A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities

Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for the rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged, including the study of the gut microbiome and its health implications and the role of microbial communities in global ecosystems. However, all the critical steps in this framework, from model construction to simulation, require the use of powerful linear optimization solvers, with the choice often relying on commercial solvers for their well-known computational efficiency. In this work, I benchmark a total of six solvers (two commercial and four open source) and measure their performance to solve linear and mixed-integer linear problems of increasing complexity. Although commercial solvers are still the fastest, at least two open-source solvers show comparable performance. These results show that genome-scale metabolic modeling does not need to be hindered by commercial licensing schemes and can become a truly open science framework for solving urgent societal challenges.IMPORTANCEModeling the metabolism of organisms and communities allows for computational exploration of their metabolic capabilities and testing their response to genetic and environmental perturbations. This holds the potential to address multiple societal issues related to human health and the environment. One of the current limitations is the use of commercial optimization solvers with restrictive licenses for academic and non-academic use. This work compares the performance of several commercial and open-source solvers to solve some of the most complex problems in the field. Benchmarking results show that, although commercial solvers are indeed faster, some of the open-source options can also efficiently tackle the hardest problems, showing great promise for the development of open science applications.

Microbial interactions shape cheese flavour formation

Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, we studied the roles of microbial interactions in flavour formation in a year-long Cheddar cheese making process, using a commercial starter culture containing Streptococcus thermophilus and Lactococcus strains. By using an experimental strategy whereby certain strains were left out from the starter culture, we show that S. thermophilus has a crucial role in boosting Lactococcus growth and shaping flavour compound profile. Controlled milk fermentations with systematic exclusion of single Lactococcus strains, combined with genomics, genome-scale metabolic modelling, and metatranscriptomics, indicated that S. thermophilus proteolytic activity relieves nitrogen limitation for Lactococcus and boosts de novo nucleotide biosynthesis. While S. thermophilus had large contribution to the flavour profile, Lactococcus cremoris also played a role by limiting diacetyl and acetoin formation, which otherwise results in an off-flavour when in excess. This off-flavour control could be attributed to the metabolic re-routing of citrate by L. cremoris from diacetyl and acetoin towards α-ketoglutarate. Further, closely related Lactococcus lactis strains exhibited different interaction patterns with S. thermophilus, highlighting the significance of strain specificity in cheese making. Our results highlight the crucial roles of competitive and cooperative microbial interactions in shaping cheese flavour profile.

Abstract 5660: IGM-7354, an immunocytokine with IL-15 fused to an anti-PD-L1 IgM, induces NK and CD8+ T cell mediated cytotoxicity of PD-L1-positive tumor cells

Immunostimulatory cytokines are a promising immunotherapy for the treatment of advanced malignancies, but generally have been associated with severe toxicities when administered systemically. The recent development of antibody-cytokine fusion proteins, or immunocytokines, aims to localize cytokine activity to the tumor microenvironment and thus improve their therapeutic index. We have developed IGM-7354, a high affinity, high avidity anti-PD-L1 pentameric IgM antibody with an IL-15Rα chain and IL-15 fused to the joining (J) chain. The IGM-7354 immunocytokine was designed to deliver IL-15-mediated stimulation of NK and CD8+ T cells to PD-L1-expressing tumors and antigen-presenting cells, to enhance anti-tumor immune responses. The multivalent binding of IGM-7354 to PD-L1 provided a stronger binding avidity for human PD-L1 than the monovalent binding of IL-15 to IL-15Rb as confirmed in kinetic binding assays. In vitro IGM-7354 induced the proliferation of a cytotoxic T cell line responsive to IL-15 stimulation and enhanced the proliferation of NK and CD8+ T cells from healthy donor human PBMCs. In cytotoxicity assays with human PBMC and PD-L1+ cancer cell lines, IGM-7354 enhanced cancer cell killing through NK and CD8+ T cell expansion and cytotoxic activity, evidenced by Ki67 and Granzyme B upregulation in these cell populations. Next, in vivo pharmacodynamic studies were performed in two humanized mouse models: non-tumor-bearing BRGSF-HIS mice engrafted with human CD34+ cells, and PD-L1+ MDA-MB-231 tumor-bearing MHC-/- NSG mice engrafted with human PBMCs. In the BRGSF model, IGM-7354 increased NK cell activation and Granzyme B expression as well as NK and CD8+ T cell proliferation. In the tumor-bearing mouse model, IGM-7354 dose-dependently increased NK and CD8+ T cell proliferation in blood and infiltration of lymphocytes into the tumor. This pharmacodynamic activity correlated with IGM-7354 anti-tumor activity in the MDA-MB-231 model. Lastly, IGM-7354 increased the proliferation of NK and CD8+ T cells in cynomolgus monkeys and particularly induced the expansion of effector memory CD8+ T cells in the periphery. In summary, IGM-7354 induces NK and CD8+ T cell proliferation in both in vitro and in vivo preclinical models, resulting in the killing of PD-L1+ tumor cells. The strong avidity of IGM-7354 for PD-L1 may enhance IL-15 delivery to tumors and antigen-presenting cells and thus provide a more favorable safety profile. A Phase 1 clinical trial is planned.

