Supplementary Table S1. Selection Criteria; Supplementary Table S2. Recruiting Sites, Principal Investigators, and Patient Numbers; Supplementary Table S3. Study Members; Supplementary Table S4. List of antibodies used for immunohistochemistry analysis; Supplementary Table S5. Cutoff values for the quantitative assessment of biomarkers by immunohistochemistry; Supplementary Table S6. The 77-gene panel by the AVENIO ctDNA Expanded Kit used for targeted NGS on plasma samples; Supplementary Table S7. Representativeness of study participants; Supplementary Table S8. Association of baseline clinical and pathologic characteristics of trial participants included in the efficacy analysis with clinical benefit; Supplementary Table S9. Relative dose intensity and drug discontinuation; Supplementary Table S10. All causality AEs according to NCI-CTCAE version 4.0.3 occurring in at least 5% of the patients; Supplementary Table S11. Adverse events of special interest according to NCI-CTCAE version 4.0.3; Supplementary Table S12. Baseline clinical and pathologic characteristics of trial participants included in the retinoblastoma and signature subsets; Supplementary Table S13. Tumor best response according to RECIST version 1.1 of trial participants included in the retinoblastoma and signature subsets; Supplementary Table S14. Association of biomarkers and composite signatures with clinical benefit.

Summary of all adverse events according to NCI-CTCAE version 4.0.3.

Kaplan-Meier analyses of investigator-assessed progression-free survival and overall survival in the efficacy population.

The level of mutant and wild-type circulating DNA in baseline plasma samples by patient.

(A) Longitudinal ctDNA quantification during study treatment. (B) Variations of ctDNA during study treatment. (C, D) Kaplan-Meier analyses of investigator-assessed progression-free survival according to the ctDNA detection after 2 weeks and 12 weeks of study treatment.

Background PHERGain was designed to assess the feasibility, safety, and efficacy of a chemotherapy-free treatment based on a dual human epidermal growth factor receptor 2 (HER2) blockade with trastuzumab and pertuzumab in patients with HER2-positive early breast cancer (EBC). It used an 18 fluorine-fluorodeoxyglucose-PET-based, pathological complete response (pCR)-adapted strategy. Methods PHERGain was a randomised, open-label, phase 2 trial that took place in 45 hospitals in seven European countries. It randomly allocated patients in a 1:4 ratio with centrally confirmed, HER2-positive, stage I-IIIA invasive, operable breast cancer with at least one PET-evaluable lesion to either group A, where patients received docetaxel (75 mg/m 2 , intravenous), carboplatin (area under the curve 6 mg/mL per min, intravenous), trastuzumab (600 mg fixed dose, subcutaneous), and pertuzumab (840 mg loading dose followed by 420 mg maintenance doses, intravenous; TCHP), or group B, where patients received trastuzumab and pertuzumab with or without endocrine therapy, every 3 weeks. Random allocation was stratified by hormone receptor status. Centrally reviewed PET was conducted at baseline and after two treatment cycles. Patients in group B were treated according to on-treatment PET results. Patients in group B who were PET-responders continued with trastuzumab and pertuzumab with or without endocrine therapy for six cycles, while PET-non-responders were switched to receive six cycles of TCHP. After surgery, patients in group B who were PET-responders who did not achieve a pCR received six cycles of TCHP, and all patients completed up to 18 cycles of trastuzumab and pertuzumab. The primary endpoints were pCR in patients who were group B PET-responders after two treatment cycles (the results for which have been reported previously) and 3-year invasive disease-free survival (iDFS) in patients in group B. The study is registered with ClinicalTrials.gov (NCT03161353) and is ongoing. Findings Between June 26, 2017, and April 24, 2019, a total of 356 patients were randomly allocated (71 patients in group A and 285 patients in group B), and 63 (89%) and 267 (94%) patients proceeded to surgery in groups A and B, respectively. At this second analysis (data cutoff: Nov 4, 2022), the median duration of follow-up was 433 months (range 00-630). In group B, the 3-year iDFS rate was 948% (95% CI 914-971; p=0001), meeting the primary endpoint. No new safety signals were identified. Treatment-related adverse events and serious adverse events (SAEs) were numerically higher in patients allocated to group A than to group B (grade >= 3 62% vs 33%; SAEs 28% vs 14%). Group B PET-responders with pCR presented the lowest incidence of treatment-related grade 3 or higher adverse events (1%) without any SAEs. Interpretation Among HER2-positive EBC patients, a PET-based, pCR-adapted strategy was associated with an excellent 3-year iDFS. This strategy identified about a third of patients who had HER2-positive EBC who could safely omit chemotherapy. Copyright (c) 2024 Elsevier Ltd. All rights reserved.

