histologically, GNH DPMs were enriched in biphasic subtype (80% vs. 14.5%) and showed abundant tumor-infiltrating lymphocytes (TILs). Genomic analysis revealed a higher frequency of TP53 alterations, whereas SETDB1 mutations were present in nearly all and only in this subset. The clinicopathologic and molecular findings were further validated in a separate cohort. Despite the younger age, patients with GNH DPMs had a shorter overall survival (10.9 vs. 25.4 months, P = 0.004); the poor prognostic impact of GNH remained significant after controlling for biphasic histology. Of three patients with GNH DPMs who received immune checkpoint blockade, two achieved a clinician-assessed partial response., Conclusions: GNH defines an aggressive subtype of mainly biphasic DPMs in younger patients with recurrent alterations in SETDB1 and TP53. The enrichment in biphasic histology and TILs, together with our preliminary immune checkpoint blockade response data and anecdotal clinical trial data, suggests that further evaluation of immunotherapy may be warranted in this subset., (©2024 American Association for Cancer Research.)

Epigenetic dependencies have become evident in many cancers. On the basis of antagonism between BAF/SWI-SNF and PRC2 in SMARCB1-deficient sarcomas, we recently completed the clinical trial of the EZH2 inhibitor tazemetostat. However, the principles of tumor response to epigenetic therapy in general, and tazemetostat in particular, remain unknown. Using functional genomics and diverse experimental models, we define molecular mechanisms of tazemetostat resistance in SMARCB1-deficient tumors. We found distinct acquired mutations that converge on the RB1/E2F axis and decouple EZH2-dependent differentiation and cell-cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest, suggests a general mechanism for effective therapy, and provides prospective biomarkers for therapy stratification, including PRICKLE1. On the basis of this, we develop a combination strategy to circumvent tazemetostat resistance using bypass targeting of AURKB. This offers a paradigm for rational epigenetic combination therapy suitable for translation to clinical trials for epithelioid sarcomas, rhabdoid tumors, and other epigenetically dysregulated cancers., Significance: Genomic studies of patient epithelioid sarcomas and rhabdoid tumors identify mutations converging on a common pathway for response to EZH2 inhibition. Resistance mutations decouple drug-induced differentiation from cell-cycle control. We identify an epigenetic combination strategy to overcome resistance and improve durability of response, supporting its investigation in clinical trials. See related commentary by Paolini and Souroullas, p. 903. This article is featured in Selected Articles from This Issue, p. 897., (©2024 American Association for Cancer Research.)

