Time is ticking faster for long genes in aging

Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.

Progenitor Cell Sources for 3D Bioprinting of Lymphatic Vessels and Potential Clinical Application

The lymphatic system maintains tissue fluid homeostasis and it is involved in the transport of nutrients and immunosurveillance. It also plays a pivotal role in both pathological and regenerative processes. Lymphatic development in the embryo occurs by polarization and proliferation of lymphatic endothelial cells from the lymph sacs, that is, lymphangiogenesis. Alternatively, lymphvasculogenesis further contributes to the formation of lymphatic vessels. In adult tissues, lymphatic formation rarely occurs under physiological conditions, being restricted to pathological processes. In lymphvasculogenesis, progenitor cells seem to be a source of lymphatic vessels. Indeed, mesenchymal stem cells, adipose stem cells, endothelial progenitor cells, and colony-forming endothelial cells are able to promote lymphatic regeneration by different mechanisms, such as direct differentiation and paracrine effects. In this review, we summarize what is known on the diverse stem/progenitor cell niches available for the lymphatic system, emphasizing the potential that these cells hold for lymphatic tissue engineering through 3D bioprinting and their translation to clinical application.

3D bioprinted breast tumor-stroma models for pre-clinical drug testing

The use of three-dimensional (3D) bioprinting has been proposed for the reproducible production of 3D disease models that can be used for high-throughput drug testing and personalized medicine. However, most such models insufficiently reproduce the features and environment of real tumors. We report the development of bioprinted in vitro 3D tumor models for breast cancer, which physically and biochemically mimic important aspects of the native tumor microenvironment, designed to study therapeutic efficacy. By combining a mix of breast decellularized extracellular matrix and methacrylated hyaluronic acid with tumor-derived cells and non-cancerous stromal cells of biological relevance to breast cancer, we show that biological signaling pathways involved in tumor progression can be replicated in a carefully designed tumor-stroma environment. Finally, we demonstrate proof-of-concept application of these models as a reproducible platform for investigating therapeutic responses to commonly used chemotherapeutic agents.

Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin

Inflammation is known to play a critical role in all stages of tumorigenesis; however, less is known about how it predisposes the tissue microenvironment preceding tumor formation. Recessive dystrophic epidermolysis bullosa (RDEB), a skin-blistering disease secondary to COL7A1 mutations and associated with chronic wounding, inflammation, fibrosis, and cutaneous squamous cell carcinoma (cSCC), models this dynamic. Here, we used single-cell RNA sequencing (scRNAseq) to analyze gene expression patterns in skin cells from a mouse model of RDEB. We uncovered a complex landscape within the RDEB dermal microenvironment that exhibited altered metabolism, enhanced angiogenesis, hyperproliferative keratinocytes, infiltration and activation of immune cell populations, and inflammatory fibroblast priming. We demonstrated the presence of activated neutrophil and Langerhans cell subpopulations and elevated expression of PD-1 and PD-L1 in T cells and antigen-presenting cells, respectively. Unsupervised clustering within the fibroblast population further revealed two differentiation pathways in RDEB fibroblasts, one toward myofibroblasts and the other toward a phenotype that shares the characteristics of inflammatory fibroblast subsets in other inflammatory diseases as well as the IL-1-induced inflammatory cancer-associated fibroblasts (iCAFs) reported in various cancer types. Quantitation of inflammatory cytokines indicated dynamic waves of IL-1α, TGF-β1, TNF, IL-6, and IFN-γ concentrations, along with dermal NF-κB activation preceding JAK/STAT signaling. We further demonstrated the divergent and overlapping roles of these cytokines in inducing inflammatory phenotypes in RDEB patients as well as RDEB mouse-derived fibroblasts together with their healthy controls. In summary, our data have suggested a potential role of inflammation, driven by the chronic release of inflammatory cytokines such as IL-1, in creating an immune-suppressed dermal microenvironment that underlies RDEB disease progression.

Regulation of advanced therapies in Europe: Are we on the right track?

Sixteen years after regulating advanced therapy medicinal products (ATMPs) in the European Union, few ATMPs have gained marketing authorization. Additionally, market withdrawals for commercial reasons and a lack of reimbursement are de facto blocking patient access. Here, we pinpoint the major factors underlying this roadblock and how to circumvent it.

Combination of 3D printing and electrospinning to develop chitin/gelatin/PVA scaffolds

In this study, novel scaffolds based on natural polymers were developed by combining 3D printing (3DP) and electrospinning (ES) techniques. ES ink was prepared with gelatin and poly(vinyl alcohol) (PVA), while 3DP ink was prepared with gelatin and chitin. Different biopolymers were used to confer unique properties to each ink and obtain a multilayered scaffold suitable for tissue regeneration. First, gelatin is able to exhibit the characteristics needed for both inks since gelatin chains contain arginine-glycine-aspartic (RGD) motifs, an important sequence in the promotion of cell adhesion, which gives gelatin an improved biological behavior in comparison to other polymers. Additionally, PVA was selected for ES ink to facilitate gelatin spinnability, and chitin was incorporated into 3DP ink as reinforcement to provide mechanical support and protection to the overall design. In this work, chitin was extracted from fruit fly pupae. The high extraction yield and purity of the chitin obtained from the fruit fly pupae confirmed that this pupa is an alternative source to produce chitin. Once the chitin was characterized, both inks were prepared and rheological analysis was carried out in order to confirm the shear thinning behavior required for additive manufacturing processes. The combination of 3DP and ES processes resulted in porous scaffolds, which were proven biocompatible, highlighting their potential for biomedical applications. 

