Patterns of brachyury expression in chordomas.

INTRODUCTION: Chordomas are rare malignant midline tumors, presumed to arise from notochordal remnants. This was further suggested by the discovery of the brachyury in chordomas pathogenesis. Its immunohistochemical expression has become the principal adjunct in the diagnosis of chordomas. However, studies about brachyury expression in chordomas are not fully comparable, mainly because they use different primary antibodies. Thus, the aim of this study is to investigate the expression of brachyury expression in a series of chordomas in conjunction to clinicopathological characteristics and to review the relevant literature providing all the details needed in the immunohistochemical study of brachyury. MATERIALS AND METHODS: This is a retrospective study of 62 chordomas, diagnosed over a 22-year period. No dedifferentiated or poorly differentiated cases were included. A monoclonal primary antibody (clone A-4) was used and brachyury expression was evaluated by the H-score. Clinicopathological parameters studied were age, sex, tumor localization, decalcification status and tissue age. Fetal notochords were used for comparison. RESULTS: Mean H-score of nuclear brachyury expression was 129.8. The tissue age significantly influenced brachyury expression, the older samples expressing less brachyury. Decalcification demonstrated a trend to weaken brachyury expression. Clinical characteristics were not correlated with the patterns of brachyury expression. Notochords were negative. Literature review reveals several polyclonal antibodies used and a positivity of 75%-100% in chordomas with even more variable results in notochords. CONCLUSION: In chordomas, as in other tumor types, an uniformization of studies about brachyury expression is needed, by considering the clone used, and the decalcification and the age of the sample, given the growing importance of brachyury in diagnosis and therapeutic steps.

Higher Virulence of Diplodia seriata Isolates on Vines of cv. Cabernet Sauvignon Associated with 10-Year-Old Wood Compared to Young Tissue.

Botryosphaeria dieback (BD) occurs in young and old plants. In the field, the prevalence and severity of the disease increase proportionally with the age of vineyards. Among the pathogens that cause BD, Diplodia seriata is the most prevalent species in Chile and other countries with a Mediterranean climate. To date, no information is available on the susceptibility of adult wood to infection by this pathogen since most of the pathogenicity tests have been carried out on 1- or 2-year-old shoots or detached canes. Therefore, a pathogenicity test was carried out on plants under field conditions, with inoculations in 1-year-old shoots and 2- and 10-year-old wood in grapevine cv. Cabernet Sauvignon. A pathogenicity test was carried out with two isolates of D. seriata. The results for the plants show that D. seriata was significantly more aggressive on the 10-year-old than on the one- or two-year-old tissue, where the lesions were 4.3 and 2.3 cm on average, respectively. These results were compared with the lesions obtained from two-year-old canes after the isolates were activated in grape berries. Also, the Chilean isolates of D. seriata were compared phylogenetically with those from other countries, and no major differences were found between them. Our results are consistent with the damage observed in the field, contributing to the knowledge of the epidemiology of this disease in Mediterranean climates. In the future, the effect observed in cv. Cabernet Sauvignon with D. seriata on virulence at different tissue ages should be tested for other BD-causing agents and wine varieties.

Assessing bone maturity: Compositional and mechanical properties of rib cortical bone at different ages.

Understanding what maturity entails for bone, when it arrives, and its pre- and post-maturity traits and properties are very important for understanding its evolution and physiology. There is a clear but fine distinction between the chronological age of bone (the age of its donor) and the tissue age of the bone packets it comprises at the microscopic level. Whole bone fragility changes with age due to mass and architecture effects, but so do the properties of bone at the tissue level. Tissue age and tissue-level properties are therefore increasingly attracting a great deal of attention recently. The present study investigated compositional and material changes in the hydroxyapatite crystals, the collagenous phase, changes in bone matrix composition and its nanoindentation properties and their decline with chronological age in later life. The aim was to track the age threshold at which cortical bone arrives at maturity and what happens following that threshold. To do so FTIR, DSC/TGA, XRD, nanoindentation and microindentation were used to investigate rib cortical bone material across a cohort of 86 individuals from one ethnic group with age spanning between 17 and 82 years. Results of this cross-sectional study showed a clear increase in mineral content relative to the organic and water contents across all ages. Furthermore, an increase in crystal size and consequent decrease in strain (coherence length) was detected associated with secondary mineralisation and an increase in carbonate substitution. Overall, we observe a number of modifications which contribute to a typical functional behaviour of bone showing an increase in both indentation modulus and hardness until the age of about 35 after which both of these properties decline gradually and concomitantly to other physicochemical changes and seemingly until the end of one's life.

Cortical bone material / compositional properties in growing children and young adults aged 1.5-23 years, as a function of gender, age, metabolic activity, and growth spurt.

