Ratio of electron donor to acceptor influences metabolic specialization and denitrification dynamics in Pseudomonas aeruginosa in a mixed carbon medium

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, I. H., Mullen, S., Ciccarese, D., Dumit, D., Martocello, D. E., Toyofuku, M., Nomura, N., Smriga, S., & Babbin, A. R. Ratio of electron donor to acceptor influences metabolic specialization and denitrification dynamics in Pseudomonas aeruginosa in a mixed carbon medium. Frontiers in Microbiology, 12, (2021): 711073, https://doi.org/10.3389/fmicb.2021.711073.Denitrifying microbes sequentially reduce nitrate (NO3–) to nitrite (NO2–), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx–) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx–. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.Funding for this work was provided by Simons Foundation award 622065 and an MIT Environmental Solutions Initiative seed grant to AB. Additional support was received by the MIT Ferry Fund

Wide spetcrum mutational analysis of metastatic renal cell cancer : a retrospective next generation sequencing approach

Renal cell cancer (RCC) is characterized by histological and molecular heterogeneity that may account for variable response to targeted therapies. We evaluated retrospectively with a next generation sequencing (NGS) approach using a pre-designed cancer panel the mutation burden of 32 lesions from 22 metastatic RCC patients treated with at least one tyrosine kinase or mTOR inhibitor. We identified mutations in the VHL, PTEN, JAK3, MET, ERBB4, APC, CDKN2A, FGFR3, EGFR, RB1, TP53 genes. Somatic alterations were correlated with response to therapy. Most mutations hit VHL1 (31,8%) followed by PTEN (13,6%), JAK3, FGFR and TP53 (9% each). Eight (36%) patients were wild-type at least for the genes included in the panel. A genotype concordance between primary RCC and its secondary lesion was found in 3/6 cases. Patients were treated with Sorafenib, Sunitinib and Temsirolimus with partial responses in 4 (18,2%) and disease stabilization in 7 (31,8%). Among the 4 partial responders, 1 (25%) was wild-type and 3 (75%) harbored different VHL1 variants. Among the 7 patients with disease stabilization 2 (29%) were wild-type, 2 (29%) PTEN mutated, and single patients (14% each) displayed mutations in VHL1, JAK3 and APC/CDKN2A. Among the 11 non-responders 7 (64%) were wild-type, 2 (18%) were p53 mutated and 2 (18%) VHL1 mutated. No significant associations were found among RCC histotype, mutation variants and response to therapies. In the absence of predictive biomarkers for metastatic RCC treatment, a NGS approach may address single patients to basket clinical trials according to actionable molecular specific alterations.Peer reviewe

Early primary tumor response in metastatic RCC patients treated with immune checkpoint inhibitors-based combinations

Background: 25-30% of renal cell carcinoma presents with metastases (mRCC) at diagnosis. The activity of immune checkpoint inhibitor (ICI)-combinations on the primary tumor (PT) is debated. Patients andMethods: mRCC patients (pts) with PT who received first-line nivolumab plus ipilimumab (N/I) or pembrolizumab plus axitinib (P/A) were included. We investigated the early primary tumor response (EPTR) at the first radiological assessment. Results: 73 pts were included. The median early reduction of the PT longest diameter was 12.4% with P/A versus 6.2% with N/I (p = 0.42). We evaluated if the type of EPTR could affect the metastases response. Among pts with PT stable disease (SD), 8.3% had metastatic disease progression (PD) with P/A and 34.8% with N/I. Early PT partial response (PR) was associated with no metastatic PD with both N/I and P/A. The 2 pts with PT PD had also metastatic PD to P/A. Of the 3 PT with PD to N/I, 1 had metastatic SD and 2 PD. In the overall population, of the 94.1% without PT progression (PR+SD), 47.5% had metastatic PR, 35.6% SD, 16.9% PD. Conclusions: ICIs-combinations achieved an early PT PR in about 10-20%, without any complete responses. Only a small percentage of PT had an early PD, mainly associated with metastatic PD. However, among those PT without an early progression, metastatic PR can be achieved in approximately 50% of cases