Age or lifestyle-induced accumulation of genotoxicity is associated with a length-dependent decrease in gene expression

DNA damage has long been advocated as a molecular driver of aging. DNA damage occurs in a stochastic manner, and is therefore more likely to accumulate in longer genes. The length-dependent accumulation of transcription-blocking damage, unlike that of somatic mutations, should be reflected in gene expression datasets of aging. We analyzed gene expression as a function of gene length in several single-cell RNA sequencing datasets of mouse and human aging. We found a pervasive age-associated length-dependent underexpression of genes across species, tissues, and cell types. Furthermore, we observed length-dependent underexpression associated with UV-radiation and smoke exposure, and in progeroid diseases, Cockayne syndrome, and trichothiodystrophy. Finally, we studied published gene sets showing global age-related changes. Genes underexpressed with aging were significantly longer than overexpressed genes. These data highlight a previously undetected hallmark of aging and show that accumulation of genotoxicity in long genes could lead to reduced RNA polymerase II processivity.

Ex Vivo Maturation of 3D-Printed, Chondrocyte-Laden, Polycaprolactone-Based Scaffolds Prior to Transplantation Improves Engineered Cartilage Substitute Properties and Integration

OBJECTIVE

The surgical management of nasal septal defects due to perforations, malformations, congenital cartilage absence, traumatic defects, or tumors would benefit from availability of optimally matured septal cartilage substitutes. Here, we aimed to improve in vitro maturation of 3-dimensional (3D)-printed, cell-laden polycaprolactone (PCL)-based scaffolds and test their in vivo performance in a rabbit auricular cartilage model.

DESIGN

Rabbit auricular chondrocytes were isolated, cultured, and seeded on 3D-printed PCL scaffolds. The scaffolds were cultured for 21 days in vitro under standard culture media and normoxia or in prochondrogenic and hypoxia conditions, respectively. Cell-laden scaffolds (as well as acellular controls) were implanted into perichondrium pockets of New Zealand white rabbit ears (N = 5 per group) and followed up for 12 weeks. At study end point, the tissue-engineered scaffolds were extracted and tested by histological, immunohistochemical, mechanical, and biochemical assays.

RESULTS

Scaffolds previously matured in vitro under prochondrogenic hypoxic conditions showed superior mechanical properties as well as improved patterns of cartilage matrix deposition, chondrogenic gene expression (COL1A1, COL2A1, ACAN, SOX9, COL10A1), and proteoglycan production in vivo, compared with scaffolds cultured in standard conditions.

CONCLUSIONS

In vitro maturation of engineered cartilage scaffolds under prochondrogenic conditions that better mimic the in vivo environment may be beneficial to improve functional properties of the engineered grafts. The proposed maturation strategy may also be of use for other tissue-engineered constructs and may ultimately impact survival and integration of the grafts in the damaged tissue microenvironment.

Photonic Technology for In Vivo Monitoring of Hypoxia-Ischemia

Surveillance of physiological parameters of newborns during delivery triggers medical decision-making, can rescue life and health, and helps avoid unnecessary cesareans. Here, the development of a photonic technology for monitoring perinatal asphyxia is presented and validated in vivo in a preclinical stage. Contrary to state of the art, the technology provides continuous data in real-time in a non-invasive manner. Moreover, the technology does not rely on a single parameter as pH or lactate, instead monitors changes of the entirety of physiological parameters accessible by Raman spectroscopy. By a fiber-coupled Raman probe that is in controlled contact with the skin of the subject, near-infrared Raman spectra are measured and analyzed by machine learning algorithms to develop classification models. As a performance benchmarking, various hybrid and non-hybrid classifiers are tested. In an asphyxia model in newborn pigs, more than 1000 Raman spectra are acquired at three different clinical phases-basal condition, hypoxia-ischemia, and post-hypoxia-ischemia stage. In this preclinical proof-of-concept study, figures of merit reach 90% levels for classifying the clinical phases and demonstrate the power of the technology as an innovative medical tool for diagnosing a perinatal adverse outcome.

Trends in Tissue Bioprinting, Cell-Laden Bioink Formulation, and Cell Tracking

Use of three-dimensional bioprinting for the in vitro engineering of tissues has boomed during the past five years. An increasing number of commercial bioinks are available, with suitable mechanical and rheological characteristics and excellent biocompatibility. However, cell-laden bioinks based on a single polymer do not properly mimic the complex extracellular environment needed to tune cell behavior, as required for tissue and organ formation. Processes such as cell aggregation, migration, and tissue patterning should be dynamically monitored, and progress is being made in these areas, most prominently derived from nanoscience. We review recent developments in tissue bioprinting, cellularized bioink formulation, and cell tracking, from both chemistry and cell biology perspectives. We conclude that an interdisciplinary approach including expertise in polymer science, nanoscience, and cell biology/tissue engineering is required to drive further advancements in this field toward clinical application.

Triku: a feature selection method based on nearest neighbors for single-cell data

Background

Feature selection is a relevant step in the analysis of single-cell RNA sequencing datasets. Most of the current feature selection methods are based on general univariate descriptors of the data such as the dispersion or the percentage of zeros. Despite the use of correction methods, the generality of these feature selection methods biases the genes selected towards highly expressed genes, instead of the genes defining the cell populations of the dataset.

