InfectionCMA: A Cell MicroArray Approach for Efficient Biomarker Screening in In Vitro Infection Assays

The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the scientific community to acquire knowledge in real-time, when total lockdowns and the interruption of flights severely limited access to reagents as the global pandemic became established. This unique reality made researchers aware of the importance of designing efficient in vitro set-ups to evaluate infectious kinetics. Here, we propose a histology-based method to evaluate infection kinetics grounded in cell microarray (CMA) construction, immunocytochemistry and in situ hybridization techniques. We demonstrate that the chip-like organization of the InfectionCMA has several advantages, allowing side-by-side comparisons between diverse cell lines, infection time points, and biomarker expression and cytolocalization evaluation in the same slide. In addition, this methodology has the potential to be easily adapted for drug screening. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Funding text 1: Funding: The Portuguese Foundation for Science and Technology (FCT) funded this project through the Research4COVID19 projects 109_596696487 and RESEARCH COVID-19 projects Ref. 510. FCT also financed the Ph.D. grant to R.J.P. (SFRH/BD/145217/2019) and M.N. (2020.04720.BD). i3S is supported by FEDER–Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020–Operational Program for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Inovação in the framework of the project ‘Institute for Research and Innovation in Health Sciences’ (POCI-01-0145-FEDER-007274).; Funding text 2: The Portuguese Foundation for Science and Technology (FCT) funded this project through the Research4COVID19 projects 109_596696487 and RESEARCH COVID-19 projects Ref. 510. FCT also financed the Ph.D. grant to R.J.P. (SFRH/BD/145217/2019) and M.N. (2020.04720.BD). i3S is supported by FEDER?Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020?Operational Program for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT/Minist?rio da Ci?ncia, Tecnologia e Inova??o in the framework of the project ?Institute for Research and Innovation in Health Sciences? (POCI-01-0145-FEDER-007274)

Multi-tissue transcriptomic-informed in silico investigation of drugs for the treatment of dengue fever disease

Transcriptomics, proteomics and pathogen-host interactomics data are being explored for the in silico–informed selection of drugs, prior to their functional evaluation. The effectiveness of this kind of strategy has been put to the test in the current COVID-19 pandemic, and it has been paying off, leading to a few drugs being rapidly repurposed as treatment against SARS-CoV-2 infection. Several neglected tropical diseases, for which treatment remains unavailable, would benefit from informed in silico investigations of drugs, as performed in this work for Dengue fever disease. We analyzed transcriptomic data in the key tissues of liver, spleen and blood profiles and verified that despite transcriptomic differences due to tissue specialization, the common mechanisms of action, “Adrenergic receptor antagonist”, “ATPase inhibitor”, “NF-kB pathway inhibitor” and “Serotonin receptor antagonist”, were identified as druggable (e.g., oxprenolol, digoxin, auranofin and palonosetron, respectively) to oppose the effects of severe Dengue infection in these tissues. These are good candidates for future functional evaluation and clinical trials.Funding was provided by FEDER, Fundo Europeu de Desenvolvimento Regional funds, through the COMPETE 2020, Competitiveness and Internationalization Operational Programme (POCI), Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Inovação, in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274)

Shedding light on the african enigma: In vitro testing of homo sapiens-helicobacter pylori coevolution

The continuous characterization of genome-wide diversity in population and case- cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the longstanding associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual humanand bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.Funds were guaranteed by the project “Advancing cancer research: from basic knowledge to application”; NORTE-01-0145-FEDER-000029; Projetos Estruturados de I & D & I, funded by Norte 2020-Programa Operacional Regional do Norte. i3S is financed by FEDER-Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020-Competitiveness and Internationalization Operational Programme (POCI), Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274)

Effect of Weight Loss after Bariatric Surgery on Thyroid-Stimulating Hormone Levels in Patients with Morbid Obesity and Normal Thyroid Function

