Minimum Information and Quality Standards for Conducting, Reporting, and Organizing In Vitro Research

Critical appraisal tools used in systematic reviews of in vitro cell culture studies: A methodological study

Systematic reviews (SRs) of preclinical studies are marked with poor methodological quality. In vitro studies lack assessment tools to improve the quality of preclinical research. This methodological study aimed to identify, collect, and analyze SRs based on cell culture studies to highlight the current appraisal tools utilized to support the development of a validated critical appraisal tool for cell culture in vitro research. SRs, scoping reviews, and meta-analyses that included cell culture studies and used any type of critical appraisal tool were included. Electronic search, study selection, data collection and methodological quality (MQ) assessment tool were realized. Further, statistical analyses regarding possible associations and correlations between MQ and collected data were performed. After the screening process, 82 studies remained for subsequent analysis. A total of 32 different appraisal tools were identified. Approximately 60% of studies adopted pre-structured tools not designed for cell culture studies. The most frequent instruments were SYRCLE (n = 14), OHAT (n = 9), Cochrane Collaboration's tool (n = 7), GRADE (n = 6), CONSORT (n = 5), and ToxRTool (n = 5). The studies were divided into subgroups to perform statistical analyses. A significant association (OR = 5.00, 95% CI = 1.54-16.20, p = 0.008) was found between low MQ and chronic degenerative disorders as topic of SR. Several challenges in collecting information from the included studies led to some modifications related to the previously registered protocol. These results may serve as a basis for further development of a critical appraisal tool for cell culture studies capable of capturing all the essential factors related to preclinical research, therefore enhancing the practice of evidence-based.

HIV-1 Tat amino acid residues that influence Tat-TAR binding affinity: a scoping review

HIV-1 remains a global health concern and to date, nearly 38 million people are living with HIV. The complexity of HIV-1 pathogenesis and its subsequent prevalence is influenced by several factors including the HIV-1 subtype. HIV-1 subtype variation extends to sequence variation in the amino acids of the HIV-1 viral proteins. Of particular interest is the transactivation of transcription (Tat) protein due to its key function in viral transcription. The Tat protein predominantly functions by binding to the transactivation response (TAR) RNA element to activate HIV-1 transcriptional elongation. Subtype-specific Tat protein sequence variation influences Tat-TAR binding affinity. Despite several studies investigating Tat-TAR binding, it is not clear which regions of the Tat protein and/or individual Tat amino acid residues may contribute to TAR binding affinity. We, therefore, conducted a scoping review on studies investigating Tat-TAR binding. We aimed to synthesize the published data to determine (1) the regions of the Tat protein that may be involved in TAR binding, (2) key Tat amino acids involved in TAR binding and (3) if Tat subtype-specific variation influences TAR binding. A total of thirteen studies met our inclusion criteria and the key findings were that (1) both N-terminal and C-terminal amino acids outside the basic domain (47-59) may be important in increasing Tat-TAR binding affinity, (2) substitution of the amino acids Lysine and Arginine (47-59) resulted in a reduction in binding affinity to TAR, and (3) none of the included studies have investigated Tat subtype-specific substitutions and therefore no commentary could be made regarding which subtype may have a higher Tat-TAR binding affinity. Future studies investigating Tat-TAR binding should therefore use full-length Tat proteins and compare subtype-specific variations. Studies of such a nature may help explain why we see differential pathogenesis and prevalence when comparing HIV-1 subtypes.

Read-across approaches: current applications and regulatory acceptance in Korea, Japan, and China

The aim of this paper was to investigate the current status of read-across approaches in the Republic of Korea, Japan, and China in terms of applications and regulatory acceptance. In the Republic of Korea, over the last 6 years, approximately 8% of safety data records used for chemical registrations were based upon read-across, and a guideline published on the use of read-across results in 2017. In Japan, read-across is generally accepted for screening hazard classification of toxicological endpoints according to the Chemical Substances Control Law (CSCL). In China, read-across data, along with data from other animal alternatives are accepted as a data source for chemical registrations, but could be only considered when testing is not technically feasible. At present, read-across is not widely used for chemical registrations and regulatory acceptance of read-across may differ among countries in Asia. With consideration of the advantages and limitations of read-across, it is expected that read-across may soon gradually be employed in Asian countries. Thus, regulatory agencies need to prepare for this progression.

What do we know about the mechanisms of action of probiotics on factors involved in the pathogenesis of periodontitis? A scoping review of in vitro studies

OBJECTIVE

Probiotics are increasingly used in oral prevention and treatment conditions, but little is known about their abilities. The aim of this review is to clarify, summarize and disseminate current knowledge about the mode of action of in vitro probiotics on factors involved in the pathogenesis of periodontitis.

METHOD

2495 articles were identified in three databases (Medline, Web of Science, SpringerLink) and 26 studies included in this scoping review.

