Identification of a proteomic signature for predicting immunotherapy response in patients with metastatic non-small cell lung cancer.

BACKGROUND: Immunotherapy has improved survival rates in cancer patients, but identifying those who will respond to treatment remains a challenge. Recent advances in proteomic technologies have enabled the identification and quantification of nearly all expressed proteins in a single experiment. Integration of mass spectrometry with other high-throughput technologies has paved the way for comprehensive and systematic analysis of the plasma proteome in cancer, facilitating early diagnosis and personalized treatment. In this context, the objective of our study was to investigate the predictive and prognostic value of plasma proteome analysis using the SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) strategy in newly diagnosed NSCLC patients who received pembrolizumab therapy. METHODS: For this purpose, 64 newly diagnosed advanced NSCLC patients treated with pembrolizumab therapy were enrolled and blood samples were collected from all patients before and during therapy. In total 171 blood samples were collected, and plasma samples were analysed employing SWATH-MS strategy. Next, we compared the plasma protein expression of metastatic NSCLC patients prior to receiving pembrolizumab treatment and divided the cohort into two groups in order to identify a proteomic signature that allow us to predict immunotherapy response. RESULTS: Proteomic analyses by SWATH-MS strategy allow us to identified 324 differentially expressed proteins between responder and non-responder patients. In addition, we developed a predictive model and found a combination of seven proteins, including ATG9A, DCDC2, HPS5, FIL1L, LZTL1, PGTA, and SPTN2, with stronger predictive value than PD-L1 expression alone. Additionally, survival analyses showed that low levels of ATG9A, DCDC2, and HPS5 were associated with longer progression-free survival (PFS) and overall survival (OS), while low levels of SPTN2 were associated with worse OS. CONCLUSIONS: Our work highlights the potential value of proteomic technologies to detect predictive biomarkers in blood samples of NSCLC patients. These analyses shed light on the correlation between the response to immunotherapy in patients with NSCLC and the set of 7 proteins.

Intratumoral delivery of immunotherapy to treat breast cancer: current development in clinical and preclinical studies.

Breast cancer poses one of the largest threats to women's health. Treatment continues to improve for all the subtypes of breast cancer, but some subtypes, such as triple negative breast cancer, still present a significant treatment challenge. Additionally, metastasis and local recurrence are two prevalent problems in breast cancer treatment. A newer type of therapy, immunotherapy, may offer alternatives to traditional treatments for difficult-to-treat subtypes. Immunotherapy engages the host's immune system to eradicate disease, with the potential to induce long-lasting, durable responses. However, systemic immunotherapy is only approved in a limited number of indications, and it benefits only a minority of patients. Furthermore, immune related toxicities following systemic administration of potent immunomodulators limit dosing and, consequently, efficacy. To address these safety considerations and improve treatment efficacy, interest in local delivery at the site of the tumor has increased. Numerous intratumorally delivered immunotherapeutics have been and are being explored clinically and preclinically, including monoclonal antibodies, cellular therapies, viruses, nucleic acids, cytokines, innate immune agonists, and bacteria. This review summarizes the current and past intratumoral immunotherapy clinical landscape in breast cancer as well as current progress that has been made in preclinical studies, with a focus on delivery parameters and considerations.

Estimated Impact of Nirsevimab on the Incidence of Respiratory Syncytial Virus Infections Requiring Hospital Admission in Children < 1 Year, Weeks 40, 2023, to 8, 2024, Spain.

BACKGROUND: Data from the sentinel surveillance system of severe acute respiratory infections in Spain were used to estimate the impact of administration of nirsevimab to children born from 1 April 2023 onwards. METHODS: Estimated RSV hospitalisations in < 1-year-olds during weeks 40, 2023, to 8, 2024, were compared to the number that would be expected after accounting for the background change in RSV circulation in the 2023/24 season, compared to 2022/23. RESULTS: We estimated 9364-9875 RSV hospitalisations less than expected, corresponding to a 74%-75% reduction.

Phenotypic selection patterns in a hybrid zone between two Calceolaria species with contrasting pollinators: insights from field surveys and fitness assessments.

Hybrid zones provide natural experimental settings to test hypotheses about species divergence. We concentrated on a hybrid swarm in which oil-collecting bees and flower-pecking birds act as pollinators of two Calceolaria species. We asked whether both pollinators contributed to flower divergence by differentially promoting prezygotic fitness at the phenotypic extremes that represent parentals. We studied pollinator-mediated selection on phenotypic traits critical in plant-pollinator mechanical interaction, namely plant height, reward-to-stigma distance, and flower shape. We utilised the quantity and quality of pollen deposited as fitness measures and distinguished between the contribution of the two pollinator types. Results showed uni- and bivariate disruptive selection for most traits through pollen grains deposited by both pollinators. Bird-mediated fitness favoured low plants with a long reward-to-stigma distance and a straight corolla, while bee-mediated fitness favoured tall plants with a short reward-to-stigma distance and curved corolla. In addition, stabilising selection at one end of the phenotypic range showed a bird-mediated reproductive asymmetry within the swarm. The disruptive pattern was countered, albeit weakly, by hybrids receiving higher-quality pollen on the stigmas. Results suggest that pollinator-mediated selection promotes divergence of integrated flower phenotypes mechanically adjusted either to bees or birds underscoring the importance of pollinator specialisation in diversification.