Citation Format: Thierry D. Giffon, Melanie Desbois, Poonam Yakkundi, Susan Calhoun, Keerthana Sekar, Carolyn Denson, Tasnim Kothambawala, Alexander Pearson, Sivani Pandey, Deepal Pandya, Rodnie Rosete, Daniel Machado, Pat Raichlen, Dean Ng, Abhinav R. Jain, Roel Funke, Eric Humke, Paul R. Hinton, Beatrice Wang, Bruce A. Keyt, Maya F. Kotturi, Angus M. Sinclair. IGM-7354, an immunocytokine with IL-15 fused to an anti-PD-L1 IgM, induces NK and CD8+ T cell mediated cytotoxicity of PD-L1-positive tumor cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5660.

Ecological modelling approaches for predicting emergent properties in microbial communities

Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties-patterns or functions that cannot be deduced linearly from the properties of the constituent parts-underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that emergent properties are a consequence of interactions within the community, their non-linear nature makes mathematical modelling imperative for establishing the quantitative link between community structure and function. As the need for conservation and rational modulation of microbial ecosystems is increasingly apparent, so is the consideration of the benefits and limitations of the approaches to model emergent properties. Here we review ecosystem modelling approaches from the viewpoint of emergent properties. We consider the scope, advantages and limitations of Lotka-Volterra, consumer-resource, trait-based, individual-based and genome-scale metabolic models. Future efforts in this research area would benefit from capitalizing on the complementarity between these approaches towards enabling rational modulation of complex microbial ecosystems.

The genomic basis of the plant island syndrome in Darwin's giant daisies

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies.

Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.

Abstract 3438: Enhanced NK and CD8+ T cell proliferation, tumor cytotoxicity and reversal of T cell exhaustion with IGM-7354, an anti-PD-L1 IgM antibody and IL-15 cytokine fusion

Anti-PD-1/PD-L1 therapies are efficacious in certain cancer indications, but often patients relapse following a primary response Therefore rational combinations are needed to enhance initial and durable responses of anti-PD-1/PD-L1 therapies. Immunostimulatory cytokine, IL-15 is an attractive combination partner to enhance anti-tumor NK and memory CD8+ T cell expansion and survival. We are developing IGM-7354, a high affinity, high avidity anti-PD-L1 pentameric IgM antibody with an IL-15Rα chain and IL-15 fused to the joining (J) chain, designed to deliver IL-15 to PD-L1 expressing tumors for enhancing anti-tumor immune responses. IGM-7354 was generated by grafting heavy chain variable regions of a high affinity humanized anti-PD-L1 IgG onto the IgM heavy chain framework, co-expressed with the light chain and the J chain which included a single IL-15Rα and IL-15 fusion. Binding ELISAs were performed using recombinant antigens. IGM-7354 bound human and cynomolgus monkey PD-L1 with similar affinities but did not bind to rat or mouse PD-L1. In addition, the IL-15 component of IGM-7354 bound to human and cynomolgus β chain of the trimeric IL-15 receptor with similar affinities, but with weaker binding affinity to rodent IL-15Rβ. Using in vitro assays with human and cynomolgus monkey PBMCs, IGM-7354 dose-dependently enhanced the proliferation of NK and CD8+ T cells. Furthermore, in an in vitro MLR setting, IGM-7354 was able to reverse T cell exhaustion beyond that of an IL-15/IL15Rα complex or anti-PD-L1 IgM or IgG alone, as demonstrated by an increase in activation and effector cytokine secretion. In vitro cytotoxicity and ADCC assays were performed with luciferase-tagged human cancer cell lines and PBMCs. IGM-7354 enhanced in vitro killing of PD-L1-expressing cancer cells by human PBMCs in monotherapy and in combination with other therapeutic agents. Efficacy and pharmacodynamic studies in an MDA-MB-231 xenograft mouse model showed dose-dependent increases in circulating NK and CD8+ T cells and tumor-infiltrating lymphocytes, which correlated with tumor regression. In cynomolgus monkeys, IGM-7354 markedly induced the proliferation of NK and CD8+ T cells in a dose-dependent manner with a preferential expansion of effector memory CD8+ T cells and γδ T cells in the periphery. IGM-7354 stimulates NK and CD8+ T cell expansion in vitro and in vivo plus induces tumor regressions in mouse tumor models in monotherapy or combination with various agents. This approach may enhance tumor localization of the immunostimulatory cytokine IL-15 through high affinity and high avidity binding to PD-L1 thereby improving anti-tumor responses and minimizing toxicity.

Citation Format: Thierry Giffon, Melanie Desbois, Poonam Yakkundi, Keerthana Sekar, Marigold Manlusoc, Rodnie Rosete, Daniel Machado, Susan Calhoun, Tasnim Kothambawala, Dean Ng, Vu Tran, Avneesh Saini, Abhinav Jain, Beatrice Wang, Maya Kotturi, Bruce Keyt, Angus Sinclair. Enhanced NK and CD8+ T cell proliferation, tumor cytotoxicity and reversal of T cell exhaustion with IGM-7354, an anti-PD-L1 IgM antibody and IL-15 cytokine fusion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3438.

Psychiatric intervention on patients recovering from hospitalization due to Covid-19

Introduction

According to recent reports Covid-19 patients may exhibit psychiatric co-morbidities that cause dysfunction, loss of autonomy and emotional suffering even after the physical illness is treated. Considering the high impact Covid-19 may have on mental health, we have created a psychiatric consultation dedicated to the study, observation and support of patients that developed mental illness after being hospitalized due to Covid-19.

