Regulation of human neutrophil IL-1ß secretion induced by Escherichia coli O157:H7 responsible for hemolytic uremic syndrome.

Shiga-toxin producing Escherichia coli (STEC) infections can cause from bloody diarrhea to Hemolytic Uremic Syndrome. The STEC intestinal infection triggers an inflammatory response that can facilitate the development of a systemic disease. We report here that neutrophils might contribute to this inflammatory response by secreting Interleukin 1 beta (IL-1ß). STEC stimulated neutrophils to release elevated levels of IL-1ß through a mechanism that involved the activation of caspase-1 driven by the NLRP3-inflammasome and neutrophil serine proteases (NSPs). Noteworthy, IL-1ß secretion was higher at lower multiplicities of infection. This secretory profile modulated by the bacteria:neutrophil ratio, was the consequence of a regulatory mechanism that reduced IL-1ß secretion the higher were the levels of activation of both caspase-1 and NSPs, and the production of NADPH oxidase-dependent reactive oxygen species. Finally, we also found that inhibition of NSPs significantly reduced STEC-triggered IL-1ß secretion without modulating the ability of neutrophils to kill the bacteria, suggesting NSPs might represent pharmacological targets to be evaluated to limit the STEC-induced intestinal inflammation.

Concurrent inhibition of ALK and SRC kinases disrupts the ALK lung tumor cell proteome.

Precision oncology has revolutionized the treatment of ALK-positive lung cancer with targeted therapies. However, an unmet clinical need still to address is the treatment of refractory tumors that contain drug-induced resistant mutations in the driver oncogene or exhibit resistance through the activation of diverse mechanisms. In this study, we established mouse tumor-derived cell models representing the two most prevalent EML4-ALK variants in human lung adenocarcinomas and characterized their proteomic profiles to gain insights into the underlying resistance mechanisms. We showed that Eml4-Alk variant 3 confers a worse response to ALK inhibitors, suggesting its role in promoting resistance to targeted therapy. In addition, proteomic analysis of brigatinib-treated cells revealed the upregulation of SRC kinase, a protein frequently activated in cancer. Co-targeting of ALK and SRC showed remarkable inhibitory effects in both ALK-driven murine and ALK-patient-derived lung tumor cells. This combination induced cell death through a multifaceted mechanism characterized by profound perturbation of the (phospho)proteomic landscape and a synergistic suppressive effect on the mTOR pathway. Our study demonstrates that the simultaneous inhibition of ALK and SRC can potentially overcome resistance mechanisms and enhance clinical outcomes in ALK-positive lung cancer patients. ONE SENTENCE SUMMARY: Co-targeting ALK and SRC enhances ALK inhibitor response in lung cancer by affecting the proteomic profile, offering hope for overcoming resistance and improving clinical outcomes.

Phenotypes of Metabolic Dysfunction-Associated Steatotic Liver Disease-Associated Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) typically develops as a consequence of liver cirrhosis, but HCC epidemiology has evolved drastically in recent years. Metabolic dysfunction-associated steatotic liver disease (MASLD), including metabolic dysfunction-associated steatohepatitis, has emerged as the most common chronic liver disease worldwide and a leading cause of HCC. A substantial proportion of MASLD-associated HCC (MASLD-HCC) also can develop in patients without cirrhosis. The specific pathways that trigger carcinogenesis in this context are not elucidated completely, and recommendations for HCC surveillance in MASLD patients are challenging. In the era of precision medicine, it is critical to understand the processes that define the profiles of patients at increased risk of HCC in the MASLD setting, including cardiometabolic risk factors and the molecular targets that could be tackled effectively. Ideally, defining categories that encompass key pathophysiological features, associated with tailored diagnostic and treatment strategies, should facilitate the identification of specific MASLD-HCC phenotypes. In this review, we discuss MASLD-HCC, including its epidemiology and health care burden, the mechanistic data promoting MASLD, metabolic dysfunction-associated steatohepatitis, and MASLD-HCC. Its natural history, prognosis, and treatment are addressed specifically, as the role of metabolic phenotypes of MASLD-HCC as a potential strategy for risk stratification. The challenges in identifying high-risk patients and screening strategies also are discussed, as well as the potential approaches for MASLD-HCC prevention and treatment.