Left ventricular shape index and eccentricity index with ECG-gated Nitrogen-13 ammonia PET/CT in patients with myocardial infarction, ischemia, and normal perfusion.

BACKGROUND: LV geometry with shape index (SI) and eccentricity index (EI) measured by myocardial perfusion positron emission tomography/computed tomography (PET/CT) may allow the evaluation of left ventricular (LV) adverse remodeling. This first study aims to explore the relationship of SI and EI values acquired by Nitrogen-13 ammonia PET/CT in patients with normal perfusion, ischemia, and myocardial infarction. And evaluate the correlations between the variables of LV geometry, and with the variables of LV function. METHODS AND RESULTS: One hundred and forty patients who underwent an electrocardiogram (ECG)-gated PET/CT were selected and classified into 4 groups according to ischemia or infarction burden (normal perfusion, mild ischemia, moderate-severe ischemia, and infarction). The variables were automatically retrieved using dedicated software (QPS/QGS; Cedars-Sinai, Los Angeles, CA, USA). On multicomparison analysis (one-way ANOVA and Dunnett's Test), subjects in the infarction group had significant higher values of SI end-diastolic rest (P < 0.001), and stress (P = 0.003), SI end-systolic rest (P = 0.002) and stress (P < 0.001) as well as statistically significant lower values of EI rest (P < 0.001) and stress (P < 0.001) when compared with all other groups. Regarding Pearson correlation, in the infarcted group all the variables of SI and EI were significantly correlated (P < 0.001) with strong correlation coefficients (>0.60). SI end-systolic correlated significantly with the variables of LV function independently of the group of patients (P < 0.05). CONCLUSIONS: Shape and eccentricity indices differ in patients with myocardial infarction as compared to patients with ischemia or normal perfusion. This encourage further research in their potential for detecting LV adverse remodeling.

Albocycline Is the Main Bioactive Antifungal Compound Produced by Streptomyces sp. OR6 against Verticillium dahliae.

Verticillium wilt is a soil-borne fungal disease that affects olive trees (Olea europaea) and poses a serious threat to their cultivation. The causal agent of this disease is Verticillium dahliae, a pathogen that is difficult to control with conventional methods. Therefore, there is a need to explore alternative strategies for the management of Verticillium wilt. In this study, we aimed to isolate and characterize actinobacteria from the rhizosphere of olive trees that could act as potential biocontrol agents against V. dahliae. We selected a Streptomyces sp. OR6 strain based on its in vitro antifungal activity and its ability to suppress the pathogen growth in soil samples. We identified the main active compound produced by this strain as albocycline, a macrolide polyketide with known antibacterial properties and some antifungal activity. Albocycline was able to efficiently suppress the germination of conidiospores. To our knowledge, this is the first report of albocycline as an effective agent against V. dahliae. Our results suggest that Streptomyces sp. OR6, or other albocycline-producing strains, could be used as a promising tool for the biological control of Verticillium wilt.

Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain).

Acidithiobacillus thiooxidans is of paramount importance in the development of biomining technologies. Being widely recognized as an extreme acidophile, extensive research has been dedicated to understanding its significant role in the extraction of several ores in recent years. However, there still exist significant molecular uncertainties surrounding this species. This study focuses on developing a taxonomic assignment method based on the sequencing of the 16S-5S rRNA cluster, along with a qPCR-based technology enabling precise growth determination. Additionally, an approach to understanding its response to acid stress is explored through RT-PCR and MALDI-TOF analysis. Our findings indicate that when subjected to pH levels below 1, the cell inhibits central (carbon fixation and metabolism) and energy (sulfur metabolism) metabolism, as well as chaperone synthesis, suggesting a potential cellular collapse. Nevertheless, the secretion of ammonia is enhanced to raise the environmental pH, while fatty acid synthesis is upregulated to reinforce the cell membrane.

From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus.

Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.

Waiting time dictates impact of frailty: A Spanish multicenter prospective study.