Objectives

We aim at 1) describe the profile of patients that developed psychiatric comorbidities following a hospitalization due to Covid-19 and 2) recognize and treat early psychiatric symptoms in Covid-19 patients.

Methods

Based on what was described in other epidemic crisis, we established a semi-structured interview to evaluate several dimensions of the patients’ life that may have been affected by Covid-19 and that may impact on mental health. The interview included the Depression, Anxiety and Stress Scale (DASS-21), the Impact of Event Scale – Revised (IES-R) and the Insomnia Severity Index (ISI). Each patient was observed multiple times over several months. Our evaluation was done in parallel with consultations in Internal Medicine.

Results

Most patients complained of symptoms directly related with the infection of SARS-CoV-2, namely fatigue, short breath and reduced tolerance to efforts. Importantly, many patients also reported de novo or aggravation of anxiety, stress, depression, sleep disturbances and grief often associated with feelings of existential emptiness and lack of purpose.

Conclusions

Hospitalization due to Covid-19 has a high impact on mental health, raising important questions on purpose and emptiness. An early psychiatric intervention is highly recommended.

Disclosure

No significant relationships.

Bulimia nervosa and borderline personality disorder - case report and literature review

Introduction

Bulimia Nervosa (BN) is a debilitating eating disorder characterized by binging and purging episodes generally accompanied by excessive concern with body weight and shape as well as body image disturbance. BN and Borderline Personality Disorder (BPD) may co-occur. In fact, studies estimate that one quarter to one third of patients with BN also meet criteria for BPD. However not much is known about the relationship between these two diseases. Nevertheless, the high comorbidity rate might not be surprising as both BN and BPD may share interacting aetiologies and common core symptoms such as impulsivity and emotional instability. So far, only very little is known about the clinical presentation of patients with both BN and BPD and their response to treatment.

Objectives

Literature review on BN and comorbid BPD. An illustrative clinical case is presented.

Methods

Case report and non-systematic review of the literature - sources obtained through search on Pubmed.gov database.

Results

Female, 19-year-old, student, lived with her mother and stepfather. Developed a poor relationship with her body image due to dental problems during high school. The patient started to binge eat, exhibit compensatory behaviors, restrictive eating pattern, body dissatisfaction and emotional instability while maintaining a normal BMI. Over the last year, she started a self-destructive behavior with slight improvement of BN symptoms.

Conclusions

Special attention should be given to patients suffering from BN and comorbid BPD as they present greater risk of recurrent suicide attempts and non-suicidal self-injury, as well as lower rates of remission. Early interventions that target impulsivity and problematic eating behavior may mitigate risk of future borderline personality features.

Disclosure

No significant relationships.

Impact of Covid-19 on mental health of Portuguese health professionals – longitudinal study, phase I

Introduction

The Covid-19 pandemic brought enormous challenges for health professionals. As in past epidemics, the uncertainty, danger and fear of contamination and an excessive load of work under dramatic conditions may contribute to aggravate the mental health of health professionals.

Objectives

Explore how the Covid-19 crisis impacted the mental health of healthcare workers and how their mental status relates with perspectives on the recent past and near future.

Methods

A longitudinal study will be applied in two phases, Q1 and Q2, one year apart, to evaluate depression, anxiety and post-traumatic stress among health professionals from a healthcare center in Portugal. Phase Q1 is concluded and comprised the Depression, Anxiety and Stress Scale (DASS-21), the Impact of Event Scale – Revised (IES-R) and a questionnaire about the past and the future.

Results

The IES-R scale revealed that nurses are at a higher risk of developing post-traumatic stress disorder (PTSD) than other professionals. The levels of depression and anxiety in the DASS-21 show no significant differences. Interestingly, professionals who worked almost exclusively at inpatient wards show higher levels of depression, anxiety and stress than those who worked at several hospital units (emergency, inpatient and outpatient units). A positive correlation was found between depression and anxiety and negative perspectives about the past and the future.

Conclusions

Covid-19 posed a terrible challenge for health professionals. Its impact on the mental health of healthcare workers may be significant even after the pandemic is under control.

Disclosure

No significant relationships.

Predictive and Therapeutic Implications of a Novel PLCγ1/SHP2-Driven Mechanism of Cetuximab Resistance in Metastatic Colorectal Cancer

PURPOSE

Cetuximab is an EGFR-targeted therapy approved for the treatment of RAS wild-type (WT) metastatic colorectal cancer (mCRC). However, about 60% of these patients show innate resistance to cetuximab. To increase cetuximab efficacy, it is crucial to successfully identify responder patients, as well as to develop new therapeutic approaches to overcome cetuximab resistance.

EXPERIMENTAL DESIGN

We evaluated the value of EGFR effector phospholipase C gamma 1 (PLCγ1) in predicting cetuximab responses, by analyzing progression-free survival (PFS) of a multicentric retrospective cohort of 94 treated patients with mCRC (log-rank test and Cox regression model). Furthermore, we used in vitro and zebrafish xenotransplant models to identify and target the mechanism behind PLCγ1-mediated resistance to cetuximab.

