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Testicular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression. Testicular germ cell tumours (TGCT) are the most common cancers in young men. Here, the authors analyse the genomic landscape of TGCT using data from the Genomics England 100,000 Genomes Project, revealing divergent evolutionary trajectories and the prevalence of human leukocyte antigen loss.

Immunotherapy in soft tissue sarcoma (STS) has experienced a surge of interest in the past decade, contributing to an expanding number of therapeutic options for this extremely heterogenous group of rare malignancies. Immune checkpoint inhibitors (CPIs) targeting the PD-1 and CTLA-4 axes have demonstrated promising responses in a select number of STS subtypes, including rarer subtypes, such as alveolar soft part sarcoma, SWI/SNF-deficient sarcomas, clear cell sarcoma, and angiosarcoma. Multiple pan-subtype sarcoma trials have facilitated the study of possible predictive biomarkers of the CPI response. It has also become apparent that certain therapies, when combined with CPIs, can enhance response rates, although the specific mechanisms of this possible synergy remain unconfirmed in STS. In addition to CPIs, several other immune targeting agents, including anti-tumour-associated macrophage and antigen-directed therapies, are now under assessment in STS with promising efficacy in some subtypes. In this article, we review the state of the art in immunotherapy in STS, highlighting the pre-clinical and clinical data available for this promising therapeutic strategy.

Solitary fibrous tumour is a rare, translocation-associated soft-tissue sarcoma that can be subclassified into typical, malignant, and dedifferentiated variants on the basis of the presence or absence of histological features that are associated with the more aggressive clinical phenotype. [...]these results must be appraised in the context of the currently low level of validation of Choi criteria as a surrogate for patient survival in soft-tissue sarcoma subtypes other than gastrointestinal stromal tumour.6 The reported discrepancy between investigators' assessments and central radiology review in the Choi response assessment of 16 (24%) of 66 evaluable solitary fibrous tumour patients (nine in the typical solitary fibrous tumour cohort and seven in the malignant or dedifferentiated solitary fibrous tumour cohort)1,2 also raises questions regarding the replicability and applicability of Choi criteria in routine clinical practice. The comparison of patient survival in this trial to historical controls is subject to the typical limitations of cross-trial comparisons, particularly given that earlier studies did not use the same rigorous delineation between variants of solitary fibrous tumour.7,8 Further work to validate the use of Choi criteria and other response assessment modalities (eg, PET-CT), for patient survival will be important to confirm the benefit of pazopanib to patients with solitary fibrous tumour.9 The collection of prospective data on patients' quality of life would add considerably to the appraisal of benefit and would provide important and useful information for funding organisations—a relevant consideration given that pazopanib is not routinely available to all patients with soft-tissue sarcoma in Europe.

Malignant peripheral nerve sheath tumours (MPNST) are aggressive sarcomas that have nerve sheath differentiation and can present at any anatomical site. They can arise from precursor neurofibroma in the context of neurofibromatosis type 1 (NF1) or as de novo and sporadic tumours in the absence of an underlying genetic predisposition. The primary therapeutic approach is most often radical surgery, with non-surgical modalities playing an important role, especially in locally advanced or metastatic cases. The aim of multimodality approaches is to optimize both local and systemic control while keeping to a minimum acute and late treatment morbidity. Advances in the understanding of the underlying biology of MPNSTs in both sporadic and NF-1-related contexts are essential for the management and implementation of novel therapeutic approaches.

Soft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research. Characterising the molecular profile of soft tissue sarcomas (STS) remains critical. Here, the authors analyse samples from 321 STS patients across 11 histological subtypes using proteomics and identify prognostic signatures that can be applied to multiple subtypes.

Opinion statement Two recently reported phase III randomised control trials (RCTs) have resulted in the registration of two new systemic therapies for advanced soft tissue sarcoma. Both of these trials’ designs were informed by phase II data that guided the selection of sensitive STS diagnoses, enabling the demonstration of benefit in certain subtypes. A number of other phase III trials reported in the last 18 months have seemingly fit into a recurrent pattern of failure—promising efficacy signals in earlier phase studies being lost in the survival follow-up of large, highly heterogeneous cohorts. Greater effort is needed to identify histological and molecularly defined subgroups associated with differential treatment response in order to avoid the tremendous disappointment and loss of resources associated with a failed phase III trial. Additionally, improvements in available treatment of advanced STS have underpinned a prolongation in overall survival (OS). Consequently, surrogate efficacy endpoints are of increasing importance to STS drug trials. Whilst progression-free survival (PFS) should arguably replace overall survival as the primary endpoint of choice in first-line studies, more work is required to provide definitive validation of surrogacy, as well as developing more sophisticated techniques of assessing radiological response and expanding the inclusion of quality-of-life-related endpoints.

Delays in peer reviewed publication may have consequences for both assessment of scientific prowess in academics as well as communication of important information to the knowledge receptor community. We present an analysis on the perspectives of authors publishing in conservation biology journals regarding their opinions on the importance of speed in peer-review as well as how to improve review times. Authors were invited to take part in an online questionnaire, of which the data was subjected to both qualitative (open coding, categorizing) and quantitative analyses (generalized linear models). We received 637 responses to a total of 6,547 e-mail invitations sent. Peer-review speed was generally perceived as slow, with authors experiencing a typical turnaround time of 14 weeks while their perceived optimal review time is six weeks. Male and younger respondents seem to have higher expectations of review speed than females and older respondents. Majority of participants attributed lengthy review times to the 'stress' on the peer-review system (i.e., reviewer and editor fatigue), while editor persistence and journal prestige were believed to speed up the review process. Negative consequences of lengthy review times appear to be greater for early career researchers and can also have impact on author morale (e.g. motivation or frustration). Competition among colleagues were also of concern to respondents. Incentivizing peer review was among the top suggested alterations to the system along with training graduate students in peer review, increased editorial persistence, and changes to the norms of peer-review such as opening the peer-review process to the public. It is clear that authors surveyed in this study view the peer-review system as under stress and we encourage scientists and publishers to push the envelope for new peer review models.