LBA506 Background: PHERGain is assessing the feasibility of a CT-free treatment based on a dual HER2 blockade with trastuzumab and pertuzumab (HP) in patients (pts) with HER2[+] EBC using a PET-based, pathologic complete response (pCR)-adapted strategy. In an earlier analysis of this study, a total of 227 (79.7%) of 285 pts included in group B were PET-responder (RX), of whom 86 of 227 (37.9%, 95% CI, 31.6 to 44.5; p<0.0001) achieved a pCR, reaching the first primary endpoint (Perez-Garcia JM, Lancet Oncol 2021). Methods: Details of the trial design and study population have been previously reported. Here, we present the results of the second primary endpoint, 3-year iDFS, among pts included in group B who underwent surgery based on an intent-to-treat (ITT) analysis. In brief, group B included centrally-confirmed, stage I-IIIA, HER2[+] EBC pts that were initially treated with HP (± endocrine therapy), introducing CT in pts without PET response after two treatment cycles and/or pCR. The binomial design tested the null hypothesis that the true 3-year iDFS rate was ≤89.0% against the alternative that the 3-year iDFS was >95%. We estimated that enrolling 284 pts in group B would provide 80% power at a nominal level of one-sided α of 0.025, assuming a 25% dropout rate. Results: Between June 26, 2017 and April 24, 2019, 356 pts were randomly assigned (71 pts in group A and 285 pts in group B) and 63 (89.0%) and 267 (93.7%) pts proceeded to surgery in groups A and B, respectively. In group B, the 3-year iDFS rate for the ITT population was 95.4% (95% CI, 92.8 to 98), meeting the second primary endpoint (p<0.001). After a median follow-up of 43.3 months (range, 2.4-63.0), a total of 12 iDFS events were reported, including eight distant recurrences (3.0%), three locoregional ipsilateral recurrences (1.1%), and one non-related death (0.4%). Among group B/PET-RX pts with pCR that did not receive CT as part of study treatment (n = 86), only one patient had an invasive event (locoregional ipsilateral recurrence) for a 3-year iDFS rate of 98.8% (95% CI, 96.3 to 100.0). Treatment-related adverse events (AEs) and serious adverse events (SAEs) were higher in pts allocated to group A than to group B (grade ≥3, 61.8% vs. 32.9% [p<0.001]; SAEs, 27.9% vs. 13.8% [p=0.01]). Group B/PET-RX pts with pCR presented the lowest incidence of treatment-related grade ≥3 AEs (1.2%) without any SAEs. No treatment-related deaths were reported. Conclusions: Among HER2[+] EBC pts, a PET-based, pCR-adapted strategy was associated with a substantial 3-year iDFS. These results appear comparable to those reported in several studies for the combination of neoadjuvant CT and dual HER2 blockade. This strategy identifies about a third of HER2[+] EBC pts who may safely omit CT with significantly reduced toxicity. Clinical trial information: NCT5732164 .

Stress granules (SGs) are highly conserved cytoplasmic condensates that assemble in response to stress and contribute to maintaining protein homeostasis. These membraneless organelles are dynamic, disassembling once the stress is no longer present. Persistence of SGs due to mutations or chronic stress has been often related to age-dependent protein-misfolding diseases in animals. Here, we find that the metacaspase MC1 is dynamically recruited into SGs upon proteotoxic stress in Arabidopsis (Arabidopsis thaliana). Two predicted disordered regions, the prodomain and the 360 loop, mediate MC1 recruitment to and release from SGs. Importantly, we show that MC1 has the capacity to clear toxic protein aggregates in vivo and in vitro, acting as a disaggregase. Finally, we demonstrate that overexpressing MC1 delays senescence and this phenotype is dependent on the presence of the 360 loop and an intact catalytic domain. Together, our data indicate that MC1 regulates senescence through its recruitment into SGs and this function could potentially be linked to its remarkable protein aggregate-clearing activity.