Off-label use of dalbavancin in children: a case series.

INTRODUCTION: Dalbavancin is an antibiotic active against most Gram-positive bacteria approved for acute bacterial skin and skin structure infections (ABSSSI). Owing to its long half-life, it is being increasingly used for other indications. PATIENTS AND METHODS: We present a case series of children and adolescents treated with dalbavancin for osteoarticular, catheter-related and other non-ABSSSI infections. RESULTS: Dalbavancin was prescribed to 15 patients. Six (40%) were female and median age at prescription was 11.9 (IQR 1.3-18.0) years. Most of them (12/15) had significant comorbidities. Patients presented mainly with deep surgical site infections, osteoarticular infections and central-line-associated bloodstream infections. The most common isolate was Staphylococcus aureus followed by Staphylococcus epidermidis. Major reasons to prescribe dalbavancin were to ensure compliance and patients' convenience. Two patients discontinued the drug due to adverse events possibly related to it. The rest of the patients completed the treatment with dalbavancin, with a median duration of 56 days (IQR 17.5, 115.5). All achieved complete resolution and present no relapse after a median follow-up of 9.9 months (IQR 4.8, 16.6). CONCLUSIONS: Dalbavancin was a safe, effective and convenient alternative in selected paediatric patients with complicated non-ABSSSI infections caused by Gram-positive bacteria.

T-Cell Immune Responses in Newborns and Long-Term Sequelae in Congenital Cytomegalovirus Infection (CYTRIC Study).

OBJECTIVE: The objective of this study was to assess the role of T-lymphocyte immune responses in newborns with congenital cytomegalovirus (CMV) infection (cCMV) and their potential association with the development of long-term sequelae. STUDY DESIGN: A multicenter, prospective study from 2017 to 2022 was conducted across 8 hospitals in Spain. Blood samples were collected within the first month of life from neonates diagnosed with cCMV. Intracellular cytokine staining was employed to evaluate the presence of CMV-specific interferon-gamma (IFN-γ)-producing CD8+ and CD4+ T lymphocytes (CMV-IFN-γ-CD8+/CD4+) using flow cytometry. The development of sequelae, including hearing loss and neurologic impairment, was assessed during follow-up. RESULTS: In total, 64 newborns were included; 42 infants (65.6%) had symptomatic cCMV. The median age at the last follow-up visit was 25.3 months (IQR 20.1-34.4). Eighteen infants had long-term sequelae (28.1%), predominantly hearing loss (20.3%) and neurologic disorders (15.6%). No relationship was observed between total count or percentage of CMV-specific IFN-γ-CD8+ or CD4+ lymphocytes and long-term sequelae. Multivariable analysis demonstrated an association between lower total lymphocyte count and long-term sequelae (aOR 0.549, 95% CI: 0.323-0.833), which requires further study. CONCLUSIONS: CMV-specific IFN-γ-CD4+ and CD8+ T-lymphocyte responses in neonates with cCMV were not predictive of long-term sequelae.

Coronavirus disease 2019 is associated with long-term depressive symptoms in Spanish older adults with overweight/obesity and metabolic syndrome.

