Prospects for the discovery of robust and reproducible biomarkers have improved considerably with the development of sensitive omics platforms that can enable measurement of biological molecules at an unprecedented scale. With technical barriers to success lowering, the challenge is now moving into the analytical domain. Genome-wide discovery presents a problem of scale and multiple testing as standard statistical methods struggle to distinguish signal from noise in increasingly complex biological systems. Machine learning and AI methods are good at finding answers in large datasets, but they have a tendency to overfit solutions. It may be possible to find a local answer or mechanism in a specific patient sample or small group of samples, but this may not generalise to wider patient populations due to the high likelihood of false discovery. The rise of explainable AI offers to improve the opportunity for true discovery by providing explanations for predictions that can be explored mechanistically before proceeding to costly and time-consuming validation studies. This review aims to introduce some of the basic concepts of machine learning and AI for biomarker discovery with a focus on post hoc explanation of predictions. To illustrate this, we consider how explainable AI has already been used successfully, and we explore a case study that applies AI to biomarker discovery in rheumatoid arthritis, demonstrating the accessibility of tools for AI and machine learning. We use this to illustrate and discuss some of the potential challenges and solutions that may enable AI to critically interrogate disease and response mechanisms.

Endometriosis is a gynecological inflammatory disorder characterized by the development of endometrial-like cells outside the uterine cavity. This disease is associated with a wide range of clinical presentations, such as debilitating pelvic pain and infertility issues. Endometriosis diagnosis is not easily discovered by ultrasound or clinical examination. Indeed, difficulties in noninvasive endometriosis diagnosis delay the confirmation and management of the disorder, increase symptoms, and place a significant medical and financial burden on patients. So, identifying specific and sensitive biomarkers for this disease should therefore be a top goal. Exosomes are extracellular vesicles secreted by most cell types. They transport between cells' bioactive molecules such as noncoding RNAs and proteins. MicroRNAs and long noncoding RNAs which are key molecules transferred by exosomes have recently been identified to have a significant role in endometriosis by modulating different proteins and their related genes. As a result, the current review focuses on exosomal micro-and-long noncoding RNAs that are involved in endometriosis disease. Furthermore, major molecular mechanisms linking corresponding RNA molecules to endometriosis development will be briefly discussed to better clarify the potential functions of exosomal noncoding RNAs in the therapy and diagnosis of endometriosis.

Pancreatic β cell clusters produce insulin and play a central role in glucose homeostasis. The regenerative capacity of mammalian β cells is limited and the loss of β cells causes diabetes. In contrast, zebrafish β cell clusters have a high regenerative capacity, making them an attractive model to study β cell cluster regeneration. How zebrafish β cell clusters regenerate, when the regeneration process is complete, and the identification of the cellular source of regeneration are fundamental questions that require investigation. Here, using larval and adult zebrafish, we demonstrate that pancreatic β cell clusters undergo a two-step regeneration process, regenerating functionality and then β cell numbers. Additionally, we found that all regenerating pancreatic β cells arose from Neurod1-expressing cells and that cells from different lineages contribute to both functional and β cell number recovery throughout their life. Furthermore, we found that during development and neogenesis, as well as regeneration, all β cells undergo Neurod1expression in zebrafish. Together, these results shed light on the fundamental cellular mechanisms underlying β cell cluster development, neogenesis, and regeneration.

Photoreceptor outer segments are surrounded by a carbohydrate-rich matrix, the interphotoreceptor matrix, necessary for physiological retinal function. Few roles for molecules characterizing the interphotoreceptor matrix have been clearly defined. Recent studies have found the presence of nonsense mutations in the interphotoreceptor matrix proteoglycan 2 (IMPG2) gene in patients affected by retinal dystrophies. IMPG2 encodes for a proteoglycan synthesized by photoreceptors and secreted in the interphotoreceptor matrix. Little is known about the structure and function of this protein, we thus decided to characterize zebrafish impg2. In zebrafish there are two Impg2 proteins, Impg2a and Impg2b. We generated a phylogenetic tree based on IMPG2 protein sequence similarity among vertebrates, showing a significant similarity between humans and teleosts. The human and zebrafish proteins share conserved domains, as also shown by homology models. Expression analyses of impg2a and impg2b show a continued expression in the photoreceptor layer starting from developmental stages and continuing through adulthood. Between 1 and 6 months post-fertilization, there is a significant shift of Impg2 expression toward the outer segment region, suggesting an increase in secretion. This raises intriguing hypotheses about its possible role(s) during retinal maturation, laying the groundwork for the generation of most needed models for the study of IMPG2-related inherited retinal dystrophies.