Abstract Purpose: To assess the efficacy and exploratory biomarkers of continuing palbociclib plus endocrine therapy (ET) beyond progression on prior palbociclib-based regimen in patients with hormone receptor–positive/HER2-negative (HR+/HER2−) advanced breast cancer (ABC). Patients and Methods: The multicenter, open-label, phase II BioPER trial included women who had experienced a progressive disease (PD) after having achieved clinical benefit on the immediately prior palbociclib plus ET regimen. Palbociclib (125 mg, 100 mg, or 75 mg daily orally for 3 weeks and 1 week off as per prior palbociclib-based regimen) plus ET of physician's choice were administered in 4-week cycles until PD or unacceptable toxicity. Coprimary endpoints were clinical benefit rate (CBR) and percentage of tumors with baseline loss of retinoblastoma (Rb) protein expression. Additional endpoints included safety and biomarker analysis. Results: Among 33 patients enrolled, CBR was 34.4% [95% confidence interval (CI), 18.6–53.2; P < 0.001] and 13.0% of tumors (95% CI, 5.2–27.5) showed loss of Rb protein expression, meeting both coprimary endpoints. Median progression-free survival was 2.6 months (95% CI, 1.8–6.7). No new safety signals were reported. A signature that included baseline mediators of therapeutic resistance to palbociclib and ET (low Rb score, high cyclin E1 score, ESR1 mutation) was independently associated with shorter median progression-free survival (HR, 22.0; 95% CI, 1.71–282.9; P = 0.018). Conclusions: Maintaining palbociclib after progression on prior palbociclib-based regimen seems to be a reasonable, investigational approach for selected patients. A composite biomarker signature predicts a subset of patients who may not derive a greater benefit from palbociclib rechallenge, warranting further validation in larger randomized controlled trials.

Bacterial pathogens possess complex type III effector (T3E) repertoires that are translocated inside the host cells to cause disease. However, only a minor proportion of these effectors have been assigned a function. Here, we show that the T3E AWR5 from the phytopathogen Ralstonia solanacearum is an inhibitor of TOR, a central regulator in eukaryotes that controls the switch between cell growth and stress responses in response to nutrient availability. Heterologous expression of AWR5 in yeast caused growth inhibition and autophagy induction coupled to massive transcriptomic changes, unmistakably reminiscent of TOR inhibition by rapamycin or nitrogen starvation. Detailed genetic analysis of these phenotypes in yeast, including suppression of AWR5-induced toxicity by mutation of CDC55 and TPD3 , encoding regulatory subunits of the PP2A phosphatase, indicated that AWR5 might exert its function by directly or indirectly inhibiting the TOR pathway upstream PP2A. We present evidence in planta that this T3E caused a decrease in TOR-regulated plant nitrate reductase activity and also that normal levels of TOR and the Cdc55 homologues in plants are required for R. solanacearum virulence. Our results suggest that the TOR pathway is a bona fide T3E target and further prove that yeast is a useful platform for T3E function characterisation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Antimicrobial peptides (AMPs) have potent and durable antimicrobial activity to a wide range of fungi and bacteria. The growing problem of drug-resistant pathogenic microorganisms, together with the lack of new effective compounds, has stimulated interest in developing AMPs as anti-infective molecules. PAF102 is an AMP that was rationally designed for improved antifungal properties. This cell penetrating peptide has potent and specific activity against major fungal pathogens. Cecropin A is a natural AMP with strong and fast lytic activity against bacterial and fungal pathogens, including multidrug resistant pathogens. Both peptides, PAF102 and Cecropin A, are alternative antibiotic compounds. However, their exploitation requires fast, cost-efficient production systems. Here, we developed an innovative system to produce AMPs in Pichia pastoris using the oleosin fusion technology. Oleosins are plant-specific proteins with a structural role in lipid droplet formation and stabilization, which are used as carriers for recombinant proteins to lipid droplets in plant-based production systems. This study reports the efficient production of PAF102 in P. pastoris when fused to the rice plant Oleosin 18, whereas no accumulation of Cecropin A was detected. The Ole18-PAF102 fusion protein targets the lipid droplets of the heterologous system where it accumulates to high levels. Interestingly, the production of this fusion protein induces the formation of lipid droplets in yeast cells, which can be additionally enhanced by the coexpression of a diacylglycerol transferase gene that allows a three-fold increase in the production of the fusion protein. Using this high producer strain, PAF102 reaches commercially relevant yields of up to 180 mg/l of yeast culture. Moreover, the accumulation of PAF102 in the yeast lipid droplets facilitates its downstream extraction and recovery by flotation on density gradients, with the recovered PAF102 being biologically active against pathogenic fungi. Our results demonstrate that plant oleosin fusion technology can be transferred to the well-established P. pastoris cell factory to produce the PAF102 antifungal peptide, and potentially other AMPs, for multiple applications in crop protection, food preservation and animal and human therapies.