Results

Triku is a feature selection method that favors genes defining the main cell populations. It does so by selecting genes expressed by groups of cells that are close in the k-nearest neighbor graph. The expression of these genes is higher than the expected expression if the k-cells were chosen at random. Triku efficiently recovers cell populations present in artificial and biological benchmarking datasets, based on adjusted Rand index, normalized mutual information, supervised classification, and silhouette coefficient measurements. Additionally, gene sets selected by triku are more likely to be related to relevant Gene Ontology terms and contain fewer ribosomal and mitochondrial genes.

Conclusion

Triku is developed in Python 3 and is available at https://github.com/alexmascension/triku.

The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing

Background: The advent of single-cell RNA sequencing (scRNAseq) and additional single-cell omics technologies have provided scientists with unprecedented tools to explore biology at cellular resolution. However, reaching an appropriate number of good quality reads per cell and reasonable numbers of cells within each of the populations of interest are key to infer relevant conclusions about the underlying biology of the dataset. For these reasons, scRNAseq studies are constantly increasing the number of cells analysed and the granularity of the resultant transcriptomics analyses.

Methods: We aimed to identify previously described fibroblast subpopulations in healthy adult human skin by using the largest dataset published to date (528,253 sequenced cells) and an unsupervised population-matching algorithm.

Results: Our reanalysis of this landmark resource demonstrates that a substantial proportion of cell transcriptomic signatures may be biased by cellular stress and response to hypoxic conditions.

Conclusions: We postulate that careful design of experimental conditions is needed to avoid long processing times of biological samples. Additionally, computation of large datasets might undermine the extent of the analysis, possibly due to long processing times.

Human Hair Follicle-Derived Mesenchymal Stromal Cells from the Lower Dermal Sheath as a Competitive Alternative for Immunomodulation

Mesenchymal stromal cells (MSCs) have unique immunomodulatory capacities. We investigated hair follicle-derived MSCs (HF-MSCs) from the dermal sheath, which are advantageous as an alternative source because of their relatively painless and minimally risky extraction procedure. These cells expressed neural markers upon isolation and maintained stemness for a minimum of 10 passages. Furthermore, HF-MSCs showed responsiveness to pro-inflammatory environments by expressing type-II major histocompatibility complex antigens (MHC)-II to a lesser extent than adipose tissue-derived MSCs (AT-MSCs). HF-MSCs effectively inhibited the proliferation of peripheral blood mononuclear cells equivalently to AT-MSCs. Additionally, HF-MSCs promoted the induction of CD4+CD25+FOXP3+ regulatory T cells to the same extent as AT-MSCs. Finally, HF-MSCs, more so than AT-MSCs, skewed M0 and M1 macrophages towards M2 phenotypes, with upregulation of typical M2 markers CD163 and CD206 and downregulation of M1 markers such as CD64, CD86, and MHC-II. Thus, we conclude that HF-MSCs are a promising source for immunomodulation.

Identification of Hypoxia-Ischemia by chemometrics considering systemic changes of the physiology

Perinatal asphyxia represents a major medical disorder and is related to around a fourth of all neonatal deaths worldwide. Specific thresholds for lactate or pH levels define the gold standard for detecting hypoxic-ischemic events as physiological abnormalities. In contrast to current gold standard, we analyze the systemic picture, represented by the whole set of biochemical parameters from blood gas analysis, by multiparametric machine learning algorithms. In a swine model with 22 objects, we investigate the impact of neonatal hypoxic-ischemic encephalopathy on 18 individual physiological parameters. In a first approach, we study the statistical significance of individual parameters by univariate analysis methods. In a second approach, we take the most relevant parameters as input for the development of predictive models by different hybrid and non hybrid classification algorithms. The predictive power of our multiparametric models outperforms by far the limited performance of pH and lactate as reliable indicators, despite strong correlation with hypoxic-ischemic events. We have been able to detect hypoxic-ischemic events even one hour after the episode, with accuracies close to 100% in contrast to pH or lactate-based diagnosis with 62% and 78%, respectively. By all machine learning algorithms, lactate is recognized as the main contributor due to its longer-term evidence of hypoxia-ischemia episodes. However, substantial improvement of the diagnosis is achieved by predictions based on a systemic picture of different physiological parameters. Our results prove the potential applicability of our method as a support tool for decision-making that will allow obstetricians to identify hypoxic ischemic episodes more accurately during labor.

Challenges and Opportunities for the Translation of Single-Cell RNA Sequencing Technologies to Dermatology

Skin is a complex and heterogeneous organ at the cellular level. This complexity is beginning to be understood through the application of single-cell genomics and computational tools. A large number of datasets that shed light on how the different human skin cell types interact in homeostasis-and what ceases to work in diverse dermatological diseases-have been generated and are publicly available. However, translation of these novel aspects to the clinic is lacking. This review aims to summarize the state-of-the-art of skin biology using single-cell technologies, with a special focus on skin pathologies and the translation of mechanistic findings to the clinic. The main implications of this review are to summarize the benefits and limitations of single-cell analysis and thus help translate the emerging insights from these novel techniques to the bedside.

