Proteomics and Phospho-Proteomics Profiling of the Co-Formulation of Type I and II Interferons, HeberFERON, in the Glioblastoma-Derived Cell Line U-87 MG.

HeberFERON, a co-formulation of Interferon (IFN)-α2b and IFN-γ, has effects on skin cancer and other solid tumors. It has antiproliferative effects over glioblastoma multiform (GBM) clones and cultured cell lines, including U-87 MG. Here, we report the first label-free quantitative proteomic and phospho-proteomic analyses to evaluate changes induced by HeberFERON after 72 h incubation of U-87 MG that can explain the effect on cellular proliferation. LC-MS/MS, functional enrichment and networking analysis were performed. We identified 7627 proteins; 122 and 211 were down- and up-regulated by HeberFERON (fold change > 2; p < 0.05), respectively. We identified 23,549 peptides (5692 proteins) and 8900 phospho-peptides; 523 of these phospho-peptides (359 proteins) were differentially modified. Proteomic enrichment showed IFN signaling and its control, direct and indirect antiviral mechanisms were the main modulated processes. Phospho-proteome enrichment displayed the cell cycle as one of the most commonly targeted events together with cytoskeleton organization; translation/RNA splicing, autophagy and DNA repair, as represented biological processes. There is a high interconnection of phosphoproteins in a molecular network; mTOR occupies a centric hub with interactions with translation machinery, cytoskeleton and autophagy components. Novel phosphosites and others with unknown biological functionality in key players in the aforementioned processes were regulated by HeberFERON and involved CDK and ERK kinases. These findings open new experimental hypotheses regarding HeberFERON action. The results obtained contribute to a better understanding of HeberFERON effector mechanisms in the context of GBM treatment.

Diagnostic Accuracy of Blood-Based Biomarker Panels: A Systematic Review.

Background: Because of high prevalence of Alzheimer's disease (AD) in low- and middle-income countries (LMICs), there is an urgent need for inexpensive and minimally invasive diagnostic tests to detect biomarkers in the earliest and asymptomatic stages of the disease. Blood-based biomarkers are predicted to have the most impact for use as a screening tool and predict the onset of AD, especially in LMICs. Furthermore, it has been suggested that panels of markers may perform better than single protein candidates. Methods: Medline/Pubmed was searched to identify current relevant studies published from January 2016 to December 2020. We included all full-text articles examining blood-based biomarkers as a set of protein markers or panels to aid in AD's early diagnosis, prognosis, and characterization. Results: Seventy-six articles met the inclusion criteria for systematic review. Majority of the studies reported plasma and serum as the main source for biomarker determination in blood. Protein-based biomarker panels were reported to aid in AD diagnosis and prognosis with better accuracy than individual biomarkers. Conventional (amyloid-beta and tau) and neuroinflammatory biomarkers, such as amyloid beta-42, amyloid beta-40, total tau, phosphorylated tau-181, and other tau isoforms, were the most represented. We found the combination of amyloid beta-42/amyloid beta-40 ratio and APOEε4 status to be most represented with high accuracy for predicting amyloid beta-positron emission tomography status. Conclusion: Assessment of Alzheimer's disease biomarkers in blood as a non-invasive and cost-effective alternative will potentially contribute to early diagnosis and improvement of therapeutic interventions. Given the heterogeneous nature of AD, combination of markers seems to perform better in the diagnosis and prognosis of the disease than individual biomarkers.

Scalable Bio Marker Combinations for Early Stroke Diagnosis: A Systematic Review.