Trabajo presentado al EMBO Workshop: Protein quality control: From mechanisms to disease, celebrado en Costa de la Calma (Mallorca-Espana) del 28 de abril al 3 de mayo de 2019.

Filamentous fungi encode distinct antifungal proteins (AFPs) that offer great potential to develop new antifungals. Fungi are considered immune to their own AFPs as occurs in Penicillium chrysogenum, the producer of the well-known PAF. The Penicillium digitatum genome encodes only one afp gene (afpB), and the corresponding protein (AfpB) belongs to the class B phylogenetic cluster. Previous attempts to detect AfpB were not successful. In this work, immunodetection confirmed the absence of AfpB accumulation in wild type and previous recombinant constitutive P. digitatum strains. Biotechnological production and secretion of AfpB were achieved in P. digitatum with the use of a P. chrysogenum-based expression cassette and in the yeast Pichia pastoris with the α-factor signal peptide. Both strategies allowed proper protein folding, efficient production and single-step purification of AfpB from culture supernatants. AfpB showed antifungal activity higher than the P. chrysogenum PAF against the majority of the fungi tested, especially against Penicillium species and including P. digitatum, which was highly sensitive to the self-AfpB. Spectroscopic data suggest that native folding is not required for activity. AfpB also showed notable ability to withstand protease and thermal degradation and no haemolytic activity, making AfpB a promising candidate for the control of pathogenic fungi.

The plant pathogenic bacterium Ralstonia solanacearum injects more than 70 effector proteins (virulence factors) into the host plant cells via the needle-like structure of a type III secretion system. The type III secretion system effector proteins manipulate host regulatory networks to suppress defense responses with diverse molecular activities. Uncovering the molecular function of these effectors is essential for a mechanistic understanding of R. solanacearum pathogenicity. However, few of the effectors from R. solanacearum have been functionally characterized, and their plant targets remain largely unknown. Here, we show that the ChaC domain-containing effector RipAY/RSp1022 from R. solanacearum exhibits γ-glutamyl cyclotransferase (GGCT) activity to degrade the major intracellular redox buffer, glutathione. Heterologous expression of RipAY, but not other ChaC family proteins conserved in various organisms, caused growth inhibition of yeast Saccharomyces cerevisiae, and the intracellular glutathione level was decreased to ∼30% of the normal level following expression of RipAY in yeast. Although active site mutants of GGCT activity were non-toxic, the addition of glutathione did not reverse the toxicity, suggesting that the toxicity might be a consequence of activity against other γ-glutamyl compounds. Intriguingly, RipAY protein purified from a bacterial expression system did not exhibit any GGCT activity, whereas it exhibited robust GGCT activity upon its interaction with eukaryotic thioredoxins, which are important for intracellular redox homeostasis during bacterial infection in plants. Our results suggest that RipAY has evolved to sense the host intracellular redox environment, which triggers its enzymatic activity to create a favorable environment for R. solanacearum infection.

Type III effectors (T3E) are key virulence proteins that are injected by bacterial pathogens inside the cells of their host to subvert cellular processes and contribute to disease. The budding yeast Saccharomyces cerevisiae represents an important heterologous system for the functional characterisation of T3E proteins in a eukaryotic environment. Importantly, yeast contains eukaryotic processes with low redundancy and are devoid of immunity mechanisms that counteract T3Es and mask their function. Expression in yeast of effectors from both plant and animal pathogens that perturb conserved cellular processes often resulted in robust phenotypes that were exploited to elucidate effector functions, biochemical properties, and host targets. The genetic tractability of yeast and its amenability for high-throughput functional studies contributed to the success of this system that, in recent years, has been used to study over 100 effectors. Here, we provide a critical view on this body of work and describe advantages and limitations inherent to the use of yeast in T3E research. "Favourite" targets of T3Es in yeast are cytoskeleton components and small GTPases of the Rho family. We describe how mitogen-activated protein kinase (MAPK) signalling, vesicle trafficking, membrane structures, and programmed cell death are also often altered by T3Es in yeast and how this reflects their function in the natural host. We describe how effector structure-function studies and analysis of candidate targeted processes or pathways can be carried out in yeast. We critically analyse technologies that have been used in yeast to assign biochemical functions to T3Es, including transcriptomics and proteomics, as well as suppressor, gain-of-function, or synthetic lethality screens. We also describe how yeast can be used to select for molecules that block T3E function in search of new antibacterial drugs with medical applications. Finally, we provide our opinion on the limitations of S. cerevisiae as a model system and its most promising future applications.