Bone material / compositional properties are significant determinants of bone quality, thus strength. Raman spectroscopic analysis provides information on the quantity and quality of all three bone tissue components (mineral, organic matrix, and tissue water). The overwhelming majority of the published reports on the subject concern adults. We have previously reported on these properties in growing children and young adults, in the cancellous compartment. The purpose of the present study was to create normative reference data of bone material / compositional properties for children and young adults, in the cortical compartment. We performed Raman (Senterra (Bruker Optik GmbH), 50× objective, with an excitation of 785 nm (100 mW) and a lateral resolution of ~0.6 µm) microspectroscopic analysis of transiliac bone samples from 54 individuals between 1.5 and 23 years of age, with no known metabolic bone disease, and which have been previously used to establish histomorphometric, bone mineralization density distribution, and cancellous bone quality reference values. The bone quality indices that were determined were: mineral/matrix ratio (MM) from the integrated areas of the v2PO4 (410-460 cm-1) and the amide III (1215-1300 cm-1) bands, tissue water in nanopores approximated by the ratio of the integrated spectral area ~ 494-509 cm-1 to Amide III band, the glycosaminoglycan (GAG) content (ratio of integrated area 1365-1390 cm-1 to the Amide III band, the sulfated proteoglycan (sPG) content as the ratio of the integrated peaks ~1062 cm-1 and 1365-1390 cm-1, the pyridinoline (Pyd) content estimated from the ratio of the absorbance height at 1660 cm-1 / area of the amide I (1620-1700 cm-1) band, and the mineral maturity / crystallinity (MMC) estimated from the inverse of the full width at half height of the v1PO4 (930-980 cm-1) band. Analyses were performed at the three distinct cortical surfaces (endosteal, osteonal, periosteal) at specific anatomical microlocations, namely the osteoid, and the three precisely known tissue ages based on the presence of fluorescence double labels. Measurements were also taken in interstitial bone, a much older tissue that has undergone extensive secondary mineralization. Overall, significant dependencies of the measured parameters on tissue age were observed, while at any given tissue age, sex and subject age were minimal confounders. The established Raman database in the cortical compartments complements the previously published one in cancellous bone, and provides healthy baseline bone quality indices that may serve as a valuable tool to identify alterations due to pediatric disease.

PD-L1 expression in head and neck cancer tissue specimens decreases with time.

BACKGROUND: PD-L1 immunohistochemical expression is used as an important theranostic marker in various malignancies, including head and neck squamous cell carcinoma (HNSCC) where the combined positive score (CPS) guides treatment decisions. Despite indirect evidence that there is loss of antigenicity for archived tissues, there is no direct comparison between PD-L1 expression of the same tissue upon arrival and after its storage. MATERIAL AND METHODS: We compared the immunohistochemical expression of PD-L1 (22C3) in 106 HNSCC upon their arrival and after their storage (interval ranging from 20 to 48 months, mean 30.8 months). The evaluation was performed by two different pathologists' groups. RESULTS: We found a statistically significant decrease in the PD-L1 tumor proportional score (TPS), immune cells expression (IC) and CPS between the initial and the newly stained slides. CONCLUSION: This is the first study comparing PD-L1 expression between a tissue and "himself" later in time, highlighting an important decrease in expression by tumor and immune cells, and suggesting that an immediate rather than a retrospective assay of PD-L1 expression should be preferable in the routine practice. DATA AVAILABILITY: Data are available upon reasonable request.

A Blood-Bone-Tooth Model for Age Prediction in Forensic Contexts.

The development of age prediction models (APMs) focusing on DNA methylation (DNAm) levels has revolutionized the forensic age estimation field. Meanwhile, the predictive ability of multi-tissue models with similar high accuracy needs to be explored. This study aimed to build multi-tissue APMs combining blood, bones and tooth samples, herein named blood-bone-tooth-APM (BBT-APM), using two different methodologies. A total of 185 and 168 bisulfite-converted DNA samples previously addressed by Sanger sequencing and SNaPshot methodologies, respectively, were considered for this study. The relationship between DNAm and age was assessed using simple and multiple linear regression models. Through the Sanger sequencing methodology, we built a BBT-APM with seven CpGs in genes ELOVL2, EDARADD, PDE4C, FHL2 and C1orf132, allowing us to obtain a Mean Absolute Deviation (MAD) between chronological and predicted ages of 6.06 years, explaining 87.8% of the variation in age. Using the SNaPshot assay, we developed a BBT-APM with three CpGs at ELOVL2, KLF14 and C1orf132 genes with a MAD of 6.49 years, explaining 84.7% of the variation in age. Our results showed the usefulness of DNAm age in forensic contexts and brought new insights into the development of multi-tissue APMs applied to blood, bone and teeth.

Breast cancer treatment and its effects on aging.