Background: Several studies have reported that morbid obesity is associated with increased thyroid-stimulating hormone (TSH) levels. However, it is not clear what is the impact of bariatric surgery on postoperative thyroid function. The aim of this study was to evaluate the effect of weight loss after bariatric surgery on TSH levels in euthyroid patients with morbid obesity. Methods: We performed a retrospective observational study of 949 euthyroid patients (86.1% female; age 42.0 ± 10.3 years, BMI 44.3 ± 5.7 kg/m2) with morbid obesity submitted to bariatric surgery (laparoscopic adjustable gastric band, Roux-en-Y gastric bypass, or sleeve gastrectomy). Patients were subdivided in two groups: normal TSH group (TSH <2.5 mU/L) and high-normal TSH group (TSH ≥2.5 mU/L). The impact of anthropometric parameters, comorbidities, TSH, free thyroxine (FT4), free triiodothyronine (FT3), type of surgery, and excessive body weight loss (EBWL) on TSH variation 12 months after surgery was evaluated. Results: The high-normal TSH group (24.3% of patients) included more women, presented a higher BMI, higher systolic blood pressure, and higher FT3 levels. There was a significant decrease of TSH 12 months after surgery that was more marked in the high-normal TSH group (normal TSH group: 1.57 ± 0.49 to 1.53 ± 0.69 mIU/L, p = 0.063; high-normal TSH group: 3.23 ± 0.59 to 2.38 ± 0.86 mIU/L, p < 0.001). In a multivariate analysis, after adjusting for relevant covariates, EBWL, baseline BMI, and baseline FT3 were significantly associated with TSH decrease 12 months after bariatric surgery. Conclusion: Bariatric surgery promotes a decrease of TSH that is significantly greater in patients with high-normal TSH and is independently associated with EBWL after surgery

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

A few molecularly proven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases of symptomatic reinfection are currently known worldwide, with a resolved first infection followed by a second infection after a 48 to 142-day intervening period. We report a multiple-component study of a clinically severe and prolonged viral shedding coronavirus disease 2019 (COVID-19) case in a 17-year-old Portuguese female. She had two hospitalizations, a total of 19 RT-PCR tests, mostly positive, and criteria for releasing from home isolation at the end of 97 days. The viral genome was sequenced in seven serial samples and in the diagnostic sample from her infected mother. A human genome-wide array (>900 K) was screened on the seven samples, and in vitro culture was conducted on isolates from three late samples. The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient's mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency. The 900 K profiles confirmed the identity of the patient in the serial samples, and they allowed us to infer that she had polygenic risk scores for hospitalization and severe respiratory disease within the normal distributions for a Portuguese population cohort. The early-on dynamic co-infection may have contributed to the severity of COVID-19 in this otherwise healthy young patient, and to her prolonged SARS-CoV-2 shedding profile.The authors acknowledge the support of the i3S Scientific Platforms BioSciences Screening and Genomics, members of the national infrastructure PPBI-Portuguese Platform of Bioimaging (PPBI-POCI-01-0145-FEDER-022122), PT-OPENSCREEN, GenomePT project (POCI-01-0145-FEDER-022184)

Mapping Helminth Co-Infection and Co-Intensity: Geostatistical Prediction in Ghana

Urinary schistosomiasis and hookworm infections cause considerable morbidity in school age children in West Africa. Severe morbidity is predominantly observed in individuals infected with both parasite types and, in particular, with heavy infections. We investigated for the first time the distribution of S. haematobium and hookworm co-infections and distribution of co-intensity of these parasites in Ghana. Bayesian geostatistical models were developed to generate a national co-infection map and national intensity maps for each parasite, using data on S. haematobium and hookworm prevalence and egg concentration (expressed as eggs per 10 mL of urine for S. haematobium and expressed as eggs per gram of faeces for hookworm), collected during a pre-intervention baseline survey in Ghana, 2008. In contrast with previous findings from the East Africa region, we found that both S. haematobium and hookworm infections are highly focal, resulting in small, localized clusters of co-infection and areas of high co-intensity. Overlaying on a single map the co-infection and the intensity of multiple parasite infections allows identification of areas where parasite environmental contamination and morbidity are at its highest, while providing an evidence base for the assessment of the progress of successive rounds of mass drug administration (MDA) in integrated parasitic disease control programs