Pathogenic bacteria manipulate their hosts by delivering a number of virulence proteins -called effectors- directly into the plant or animal cells. Recent findings have shown that such effectors can suffer covalent modifications inside the eukaryotic cells. Here, we summarize the recent reports where effector modifications by the eukaryotic machinery have been described. We restrict our focus on proteins secreted by the type III or type IV systems, excluding other bacterial toxins. We describe the known examples of effectors whose enzymatic activity is triggered by interaction with plant and animal cell factors, including GTPases, E2-Ubiquitin conjugates, cyclophilin and thioredoxins. We focus on the structural interactions with these factors and their influence on effector function. We also review the described examples of host-mediated post-translational effector modifications which are required for proper subcellular location and function. These host-specific covalent modifications include phosphorylation, ubiquitination, SUMOylation, and lipidations such as prenylation, fatty acylation and phospholipid binding.

The soil-borne plant pathogen Ralstonia solanacearum is the causing agent of bacterial wilt, a devastating disease of wide geographical distribution and host range with enormous economic impact worldwide. To cause disease, R. solanacearum injects a suite of type III effector (T3E) proteins into its hosts, from which only a few have been assigned a function, as it is the case for the T3E repertoires of other bacterial pathogens. Using yeast as a model system, we show that expression of the R. solanacearum awr type III effector family caused growth inhibition to different extents, and AWR5 displayed the most dramatic effect on yeast cells. Production of the full-length AWR5 protein in yeast targeted a cellular process leading to a growth inhibition and reduced cell size, but not involving an evident cell cycle arrest or cell death. Furthermore, we demonstrate that AWR5 is an inhibitor of TOR (target of rapamycin), a central regulator in eukaryotes that controls the switch between cell growth and stress responses in response to nutrient availability. Heterologous expression of awr5 in yeast caused autophagy induction coupled to massive transcriptomic changes, unmistakably reminiscent of TOR inhibition by rapamycin or by nitrogen starvation. The observation that deletion of two components of the PP2A heterotrimeric forms -CDC55 and TPD3- and mutation in SCH9 abolished the dramatic growth defect of cells expressing awr5 indicates AWR5 might exert its function by directly or indirectly inhibiting the TOR pathway upstream PP2A and Sch9. We speculate targeting of TOR pathways might be conserved among AWR2, AWR4 and AWR5, since their expression in yeast leads to similar downstream transcriptional responses. Also, we present evidence in planta that AWR5 T3E caused a reduction in TOR-regulated plant nitrate reductase activity and that the bacterial growth inhibition caused by delivery of AWR5 into host cells was mediated by TOR. Our work demonstrates that yeast is a powerful model for T3E function discovery and reveals not only a new mode of action for T3Es but also a new virulence target that might be conserved across kingdoms.

This study aimed to present the logical structure and core functions of a software module for recording, processing and reporting information relating to performance control in beef cattle. The research comprised a literature review on several control systems used in other countries, international guidelines and recommendation in the field and a syntheses of key issues that led to the successful implementation of an information module that takes into account these requirements, described in this article. The results of scientific investigations illustrate that the process of collecting and inputting data has a important role in the process of performance recording in its early stage and although the performance indexes for each animal can be already useful in practice, the software needs a period of 3-5 years of continuously recording the data in order to become fully mature.

We present here the characterization of a new gene family, awr, found in all sequenced Ralstonia solanacearum strains and in other bacterial pathogens. We demonstrate that the five paralogues in strain GMI1000 encode type III-secreted effectors and that deletion of all awr genes severely impairs its capacity to multiply in natural host plants. Complementation studies show that the AWR (alanine-tryptophan-arginine tryad) effectors display some functional redundancy, although AWR2 is the major contributor to virulence. In contrast, the strain devoid of all awr genes (Δawr1-5) exhibits enhanced pathogenicity on Arabidopsis plants. A gain-of-function approach expressing AWR in Pseudomonas syringae pv. tomato DC3000 proves that this is likely due to effector recognition, because AWR5 and AWR4 restrict growth of this bacterium in Arabidopsis. Transient overexpression of AWR in nonhost tobacco species caused macroscopic cell death to varying extents, which, in the case of AWR5, shows characteristics of a typical hypersensitive response. Our work demonstrates that AWR, which show no similarity to any protein with known function, can specify either virulence or avirulence in the interaction of R. solanacearum with its plant hosts.