RESULTS

In this study, levels of PLCγ1 were found increased in RAS WT tumors and were able to predict cetuximab responses in clinical samples and in vitro and in vivo models. Mechanistically, PLCγ1 expression was found to bypass cetuximab-dependent EGFR inhibition by activating ERK and AKT pathways. This novel resistance mechanism involves a noncatalytic role of PLCγ1 SH2 tandem domains in the propagation of downstream signaling via SH2-containing protein tyrosine phosphatase 2 (SHP2). Accordingly, SHP2 inhibition sensitizes PLCγ1-resistant cells to cetuximab.

CONCLUSIONS

Our discoveries reveal the potential of PLCγ1 as a predictive biomarker for cetuximab responses and suggest an alternative therapeutic approach to circumvent PLCγ1-mediated resistance to cetuximab in patients with RAS WT mCRC. In this way, this work contributes to the development of novel strategies in the medical management and treatment of patients with mCRC.

Unlocking the genomic potential of aerobes and phototrophs for the production of nutritious and palatable microbial food without arable land or fossil fuels

The increasing world population and living standards urgently necessitate the transition towards a sustainable food system. One solution is microbial protein, i.e. using microbial biomass as alternative protein source for human nutrition, particularly based on renewable electron and carbon sources that do not require arable land. Upcoming green electrification and carbon capture initiatives enable this, yielding new routes to H2, CO2 and CO2-derived compounds like methane, methanol, formic- and acetic acid. Aerobic hydrogenotrophs, methylotrophs, acetotrophs and microalgae are the usual suspects for nutritious and palatable biomass production on these compounds. Interestingly, these compounds are largely un(der)explored for purple non-sulfur bacteria, even though these microbes may be suitable for growing aerobically and phototrophically on these substrates. Currently, selecting the best strains, metabolisms and cultivation conditions for nutritious and palatable microbial food mainly starts from empirical growth experiments, and mostly does not stretch beyond bulk protein. We propose a more target-driven and efficient approach starting from the genome-embedded potential to tuning towards, for instance, essential amino- and fatty acids, vitamins, taste,... Genome-scale metabolic models combined with flux balance analysis will facilitate this, narrowing down experimental variations and enabling to get the most out of the 'best' combinations of strain and electron and carbon sources.

From random point processes to hierarchical cavity master equations for stochastic dynamics of disordered systems in random graphs: Ising models and epidemics

We start from the theory of random point processes to derive n-point coupled master equations describing the continuous dynamics of discrete variables in random graphs. These equations constitute a hierarchical set of approximations that generalize and improve the cavity master equation (CME), a recently obtained closure for the usual master equation representing the dynamics. Our derivation clarifies some of the hypotheses and approximations that originally led to the CME, considered now as the first order of a more general technique. We tested the scheme in the dynamics of three models defined over diluted graphs: the Ising ferromagnet, the Viana-Bray spin-glass, and the susceptible-infectious-susceptible model for epidemics. In the first two, the equations perform similarly to the best-known approaches in literature. In the latter, they outperform the well-known pair quenched mean-field approximation.

711 IGM-7354 is an anti-PD-L1 IgM antibody and IL-15 cytokine fusion that enhances NK and CD8+ T cell proliferation and tumor cytotoxicity plus potently reverses T cell exhaustion

Background

While approved PD-1/PD-L1 inhibitory antibodies have demonstrated clinical efficacy in certain cancer patients, relapse following a primary response is often observed. Enhancing anti-tumor immune responses with an immunostimulatory cytokine, IL-15 is an attractive combination strategy to enhance anti-tumor NK and memory CD8+ T cell expansion and survival. We have developed IGM-7354, a high affinity, high avidity anti-PD-L1 pentameric IgM antibody with an IL-15Rα chain and IL-15 fused to the joining (J) chain, designed to deliver IL-15 to PD-L1 expressing tumors for enhancing anti-tumor immune responses.

Methods

IGM-7354 was generated by grafting heavy chain variable regions of a high affinity humanized anti-PD-L1 IgG onto the IgM heavy chain framework, co-expressed with the light chain and the J chain which included a single IL-15Rα and IL-15 fusion. Binding ELISAs were performed using recombinant antigens. Human and cynomolgus monkey PBMCs were used for potency testing. Reversal of T cell exhaustion was tested using in vitro MLR. In vitro cytotoxicity assays were performed with luciferase-tagged MDA-MB-231 cells and PBMCs. In vivo pharmacodynamic studies were conducted in mice and cynomolgus monkeys.

Results

IGM-7354 bound human and cynomolgus monkey PD-L1 with the same affinity but did not bind to rat or mouse PD-L1. In addition, the IL-15 component of IGM-7354 bound to human and cynomolgus β chain of the trimeric IL-15 receptor with similar affinities, but with weaker binding affinity to rodent IL-15Rβ. Using in vitro assays with PBMCs, IGM-7354 dose dependently enhanced the proliferation of human and cynomolgus monkey NK and CD8+ T cells. Furthermore, IGM-7354 was able to reverse T cell exhaustion in an in vitro MLR beyond that of an IL-15/IL15Rα complex or anti-PD-L1 IgM or IgG alone, as demonstrated by an increase in activation and effector cytokine secretion. IGM-7354 also enhanced in vitro killing of PD-L1-expressing MDA-MB-231 breast cancer cells by human PBMCs. Pharmacodynamic studies in an MDA-MB-231 xenograft mouse model showed dose-dependent increases in circulating NK and CD8+ T cells and tumor infiltrating lymphocytes, which correlated with tumor regression. In cynomolgus monkeys, intravenous administration of IGM-7354 was well tolerated and dose dependently induced the proliferation of NK and CD8+ T cells.