Background & Aims: Frailty is prevalent in liver transplant (LT) candidates. It is considered an independent predictor of adverse outcomes pre- and post-transplant according to data obtained in the United States. We aimed to externally validate the liver frailty index (LFI) in a multicenter cohort of LT candidates. Methods: Outpatients with cirrhosis were prospectively recruited from five Spanish centers (2018-2020). Patients were defined as "frail" by an optimal cut-off of LFI ≥4.5. Patients were followed for at least 6 months to study associations of pre-LT frailty with pre- and post-transplant mortality, length of hospital and intensive care unit (ICU) stays, risk of early (<30 days) and late (30-90 days) post-transplant complications, retransplantation and cardiovascular events. Results: Of 212 patients included, 45 patients (21%) were frail pre-LT, and the median LFI was 3.9 (IQR 3.5-4.4). After a median waiting time of 78 days, 2% died or were delisted for clinical worsening. The LFI at baseline was not predictive of mortality/delisting in LT candidates in univariable or multivariable analyses after adjusting for age and MELD-Na score (hazard ratio 1.48; p = 0.586). In contrast, compared to non-frail patients, frail LT candidates had a significantly higher length of hospital stay (9 vs. 13 days; p = 0.001) and rate of early (<30 days) post-transplant complications (55% vs. 100%; p = 0.021). Conclusions: In the context of a short LT waiting time, frailty does not impact pretransplant mortality and/or delisting. In contrast, LT frailty is predictive of higher post-transplant complication rates and length of hospital stay. Whether strategies aimed at pre- and/or re-habilitation are beneficial in settings with short waiting times needs to be confirmed in prospective studies. Impact and implications: Literature is scarce on the actual impact of physical frailty on adverse outcomes in the liver transplant scenario outside North America. Evidence-based justification to extend the use of objective frailty tools in the decision-making processes in other liver transplant settings is needed. This study is the first to evaluate the predictive value of the liver frailty index in outpatients in the European liver transplant setting, showing that in a low MELD, high access system, frailty does not impact pretransplant mortality and/or delisting but is predictive of higher complication rates and longer post-transplant length of stay. In practical ways, physicians should consider physical frailty as a vital sign to be measured systematically and routinely during clinic visits; researchers are encouraged to initiate prospective studies to evaluate the benefit of applying strategies aimed at pre- and or re-habilitation in liver transplant settings with short waiting times.

Bidimensional Analyses of the Intra- and Extracellular Proteomes of Steroid Producer Mycobacteria.

The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. However, those industrially relevant mycobacteria have received less attention, even though the steroid market sales in 2021 were estimated in $56.45 billion.The extracellular proteome, due to its relevance in the sterol processing and uptake, and the intracellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. Both, monodimensional gels, as preparatory analysis, and bidimensional gels as proteome analysis are described. As a proof of concept, the protein extraction methods for both sub-proteomes of Mycobacterium are described. Thus, procedures and relevant key points of these proteome analyses are fully detailed.

Changes in the Microbial Composition of the Rhizosphere of Hop Plants Affected by Verticillium Wilt Caused by Verticillium nonalfalfae.

Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium nonalfalfae. As both healthy and diseased plants coexist in the same field, we focused this study on the detection of putative differences in the microbial communities associated with the two types of plants. Bacterial communities were characterized by sequencing the V4 region of the 16S rRNA gene, whereas sequencing of the ITS2 region was performed for fungal communities. The bacterial community was dominated by phyla Proteobacteria, Acidobacteriota, Bacteroidota, Actinobacteriota, Planctomycetota, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota, which are typically found in crop soils throughout the world. At a fungal level, Fusarium sp. was the dominant taxon in both bulk and rhizosphere soils. Verticillium sp. levels were very low in all samples analyzed and could only be detected by qPCR in the rhizosphere of diseased plants. The rhizosphere of diseased plants underwent important changes with respect to the rhizosphere of healthy plants where significant increases in potentially beneficial fungi such as the basidiomycetes Ceratobasidium sp. and Mycena sp., the zygomycete Mortierella sp., and a member of Glomeralles were observed. However, the rhizosphere of diseased plants experienced a decrease in pathogenic basidiomycetes that can affect the root system, such as Thanatephorus cucumeris (the teleomorph of Rhizoctonia solani) and Calyptella sp.

Maintenance olaparib in patients with platinum-sensitive relapsed ovarian cancer: Outcomes by somatic and germline BRCA and other homologous recombination repair gene mutation status in the ORZORA trial.