The Cardiovascular Toxicity of Abiraterone and Enzalutamide in Prostate Cancer

We analyzed the cardiovascular toxicities related to the use of abiraterone and enzalutamide in prostate cancer. We found that these agents are associated with an increased risk of all- and high-grade cardiac toxicity as well as an increased risk of all- and high-grade hypertension. Follow-up for the onset of treatment-related cardiovascular events should be considered in these patients treated with abiraterone and enzalutamide.Introduction: The cardiovascular toxicity related to abiraterone and enzalutamide has been previously studied by our group. In this analysis, we aim to update our previous findings related to abiraterone and enzalutamide, including the new available evidence, both in castration-resistant and hormone-sensitive prostate cancer. Patients and Methods: Prospective studies were identified by searching the MEDLINE/PubMed, Cochrane Library, and ASCO Meeting abstracts. Combined relative risks (RRs) and 95% confidence intervals (Cis) were calculated using fixed- or random-effects methods. Results: We included 7 articles in this meta-analysis, covering a total of 8660 patients who were used to evaluate cardiovascular toxicity. The use of new hormonal agents was associated with an increased risk of all-grade (RR, 1.36; 95% CI, 1.13-1.64; P = .001) and high-grade (RR, 1.84; 95% CI, 1.21-2.80; P = .004) cardiac toxicity. The use of new hormonal agents was also associated with an increased risk of all-grade (RR, 1.98; 95% CI, 1.62-2.43; P = .001) and high-grade (RR, 2.26; 95% CI, 1.84-2.77; P = .004) hypertension compared with the controls. Abiraterone was found to significantly increase the risk of both cardiac toxicity and hypertension, whereas enzalutamide significantly increases only the risk of hypertension. No differences were found based on the dose of prednisone used with abiraterone. The major limitation of this study is that data are available only as aggregate, and no single-patient information could be analyzed. Conclusions: Abiraterone and enzalutamide significantly increase the incidence and RR of cardiovascular toxicity in patients affected by metastatic prostate cancer. Follow-up for the onset of treatment-related cardiovascular events should therefore be considered in these patients. (C) 2017 Elsevier Inc. All rights reserved

Structured reporting for fibrosing lung disease: a model shared by radiologist and pulmonologist

Objectives: To apply the Delphi exercise with iterative involvement of radiologists and pulmonologists with the aim of defining a structured reporting template for high-resolution computed tomography (HRCT) of patients with fibrosing lung disease (FLD). Methods: The writing committee selected the HRCT criteria\ue2\u80\u94the Delphi items\ue2\u80\u94for rating from both radiology panelists (RP) and pulmonology panelists (PP). The Delphi items were first rated by RPs as \ue2\u80\u9cessential\ue2\u80\u9d, \ue2\u80\u9coptional\ue2\u80\u9d, or \ue2\u80\u9cnot relevant\ue2\u80\u9d. The items rated \ue2\u80\u9cessential\ue2\u80\u9d by < 80% of the RP were selected for the PP rating. The format of reporting was rated by both RP and PP. Results: A total of 42 RPs and 12 PPs participated to the survey. In both Delphi round 1 and 2, 10/27 (37.7%) items were rated \ue2\u80\u9cessential\ue2\u80\u9d by more than 80% of RP. The remaining 17/27 (63.3%) items were rated by the PP in round 3, with 2/17 items (11.7%) rated \ue2\u80\u9cessential\ue2\u80\u9d by the PP. PP proposed additional items for conclusion domain, which were rated by RPs in the fourth round. Poor consensus was observed for the format of reporting. Conclusions: This study provides a template for structured report of FLD that features essential items as agreed by expert thoracic radiologists and pulmonologists

Influence of temporal and spatial heterogeneity on microbial spatial self-organization

In this thesis work, I investigated the influences of environmental heterogeneities on the spatial self-organization of microbial communities. I took a reductionist approach using isogenic cross feeding strains grown under controlled environmental conditions. The environmental heterogeneities investigated in this research study include local nutrient availability, temporal fluctuations in environmental conditions, physical structures, and spatial distance between interacting individuals. In Chapter 1, I describe the main knowledge gaps regarding spatiotemporal heterogeneities as drivers of microbial spatial organization and community composition. In Chapter 2, I review the methods and current state of research in synthetic ecology to investigate the causes and consequences of microbial spatial self-organization. I described the properties of patterns of self-organization and propose methods to quantify them. Finally, I give an overview on the existing methods to engineer the spatial organization of microbial communities. In Chapter 3, I co-authored a research article on the influence of local nutrient concentrations on spatial organization and the maintenance of diversity during expansion of a cross-feeding community. I provided an agent-based model developed by Benedict Borer (ETHZ, STEP) that describes the influence of spatial organization on the reproductive success of lineages with consequences on the maintenance of genetic diversity during range expansion. I contributed to the experimental results, to the formulation of the main research question, and to the writing of the manuscript. In Chapter 4, I investigate patterns of spatial self-organization that emerge during range expansion of a cross feeding community under temporal fluctuations in the available electron acceptor. I used an updated version of the model presented in Chapter 3 to explain the mechanisms that enable the persistence of the community during fluctuating conditions and preserve genetic diversity. In Chapter 5, I describe how physical objects on a surface influence spatial self-organization and interspecific diversity during range expansion. I found that physical objects have differing effects depending on the types of interactions (competition and mutualism) present between genotypes. More specifically, I found that competitive interactions maintain higher diversity at the expanding edge compared to mutualistic interactions. In Chapter 6, I illustrate how the strength of a mutualistic interaction determines whether individuals are likely to develop into colonies. More specifically, I show that colony abundance, size and interspecific distance all depend on the strength of the interaction. I found that the mutualistic component of the net interaction determines the number of colonies and interspecific distances while the competitive component of the net interaction determines colony size. In Chapter 7, I discuss the main outcome of the research work and I describe new direction of future investigations