BACKGROUND: The coronavirus disease 2019 (COVID-19) has serious physiological and psychological consequences. The long-term (>12 weeks post-infection) impact of COVID-19 on mental health, specifically in older adults, is unclear. We longitudinally assessed the association of COVID-19 with depression symptomatology in community-dwelling older adults with metabolic syndrome within the framework of the PREDIMED-Plus cohort. METHODS: Participants (n = 5486) aged 55-75 years were included in this longitudinal cohort. COVID-19 status (positive/negative) determined by tests (e.g. polymerase chain reaction severe acute respiratory syndrome coronavirus 2, IgG) was confirmed via event adjudication (410 cases). Pre- and post-COVID-19 depressive symptomatology was ascertained from annual assessments conducted using a validated 21-item Spanish Beck Depression Inventory-II (BDI-II). Multivariable linear and logistic regression models assessed the association between COVID-19 and depression symptomatology. RESULTS: COVID-19 in older adults was associated with higher post-COVID-19 BDI-II scores measured at a median (interquartile range) of 29 (15-40) weeks post-infection [fully adjusted ß = 0.65 points, 95% confidence interval (CI) 0.15-1.15; p = 0.011]. This association was particularly prominent in women (ß = 1.38 points, 95% CI 0.44-2.33, p = 0.004). COVID-19 was associated with 62% increased odds of elevated depression risk (BDI-II ≥ 14) post-COVID-19 when adjusted for confounders (odds ratio; 95% CI 1.13-2.30, p = 0.008). CONCLUSIONS: COVID-19 was associated with long-term depression risk in older adults with overweight/obesity and metabolic syndrome, particularly in women. Thus, long-term evaluations of the impact of COVID-19 on mental health and preventive public health initiatives are warranted in older adults.

Bioinformatics tools for the study of bioactive peptides from vegetal sources: evolution and future perspectives.

Bioactive peptides from vegetal sources have been shown to have functional properties as anti-inflammatory, antioxidant, antihypertensive or antidiabetic capacity. For this reason, they have been proposed as an interesting and promising alternative to improve human health. In recent years, the numerous advances in the bioinformatics field for in silico prediction have speeded up the discovery of bioactive peptides, also reducing the associated costs when using an integrated approach between the classical and bioinformatics discovery. This review aims to provide an overview of the evolution, limitations and latest advances in the field of bioinformatics and computational tools, and specifically make a critical and comprehensive insight into computational techniques used to study the mechanism of interaction that allows the explanation of plant bioactive peptide functionality. In particular, molecular docking is considered key to explain the different functionalities that have been previously identified. The assumptions to simplify such a high complex environment implies a degree of uncertainty that can only be guaranteed and validated by in vitro or in vivo studies, however, the combination of databases, software and bioinformatics applications with the classical approach has become a promising procedure for the study of bioactive peptides.

DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation.

Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.

New PFASs Identified in AFFF Impacted Groundwater by Passive Sampling and Nontarget Analysis.

Monitoring contamination from per- and polyfluoroalkyl substances (PFASs) in water systems impacted by aqueous film-forming foams (AFFFs) typically addresses a few known PFAS groups. Given the diversity of PFASs present in AFFFs, current analytical approaches do not comprehensively address the range of PFASs present in these systems. A suspect-screening and nontarget analysis (NTA) approach was developed and applied to identify novel PFASs in groundwater samples contaminated from historic AFFF use. A total of 88 PFASs were identified in both passive samplers and grab samples, and these were dominated by sulfonate derivatives and sulfonamide-derived precursors. Several ultrashort-chain (USC) PFASs (≤C3) were detected, 11 reported for the first time in Australian groundwater. Several transformation products were identified, including perfluoroalkane sulfonamides (FASAs) and perfluoroalkane sulfinates (PFASis). Two new PFASs were reported (((perfluorohexyl)sulfonyl)sulfamic acid; m/z 477.9068 and (E)-1,1,2,2,3,3,4,5,6,7,8,8,8-tridecafluorooct-6-ene-1-sulfonic acid; m/z 424.9482). This study highlights that several PFASs are overlooked using standard target analysis, and therefore, the potential risk from all PFASs present is likely to be underestimated.

Highly Concentrated Linear Guanidine Amides from the Marine Sipunculid Phascolosoma granulatum.