Introduction: ERBB2 amplification in lung cancer remains poorly characterized. HER2 (encoded by ERBB2) is a transmembrane tyrosine kinase capable of ligand-independent dimerization and signaling when overexpressed, and a common cause of HER2 overexpression is ERBB2 amplification. Here, we evaluated the clinicopathologic and genomic characteristics of ERBB2-amplified NSCLC and explored a HER2 antibody-drug conjugate (ADC) therapeutic strategy., Methods: Our institutional next-generation DNA sequencing data (OncoPanel) from 5769 NSCLC samples (5075 patients) were queried for cases having high-level ERBB2 amplification (≥6 copies). Clinical and demographic characteristics were extracted from the electronic medical records. Efficacy of the pan-ERBB inhibitor afatinib or HER2 ADCs (trastuzumab deruxtecan and trastuzumab emtansine) was evaluated in NSCLC preclinical models and patients with ERBB2 amplification., Results: High-level ERBB2 amplification was identified in 0.9% of lung adenocarcinomas and reliably predicted overexpression of HER2. ERBB2 amplification events are detected in two distinct clinicopathologic and genomic subsets of NSCLC: as the sole mitogenic driver in tumors arising in patients with a smoking history or as a concomitant alteration with other mitogenic drivers in patients with a light or never smoking history. We further reveal that trastuzumab deruxtecan is effective therapy in in vitro and in vivo preclinical models of NSCLC harboring ERBB2 amplification and report two cases of clinical activity of an anti-HER2 ADC in patients who acquired ERBB2 amplification after previous targeted therapy., Conclusions: High-level ERBB2 amplification reliably predicts HER2 overexpression in patients with NSCLC, and HER2 ADC is effective therapy in this population., Competing Interests: Disclosure Dr. Nishino reports receiving grants from Daiichi Sankyo, Canon Medical Systems, and Konica Minolta and consulting fees from AstraZeneca. Dr. Paweletz reports having sponsored research agreements with Daiichi Sankyo, Bicycle Therapeutics, Transcenta, Bicara Therapeutics, AstraZeneca, Intellia Therapeutics, Janssen Pharmaceuticals, Mirati Therapeutics, Array Biopharma, Bristol-Myers Squibb, Takeda Pharmaceutical Company, KSQ Therapeutics, and IMPACT Therapeutics; having received consulting fees from XSphera Biosciences; owning stocks of XSphera Biosciences; having received payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Bio-Rad. Dr. Rudin has consulted regarding oncology drug development with AbbVie, Amgen, AstraZeneca, D2G, Daiichi Sankyo, Epizyme, Genentech/Roche, Ipsen, Jazz, Kowa, Eli Lilly, Merck, and Syros; served on the scientific advisory boards of Auron, Bridge Medicines, DISCO, Earli, and Harpoon Therapeutics. Dr. Ladanyi reports receiving consulting fees from AstraZeneca. Dr. Somwar reports receiving financial support from National Institutes of Health/National Cancer Institute provided to his institution and grants and reagents from Helsinn Health Care, Merus, Elevation Oncology, and Loxo Oncology, provided to his institution for unrelated projects. Dr. Jänne reports receiving grants from AstraZeneca, Daiichi Sankyo, PUMA, Eli Lilly, Boehringer Ingelheim, Revolution Medicines and Takeda Oncology paid to this institution; consulting fees from AstraZeneca, Boehringer Ingelheim, Pfizer, Roche/Genentech, Chugai Pharmaceuticals, Eli Lilly pharmaceuticals, SFJ Pharmaceuticals, Voronoi, Daiichi Sankyo, Biocartis, Novartis, Takeda Oncology, Mirati Therapeutics, Transcenta, Silicon Therapeutics, Syndax, Nuvalent, Bayer, Esai, Allorion Therapeutics, Accutar Biotech, Abbvie, Monte Rosa, Scorpion Therapeutics, Merus, Frontier Medicines, Hongyun Biotechnology, Duality and Blueprint Medicine paid to him; stocks in Gatekeeper Pharmaceuticals; and post-marketing royalties from LabCorp paid to him and his institution. Dr. Sholl reports receiving consulting fees from AstraZeneca; research support from Bristol-Myers Squibb and Genentech provided to her institution, and consulting fees from Eli Lilly and Genentech to her institution. The remaining authors declare no conflict of interest., (Copyright © 2023 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.)

BRCA1-associated protein 1 (BAP1) has emerged as a major tumor suppressor gene in diverse cancer types, notably in malignant pleural mesothelioma (DPM), and has also been identified as a germline cancer predisposition gene for DPM and other select cancers. However, its role in the response to DNA damage has remained unclear. Here, we show that BAP1 inactivation is associated with increased DNA damage both in Met-5A human mesothelial cells and human DPM cell lines. Through proteomic analyses, we identified PRKDC as an interaction partner of BAP1 protein complexes in DPM cells and 293 T human embryonic kidney cells. PRKDC encodes the catalytic subunit of DNA protein kinase (DNA-PKcs) which functions in the nonhomologous end-joining (NHEJ) pathway of DNA repair. Double-stranded DNA damage resulted in prominent nuclear expression of BAP1 in DPM cells and phosphorylation of BAP1 at serine 395. A plasmid-based NHEJ assay confirmed a significant effect of BAP1 knockdown on cellular NHEJ activity. Combination treatment with X-ray irradiation and gemcitabine (as a radiosensitizer) strongly suppressed the growth of BAP1-deficient cells. Our results suggest reciprocal positive interactions between BAP1 and DNA-PKcs, based on phosphorylation of BAP1 by the latter and deubiquitination of DNA-PKcs by BAP1. Thus, functional interaction of BAP1 with DNA-PKcs supports a role for BAP1 in NHEJ DNA repair and may provide the basis for new therapeutic strategies and new insights into its role as a tumor suppressor., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)