Conclusions

IGM-7354 stimulates NK and CD8+ T cell expansion in vitro and in vivo plus induces tumor regressions in mouse tumor models. This approach may enhance tumor localization of the immunostimulatory cytokine IL-15 through high affinity and high avidity binding to PD-L1 thereby improving anti-tumor responses and minimizing toxicity.

Ethics Approval

All animal studies were conducted according to approved Institutional Animal Care and Use Committee (IACUC) protocols of the testing facilities.

Metabolic memory underlying minimal residual disease in breast cancer

Tumor relapse from treatment-resistant cells (minimal residual disease, MRD) underlies most breast cancer-related deaths. Yet, the molecular characteristics defining their malignancy have largely remained elusive. Here, we integrated multi-omics data from a tractable organoid system with a metabolic modeling approach to uncover the metabolic and regulatory idiosyncrasies of the MRD. We find that the resistant cells, despite their non-proliferative phenotype and the absence of oncogenic signaling, feature increased glycolysis and activity of certain urea cycle enzyme reminiscent of the tumor. This metabolic distinctiveness was also evident in a mouse model and in transcriptomic data from patients following neo-adjuvant therapy. We further identified a marked similarity in DNA methylation profiles between tumor and residual cells. Taken together, our data reveal a metabolic and epigenetic memory of the treatment-resistant cells. We further demonstrate that the memorized elevated glycolysis in MRD is crucial for their survival and can be targeted using a small-molecule inhibitor without impacting normal cells. The metabolic aberrances of MRD thus offer new therapeutic opportunities for post-treatment care to prevent breast tumor recurrence.

LONG-PULSED ND:YAG LASER TO TREAT TELANGIECTASIA OF THE NOSE: A COMPREHENSIVE 5-YEAR SINGLE CENTER STUDY

Telangiectases of the nose are of esthetic concern and treatment is warranted. The study provides the results of 5 years of treatment of telangiectases of the nose region with the long-pulsed Nd:YAG 1,064 nm laser. A retrospective analysis was conducted in patients of Fitzpatrick skin type II-V. Exclusion criteria were patients with a previous history of treatment of the nose region, pregnant or lactating patients or patients with unrealistic expectations regarding the treatment risks, limitations and results. Standardized photographs were obtained before each session and at least 2 months after the last treatment session. A long-pulsed Nd:YAG 1,064 nm laser was used with a spot size of 2.5mm, fluence of 100 - 175 J/cm2, pulse duration of up to 135ms and repetition rate of 2-4 Hz. The follow-up ranged from 2 months to 5 years. The number of laser sessions varied from 1 to 5 monthly. Assessment was made by comparing pre-treatment and post-treatment photographs by two independent specialists and also by the patients' own assessment. All patients presented improvement of the vascular alterations. Evaluation of independent specialists as well as the evaluation of the patients themselves showed a high degree of satisfaction with the treatment. The treatment presented only few transitory side effects. Treatment of telangiectasia on the nose skin with the long-pulsed Nd:YAG 1,064 nm laser demonstrated to be safe and effective even in darker pigmented skin. The major limitation of this study is its retrospective nature.

Bleuler’s a or autism spectrum disorder in adults?

Introduction

Nowadays we know that autism spectrum disorders (ASD) and Schizophrenic spectrum (SS) are different types of disorders in their etiology, symptoms and prognosis, but the clinical distinction is often difficult to make due to comorbidity and similar symptoms.

Objectives

With this project, the authors intend to explore the differential diagnosis between ASD and SS specially when we talk about critical ages of onset.

Methods

An analysis of articles searched on Pubmed (articles between 2010-2020) with the key words “adult autism”, “childhood onset schizophrenia”, “childhood psychosis”.

Results

Early-onset schizophrenia (EOS) is defined as occurring before age 18 years. The condition share key diagnostic symptoms with adult-onset schizophrenia (AOS) but his prognoses and comorbidities differ. Autism spectrum disorder (ASD) is a common neurodevelopmental disorder characterized by difficulties since early childhood across reciprocal social communication and restricted interests and behaviors. ASD is a lifelong neurodevelopmental disorder, however there is a lack of answers and research for adults with ASD. There are shared aspects of odd thinking, rigid behaviors and impaired socialization in schizophrenia and ASD and COS seems to have a strong relationship with ASD, being comorbid in up to 50% of cases.

Conclusions

Usually the evaluation of the developmental history of the person, prodrome and onset, its course and the presence of positive symptoms of schizophrenia is enough to help us find a diagnosis. Unfortunately, in some ages the conclusion is not so easy to find. However is essential to determine whether the clinical manifestations belong to the autistic spectrum, the schizophrenic or result from comorbidity.

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly lactic and acetic acid bacteria) and yeasts (family Saccharomycetaceae), realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microorganisms) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open the niche for the followers by making available metabolites such as amino acids and lactate. Through metabolomics, transcriptomics and large-scale mapping of inter-species interactions, we show how microorganisms poorly suited for milk survive in-and even dominate-the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.