The chemical diversity of annelids, particularly those belonging to the class Sipuncula, remains largely unexplored. However, as part of a Marine Biodiscovery program in Ireland, the peanut worm Phascolosoma granulatum emerged as a promising source of unique metabolites. The purification of the MeOH/CH2Cl2 extract of this species led to the isolation of six new linear guanidine amides, named phascolosomines A-F (1-6). NMR analysis allowed for the elucidation of their structures, all of which feature a terminal guanidine, central amide linkage, and a terminal isobutyl group. Notably, these guanidine amides were present in unusually high concentrations, comprising ∼3% of the dry mass of the organism. The primary concentration of the phascolosomines in the viscera is similar to that previously identified in linear amides from sipunculid worms and marine fireworms. The compounds from sipunculid worms have been hypothesized to be toxins, while those from fireworms are reported to be defensive irritants. However, screening of the newly isolated compounds for inhibitory bioactivity showed no significant inhibition in any of the assays conducted.

Uncovering the biotechnological capacity of marine and brackish water Planctomycetota.

An appealing strategy for finding novel bioactive molecules in Nature consists in exploring underrepresented and -studied microorganisms. Here, we investigated the antimicrobial and tumoral anti-proliferative bioactivities of twenty-three marine and estuarine bacteria of the fascinating phylum Planctomycetota. This was achieved through extraction of compounds produced by the Planctomycetota cultured in oligotrophic medium followed by an antimicrobial screening against ten relevant human pathogens including Gram-positive and Gram-negative bacteria, and fungi. Cytotoxic effects of the extracts were also evaluated against five tumoral cell lines. Moderate to potent activities were obtained against Enterococcus faecalis, methicillin-sensitive and methicillin-resistant Staphylococcus aureus and vancomycin-sensitive and vancomycin-resistant Enterococcus faecium. Anti-fungal effects were observed against Trichophyton rubrum, Candida albicans and Aspergillus fumigatus. The highest cytotoxic effects were observed against human breast, pancreas and melanoma tumoral cell lines. Novipirellula caenicola and Rhodopirellula spp. strains displayed the widest spectrum of bioactivities while Rubinisphaera margarita ICM_H10T affected all Gram-positive bacteria tested. LC-HRMS analysis of the extracts did not reveal the presence of any known bioactive natural product, suggesting that the observed activities are most likely caused by novel molecules, that need identification. In summary, we expanded the scope of planctomycetal species investigated for bioactivities and demonstrated that various strains are promising sources of novel bioactive compounds, which reenforces the potential biotechnological prospects offered by Planctomycetota.

Multidisciplinary approach to inherited causes of dual sensory impairment.

PURPOSE: This article presents a review of the main causes of inherited dual sensory impairment (DSI) with an emphasis on the multidisciplinary approach. METHODS: A narrative review of English literature published before January 2023 was conducted using PubMed, Medline, and Scopus databases. The different causes of inherited DSI are discussed from a multidisciplinary perspective. RESULTS: There are a wide range of dual sensory impairment (DSI), commonly referred to as blindness and deafness. While Usher syndrome is the most frequent genetic cause, other genetic syndromes such as Alport syndrome or Stickler syndrome can also lead to DSI. Various retinal phenotypes, including pigmentary retinopathy as seen in Usher syndrome, vitreoretinopathy as in Stickler syndrome, and macular dystrophy as in Alport syndrome, along with type of hearing loss (sensorineural or conductive) and additional systemic symptoms can aid in diagnostic suspicion. A thorough ophthalmologic and otorhinolaryngologic examination can help guide diagnosis, which can then be confirmed with genetic studies, crucial for determining prognosis. Effective hearing rehabilitation measures, such as hearing implants, and visual rehabilitation measures, such as low vision optical devices, are crucial for maintaining social interaction and proper development in these patients. CONCLUSIONS: While Usher syndrome is the primary cause of inherited dual sensory impairment (DSI), other genetic syndromes can also lead to this condition. A proper diagnostic approach based on retinal phenotypes and types of hearing loss can aid in ruling out alternative causes. Multidisciplinary approaches can assist in reaching a definitive diagnosis, which has significant prognostic implications.