Lack of evidence for increased transcriptional noise in aged tissues

Aging is often associated with a loss of cell type identity that results in an increase in transcriptional noise in aged tissues. If this phenomenon reflects a fundamental property of aging remains an open question. Transcriptional changes at the cellular level are best detected by single-cell RNA sequencing (scRNAseq). However, the diverse computational methods used for the quantification of age-related loss of cellular identity have prevented reaching meaningful conclusions by direct comparison of existing scRNAseq datasets. To address these issues we created Decibel, a Python toolkit that implements side-to-side four commonly used methods for the quantification of age-related transcriptional noise in scRNAseq data. Additionally, we developed Scallop, a novel computational method for the quantification of membership of single cells to their assigned cell type cluster. Cells with a greater Scallop membership score are transcriptionally more stable. Application of these computational tools to seven aging datasets showed large variability between tissues and datasets, suggesting that increased transcriptional noise is not a universal hallmark of aging. To understand the source of apparent loss of cell type identity associated with aging, we analyzed cell type-specific changes in transcriptional noise and the changes in cell type composition of the mammalian lung. No robust pattern of cell type-specific transcriptional noise alteration was found across aging lung datasets. In contrast, age-associated changes in cell type composition of the lung were consistently found, particularly of immune cells. These results suggest that claims of increased transcriptional noise of aged tissues should be reformulated.

Cell therapy as a treatment of secondary lymphedema: a systematic review and meta-analysis

Background

Lymphedema, the accumulation of interstitial fluid caused by poor lymphatic drainage, is a progressive and permanent disease with no curative treatment. Several studies have evaluated cell-based therapies in secondary lymphedema, but no meta-analysis has been performed to assess their efficacy.

Methods

We conducted a systematic review and meta-analysis of all available preclinical and clinical studies, with assessment of their quality and risk of bias.

Results

A total of 20 articles using diverse cell types were selected for analysis, including six clinical trials and 14 pre-clinical studies in three species. The meta-analysis showed a positive effect of cell-based therapies on relevant disease outcomes (quantification of edema, density of lymphatic capillaries, evaluation of the lymphatic flow, and tissue fibrosis). No significant publication bias was observed.

Conclusion

Cell-based therapies have the potential to improve secondary lymphedema. The underlying mechanisms remain unclear. Due to relevant heterogeneity between studies, further randomized controlled and blinded studies are required to substantiate the use of these novel therapies in clinical practice.

The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing

Background: The advent of single-cell RNA sequencing (scRNAseq) and additional single-cell omics technologies have provided scientists with unprecedented tools to explore biology at cellular resolution. However, reaching an appropriate number of good quality reads per cell and reasonable numbers of cells within each of the populations of interest are key to infer relevant conclusions about the underlying biology of the dataset. For these reasons, scRNAseq studies are constantly increasing the number of cells analysed and the granularity of the resultant transcriptomics analyses. Methods: We aimed to identify previously described fibroblast subpopulations in healthy adult human skin by using the largest dataset published to date (528,253 sequenced cells) and an unsupervised population-matching algorithm. Results: Our reanalysis of this landmark resource demonstrates that a substantial proportion of cell transcriptomic signatures may be biased by cellular stress and response to hypoxic conditions. Conclusions: We postulate that careful design of experimental conditions is needed to avoid long processing times of biological samples. Additionally, computation of large datasets might undermine the extent of the analysis, possibly due to long processing times.

Three-Dimensional Bioprinting Scaffolding for Nasal Cartilage Defects: A Systematic Review

BACKGROUND

In recent years, three-dimensional (3D)-printing of tissue-engineered cartilaginous scaffolds is intended to close the surgical gap and provide bio-printed tissue designed to fit the specific geometric and functional requirements of each cartilage defect, avoiding donor site morbidity and offering a personalizing therapy.

METHODS

To investigate the role of 3D-bioprinting scaffolding for nasal cartilage defects repair a systematic review of the electronic databases for 3D-Bioprinting articles pertaining to nasal cartilage bio-modelling was performed. The primary focus was to investigate cellular source, type of scaffold utilization, biochemical evaluation, histological analysis, in-vitro study, in-vivo study, animal model used, length of research, and placement of experimental construct and translational investigation.

RESULTS

From 1011 publications, 16 studies were kept for analysis. About cellular sources described, most studies used primary chondrocyte cultures. The cartilage used for cell isolation was mostly nasal septum. The most common biomaterial used for scaffold creation was polycaprolactone alone or in combination. About mechanical evaluation, we found a high heterogeneity, making it difficult to extract any solid conclusion. Regarding biological and histological characteristics of each scaffold, we found that the expression of collagen type I, collagen Type II and other ECM components were the most common patterns evaluated through immunohistochemistry on in-vitro and in-vivo studies. Only two studies made an orthotopic placement of the scaffolds. However, in none of the studies analyzed, the scaffold was placed in a subperichondrial pocket to rigorously simulate the cartilage environment. In contrast, scaffolds were implanted in a subcutaneous plane in almost all of the studies included.

CONCLUSION

The role of 3D-bioprinting scaffolding for nasal cartilage defects repair is growing field. Despite the amount of information collected in the last years and the first surgical applications described recently in humans. Further investigations are needed due to the heterogeneity on mechanical evaluation parameters, the high level of heterotopic scaffold implantation and the need for quantitative histological data.

Terminal Schwann Cell Aging: Implications for Age-Associated Neuromuscular Dysfunction

Action potential is transmitted to muscle fibers through specialized synaptic interfaces called neuromuscular junctions (NMJs). These structures are capped by terminal Schwann cells (tSCs), which play essential roles during formation and maintenance of the NMJ. tSCs are implicated in the correct communication between nerves and muscles, and in reinnervation upon injury. During aging, loss of muscle mass and strength (sarcopenia and dynapenia) are due, at least in part, to the progressive loss of contacts between muscle fibers and nerves. Despite the important role of tSCs in NMJ function, very little is known on their implication in the NMJ-aging process and in age-associated denervation. This review summarizes the current knowledge about the implication of tSCs in the age-associated degeneration of NMJs. We also speculate on the possible mechanisms underlying the observed phenotypes.