Polarization of microbial communities between competitive and cooperative metabolism

Resource competition and metabolic cross-feeding are among the main drivers of microbial community assembly. Yet the degree to which these two conflicting forces are reflected in the composition of natural communities has not been systematically investigated. Here, we use genome-scale metabolic modelling to assess the potential for resource competition and metabolic cooperation in large co-occurring groups (up to 40 members) across thousands of habitats. Our analysis reveals two distinct community types, which are clustered at opposite ends of a spectrum in a trade-off between competition and cooperation. At one end are highly cooperative communities, characterized by smaller genomes and multiple auxotrophies. At the other end are highly competitive communities, which feature larger genomes and overlapping nutritional requirements, and harbour more genes related to antimicrobial activity. The latter are mainly present in soils, whereas the former are found in both free-living and host-associated habitats. Community-scale flux simulations show that, whereas competitive communities can better resist species invasion but not nutrient shift, cooperative communities are susceptible to species invasion but resilient to nutrient change. We also show, by analysing an additional data set, that colonization by probiotic species is positively associated with the presence of cooperative species in the recipient microbiome. Together, our results highlight the bifurcation between competitive and cooperative metabolism in the assembly of natural communities and its implications for community modulation.

Stigmatizing Attitudes Toward Patients With Psychiatric Disorders Among Medical Students and Professionals

INTRODUCTION

Stigma attached to mental health encompasses discrimination and exclusion of psychiatric patients and hinders their opportunities to have more productive and fulfilling lives. Moreover, stigma also exists among health professionals, and therefore, it hampers the provision of treatment and care and the promotion of mental well-being. This manuscript intends to assess and compare the levels of stigmatization toward patients with mental illness between medical students and doctors from different specialties.

METHODS

The Portuguese version of Attribution Questionnaire (AQ-27) was used to assess the attitudes of medical students (n = 203), non-psychiatry doctors (n = 121), and psychiatry specialists (n = 29) from the University of Minho and three hospitals in the region of Braga, Portugal (Hospital de Braga, Hospital Senhora da Oliveira, and Hospital de Fafe).

RESULTS

Psychiatrists were the group that displayed lower levels of stigmatizing attitudes in all the items of the AQ-27, followed by the students. The regression analyses revealed that professional group and presence of a relative with mental illness were the factors that have a significant impact on the levels of stigmatization.

CONCLUSIONS

Mental illness stigma is widely spread in community and reaches not only general population but also health professionals. Psychiatrists presented lower levels of stigma compared with non-psychiatry physicians and medical students. We found that stigma is related with age and the presence of relatives with psychiatric disorders. These findings highlight the critical relevance of raising awareness on this topic and, therefore, break stereotypes to reduce the negative consequences of stigma.

Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

BACKGROUND

The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit genotypic and phenotypic diversity to boost yeast's industrial value is still urgently needed.

RESULTS

We analyzed 5,400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions; however, plant isolates tend to have a wider range of resistance, which may be associated with their metabolome and fluxome signatures in the tricarboxylic acid cycle and fatty acid metabolism. By deep genomic sequencing, we found that industrial strains have more genomic duplications especially affecting transcription factors, showing that they result from disparate evolutionary paths in comparison with the environmental strains, which have more indels, gene deletions, and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances.

CONCLUSIONS

These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains.

Mycobacterium marinum lymphocutaneous infection

Mycobacterium marinum is a nontuberculous mycobacteria with worldwide distribution that lives in fresh or salt water and is responsible for infections in fish, and sometimes in humans. Human disease consists mainly of cutaneous nodules, but deep structure involvement may also occur. Diagnosis of M. marinum infection remains a challenge, with a considerable time delay between onset of symptoms and diagnosis. We present a 33-year-old man with no immunosuppressive history who was seen in our department with skin nodules over his hand and forearm, distributed in a sporotrichoid pattern. His hobbies included maintaining an aquarium of tropical fish. Histological examination of the patient's skin biopsy was compatible with the diagnosis of mycobacterial infection, and the Ziehl-Neelsen staining revealed acid-fast bacilli. Molecular techniques confirmed the suspicion of M. marinum infection. A necropsy was performed on one of the patient's fish, more specifically, a Poecilia reticulata, and resulted in identification of M. marinum from its gut. The patient was treated with clarithromycin, ethambutol, and rifampicin for 9 months, with clearance of infection.

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual curation required to obtain good quality models. Here, we present an automated tool, CarveMe, for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation ready. Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. We show that CarveMe models perform closely to manually curated models in reproducing experimental phenotypes (substrate utilization and gene essentiality). Additionally, we build a collection of 74 models for human gut bacteria and test their ability to reproduce growth on a set of experimentally defined media. Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.

Hepatitis C Virus Eradication in Kidney Transplant Recipients: A Single-Center Experience in Portugal

INTRODUCTION

Hepatitis C (HCV) is a major cause of liver impairment post-kidney transplantation (KT). Anti-HCV direct-acting antivirals (DAA) made viral eradication possible.

METHODS

We performed a retrospective review of KT patients (n = 23) who received DAA at our hospital. Sustained viral response (SVR) was defined as absence of viral detection 12 weeks after cessation of therapy.

