Computational Methods for Single-Cell Imaging and Omics Data Integration

Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.

Open Healing: A Minimally Invasive Protocol with Flapless Ridge Preservation in Implant Patients

We aimed to validate the safety and efficacy of the minimally invasive “open healing” flapless technique for post-extraction socket and alveolar ridge preservation, while assessing the alveolar bone changes. The study enrolled (n = 104) patients (0.55 sex ratio), with atraumatic extraction of (N = 135) hopeless teeth, followed by either immediate placement of tissue level implants (N1 = 26), or later stage implant insertion (N2 = 109). No flap was raised in either situation. Post-extraction sockets were filled with deproteinized bovine bone granules and covered by collagen resorbable membrane—left purposely exposed during healing. This yielded an uneventful healing, with sufficient bone formation, while avoiding soft-tissue problems. The need for additional augmentation was assessed clinically and by calibrated CBCT scans at six months, before either loading (N1) or implant insertion (N2). Implant success and survival rate were evaluated at 12-, 24-, and 60-month follow-up control sessions. The inserted implants had a survival rate of 98.5% and a success rate of 94.8% at five-year follow-up. Open healing technique with flapless approach can be favorable for preserving the 3D architecture of the post-extraction socket, as well as the alveolar ridge width and height.

The Involvement of miRNAs in Pituitary Adenomas Pathogenesis and the Clinical Implications

Pituitary adenomas (PAs) account for the top three primary intracranial tumors in terms of total incidence rate. PAs can cause severe endocrine disorders and even malignant features, such as invasion, metastasis, and recurrence. Therefore, the early diagnosis and accurate prognosis would be greatly beneficial for clinical treatment of PAs. MicroRNAs (miRNAs) are small, protein-noncoding RNAs that regulate gene expression posttranscriptionally. They regulate essential physiological processes, including proliferation, growth, and apoptosis, and also they involve in the invasion and metastasis of malignant tumors. At the tissue level, differential miRNA expression in endocrine malignancies including PAs has been reported. When miRNAs have been successfully detected in various biofluids and cell-free environments, their important roles as potential screening or prognostic biomarkers have been extensively investigated. The current work reviews recent studies on the emerging roles of miRNAs in PAs and the clinical significance.

Microstructural Dynamics of the Myocardium: Orientation of the Muscle Fibers and Occurrence of Cardiomyopathies

This paper considers the Holzapfel–Ogden (HO) model to examine the behavior of the left ventricle myocardium. At the tissue level, we analyze the contributions of the orientation angle of muscle fibers (MFs) and investigate their effects on the occurrence of certain cardiomyopathies and congenital diseases at the organ level. Knowing the importance of myocardial microstructure on cardiac function, we vary the angle between the direction of collagen sheets and MFs in all layers of the myocardium (from epicardium to endocardium) to model the effects of tilted MFs. Based on the HO model in which the directions of the fibers are orthogonal and using the strain energy of HO, we construct a tensile-compression test and simulate the dynamics of a cubic sample. We recover the authors’ results exhibiting the existence of residual stresses in various directions. Then, we modify the energy of HO slightly to assess the impact of the same stress states on the system with tilted MFs. A numerical tensile-compression test performed on this new cubic sample shows that, in certain directions, the heart tissue is more resistant to shear deformations in some planes than in others. Moreover, it appears that the residual stress is smaller as the angle of orientation of the MFs is small. Furthermore, we observe that the residual stress is greater in the new model compared to the normal HO model. This could affect the heart muscle at the organ level leading to hypertrophied/dilated cardiomyopathy.

Systemic Sclerosis: From Pathophysiology to Novel Therapeutic Approaches

Systemic sclerosis (SSc) is a systemic, immune-mediated chronic disorder characterized by small vessel alterations and progressive fibrosis of the skin and internal organs. The combination of a predisposing genetic background and triggering factors that causes a persistent activation of immune system at microvascular and tissue level is thought to be the pathogenetic driver of SSc. Endothelial alterations with subsequent myofibroblast activation, excessive extracellular matrix (ECM) deposition, and unrestrained tissue fibrosis are the pathogenetic steps responsible for the clinical manifestations of this disease, which can be highly heterogeneous according to the different entity of each pathogenic step in individual subjects. Although substantial progress has been made in the management of SSc in recent years, disease-modifying therapies are still lacking. Several molecular pathways involved in SSc pathogenesis are currently under evaluation as possible therapeutic targets in clinical trials. These include drugs targeting fibrotic and metabolic pathways (e.g., TGF-β, autotaxin/LPA, melanocortin, and mTOR), as well as molecules and cells involved in the persistent activation of the immune system (e.g., IL4/IL13, IL23, JAK/STAT, B cells, and plasma cells). In this review, we provide an overview of the most promising therapeutic targets that could improve the future clinical management of SSc.