Background: Acute stroke treatment is a time-critical process in which every minute counts. Laboratory biomarkers are needed to aid clinical decisions in the diagnosis. Although imaging is critical for this process, these biomarkers may provide additional information to distinguish actual stroke from its mimics and monitor patient condition and the effect of potential neuroprotective strategies. For such biomarkers to be effectively scalable to public health in any economic setting, these must be cost-effective and non-invasive. We hypothesized that blood-based combinations (panels) of proteins might be the key to this approach and explored this possibility through a systematic review. Methods: We followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines for systematic review. Initially, the broader search for biomarkers for early stroke diagnosis yielded 704 hits, and five were added manually. We then narrowed the search to combinations (panels) of the protein markers obtained from the blood. Results: Twelve articles dealing with blood-based panels of protein biomarkers for stroke were included in the systematic review. We observed that NR2 peptide (antibody against the NR2 fragment) and glial fibrillary acidic protein (GFAP) are brain-specific markers related to stroke. Von Willebrand factor (vWF), matrix metalloproteinase 9 (MMP-9), and S100ß have been widely used as biomarkers, whereas others such as the ischemia-modified albumin (IMA) index, antithrombin III (AT-III), and fibrinogen have not been evaluated in combination. We herein propose the following new combination of biomarkers for future validation: panel 1 (NR2 + GFAP + MMP-9 + vWF + S100ß), panel 2 (NR2 + GFAP + MMP-9 + vWF + IMA index), and panel 3 (NR2 + GFAP + AT-III + fibrinogen). Conclusions: More research is needed to validate, identify, and introduce these panels of biomarkers into medical practice for stroke recurrence and diagnosis in a scalable manner. The evidence indicates that the most promising approach is to combine different blood-based proteins to provide diagnostic precision for health interventions. Through our systematic review, we suggest three novel biomarker panels based on the results in the literature and an interpretation based on stroke pathophysiology.

MMP-2: is too low as bad as too high in the cardiovascular system?

Matrix metalloproteinase (MMP)-2 cleaves a broad spectrum of substrates, including extracellular matrix components (responsible for normal tissue remodeling) and cytokines (modulators of the inflammatory response to physiological insults such as tissue damage). MMP-2 expression is elevated in many cardiovascular pathologies (e.g., myocardial infarction, hypertensive heart disease) where tissue remodeling and inflammatory responses are perturbed. Thus, it has generally been assumed that blockade of MMP-2 activity will yield therapeutic effects. Here, we provide a counterargument to this dogma based on 1) preclinical studies on Mmp2-null ( Mmp2-/-) mice and 2) clinical studies on patients with inactivating MMP2 gene mutations. Furthermore, we put forward the hypothesis that, when MMP-2 activity falls below baseline, the bioavailability of proinflammatory cytokines normally cleaved and inactivated by MMP-2 increases, leading to the production of cytokines and cardiac secretion of phospholipase A2 activity into the circulation, which stimulate systemic inflammation that perturbs lipid metabolism in target organs. Finally, we suggest that insufficient understanding of the consequences of MMP-2 deficiency remains a major factor in the failure of MMP-2 inhibitor-based therapeutic approaches. This paucity of knowledge precludes our ability to effectively intervene in cardiovascular and noncardiovascular pathologies at the level of MMP-2.

Método rápido de verificación de mutantes de Escherichia coli empleados en ingeniería genética / Rapid verification method of Escherichia coli mutants used in genetic engineering

Para las metodologías de ADN recombinante, los biólogos moleculares emplean mutantes de Escherichia coli que son adquiridos de kit comerciales o de colecciones microbianas especializadas. En la práctica estos mutantes son conservados por pases sucesivos o en un banco poco caracterizado. No seguir el sistema de lotes de siembra (lote de siembra de referencia y lotes de siembra de trabajo) y la falta de controles sistemáticos, puede llevar a la pérdida de las características originales de las cepas y afectar la calidad de los resultados experimentales. Por otra parte, la propia dinámica de los laboratorios de investigación hace que sea poco práctico realizar las extensas verificaciones propias del trabajo de las colecciones microbianas. El objetivo de este artículo es proponer un método de evaluación de pureza y estabilidad genética que permita la verificación de varios mutantes de E. coli en un solo ensayo. En él se definen los criterios de selección para el diseño de medios de cultivos específicos. Se realizan diluciones seriadas de los cultivos crecidos en medio Luria Bertani y se emplea como método de siembra las trazas de dilución. Los resultados evidencian que teniendo en cuenta las rutas metabólicas afectadas en cada mutante, se pueden agrupar varias cepas a verificar en un solo ensayo. La combinación de medios específicos permite tener un criterio de la pureza del cultivo y la estabilidad genética. Esta alternativa permite el chequeo rápido de aquellos marcadores de las cepas que son determinantes en las metodologías de ADN recombinante(AU)