A data-driven approach to decode metabolic dysfunction-associated steatotic liver disease.

Metabolic dysfunction-associated steatotic liver disease (MASLD), defined by the presence of liver steatosis together with at least one out of five cardiometabolic factors, is the most common cause of chronic liver disease worldwide, affecting around one in three people. Yet the clinical presentation of MASLD and the risk of progression to cirrhosis and adverse clinical outcomes is highly variable. It, therefore, represents both a global public health threat and a precision medicine challenge. Artificial intelligence (AI) is being investigated in MASLD to develop reproducible, quantitative, and automated methods to enhance patient stratification and to discover new biomarkers and therapeutic targets in MASLD. This review details the different applications of AI and machine learning algorithms in MASLD, particularly in analyzing electronic health record, digital pathology, and imaging data. Additionally, it also describes how specific MASLD consortia are leveraging multimodal data sources to spark research breakthroughs in the field. Using a new national-level 'data commons' (SteatoSITE) as an exemplar, the opportunities, as well as the technical challenges of large-scale databases in MASLD research, are highlighted.

Superior capsular reconstruction with the long head of the biceps tendon achieves excellent clinical results and low rotator cuff rerupture rates one year after cuff repair surgery.

PURPOSE: To analyze the clinical one-year evolution of healed and rerupture lesions in patients who received a rotator cuff repair plus Superior Capsular Reconstruction (SCR) with the long head of the biceps (LHB). Moreover, to compare this evolution between men and women. METHODS: A pilot study was conducted on patients who underwent a rotator cuff repair plus SCR with LHB between February 2021 and June 2022. All patients completed pre-operative and one-year post-operative evaluations for tendon type of tear and tendon integrity using Magnetic Resonance Imaging (MRI)after one year of the surgery. Besides, functionality was evaluated with the American Shoulder and Elbow Surgeons (ASES) score; the visual analog scale for pain (VAS); and the Constant score. RESULTS: A total of 38 patients completed the one-year final evaluation, they presented an increased functionality score to 83 and 86 in Constant and ASES scales (p < .001), respectively. Besides, 84% of the patients presented a healed cuff, while rerupture occurred in 16% of the patients. There were differences between the healed and rerupture patients in the total Constant score, with a remarkable increase in the strength subscale, almost double for patients with healed cuff (p < .001); in the same way, daily life activity score, and balance subscale increased, while pain score decreased in the healed cuff group (p < .05). There was no difference in functionality between men and women (p > .05). Besides, almost all patients achieved the MCID in both ASES and Constant total scores, irrespectively of the healing group. CONCLUSION: The cuff repair using SCR with the LHB achieved a low percentage of rerupture and a functional improvement after one year of follow-up. Patients who healed the lesion presented more strength and better performance in daily life activities than those with cuff repurture. Thus, SCR + LHB procedure can be considered an efficient technique for rotator cuff repair surgery for both men and women. Although a comparison with a control group is needed to confirm these findings.

Naphthoquinone Derivatives from Angustimassarina populi CF-097565 Display Anti-Tumour Activity in 3D Cultures of Breast Cancer Cells.

Cancer is one of the leading causes of death worldwide, with breast cancer being the second cause of cancer-related mortality among women. Natural Products (NPs) are one of the main sources for drug discovery. During a screening campaign focused on the identification of extracts from Fundación MEDINA's library inhibiting the proliferation of cancer cell lines, a significant bioactivity was observed in extracts from cultures of the fungus Angustimassarina populi CF-097565. Bioassay-guided fractionation of this extract led to the identification and isolation of herbarin (1), 1-hydroxydehydroherbarin (4) plus other three naphthoquinone derivatives of which 3 and 5 are new natural products and 2 is herein described from a natural source for the first time. Four of these compounds (1, 3, 4 and 5) confirmed a specific cytotoxic effect against the human breast cancer cell line MCF-7. To evaluate the therapeutic potential of the compounds isolated, their efficacy was validated in 3D cultures, a cancer model of higher functionality. Additionally, an in-depth study was carried out to test the effect of the compounds in terms of cell mortality, sphere disaggregation, shrinkage, and morphology. The cell profile of the compounds was also compared to that of known cytotoxic compounds with the aim to distinguish the drug mode of action (MoA). The profiles of 1, 3 and 4 showed more biosimilarity between them, different to 5, and even more different to other known cytotoxic agents, suggesting an alternative MoA responsible for their cytotoxicity in 3D cultures.