BACKGROUND: The open-label, single-arm, multicenter ORZORA trial (NCT02476968) evaluated the efficacy and safety of maintenance olaparib in patients with platinum-sensitive relapsed ovarian cancer (PSR OC) who had tumor BRCA mutations (BRCAm) of germline (g) or somatic (s) origin or non-BRCA homologous recombination repair mutations (HRRm) and were in response to their most recent platinum-based chemotherapy after ≥2 lines of treatment. METHODS: Patients received maintenance olaparib capsules (400 mg twice daily) until disease progression. Prospective central testing at screening determined tumor BRCAm status and subsequent testing determined gBRCAm or sBRCAm status. Patients with predefined non-BRCA HRRm were assigned to an exploratory cohort. The co-primary endpoints were investigator-assessed progression-free survival (PFS; modified Response Evaluation Criteria in Solid Tumors v1.1) in BRCAm and sBRCAm cohorts. Secondary endpoints included health-related quality of life (HRQoL) and tolerability. RESULTS: 177 patients received olaparib. At the primary data cut-off (17 April 2020), the median follow-up for PFS in the BRCAm cohort was 22.3 months. The median PFS (95% CI) in BRCAm, sBRCAm, gBRCAm and non-BRCA HRRm cohorts was 18.0 (14.3-22.1), 16.6 (12.4-22.2), 19.3 (14.3-27.6) and 16.4 (10.9-19.3) months, respectively. Most patients with BRCAm reported improvements (21.8%) or no change (68.7%) in HRQoL and the safety profile was as expected. CONCLUSIONS: Maintenance olaparib had similar clinical activity in PSR OC patients with sBRCAm and those with any BRCAm. Activity was also observed in patients with a non-BRCA HRRm. ORZORA further supports use of maintenance olaparib in all patients with BRCA-mutated, including sBRCA-mutated, PSR OC.

Magnetically propelled chained nanocomposites for biologically relevant media exploration.

Elongated nanostructures to be remotely and magnetically propelled in biologically relevant media, have gained attention as offering themselves as effective tools or carriers in theragnostics applications. However, the magnetic actuation associated remains challenging due to the lack of mechanical information in the media of interest, taking into account biophysical or biomedical purposes. In this study, we detail the magnetic actuation of magnetically propelled chained nanocomposites considering their dynamics, in which their velocity can be modulated in terms of the viscosity of the medium considered, given a magnetic field gradient. Simpler cases of distilled water, a water/glycerol mixture and a fluid made of cell extracts (imitating the cytosol of cells) of known viscosity are the basis experiments for the study of more complex media inside HeLa cells, murine NIH-3T3 fibroblasts and zebrafish larvae, offering the mechanical information required. The experimental results indicate that the magnetically propelled performance of the chained nanostructures can be precisely controlled in potentially changing scenarios, where drug and heat delivery, magnetic separation, or microfluidic technologies are demanded, using a magnetic field gradient and providing good estimations of the dynamical parameters involved.

Biodegradation of Pine Processionary Caterpillar Silk Is Mediated by Elastase- and Subtilisin-like Proteases.

Pine processionary caterpillar nests are made from raw silk. Fibroin protein is the main component of silk which, in the case of pine processionary caterpillar, has some unusual properties such as a higher resistance to chemical hydrolysis. Isolation of microorganisms naturally present in silk nests led to identification of Bacillus licheniformis and Pseudomonas aeruginosa strains that in a defined minimal medium were able to carry out extensive silk biodegradation. A LasB elastase-like protein from P. aeruginosa was shown to be involved in silk biodegradation. A recombinant form of this protein expressed in Escherichia coli and purified by affinity chromatography was able to efficiently degrade silk in an in vitro assay. However, silk biodegradation by B. licheniformis strain was mediated by a SubC subtilisin-like protease. Homologous expression of a subtilisin Carlsberg encoding gene (subC) allowed faster degradation compared to the biodegradation kinetics of a wildtype B. licheniformis strain. This work led to the identification of new enzymes involved in biodegradation of silk materials, a finding which could lead to possible applications for controlling this pest and perhaps have importance from sanitary and biotechnological points of view.

Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients.

Metastasis is the primary cause of death for most breast cancer (BC) patients who succumb to the disease. During the hematogenous dissemination, circulating tumor cells interact with different blood components. Thus, there are microenvironmental and systemic processes contributing to cancer regulation. We have recently published that red blood cells (RBCs) that accompany circulating tumor cells have prognostic value in metastatic BC patients. RBC alterations are related to several diseases. Although the principal known role is gas transport, it has been recently assigned additional functions as regulatory cells on circulation. Hence, to explore their potential contribution to tumor progression, we characterized the proteomic composition of RBCs from 53 BC patients from stages I to III and IV, compared with 33 cancer-free controls. In this work, we observed that RBCs from BC patients showed a different proteomic profile compared to cancer-free controls and between different tumor stages. The differential proteins were mainly related to extracellular components, proteasome, and metabolism. Embryonic hemoglobins, not expected in adults' RBCs, were detected in BC patients. Besides, lysosome-associated membrane glycoprotein 2 emerge as a new RBCs marker with diagnostic and prognostic potential for metastatic BC patients. Seemingly, RBCs are acquiring modifications in their proteomic composition that probably represents the systemic cancer disease, conditioned by the tumor microenvironment.