Metabolomic Analysis of Carbohydrate and Amino Acid Changes Induced by Hypoxia in Naked Mole-Rat Brain and Liver

Hypoxia poses a major physiological challenge for mammals and has significant impacts on cellular and systemic metabolism. As with many other small rodents, naked mole-rats (NMRs; Heterocephalus glaber), who are among the most hypoxia-tolerant mammals, respond to hypoxia by supressing energy demand (i.e., through a reduction in metabolic rate mediated by a variety of cell- and tissue-level strategies), and altering metabolic fuel use to rely primarily on carbohydrates. However, little is known regarding specific metabolite changes that underlie these responses. We hypothesized that NMR tissues utilize multiple strategies in responding to acute hypoxia, including the modulation of signalling pathways to reduce anabolism and reprogram carbohydrate metabolism. To address this question, we evaluated changes of 64 metabolites in NMR brain and liver following in vivo hypoxia exposure (7% O2, 4 h). We also examined changes in matched tissues from similarly treated hypoxia-intolerant mice. We report that, following exposure to in vivo hypoxia: (1) phenylalanine, tyrosine and tryptophan anabolism are supressed both in NMR brain and liver; (2) carbohydrate metabolism is reprogramed in NMR brain and liver, but in a divergent manner; (3) redox state is significantly altered in NMR brain; and (4) the AMP/ATP ratio is elevated in liver. Overall, our results suggest that hypoxia induces significant metabolic remodelling in NMR brain and liver via alterations of multiple metabolic pathways.

Pathological Targets for Treating Temporal Lobe Epilepsy: Discoveries From Microscale to Macroscale

Temporal lobe epilepsy (TLE) is one of the most common and severe types of epilepsy, characterized by intractable, recurrent, and pharmacoresistant seizures. Histopathology of TLE is mostly investigated through observing hippocampal sclerosis (HS) in adults, which provides a robust means to analyze the related histopathological lesions. However, most pathological processes underlying the formation of these lesions remain elusive, as they are difficult to detect and observe. In recent years, significant efforts have been put in elucidating the pathophysiological pathways contributing to TLE epileptogenesis. In this review, we aimed to address the new and unrecognized neuropathological discoveries within the last 5 years, focusing on gene expression (miRNA and DNA methylation), neuronal peptides (neuropeptide Y), cellular metabolism (mitochondria and ion transport), cellular structure (microtubule and extracellular matrix), and tissue-level abnormalities (enlarged amygdala). Herein, we describe a range of biochemical mechanisms and their implication for epileptogenesis. Furthermore, we discuss their potential role as a target for TLE prevention and treatment. This review article summarizes the latest neuropathological discoveries at the molecular, cellular, and tissue levels involving both animal and patient studies, aiming to explore epileptogenesis and highlight new potential targets in the diagnosis and treatment of TLE.

Metabolic Response to Daytime Dry Fasting in Bahá’í Volunteers—Results of a Preliminary Study

Each year in March, adherents of the Bahá’í faith abstain from eating and drinking from sunrise to sunset for 19 days. Thus, Bahá’í fasting (BF) can be considered as a form of daytime dry fasting. We investigated whether BF decreased energy expenditure after a meal and whether it improved anthropometric measures and systemic and tissue-level metabolic parameters. This was a self-controlled cohort study with 11 healthy men. We measured anthropometric parameters, metabolic markers in venous blood and pre- and postprandial energy metabolism at systemic (indirect calorimetry) and tissue (adipose tissue and skeletal muscle microdialysis) level, both before and during BF. During BF, we found reduced body weight, body mass index, body fat and blood glucose. Postprandial increase in energy expenditure was lower and diet-induced thermogenesis tended to be lower as well. In adipose tissue, perfusion, glucose supply and lipolysis were increased. In skeletal muscle, tissue perfusion did not change. Glucose supply and lipolysis were decreased. Glucose oxidation was increased, indicating improved insulin sensitivity. BF may be a promising approach to losing weight and improving metabolism and health. However, outside the context of religiously motivated fasting, skipping a meal in the evening (dinner cancelling) might be recommended, as metabolism appeared to be reduced in the evening.