HuR/ELAVL1 drives malignant peripheral nerve sheath tumor growth and metastasis

Cancer cells can develop a strong addiction to discrete molecular regulators, which control the aberrant gene expression programs that drive and maintain the cancer phenotype. Here, we report the identification of the RNA-binding protein HuR/ELAVL1 as a central oncogenic driver for malignant peripheral nerve sheath tumors (MPNSTs), which are highly aggressive sarcomas that originate from cells of the Schwann cell lineage. HuR was found to be highly elevated and bound to a multitude of cancer-associated transcripts in human MPNST samples. Accordingly, genetic and pharmacological inhibition of HuR had potent cytostatic and cytotoxic effects on tumor growth, and strongly suppressed metastatic capacity in vivo. Importantly, we linked the profound tumorigenic function of HuR to its ability to simultaneously regulate multiple essential oncogenic pathways in MPNST cells, including the Wnt/β-catenin, YAP/TAZ, RB/E2F, and BET pathways, which converge on key transcriptional networks. Given the exceptional dependency of MPNST cells on HuR for survival, proliferation, and dissemination, we propose that HuR represents a promising therapeutic target for MPNST treatment.

Human Dermal Fibroblast Subpopulations Are Conserved across Single-Cell RNA Sequencing Studies

On the basis of their differential location within the dermis and of discrete changes in gene and protein expression, two major fibroblast subtypes (papillary and reticular) have traditionally been distinguished. In the last 3 years, a number of research groups have begun to address transcriptomic heterogeneity of human skin cells at the single-cell level by determining mRNA levels of expressed genes through single-cell RNA sequencing technologies. However, the outcome of single-cell RNA sequencing studies is thus far confusing. Very little overlap was found in fibroblast subpopulations, which also varied in number and composition in each dataset. After a careful reappraisal of the transcriptomic data of 13,823 human adult dermal fibroblasts that have been sequenced to date, we show that fibroblasts may robustly be assigned to three major types (axes A‒C), which in turn are composed of 10 major subtypes (clusters), which we denominated A1‒A4, B1 and B2, and C1‒C4. These computationally determined axes and clusters represent the major fibroblast types and subtypes in adult healthy human skin across different datasets, accounting for 92.5% of the sequenced fibroblasts. They thus may provide the basis to improve our understanding of dermal homeostasis and cellular function at the transcriptomic level.

Machine Learning-Assisted Raman Spectroscopy for pH and Lactate Sensing in Body Fluids

This study presents the combination of Raman spectroscopy with machine learning algorithms as a prospective diagnostic tool capable of detecting and monitoring relevant variations of pH and lactate as recognized biomarkers of several pathologies. The applicability of the method proposed here is tested both in vitro and ex vivo. In a first step, Raman spectra of aqueous solutions are evaluated for the identification of characteristic patterns resulting from changes in pH or in the concentration of lactate. The method is further validated with blood and plasma samples. Principal component analysis is used to highlight the relevant features that differentiate the Raman spectra regarding their pH and concentration of lactate. Partial least squares regression models are developed to capture and model the spectral variability of the Raman spectra. The performance of these predictive regression models is demonstrated by clinically accurate predictions of pH and lactate from unknown samples in the physiologically relevant range. These results prove the potential of our method to develop a noninvasive technology, based on Raman spectroscopy, for continuous monitoring of pH and lactate in vivo.

Role of bulge epidermal stem cells and TSLP signaling in psoriasis

Psoriasis is a common inflammatory skin disease involving a cross‐talk between epidermal and immune cells. The role of specific epidermal stem cell populations, including hair follicle stem cells (HF‐SCs) in psoriasis is not well defined. Here, we show reduced expression of c‐JUN and JUNB in bulge HF‐SCs in patients with scalp psoriasis. Using lineage tracing in mouse models of skin inflammation with inducible deletion of c‐Jun and JunB, we found that mutant bulge HF‐SCs initiate epidermal hyperplasia and skin inflammation. Mechanistically, thymic stromal lymphopoietin (TSLP) was identified in mutant cells as a paracrine factor stimulating proliferation of neighboring non‐mutant epidermal cells, while mutant inter‐follicular epidermal (IFE) cells are lost over time. Blocking TSLP in psoriasis‐like mice reduced skin inflammation and decreased epidermal proliferation, VEGFα expression, and STAT5 activation. These findings unravel distinct roles of HF‐SCs and IFE cells in inflammatory skin disease and provide novel mechanistic insights into epidermal cell interactions in inflammation.

Creation of a multidisciplinary and multicenter study group for the use of 3D printing in general thoracic surgery: lessons learned in our first year experience

Introduction: In recent years, the use of 3D printing in medicine has grown exponentially, but the use of 3D technology has not been equally adopted by the different medical specialties. Published 3D printing activity in general thoracic surgery is scarce and has been mostly limited to case reports. The aim of this report was to reflect on the results and lessons learned from a newly created multidisciplinary and multicenter 3D unit of the Spanish Society of Thoracic Surgery (SECT). Methods: This is a pilot study to determine the feasibility and usefulness of printing 3D models for patients with thoracic malignancy or airway complications, based on real data. We designed a point-of-care 3D printing workflow involving thoracic surgeons, radiologists with experience in intrathoracic pathology, and engineers with experience in additive manufacturing. Results: In the first year of operation we generated 26 three-dimensional models out of 27 cases received (96.3%). In 9 cases a virtual model was sufficient for optimal patient handling, while in 17 cases a 3D model was printed. Per pathology, cases were classified as airway stenosis after lung transplantation (7 cases, 25.9%), tracheal pathology (7 cases, 25.9%), chest tumors (6 cases, 22.2%) carcinoid tumors (4 cases, 14.8%), mediastinal tumors (2 cases, 7.4%) and Pancoast tumors (one case, 3.7%). Conclusion: A multidisciplinary 3D laboratory is feasible in a hospital setting, and working as a multicenter group increases the number of cases and diversity of pathologies thus providing further opportunity to study the benefits of the 3D printing technology in general thoracic surgery.