Exploring the potential of phenolic and antioxidant compounds in new Rosaceae fruits.

BACKGROUND: Rosaceae fruits have been used in traditional medicine for the prevention and treatment of diseases. However, these fruits have not extensively been studied regarding their phenolic composition. Thus, this research focuses on the determination of phenolic compounds by high-performance liquid chromatography electrospray ionization time-of-flight mass spectrometry, flavan-3-ols by high-performance liquid chromatography with fluorescence detection, and the antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), and ferric reducing antioxidant power of the fruits of five species of genera Crataegus and Sorbus (Rosaceae). RESULTS: We found a total of 71 phenolic compounds from which 30 were identified in these berries for the first time. Crataegus monogyna and Crataegus laciniata revealed higher total phenolic and flavan-3-ol contents than the other species and the highest antioxidant activities. CONCLUSIONS: Therefore, the fruits evaluated have demonstrated to be important sources of bioactive compounds with huge potential for being used in nutraceutical or food scopes. Additional studies could be needed to evaluate the influence of the different production areas on the phenolic content. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Influence of augmented reality technique on the accuracy of autotransplanted teeth in surgically created sockets.

BACKGROUND: The objective of the present study was to evaluate the reliability of an augmented reality drilling approach and a freehand drilling technique for the autotransplantation of single-rooted teeth. MATERIALS AND METHODS: Forty samples were assigned to the following surgical techniques for drilling guidance of the artificial sockets: A. augmented reality technique (AR) (n = 20) and B. conventional free-hand technique (FT) (n = 20). Then, two models with 10 teeth each were submitted to a preoperative cone-beam computed tomography (CBCT) scan and a digital impression by a 3D intraoral scan. Afterwards, the autotrasplanted teeth were planned in a 3D dental implant planning software and transferred to the augmented reality device. Then, a postoperative CBCT scan was performed. Data sets from postoperative CBCT scans were aligned to the planning in the 3D implant planning software to analize the coronal, apical and angular deviations. Student's t-test and Mann-Whitney non-parametric statistical analysis were used to analyze the results. RESULTS: No statistically significant differences were shown at coronal (p = 0.123) and angular (p = 0.340) level; however, apical deviations between AR and FT study groups (p = 0.008) were statistically significant different. CONCLUSION: The augmented reality appliance provides higher accuracy in the positioning of single-root autotransplanted teeth compared to the conventional free-hand technique.

Prevalence of diagnosed and undiagnosed osteoarthrosis and associated factors in the adult general Spanish population.

OBJECTIVE: To determine the prevalence and related factors of diagnosed osteoarthrosis (DO) and undiagnosed osteoarthrosis (UO) in the general Spanish adult population. SETTING: Cross-sectional study with data from the Spanish National Health Survey 2017. PARTICIPANTS: N=23,089 adults. Three groups of people were defined: DO, UO, and no osteoarthrosis (NO). MAIN MEASUREMENTS: Sociodemographic information, lifestyle (tobacco, alcohol, physical activity, body mass index) and health factors (intensity of pain, pain drug consumption, mental health, self-perceived health status, pain involvement in daily living) were collected. Descriptive and bivariate analyses were performed, and a multinomial logistic regression model for the factors associated with each group. RESULTS: The prevalence of DO was 22.4% (95%CI=21.8;22.9) and 0.9% (95%CI=0.8;1) of UO. With respect to NO, risk factors for DO and UO included higher pain levels and pain drug consumption. Better self-perceived health status was inversely related with both. More pain involvement in daily living was associated with increased risk of DO, but reduced risk of UO. CONCLUSIONS: The prevalence of DO and UO was similar to that reported in Europe, but slightly higher than in low/middle-income countries. It was more prevalent in females, older people, people with worse perceived health status and worse mental health. Higher pain levels and pain drug consumption were risk factors for DO and UO. Better self-perceived health status was protective. Pain involvement in daily living was a risk factor for DO, but protective for UO. Different public health strategies should be considered in view of this.