RESULTS

From 1985 to September 2017, 1440 patients underwent transplantation at Hospital Santa Cruz. From a total of 32 HCV RNA+ KT recipients on follow-up, we describe the first 23 patients treated with DAA. They were 56.7 ± 9.1 years old; 22 were white, 52.2% were males, they underwent transplantation 18.8 ± 9.0 years ago, and 13 had genotype 1B, 21 were naïve, and 9 had stages F3/F4. All but 2 patients, treated with grazoprevir/elbasvir, received sofosbuvir (18 with ledispasvir, 2 with daclastavir, and 4 with simultaneous ribavirin). Pretreatment, intra-treatment, and post-treatment creatinine clearances were 61.4, 60.6, and 60.7 mL/min/1.73 m², respectively (not significant [NS]). Cyclosporine A was the basis of immunosuppression in the majority [(n = 14); pretreatment and intra-treatment levels were 79.5 ± 23.0 and 91.8 ± 26.0 ng/mL, respectively (P = .08)]; tacrolimus (n = 8) and mammalian target of rapamycin (mTOR) levels (n = 5) were also similar. One patient interrupted ribavirin after 7 weeks due to anemia; all other patients completed the treatment course without major side effects. Only 3 patients presented positive viral RNA at the fourth week of treatment and SVR was achieved in 100% of the patients 12 weeks after treatment.

CONCLUSIONS

DAA therapy was well tolerated and effective in 100% of our treated patients, without significant impact on the renal function or on the immunosuppression.

Intravenous Immunoglobulin and Rituximab in HLA Highly Sensitized Kidney Transplant Recipients

INTRODUCTION

HLA-sensitized patients are penalized both in the access to kidney transplantation (KT) and, once transplanted, in the incidence of rejections and long-term allograft survival despite aggressive induction and maintenance therapy.

METHODS

This study retrospectively evaluates the impact of combining T- and B-cell-depleting agents and intravenous immunoglobulin for induction therapy in 45 highly sensitized KT patients (anti-panel reactive antibodies >60%, positive flow cytometry crossmatch or donor specific antibodies at the time of transplantation). The outcome data included the occurrence of biopsy-proven acute rejection, new-onset proteinuria, development of leukopenia, incidence of poliomavirus infection (BK or JC virus), fungal or bacterial infection after KT, de novo neoplasia, graft function, graft loss, or death with functioning KT.

RESULTS

The average panel reactive antibody was 62.5%; 41 patients (91.1%) had ≥3 HLA mismatches with the donor and 91.1% of patients had class I or II anti-HLA antibodies. Fourteen patients (31.1%) presented pre-KT donor-specific antibodies and 6 patients (13.3%) had a positive flow cytometry cross-match at the time of transplantation. The incidence of acute rejection in the first 6 months was 24.4% and the cumulative incidence was 37.8%. Two patients were diagnosed with leukopenia in the first 6 months after KT. Two patients (4.5%) had cytomegalovirus disease, 17 patients (37.8%) were diagnosed with bacterial infections. Cutaneous neoplasms were identified in 5 patients (11.1%) and solid tumors in 4 (8.9%). The death-censored graft survival was 100% in the first 6 months and 93.5% at the last evaluation. Patient survival in the same periods was 97.8% and 93.3%, respectively.

CONCLUSIONS

Induction immunosuppressive therapy with intravenous immunoglobulin and rituximab is effective; outcomes demonstrate an excellent patient and allograft survival and allograft function over the follow-up period.

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Deregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (FH) deficient cells and developed a computational modelling approach to identify putative regulatory phosphorylation-sites of metabolic enzymes. We identified previously reported functionally relevant phosphosites and potentially novel regulatory residues in enzymes of the central carbon metabolism. In particular, we showed that pyruvate dehydrogenase (PDHA1) enzymatic activity is inhibited by increased phosphorylation in FH-deficient cells, restricting carbon entry from glucose to the tricarboxylic acid cycle. Moreover, we confirmed PDHA1 phosphorylation in human FH-deficient tumours. Our work provides a novel approach to investigate how post-translational modifications of enzymes regulate metabolism and could have important implications for understanding the metabolic transformation of FH-deficient cancers with potential clinical applications.

Combined Effect of the PGR +331C > T, CYP17A1 -34A > G and CYP19A1 1531G > A Polymorphisms on the Risk of Developing Endometriosis

Purpose To evaluate the magnitude of the association of the polymorphisms of the genes PGR, CYP17A1 and CYP19A1 in the development of endometriosis.

Methods This is a retrospective case-control study involving 161 women with endometriosis (cases) and 179 controls. The polymorphisms were genotyped by real-time polymerase chain reaction using the TaqMan system. The association of the polymorphisms with endometriosis was evaluated using the multivariate logistic regression.

Results The endometriosis patients were significantly younger than the controls (36.0 ± 7.3 versus 38.0 ± 8.5 respectively, p = 0.023), and they had a lower body mass index (26.3 ± 4.8 versus 27.9 ± 5.7 respectively, p = 0.006), higher average duration of the menstrual flow (7.4 ± 4.9 versus 6.1 ± 4.4 days respectively, p = 0.03), and lower average time intervals between menstrual periods (25.2 ± 9.6 versus 27.5 ± 11.1 days respectively, p = 0.05). A higher prevalence of symptoms of dysmenorrhea, dyspareunia, chronic pelvic pain, infertility and intestinal or urinary changes was observed in the case group when compared with the control group. The interval between the onset of symptoms and the definitive diagnosis of endometriosis was 5.2 ± 6.9 years. When comparing both groups, significant differences were not observed in the allelic and genotypic frequencies of the polymorphisms PGR +331C > T, CYP17A1 -34A > G and CYP19A1 1531G > A, even when considering the symptoms, classification and stage of the endometriosis. The combined genotype PGR +331TT/CYP17A1 -34AA/CYP19A11531AA is positively associated with endometriosis (odds ratio [OR] = 1.72; 95% confidence interval [95%CI] = 1.09–2.72).