Effect of bone marrow stromal cells in combination with biomaterials in early phases of distraction osteogenesis: An experimental study in a rabbit femur model

Acceleration of the consolidation of the distracted bone is a relevant medical need. As a platform to improve in vivo bone engineering, we developed a novel distraction osteogenesis (DO) model in a rabbit large bone (femur) and tested if the application of cultured bone marrow stromal cells (BMSCs) immediately after the osteotomy promotes the formation of bone. This report consists of two components, an animal study to evaluate the quality of the regenerate following different treatments and an in vitro study to evaluate osteogenic potential of BMSC cultures. To illuminate the mechanism of action of injected cells, we tested stem cell cultures enriched in osteogenic-BMSCs (O-BMSCs) as compared with cultures enriched in non-osteogenic BMSCs (NO-BMSCs). Finally, we included a group of animals treated with biomaterials (fibrin and ground cortical bone) in addition to cells. Injection of O-BMSCs promoted the maturity of distracted callus and decreased fibrosis. When combined with biomaterials, O-BMSCs modified the ossification pattern from endochondral to intramembranous type. The use of NO-BMSCs not only did not increase the maturity but also increased porosity of the bone. These preclinical results indicate that the BMSC cultures must be tested in vitro prior to clinical use, since a number of factors may influence their outcome in bone formation. We hypothesize that the use of osteogenic BMSCs and biomaterials could be clinically beneficial to shorten the consolidation period of the distraction and the total period of bone lengthening.

Epigenetic age-predictor for mice based on three CpG sites

Epigenetic clocks for mice were generated based on deep-sequencing analysis of the methylome. Here, we demonstrate that site-specific analysis of DNA methylation levels by pyrosequencing at only three CG dinucleotides (CpGs) in the genes Prima1, Hsf4, and Kcns1 facilitates precise estimation of chronological age in murine blood samples, too. DBA/2 mice revealed accelerated epigenetic aging as compared to C57BL6 mice, which is in line with their shorter life-expectancy. The three-CpG-predictor provides a simple and cost-effective biomarker to determine biological age in large intervention studies with mice.

Epigenetic marks are chemical modifications found throughout the genome – the DNA within cells. By influencing the activity of nearby genes, the marks govern developmental processes and help cells to adapt to changes in their surroundings. Some epigenetic marks can be gained or lost with age. A lot of aging research focuses on one type of mark, called “DNA methylation”. By measuring the presence or absence of specific methyl groups, scientists can estimate biological age – which may differ from calendar age.

Recent studies have developed computer models called epigenetic aging clocks to predict the biological age of mouse cells. These clocks use epigenetic data collected from the entire genomes of mice, and are useful for understanding how the aging process is affected by genetic parameters, diet, or other environmental factors. Yet, the genome sequencing methods used to construct most existing epigenetic clocks are expensive, labor-intensive, and cannot be easily applied to large groups of mice.

Han et al. have developed a new way to predict biological aging in mice that needs methylation information from just three particular sections of the genome. Even though this approach is much faster and less expensive than other epigenetic approaches to measuring aging, it has a similar level of accuracy to existing models. Han et al. use the new method to show that cells from different strains of laboratory mice age at different rates. Furthermore, in a strain that has a shorter life expectancy, aging seems to be accelerated.

The new approach developed by Han et al. will make it easier to study how aging in mice is affected by different interventions. Further studies will also be needed to better understand how epigenetic marks relate to biological aging.

The panniculus carnosus muscle: an evolutionary enigma at the intersection of distinct research fields

The panniculus carnosus is a thin striated muscular layer intimately attached to the skin and fascia of most mammals, where it provides skin twitching and contraction functions. In humans, the panniculus carnosus is conserved at sparse anatomical locations with high interindividual variability, and it is considered of no functional significance (most possibly being a remnant of evolution). Diverse research fields (such as anatomy, dermatology, myology, neuroscience, surgery, veterinary science) use this unique muscle as a model, but several unknowns and misconceptions remain in the literature. In this article, we review what is currently known about panniculus carnosus structure, development, anatomical location, response to environmental stimuli and potential function(s), with the aim of putting together the evidence arising from the different research communities and raising interest in this unique muscle, which we postulate as an ideal model for both vascular and muscular research.

SOX2 expression diminishes with ageing in several tissues in mice and humans

SOX2 (Sex-determining region Y box 2) is a transcription factor expressed in several foetal and adult tissues and its deregulated activity has been linked to chronic diseases associated with ageing. Nevertheless, the level of SOX2 expression in aged individuals at the tissue level has not previously been examined. In this work, we show that SOX2 expression decreases significantly in the brain with ageing, in both humans and rodents. The administration of resveratrol for 6 months in mice partly attenuated this reduction. We also identified an age-related decline in SOX2 mRNA and protein expression in several other organs, namely, the lung, heart, kidney, spleen and liver. Moreover, peripheral blood mononuclear cells (PBMCs) from elderly expressed lower levels of SOX2 than those from young individuals. Mechanistically, SOX2 expression inversely correlates with p16^Ink4a levels. Together, these data show a widespread decrease in SOX2 with age, suggesting that the decline in SOX2 expression might be used as a biomarker of ageing.

