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.

Elastin and collagen fibres in cutaneous wound healing.

Skin forms the outer barrier of the body. Upon injury, successful wound healing in normal skin restores tissue damage and counteracts the loss of extracellular matrix (ECM) proteins and cells. Collagens and elastin are the most abundant structural proteins of the ECM. In homeostasis, collagen type I is the prevalent form, but it is replaced by type III collagen upon wounding, and only later remodelled. In turn, unsuccessful healing results in scars, which tend to be inflexible and inelastic as compared to normal elastic dermis. Scar inelasticity may be due to the absence of mature elastin fibre formation and cross-linking. In this review, the available information on the process of formation of new collagen and elastic fibres during wound healing is analysed. The distinct roles of elastin and collagen proteins during healing are revisited and future research directions proposed which may help improve clinical management of open wounds and scars.

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.

Distinct Patterns of Hair Graft Survival After Transplantation Into 2 Nonhealing Ulcers: Is Location Everything?

BACKGROUND: Studies highlighting the role of hair follicles (HFs) in wound healing have raised the challenge of bringing this knowledge to clinical applications. A successful translation is the transplantation of scalp HFs into chronic wounds to promote healing. OBJECTIVE: To characterize scar formation and hair growth in nonhealing ulcers after transplantation. PATIENTS AND METHODS: Nonhealing ulcers were treated with hair transplantation to promote wound healing. Hair follicles were harvested from the patient's scalp and inserted into the wound bed. Wound repair and hair growth were assessed clinically. Further analyses were performed in situ, using biopsies from the central and peripheral scar. RESULTS: Rapid wound closure and differences of scar quality and hair growth between the central and peripheral wound areas were observed: the periphery healed with no hair shaft survival and an almost scarless appearance, the center healed with a fibrotic scar, with some hair shaft growth. In situ analyses revealed differences in dermal remodeling and collagen formation between central and peripheral scar areas. CONCLUSION: Besides confirming the effectiveness of this therapy to promote wound healing in human skin, location-dependent disparities in scar quality and hair growth raise the intriguing question whether they are due to clinically important differences in mechanical forces and/or wound microenvironments between ulcer center and periphery.

Pericytes in Cutaneous Wound Healing.

Most of the studies on cutaneous wound healing are focused on epidermal closure. This is obviously important, as the epidermis constitutes the main barrier that separates the inner organism from the environment. However, dermal remodeling is key to achieve long-lasting healing of the area that was originally wounded. In this chapter, we summarize what is known on the stromal components that strongly influence the outcome of healing and postulate that dedifferentiation of stably differentiated cells plays a major role in the initial response to wounding, as well as in long-term wound remodeling. Specifically, we explore the available evidence implicating skin pericytes, endothelial cells, Schwann cells, and macrophages as major players in a complex symphony of cellular plasticity and signaling events whose balance will promote healing (by tissue regeneration or repair) or fibrosis.

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.

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/ .

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.

Does Schwann cell dedifferentiation originate dermal neurofibromas?

Dermal neurofibromas are characteristic of neurofibromatosis type one (NF1), and their developmental origin still unsolved. Although NF1 loss is required for neurofibroma initiation, some features of these benign tumors resemble a skin injury state and cutaneous trauma or other insults might support tumor development. Since adult terminal Schwann cells ensheathing nerve endings are able to dedifferentiate into a progenitor-like state in response to nerve crushing, we hypothesized that dedifferentiation of NF1-/- Schwann cells could be at the origin of human dermal neurofibromas. In support of this, here we show that CDH19 (a marker specific of Schwann cell precursors) and Schwann cell dedifferentiation marker SOX2 are significantly upregulated in NF1 tumors. We posit that onset of nerve regeneration might have a role in dermal neurofibroma initiation via dedifferentiation of NF1-/- Schwann cells.

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.

Circumferential urinary sphincter surface electromyography: A novel diagnostic method for intrinsic sphincter deficiency.

AIMS: The diagnosis of intrinsic sphincter deficiency (ISD) in patients with stress urinary incontinence (SUI) is not well established. We explored the possibility of applying a new tool: minimally invasive circumferential sphincter surface electromyography (CSS-EMG) to assess the muscular integrity of the urethral sphincter in patients with SUI/ISD. METHODS: CSS-EMG of the urethral sphincter and urodynamic studies were performed in 44 women with SUI. A urethral pressure profile (UPP) was measured in four directions. Maximal urethral closure pressure (MUCP) <40 cm/H2 O or the presence of SUI without urethral hypermobility was used to define ISD. RESULTS: Twenty-one patients had urodynamic SUI, 23 had no SUI and 12 patients had ISD. The mean average rectified value (ARV) of the motor unit action potential (MUAP), an indicator of the strength of urethral rhabdosphincter, was estimated. ARV measured in the 12 o'clock quadrant during maximal contraction was the only CSS-EMG parameter that had significant predictive value for ISD. With an increase in the 12 o'clock ARV value, the likelihood of ISD decreases (Odds Ratio 0.36 95% confidence interval 0.67-0.92). In the ROC curve with ARV measured in the 12 o'clock quadrant during maximal contraction, the explained area was 0.794 (P = 0.02); implying that ARV measured at the 12 o'clock quadrant during maximal contraction was able to predict ISD significantly. CONCLUSIONS: Myogenic changes of the urethral sphincter that contribute to ISD can be assessed with CSS-EMG. This new concept for assessing the functionality of the female urethral sphincter may assist with better understanding of the pathophysiology, the diagnosis and the treatment of SUI.

Human epithelial hair follicle stem cells and their progeny: current state of knowledge, the widening gap in translational research and future challenges.