RESULTS

Twenty-three probiotic species were identified, the majority of which were Lactobacilli or Bifidobacteria. Lactobacillus rhamnosus (30.8 %) and Lactobacillus reuteri (42.3 %) were found to be the two predominantly studied probiotic species and three main mechanisms of action of probiotics could be classified as: (i) modulation of the immuno-inflammatory response, (ii) direct actions of probiotics on periodontopathogens by adhesion or nutritive competitions and/or the secretion of antimicrobial molecules and (iii) indirect actions through environmental modifications. A combination of several probiotic strains seems to be beneficial via synergistic action amplifying the functions of each strain used. However, heterogeneity of the methodologies and probiotic species included in studies leads us to consider the following avenues for future research: (i) implementation of standardized periodontal models as close as possible to in vivo periodontal conditions to identify the functions of each strain for appropriate medication, (ii) updating data about interactions within oral biofilms to identify new candidates and to predict then analyze their behavior within these biofilms.

CONCLUSION

Probiotics may have their place in the response to inter-individual variability in periodontitis, provided that the choice of the probiotic strain or combination of them will be personalized and optimal for each patient.

Therapeutic Applications of Stem Cells and Extracellular Vesicles in Emergency Care: Futuristic Perspectives

Regenerative medicine (RM) is an interdisciplinary field that aims to repair, replace or regenerate damaged or missing tissue or organs to function as close as possible to its physiological architecture and functions. Stem cells, which are undifferentiated cells retaining self-renewal potential, excessive proliferation and differentiation capacity into offspring or daughter cells that form different lineage cells of an organism, are considered as an important part of the RM approaches. They have been widely investigated in preclinical and clinical studies for therapeutic purposes. Extracellular vesicles (EVs) are the vital mediators that regulate the therapeutic effects of stem cells. Besides, they carry various types of cargo between cells which make them a significant contributor of intercellular communication. Given their role in physiological and pathological conditions in living cells, EVs are considered as a new therapeutic alternative solution for a variety of diseases in which there is a high unmet clinical need. This review aims to summarize and identify therapeutic potential of stem cells and EVs in diseases requiring acute emergency care such as trauma, heart diseases, stroke, acute respiratory distress syndrome and burn injury. Diseases that affect militaries or societies including acute radiation syndrome, sepsis and viral pandemics such as novel coronavirus disease 2019 are also discussed. Additionally, featuring and problematic issues that hamper clinical translation of stem cells and EVs are debated in a comparative manner with a futuristic perspective. Graphical Abstract.

A Family Affair: Addressing the Challenges of Factor H and the Related Proteins

Inflammation is a common denominator of diseases. The complement system, an intrinsic part of the innate immune system, is a key driver of inflammation in numerous disorders. Recently, a family of proteins has been suggested to be of vital importance in conditions characterized by complement dysregulation: the human Factor H (FH) family. This group of proteins consists of FH, Factor H-like protein 1 and five Factor H-related proteins. The FH family has been linked to infectious, vascular, eye, kidney and autoimmune diseases. In contrast to FH, the functions of the other highly homologous proteins are largely unknown and, hence, their role in the different disease-specific pathogenic mechanisms remains elusive. In this perspective review, we address the major challenges ahead in this emerging area, including 1) the controversies about the functional roles of the FH protein family, 2) the discrepancies in quantification of the FH protein family, 3) the unmet needs for validated tools and 4) limitations of animal models. Next, we also discuss the opportunities that exist for the immunology community. A strong multidisciplinary approach is required to solve these obstacles and is only possible through interdisciplinary collaboration between biologists, chemists, geneticists and physicians. We position this review in light of our own perspective, as principal investigators of the SciFiMed Consortium, a consortium aiming to create a comprehensive analytical system for the quantitative and functional assessment of the entire FH protein family.

Insufficient transparency of statistical reporting in preclinical research: a scoping review

Non-transparent statistical reporting contributes to the reproducibility crisis in life sciences, despite guidelines and educational articles regularly published. Envisioning more effective measures for ensuring transparency requires the detailed monitoring of incomplete reporting in the literature. In this study, a systematic approach was used to sample 16 periodicals from the ISI Journal Citation Report database and to collect 233 preclinical articles (including both in vitro and animal research) from online journal content published in 2019. Statistical items related to the use of location tests were quantified. Results revealed that a large proportion of articles insufficiently describe tests (median 44.8%, IQR [33.3–62.5%], k = 16 journals), software (31%, IQR [22.3–39.6%]) or sample sizes (44.2%, IQR [35.7–55.4%]). The results further point at contradictory information as a component of poor reporting (18.3%, IQR [6.79–26.7%]). No detectable correlation was found between journal impact factor and the quality of statistical reporting of any studied item. The under-representation of open-source software (4.50% of articles) suggests that the provision of code should remain restricted to articles that use such packages. Since mounting evidence indicates that transparency is key for reproducible science, this work highlights the need for a more rigorous enforcement of existing guidelines.