Schwann Cells in the Ventral Dermis Do Not Derive from Myf5-Expressing Precursors

The embryonic origin of lineage precursors of the trunk dermis is somewhat controversial. Precursor cells traced by Myf5 and Twist2 (Dermo1) promoter activation (i.e., cells of presumed dermomyotomal lineage) have been reported to generate Schwann cells. On the other hand, abundant data demonstrate that dermal Schwann cells derive from the neural crest. This is relevant because dermal precursors give rise to neural lineages, and multilineage differentiation potential qualifies them as adult stem cells. However, it is currently unclear whether neural lineages arise from dedifferentiated Schwann cells instead of mesodermally derived dermal precursor cells. To clarify these discrepancies, we traced SOX2⁺ adult dermal precursor cells by two independent Myf5 lineage tracing strains. We demonstrate that dermal Schwann cells do not belong to the Myf5⁺ cell lineage, indicating that previous tracing data reflected aberrant cre recombinase expression and that bona fide Myf5⁺ dermal precursors cannot transdifferentiate to neural lineages in physiological conditions.

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Adult Myf5-cre^Sor mice aberrantly trace dermal Schwann cells (dSCs)

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Dedifferentiated, SOX2⁺ dSCs are the neural-competent precursors in the dermis

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These findings cast doubt on the multipotency of adult skin-derived precursors

NaviSE: superenhancer navigator integrating epigenomics signal algebra

Background

Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers.

Results

We have developed NaviSE, a user-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface dynamically generated by NaviSE. NaviSE also implements an ‘epigenomics signal algebra’ that allows the combination of multiple activation and repression epigenomics signals. NaviSE provides an interactive chromosomal landscaping of the locations of superenhancers, which can be navigated to obtain annotated information about superenhancer signal profile, associated genes, gene ontology enrichment analysis, motifs of transcription factor binding sites enriched in superenhancers, graphs of the metrics evaluating the superenhancers quality, protein-protein interaction networks and enriched metabolic pathways among other features. We have parallelised the most time-consuming tasks achieving a reduction up to 30% for a 15 CPUs machine. We have optimized the default parameters of NaviSE to facilitate its use. NaviSE allows different entry levels of data processing, from sra-fastq files to bed files; and unifies the processing of multiple replicates. NaviSE outperforms the more time-consuming processes required in a non-integrated pipeline. Alongside its high performance, NaviSE is able to provide biological insights, predicting cell type specific markers, such as SOX2 and ZIC3 in embryonic stem cells, CDK5R1 and REST in neurons and CD86 and TLR2 in monocytes.

Conclusions

NaviSE is a user-friendly streamlined solution for superenhancer analysis, annotation and navigation, requiring only basic computer and next generation sequencing knowledge. NaviSE binaries and documentation are available at: https://sourceforge.net/projects/navise-superenhancer/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1698-5) contains supplementary material, which is available to authorized users.

Hair follicle-containing punch grafts accelerate chronic ulcer healing: A randomized controlled trial

BACKGROUND

A prominent role of hair follicle-derived cells in epidermal wound closure is now well established but clinical translation of basic research findings is scarce. Although skin punch grafts have been used as a therapeutic intervention to improve healing of chronic leg ulcers, they are normally harvested from nonhairy areas, thus not taking advantage of the reported role of the hair follicle as a wound-healing promoter.

OBJECTIVE

We sought to substantiate the role of hair follicles in venous leg ulcer healing by transplanting hair follicle-containing versus nonhairy punch grafts.

METHODS

This was a randomized controlled trial with intraindividual comparison of hair follicle scalp grafts and nonhairy skin grafts transplanted in parallel into 2 halves of the same ulcer.

RESULTS

Ulcer healing measured as the average percentage reduction 18 weeks postintervention was significantly increased (P = .002) in the hair follicle group with a 75.15% (SD 23.03) ulcer area reduction compared with 33.07% (SD 46.17) in the control group (nonhairy grafts).

LIMITATIONS

Sample size was small (n = 12).

CONCLUSION

Autologous transplantation of terminal hair follicles by scalp punch grafts induces better healing than punch grafts harvested from nonhairy areas. Hair punch grafting is a minimally invasive surgical procedure that appears to be effective as a therapeutic tool for chronic venous leg ulcers.

Systematic Review to Compare Urothelium Differentiation with Urethral Epithelium Differentiation in Fetal Development, as a Basis for Tissue Engineering of the Male Urethra

BACKGROUND

Tissue-engineered (TE) urethra is desirable in men with urethral disease (stricture or hypospadias) and shortage of local tissue. Although ideally a TE graft would contain urethral epithelium cells, currently, bladder epithelium (urothelium) is widely used, but morphologically different. Understanding the differences and similarities of urothelium and urethral epithelium could help design a protocol for in vitro generation of urethral epithelium to be used in TE grafts for the urethra.

PURPOSE

To understand the development toward urethral epithelium or urothelium to improve TE of the urethra.

METHODS

A literature search was done following PRISMA guidelines. Articles describing urethral epithelium and bladder urothelium development in laboratory animals and humans were selected.