Conclusions The combined analysis of the polymorphisms PGR-CYP17A1-CYP19A1 suggests a gene-gene interaction in the susceptibility to endometriosis. These results may contribute to the identification of biomarkers for the diagnosis and/or prognosis of the disease and of possible molecular targets for individualized treatments.

Selective cytotoxicity and luminescence imaging of cancer cells with a dipicolinato-based EuIII complex

Four new lanthanide complexes with the ligand dipicNH₂²⁻ (dipic = dipicolinato) show selective cancer cell toxicity and are used for cell luminescence imaging.

Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene. We show how this can be applied to different kinds of constraint-based analysis: flux distribution prediction, gene essentiality analysis, random flux sampling, elementary mode analysis, transcriptomics data integration, and rational strain design. In each case we demonstrate how this approach can lead to improved phenotype predictions and a deeper understanding of the genotype-to-phenotype link. In particular, we show that a large fraction of reaction-based designs obtained by current strain design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions result in improved prediction accuracy. The model transformation proposed in this work enables existing constraint-based methods to be used at the gene level without modification. This automatically leverages phenotype analysis from reaction to gene level, improving the biological insight that can be obtained from genome-scale models.

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.

Safety, tolerability, efficacy and pharmacodynamics of the selective JAK1 inhibitor GSK2586184 in patients with systemic lupus erythematosus

We aimed to evaluate the pharmacodynamics, efficacy, safety and tolerability of the JAK1 inhibitor GSK2586184 in adults with systemic lupus erythematosus (SLE). In this adaptive, randomized, double-blind, placebo-controlled study, patients received oral GSK2586184 50-400 mg, or placebo twice daily for 12 weeks. Primary endpoints included interferon-mediated messenger RNA transcription over time, changes in Safety of Estrogen in Lupus National Assessment-SLE Disease Activity Index score, and number/severity of adverse events. A pre-specified interim analysis was performed when ≥ 5 patients per group completed 2 weeks of treatment. In total, 84-92% of patients were high baseline expressors of the interferon transcriptional biomarkers evaluated. At interim analysis, GSK2586184 showed no significant effect on mean interferon transcriptional biomarker expression (all panels). The study was declared futile and recruitment was halted at 50 patients. Shortly thereafter, significant safety data were identified, including elevated liver enzymes in six patients (one confirmed and one suspected case of Drug Reaction with Eosinophilia and Systemic Symptoms), leading to immediate dosing cessation. Safety of Estrogen in Lupus National Assessment-SLE Disease Activity Index scores were not analysed due to the small number of patients completing the study. The study futility and safety data described for GSK2586184 do not support further evaluation in patients with SLE. Study identifiers: GSK Study JAK115919; ClinicalTrials.gov identifier: NCT01777256.

Care Partnerships: Toward Technology to Support Teens' Participation in Their Health Care

Adolescents with complex chronic illnesses, such as cancer and blood disorders, must partner with family and clinical caregivers to navigate risky procedures with life-altering implications, burdensome symptoms and lifelong treatments. Yet, there has been little investigation into how technology can support these partnerships. We conducted 38 in-depth interviews (15 with teenage adolescents with chronic forms of cancer and blood disorders, 15 with their parents, and eight with clinical caregivers) along with nine non-participant observations of clinical consultations to better understand common challenges and needs that could be supported through design. Participants faced challenges primarily concerning: 1) teens' limited participation in their care, 2) communicating emotionally-sensitive information, and 3) managing physical and emotional responses. We draw on these findings to propose design goals for sociotechnical systems to support teens in partnering in their care, highlighting the need for design to support gradually evolving partnerships in care.

Renal Transplantation in HIV-Infected Patients: The First Portuguese Review

INTRODUCTION

With the introduction of combination antiretroviral therapy (cART), prognosis of human immunodeficiency virus (HIV) infection has been improved and kidney transplantation (KT) in HIV-positive patients became possible.

METHODS

We reviewed the demographic, clinical, laboratory, and therapeutic data of all the HIV-infected patients who underwent KT between 2009 (first KT in Portugal in a HIV-infected patient) and May 2014. Case accrual was through all Portuguese KT centers where a KT in an HIV-infected patient was performed. Patients were transplanted following the American and Spanish guideline recommendations that included maintenance on cART, undetectable plasma HIV RNA copies, and absolute CD4 counts of ≥ 200 cells/μL in the last 6 months.

RESULTS

Fourteen KT were performed on men and 3 on women. The mean age of patients at the time of transplantation was 49.9 ± 11.7 years. HIV status was known for 12 ± 5 years. Eight patients had AIDS in the past and all patients received grafts from deceased donors. Twelve patients (64.7%) underwent induction therapy with basiliximab and 2 patients experienced early graft loss. In 2 patients, humoral rejection was diagnosed and in 3 patients, cellular rejection. Two patients died and an additional patient had early graft loss.

CONCLUSION

KT is a possible, but challenging, renal replacement therapy in selected HIV-positive patients. Even in those with AIDS criteria in the past, when the disease is controlled, and after the reconstitution of the immune system with cART, KT can be performed. Nevertheless, the risk-benefit ratio for each patient needs to be taken in consideration.