Is Nontarget Analysis Ready for Regulatory Application? Influence of Peak-Picking Algorithms on Data Analysis.

The use of peak-picking algorithms is an essential step in all nontarget analysis (NTA) workflows. However, algorithm choice may influence reliability and reproducibility of results. Using a real-world data set, the aim of this study was to investigate how different peak-picking algorithms influence NTA results when exploring temporal and/or spatial trends. For this, drinking water catchment monitoring data, using passive samplers collected twice per year across Southeast Queensland, Australia (n = 18 sites) between 2014 and 2019, was investigated. Data were acquired using liquid chromatography coupled to high-resolution mass spectrometry. Peak picking was performed using five different programs/algorithms (SCIEX OS, MSDial, self-adjusting-feature-detection, two algorithms within MarkerView), keeping parameters identical whenever possible. The resulting feature lists revealed low overlap: 7.2% of features were picked by >3 algorithms, while 74% of features were only picked by a single algorithm. Trend evaluation of the data, using principal component analysis, showed significant variability between the approaches, with only one temporal and no spatial trend being identified by all algorithms. Manual evaluation of features of interest (p-value <0.01, log fold change >2) for one sampling site revealed high rates of incorrectly picked peaks (>70%) for three algorithms. Lower rates (<30%) were observed for the other algorithms, but with the caveat of not successfully picking all internal standards used as quality control. The choice is therefore currently between comprehensive and strict peak picking, either resulting in increased noise or missed peaks, respectively. Reproducibility of NTA results remains challenging when applied for regulatory frameworks.

Deep MRD profiling defines outcome and unveils different modes of treatment resistance in standard- and high-risk myeloma.

Patients with multiple myeloma (MM) carrying standard- or high-risk cytogenetic abnormalities (CAs) achieve similar complete response (CR) rates, but the later have inferior progression-free survival (PFS). This questions the legitimacy of CR as a treatment endpoint and represents a biological conundrum regarding the nature of tumor reservoirs that persist after therapy in high-risk MM. We used next-generation flow (NGF) cytometry to evaluate measurable residual disease (MRD) in MM patients with standard- vs high-risk CAs (n = 300 and 90, respectively) enrolled in the PETHEMA/GEM2012MENOS65 trial, and to identify mechanisms that determine MRD resistance in both patient subgroups (n = 40). The 36-month PFS rates were higher than 90% in patients with standard- or high-risk CAs achieving undetectable MRD. Persistent MRD resulted in a median PFS of âˆ¼3 and 2 years in patients with standard- and high-risk CAs, respectively. Further use of NGF to isolate MRD, followed by whole-exome sequencing of paired diagnostic and MRD tumor cells, revealed greater clonal selection in patients with standard-risk CAs, higher genomic instability with acquisition of new mutations in high-risk MM, and no unifying genetic event driving MRD resistance. Conversely, RNA sequencing of diagnostic and MRD tumor cells uncovered the selection of MRD clones with singular transcriptional programs and reactive oxygen species-mediated MRD resistance in high-risk MM. Our study supports undetectable MRD as a treatment endpoint for patients with MM who have high-risk CAs and proposes characterizing MRD clones to understand and overcome MRD resistance. This trial is registered at www.clinicaltrials.gov as #NCT01916252.