The crucial step in any regeneration process is epithelization, i.e. the restoration of an epithelium structural and functional integrity. Epithelization requires cytoskeletal rearrangements, primarily of actin filaments and microtubules. Sponges (phylum Porifera) are early branching metazoans with pronounced regenerative abilities. Calcareous sponges have a unique step during regeneration: the formation of a temporary structure, called regenerative membrane which initially covers a wound. It forms due to the morphallactic rearrangements of exopinaco- and choanoderm epithelial-like layers. The current study quantitatively evaluates morphological changes and characterises underlying actin cytoskeleton rearrangements during regenerative membrane formation in asconoid calcareous sponge Leucosolenia variabilis through a combination of time-lapse imaging, immunocytochemistry, and confocal laser scanning microscopy. Regenerative membrane formation has non-linear stochastic dynamics with numerous fluctuations. The pinacocytes at the leading edge of regenerative membrane form a contractile actomyosin cable. Regenerative membrane formation either depends on its contraction or being coordinated through it. The cell morphology changes significantly during regenerative membrane formation. Exopinacocytes flatten, their area increases, while circularity decreases. Choanocytes transdifferentiate into endopinacocytes, losing microvillar collar and flagellum. Their area increases and circularity decreases. Subsequent redifferentiation of endopinacocytes into choanocytes is accompanied by inverse changes in cell morphology. All transformations rely on actin filament rearrangements similar to those characteristic of bilaterian animals. Altogether, we provide here a qualitative and quantitative description of cell transformations during reparative epithelial morphogenesis in a calcareous sponge.

Type 2 diabetes (T2D), associated with obesity, represents a state of metabolic inflammation and oxidative stress leading to insulin resistance and progressive insulin deficiency. Adipose-derived stem cells (ASCs) are adult mesenchymal stem/stromal cells identified within the stromal vascular fraction of adipose tissue. These cells can regulate the immune system and possess anti-inflammatory properties. ASCs are a potential therapeutic modality for inflammatory diseases including T2D. Patient-derived (autologous) rather than allogeneic ASCs may be a relatively safer approach in clinical perspectives, to avoid occasional anti-donor immune responses. However, patient characteristics such as body mass index (BMI), inflammatory status, and disease duration and severity may limit the therapeutic utility of ASCs. The current review presents human ASC (hASC) immunoregulatory mechanisms with special emphasis on those related to T lymphocytes, hASC implications in T2D treatment, and the impact of T2D and obesity on hASC immunoregulatory potential. hASCs can modulate the proliferation, activation, and functions of diverse innate and adaptive immune cells via direct cell-to-cell contact and secretion of paracrine mediators and extracellular vesicles. Preclinical studies recommend the therapeutic potential of hASCs to improve inflammation and metabolic indices in a high-fat diet (HFD)-induced T2D disease model. Discordant data have been reported to unravel intact or detrimentally affected immunomodulatory functions of ASCs, isolated from patients with obesity and/or T2D patients, in vitro and in vivo. Numerous preconditioning strategies have been introduced to potentiate hASC immunomodulation; they are also discussed here as possible options to potentiate the immunoregulatory functions of hASCs isolated from patients with obesity and T2D.

The maintenance of planar polarity in airway multiciliated cells (MCCs) has been poorly characterized. We recently reported that the direction of ciliary beating in a surgically inverted tracheal segment remained inverted beyond the time required for the turnover of cells, without adjustment to global distal-to-proximal polarity. We hypothesized that the local maintenance of tissue-level polarity occurs via locally reproduced cells. To provide further insight regarding this hypothetical property, we performed allotransplantation of an inverted tracheal segment between wild-type (donor) and tdTomato-expressing (host) rats, with and without scratching the mucosa of the transplants. The origin of cells in the transplants was assessed using tdTomato-specific immunostaining. Ciliary movement and structures were observed by high-speed video and electron microscopy to analyze MCC orientations. Variabilities in the orientations of closely and distantly located MCCs were analyzed to evaluate the local- and broad-scale coordination of polarity, respectively. The epithelium was maintained by donor-derived cells in the non-scratched inverted transplant over 6 months, beyond one cycle of turnover. The inverted orientation of MCCs was also maintained throughout the non-scratched transplant. MCCs regenerated in the scratched transplant were derived from the host and exhibited diverse orientations across the transplant. However, the orientations of adjacent regenerated MCCs were often coordinated, indicating that airway MCCs can locally coordinate their orientations. A steady-state airway may maintain MCC orientation by locally reproducing MCCs via the local coordination of polarity. This local coordination enables the formation and maintenance of tissue-level polarity in small regions after mucosal injury.

Few studies describe the sequence of morphological events that characterize spermiogenesis in birds. In this paper, the clearly observable steps of spermiogenesis are described and illustrated for the first time in a commercially important ratite, the ostrich, based on light microscopy of toluidine blue-stained plastic sections. Findings were supplemented and supported by ultrastructural observations, PNA labeling of acrosome development, and immunocytochemical labeling of isolated spermatogenic cells. Spermiogenesis in the ostrich followed the general pattern described in non-passerine birds. Eight steps were identified based on changes in nuclear shape and contents, positioning of the centriolar complex, and acrosome development. Only two steps could be recognized with certainty during development of the round spermatid which contributed to the fewer steps recorded for the ostrich compared to that described in some other bird species. The only lectin that displayed acrosome reactivity was PNA and only for the first three steps of spermiogenesis. This suggests that organizational and/or compositional changes may occur in the acrosome during development and merits further investigation. Immunological labeling provided additional evidence to support the finding of previous studies that the tip of the nucleus in the ostrich is shaped by the forming acrosome and not by the microtubular manchette. To our knowledge, this is the first complete description of spermiogenesis in ostrich and one of few in any avian species. In addition to comparative reproduction and animal science, this work has implications for evolutionary biology as the reported germ cell features provide a bridge between reptile and ratite-avian spermatogenesis.