For recombinant DNA methodologies, molecular biologists use Escherichia coli mutants acquired from commercial kits or specialized microbial strain collections. These mutants are routinely conserved by successive passages or in poorly-characterized strain banks. A failure to follow the seed lot system (reference seed lot and working seed lot) and the lack of systematic controls, can lead to the loss of original strain characteristics and affect the quality of experimental results. On the other hand, the dynamic of research laboratories makes impractical to carry out extensive verifications related to the work with microbial collections. The aim of this article is to propose a single-assay method for genetic purity and stability evaluation of multiple E. coli mutants simultaneously. For the design of specific culture media, selection criteria were defined. Serial dilutions of cultures in Luria Bertani medium were made, and track dilution was used as seeding method. The results show how a mutated metabolic pathway-oriented design permit the verification of several strains in a single trial. A criterion about culture purity and genetic stability could be obtained after combining specific media. This alternative allows for a rapid evaluation of strain key genetic markers for recombinant DNA methodologies(AU)

Método rápido de verificación de mutantes de Escherichia coli empleados en ingeniería genética / Rapid verification method of Escherichia coli mutants used in genetic engineering

Para las metodologías de ADN recombinante, los biólogos moleculares emplean mutantes de Escherichia coli que son adquiridos de kit comerciales o de colecciones microbianas especializadas. En la práctica estos mutantes son conservados por pases sucesivos o en un banco poco caracterizado. No seguir el sistema de lotes de siembra (lote de siembra de referencia y lotes de siembra de trabajo) y la falta de controles sistemáticos, puede llevar a la pérdida de las características originales de las cepas y afectar la calidad de los resultados experimentales. Por otra parte, la propia dinámica de los laboratorios de investigación hace que sea poco práctico realizar las extensas verificaciones propias del trabajo de las colecciones microbianas. El objetivo de este artículo es proponer un método de evaluación de pureza y estabilidad genética que permita la verificación de varios mutantes de E. coli en un solo ensayo. En él se definen los criterios de selección para el diseño de medios de cultivos específicos. Se realizan diluciones seriadas de los cultivos crecidos en medio Luria Bertani y se emplea como método de siembra las trazas de dilución. Los resultados evidencian que teniendo en cuenta las rutas metabólicas afectadas en cada mutante, se pueden agrupar varias cepas a verificar en un solo ensayo. La combinación de medios específicos permite tener un criterio de la pureza del cultivo y la estabilidad genética. Esta alternativa permite el chequeo rápido de aquellos marcadores de las cepas que son determinantes en las metodologías de ADN recombinante(AU)

For recombinant DNA methodologies, molecular biologists use Escherichia coli mutants acquired from commercial kits or specialized microbial strain collections. These mutants are routinely conserved by successive passages or in poorly-characterized strain banks. A failure to follow the seed lot system (reference seed lot and working seed lot) and the lack of systematic controls, can lead to the loss of original strain characteristics and affect the quality of experimental results. On the other hand, the dynamic of research laboratories makes impractical to carry out extensive verifications related to the work with microbial collections. The aim of this article is to propose a single-assay method for genetic purity and stability evaluation of multiple E. coli mutants simultaneously. For the design of specific culture media, selection criteria were defined. Serial dilutions of cultures in Luria Bertani medium were made, and track dilution was used as seeding method. The results show how a mutated metabolic pathway-oriented design permit the verification of several strains in a single trial. A criterion about culture purity and genetic stability could be obtained after combining specific media. This alternative allows for a rapid evaluation of strain key genetic markers for recombinant DNA methodologies(AU)