RESULTS

Twenty-nine studies on development of urethral epithelium and 29 studies on development of urothelium were included. Both tissue linings derive from endoderm and although adult urothelium and urethral epithelium are characterized by different gene expression profiles, the signaling pathways underlying their development are similar, including Shh, BMP, Wnt, and FGF. The progenitor of the urothelium and the urethral epithelium is the early fetal urogenital sinus (UGS). The urethral plate and the urothelium are both formed from the p63+ cells of the UGS. Keratin 20 and uroplakins are exclusively expressed in urothelium, not in the urethral epithelium. Further research has to be done on unique markers for the urethral epithelium.

CONCLUSION

This review has summarized the current knowledge about embryonic development of urothelium versus urethral epithelium and especially focuses on the influencing factors that are potentially specific for the eventual morphological differences of both cell linings, to be a basis for developmental or tissue engineering of urethral tissue.

Identification and Characterization of the Dermal Panniculus Carnosus Muscle Stem Cells

The dermal Panniculus carnosus (PC) muscle is important for wound contraction in lower mammals and represents an interesting model of muscle regeneration due to its high cell turnover. The resident satellite cells (the bona fide muscle stem cells) remain poorly characterized. Here we analyzed PC satellite cells with regard to developmental origin and purported function. Lineage tracing shows that they originate in Myf5⁺, Pax3/Pax7⁺ cell populations. Skin and muscle wounding increased PC myofiber turnover, with the satellite cell progeny being involved in muscle regeneration but with no detectable contribution to the wound-bed myofibroblasts. Since hematopoietic stem cells fuse to PC myofibers in the absence of injury, we also studied the contribution of bone marrow-derived cells to the PC satellite cell compartment, demonstrating that cells of donor origin are capable of repopulating the PC muscle stem cell niche after irradiation and bone marrow transplantation but may not fully acquire the relevant myogenic commitment.

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PC satellite cells originate from Myf5⁺, Pax3/Pax7⁺ cell lineages

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Skin and muscle wounding increase PC myofiber turnover

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Donor bone marrow cells repopulate the PC satellite niche after BMT

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Dermis-derived myogenesis originates from the PC satellite cell population

An immunohistochemical study of cytokeratins distribution of the human adult male and female urethra

Surgical treatment of diseases affecting long urethral areas represents a challenge in urology. Recent developments of tissue-engineered urethral substitutes represent a hope for patients. However finding an ideal tissue source for urethral reconstruction first requires proper understanding of the native human urethra physiology and a deep knowledge of the histological and molecular features of the native human urethra. Here we present a comprehensive characterization of male and female urethra by histological, histochemical and immunohistochemical methods with a panel of 15 antibodies. The results demonstrated that the histology of the male and female urethra depend on the area where the sample is taken along its length. Proximal areas of male and female urethra have differential expression of the epithelial basal and suprabasal layer markers CK14 and CK10 which distinguished the prostatic/membranous and proximal female urethra from the bulbar/penile and distal female areas of the urethra. The distal male (penile) and female may be further divided by the distinct expression pattern of CK19. On the other hand, the expression of CK5/6 and CK19 also make a distinction of the proximal and distal female urethra. These results should facilitate a more informed selection of donor graft tissues for urethral replacement. Besides, novel bioengineered urethral tissue approaches should take into account the characterization of the different areas of the urethra presented in this work.

Cell-based product classification procedure: What can be done differently to improve decisions on borderline products?

In June 2015, European Medicines Agency/Committee for Advanced Therapies (CAT) released the new version of the reflection paper on classification of advanced therapy medicinal products (ATMPs) established to address questions of borderline cases in which classification of a product based on genes, cells or tissues is unclear. The paper shows CAT's understanding of substantial manipulation and essential function(s) criteria that define the legal scope of cell-based medicinal products. This article aims to define the authors' viewpoint on the reflection paper. ATMP classification has intrinsic weaknesses derived from the lack of clarity of the evolving concepts of substantial manipulation and essential function(s) as stated in the EU Regulation, leading to the risk of differing interpretations and misclassification. This might result in the broadening of ATMP scope at the expense of other products such as cell/tissue transplants and blood products, or even putting some present and future clinical practice at risk of being classified as ATMP. Because of the major organizational, economic and regulatory implications of product classification, we advocate for increased interaction between CAT and competent authorities (CAs) for medicines, blood and blood components and tissues and cells or for the creation of working groups including representatives of all parties as recently suggested by several CAs.

Biology of the eyelash hair follicle: an enigma in plain sight

Because of their crucial impact on our perception of beauty, eyelashes constitute a prime target for the cosmetic industry. However, when compared with other hair shafts and the mini-organs that produce them [eyelash hair follicles (ELHFs)], knowledge on the biology underlying growth and pigmentation of eyelashes is still rudimentary. This is due in part to the extremely restricted availability of human ELHFs for experimental study, underappreciation of their important sensory and protective functions and insufficient interest in understanding why they are distinct from scalp hair follicles (HFs) (e.g. ELHFs produce shorter hair shafts, do not possess an arrector pili muscle, have a shorter hair cycle and undergo greying significantly later than scalp HFs). Here we synthesize the limited current knowledge on the biology of ELHFs, in humans and other species, their role in health and disease, the known similarities with and differences from other HF populations, and their intrinsic interethnic variations. We define major open questions in the biology of these intriguing mini-organs and conclude by proposing future research directions. These include dissecting the molecular and cellular mechanisms that underlie trichomegaly and the development of in vitro models in order to interrogate the distinct molecular controls of ELHF growth, cycling and pigmentation and to probe novel strategies for the therapeutic and cosmetic manipulation of ELHFs beyond prostaglandin receptor stimulation.