Lung-resident memory B cells (BRM cells) are elicited after influenza infections of mice, but connections to other pathogens and hosts - as well as their functional significance - have yet to be determined. We postulate that BRM cells are core components of lung immunity. To test this, we examined whether lung BRM cells are elicited by the respiratory pathogen pneumococcus, are present in humans, and are important in pneumonia defense. Lungs of mice that had recovered from pneumococcal infections did not contain organized tertiary lymphoid organs, but did have plasma cells and noncirculating memory B cells. The latter expressed distinctive surface markers (including CD69, PD-L2, CD80, and CD73) and were poised to secrete antibodies upon stimulation. Human lungs also contained B cells with a resident memory phenotype. In mice recovered from pneumococcal pneumonia, depletion of PD-L2+ B cells, including lung BRM cells, diminished bacterial clearance and the level of pneumococcus-reactive antibodies in the lung. These data define lung BRM cells as a common feature of pathogen-experienced lungs and provide direct evidence of a role for these cells in pulmonary antibacterial immunity.

AbstractObjectiveTo investigate whether vitamin D and marine derived long chain omega 3 fatty acids reduce autoimmune disease risk.DesignVitamin D and omega 3 trial (VITAL), a nationwide, randomized, double blind, placebo controlled trial with a two-by-two factorial design.SettingNationwide in the United States.Participants25 871 participants, consisting of 12 786 men ≥50 years and 13 085 women ≥55 years at enrollment.InterventionsVitamin D (2000 IU/day) or matched placebo, and omega 3 fatty acids (1000 mg/day) or matched placebo. Participants self-reported all incident autoimmune diseases from baseline to a median of 5.3 years of follow-up; these diseases were confirmed by extensive medical record review. Cox proportional hazard models were used to test the effects of vitamin D and omega 3 fatty acids on autoimmune disease incidence.Main outcome measuresThe primary endpoint was all incident autoimmune diseases confirmed by medical record review: rheumatoid arthritis, polymyalgia rheumatica, autoimmune thyroid disease, psoriasis, and all others.Results25 871 participants were enrolled and followed for a median of 5.3 years. 18 046 self-identified as non-Hispanic white, 5106 as black, and 2152 as other racial and ethnic groups. The mean age was 67.1 years. For the vitamin D arm, 123 participants in the treatment group and 155 in the placebo group had a confirmed autoimmune disease (hazard ratio 0.78, 95% confidence interval 0.61 to 0.99, P=0.05). In the omega 3 fatty acids arm, 130 participants in the treatment group and 148 in the placebo group had a confirmed autoimmune disease (0.85, 0.67 to 1.08, P=0.19). Compared with the reference arm (vitamin D placebo and omega 3 fatty acid placebo; 88 with confirmed autoimmune disease), 63 participants who received vitamin D and omega 3 fatty acids (0.69, 0.49 to 0.96), 60 who received only vitamin D (0.68, 0.48 to 0.94), and 67 who received only omega 3 fatty acids (0.74, 0.54 to 1.03) had confirmed autoimmune disease.ConclusionsVitamin D supplementation for five years, with or without omega 3 fatty acids, reduced autoimmune disease by 22%, while omega 3 fatty acid supplementation with or without vitamin D reduced the autoimmune disease rate by 15% (not statistically significant). Both treatment arms showed larger effects than the reference arm (vitamin D placebo and omega 3 fatty acid placebo).Study registrationClinicalTrials.gov NCT01351805 and NCT01169259

We present an updated mechanism for tropospheric halogen (Cl + Br + I) chemistry in the GEOS-Chem global atmospheric chemical transport model and apply it to investigate halogen radical cycling and implications for tropospheric oxidants. Improved representation of HOBr heterogeneous chemistry and its pH dependence in our simulation leads to less efficient recycling and mobilization of bromine radicals and enables the model to include mechanistic sea salt aerosol debromination without generating excessive BrO. The resulting global mean tropospheric BrO mixing ratio is 0.19 ppt (parts per trillion), lower than previous versions of GEOS-Chem. Model BrO shows variable consistency and biases in comparison to surface and aircraft observations in marine air, which are often near or below the detection limit. The model underestimates the daytime measurements of Cl2 and BrCl from the ATom aircraft campaign over the Pacific and Atlantic, which if correct would imply a very large missing primary source of chlorine radicals. Model IO is highest in the marine boundary layer and uniform in the free troposphere, with a global mean tropospheric mixing ratio of 0.08 ppt, and shows consistency with surface and aircraft observations. The modeled global mean tropospheric concentration of Cl atoms is 630 cm−3, contributing 0.8 % of the global oxidation of methane, 14 % of ethane, 8 % of propane, and 7 % of higher alkanes. Halogen chemistry decreases the global tropospheric burden of ozone by 11 %, NOx by 6 %, and OH by 4 %. Most of the ozone decrease is driven by iodine-catalyzed loss. The resulting GEOS-Chem ozone simulation is unbiased in the Southern Hemisphere but too low in the Northern Hemisphere.