Epithelial hair follicle stem cells (eHFSCs) are required to generate, maintain and renew the continuously cycling hair follicle (HF), supply cells that produce the keratinized hair shaft and aid in the reepithelialization of injured skin. Therefore, their study is biologically and clinically important, from alopecia to carcinogenesis and regenerative medicine. However, human eHFSCs remain ill defined compared to their murine counterparts, and it is unclear which murine eHFSC markers really apply to the human HF. We address this by reviewing current concepts on human eHFSC biology, their immediate progeny and their molecular markers, focusing on Keratin 15 and 19, CD200, CD34, PHLDA1, and EpCAM/Ber-EP4. After delineating how human eHFSCs may be selectively targeted experimentally, we close by defining as yet unmet key challenges in human eHFSC research. The ultimate goal is to transfer emerging concepts from murine epithelial stem cell biology to human HF physiology and pathology.

Reflections on how wound healing-promoting effects of the hair follicle can be translated into clinical practice.

Clinicians have long reported that hair-bearing areas tend to heal more rapidly than those lacking hair follicles. In the past decade, numerous scientific studies have corroborated clinical evidence, showing a direct nexus between the human hair follicle and the wound healing process. The migration of epithelial follicular stem cells to the skin surface to help in the wound re-epithelialization and the effect of the hair cycle on the wound healing rate underline the influence of the hair follicle in the healing process. In clinical practice, non-healing wounds are pathologies of high prevalence with significant associated burden costs for the healthcare system. As the population ages, the prevalence of this pathology is expected to increase in future years. The recent advances in understanding the biology of hair follicle stem cells have created the challenges of using this newly acquired knowledge in practical therapeutic applications. Chronic leg ulcers are an example of the targeted pathologies that urgently need better therapies. In this essay, our aim is to raise interest in this question, reviewing what is known in relation to the connections between hair follicles and wound healing, and elaborating on future directions that the field might take, including implications for clinical practice.

Association between EGFR gene polymorphisms, skin rash and response to anti-EGFR therapy in metastatic colorectal cancer patients.

Cetuximab and panitumumab are epidermal growth factor receptor (EGFR) inhibitors used in metastatic colorectal cancer (mCRC). Most patients develop a papulopustular rash that may predict tumor response to treatment. EGFR gene polymorphisms may also determine tumor response and appearance of skin rash. We hypothesized an association between EGFR gene polymorphisms, papulopustular rash and response to anticancer treatment. Four EGFR polymorphisms (-216, -191, CA-SSR, R521K) were analysed in 51 patients with mCRC receiving anti-EGFR. Severity of cutaneous rash and tumor response was measured following standard scales. We report an association between SNP-216 and tumor response (P = 0.003): no tumor progression occurred in TT genotype. Moreover, 92.3% of the responder patients developed skin rash, 62.9% of them presenting a grade ≥2 (P = 0.015). Thus, although underpowered, our preliminary data suggest that SNP-216 polymorphism of the EGFR gene could be useful in predicting tumor response and the appearance of severe skin rash might also be associated.

Biofabrication and Monitoring of a 3D Printed Skin Model for Melanoma.

There is an unmet need for in vitro cancer models that emulate the complexity of human tissues. 3D-printed solid tumor micromodels based on decellularized extracellular matrices (dECMs) recreate the biomolecule-rich matrix of native tissue. Herein a 3D in vitro metastatic melanoma model that is amenable for drug screening purposes and recapitulates features of both the tumor and the skin microenvironment is described. Epidermal, basement membrane, and dermal biocompatible inks are prepared by means of combined chemical, mechanical, and enzymatic processes. Bioink printability is confirmed by rheological assessment and bioprinting, and bioinks are subsequently combined with melanoma cells and dermal fibroblasts to build complex 3D melanoma models. Cells are tracked by confocal microscopy and surface-enhanced Raman spectroscopy (SERS) mapping. Printed dECMs and cell tracking allow modeling of the initial steps of metastatic disease, and may be used to better understand melanoma cell behavior and response to drugs.

A neural extracellular matrix-based method for in vitro hippocampal neuron culture and dopaminergic differentiation of neural stem cells.

BACKGROUND: The ability to recreate an optimal cellular microenvironment is critical to understand neuronal behavior and functionality in vitro. An organized neural extracellular matrix (nECM) promotes neural cell adhesion, proliferation and differentiation. Here, we expanded previous observations on the ability of nECM to support in vitro neuronal differentiation, with the following goals: (i) to recreate complex neuronal networks of embryonic rat hippocampal cells, and (ii) to achieve improved levels of dopaminergic differentiation of subventricular zone (SVZ) neural progenitor cells. METHODS: Hippocampal cells from E18 rat embryos were seeded on PLL- and nECM-coated substrates. Neurosphere cultures were prepared from the SVZ of P4-P7 rat pups, and differentiation of neurospheres assayed on PLL- and nECM-coated substrates. RESULTS: When seeded on nECM-coated substrates, both hippocampal cells and SVZ progenitor cells showed neural expression patterns that were similar to their poly-L-lysine-seeded counterparts. However, nECM-based cultures of both hippocampal neurons and SVZ progenitor cells could be maintained for longer times as compared to poly-L-lysine-based cultures. As a result, nECM-based cultures gave rise to a more branched neurite arborization of hippocampal neurons. Interestingly, the prolonged differentiation time of SVZ progenitor cells in nECM allowed us to obtain a purer population of dopaminergic neurons. CONCLUSIONS: We conclude that nECM-based coating is an efficient substrate to culture neural cells at different stages of differentiation. In addition, neural ECM-coated substrates increased neuronal survival and neuronal differentiation efficiency as compared to cationic polymers such as poly-L-lysine.

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.

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.

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.

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 arginineglycine-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.