Breast cancer is the most common cancer of women in the United States. It is also proving to be one of the most treatable. Early detection, surgical intervention, therapeutic radiation, cytotoxic chemotherapies and molecularly targeted agents are transforming the lives of patients with breast cancer, markedly improving their survival. Although current breast cancer treatments are largely successful in producing cancer remission and extending lifespan, there is concern that these treatments may have long lasting detrimental effects on cancer survivors, in part, through their impact on non-tumor cells. Presently, the impact of breast cancer treatment on normal cells, its impact on cellular function and its effect on the overall function of the individual are incompletely understood. In particular, it is unclear whether breast cancer and/or its treatments are associated with an accelerated aging phenotype. In this review, we consider breast cancer survivorship from the perspective of accelerated aging, and discuss the evidence suggesting that women treated for breast cancer may suffer from an increased rate of physical and cognitive decline that likely corresponds with underlying vulnerabilities of genome instability, epigenetic changes, and cellular senescence.

Tissue age and plant genotype affect the microbiota of apple and pear bark.

Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties.

Dual discriminative local coding for tissue aging analysis.

In aging research, morphological age of tissue helps to characterize the effects of aging on different individuals. While currently manual evaluations are used to estimate morphological ages under microscopy, such operation is difficult and subjective due to the complex visual characteristics of tissue images. In this paper, we propose an automated method to quantify morphological ages of tissues from microscopy images. We design a new sparse representation method, namely dual discriminative local coding (DDLC), that classifies the tissue images into different chronological ages. DDLC in- corporates discriminative distance learning and dual-level local coding into the basis model of locality-constrained linear coding thus achieves higher discriminative capability. The morphological age is then computed based on the classification scores. We conducted our study using the publicly avail- able terminal bulb aging database that has been commonly used in existing microscopy imaging research. To represent these images, we also design a highly descriptive descriptor that combines several complementary texture features extracted at two scales. Experimental results show that our method achieves significant improvement in age classification when compared to the existing approaches and other popular classifiers. We also present promising results in quantification of morphological ages.

Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma.

BACKGROUND: Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA). RESULTS: Our analysis reveals extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes. CONCLUSIONS: Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE to EAC progression.

Drifting Diaphyses: Asymmetry in Diametric Growth and Adaptation Along the Humeral and Femoral Length.

This study quantifies regional histomorphological variation along the human humeral and femoral diaphysis in order to gain information on diaphyseal growth and modeling drift patterns. Three thin sections at 40, 50, and 60% bone length were prepared from a modern Mexican skeletal sample with known age and sex to give a longitudinal perspective on the drifting cortex (12 adults and juveniles total, 7 male and 5 female). Point-count techniques were applied across eight cross-sectional regions of interest using the starburst sampling pattern to quantify percent periosteal and endosteal primary lamellar bone at each diaphyseal level. The results of this study show a posterio-medial drift pattern in the humerus with a posterior rotational trend along the diaphysis. In the femur, we observed a consistent lateral to anteriolateral drift and an increase in primary lamellar bone area of both, periosteal and endosteal origin, towards the distal part of the diaphysis. These observations characterize drifting diaphyses in greater detail, raising important questions about how to resolve microscopic and macroscopic cross-sectional analysis towards a more complete understanding of bone growth and mechanical adaptation. Accounting for modeling drift has the potential to positively impact age and physical activity estimation, and explain some of the significant regional variation in bone histomorphology seen within (and between) bone cross-sections due to differing ages of tissue formation. More study is necessary, however, to discern between possible drift scenarios and characterize populational variation.

Pediatric reference Raman data for material characteristics of iliac trabecular bone.

Bone material characteristics are important contributors in the determination of bone strength. Raman spectroscopic analysis provides information on mineral/matrix ratio, mineral maturity/crystallinity, relative pyridinoline (Pyd) collagen cross-link content, relative proteoglycan content and relative lipid content. However, published reference data are available only for adults. The purpose of the present study was to establish reference data of Raman outcomes pertaining to bone quality in trabecular bone for children and young adults. To this end, tissue age defined Raman microspectroscopic analysis was performed on bone samples from 54 individuals between 1.5 and 23 years with no metabolic bone disease, which have been previously used to establish histomorphometric and bone mineralization density distribution reference values. Four distinct tissue ages, three well defined by the fluorescent double labels representing early stages of bone formation and tissue maturation (days 3, 12, 20 of tissue mineralization) and a fourth representing old mature tissue at the geometrical center of the trabeculae, were analyzed. In general, significant dependencies of the measured parameters on tissue age were found, while at any given tissue age, sex and subject age were not confounders. Specifically, mineral/matrix ratio, mineral maturity/crystallinity index and relative pyridinoline collagen cross-link content index increased by 485%, 20% and 14%, respectively between days 3 and 20. The relative proteoglycan content index was unchanged between days 3 and 20 but was elevated in the old tissue compared to young tissue by 121%. The relative lipid content decreased within days 3 to 20 by -22%. Thus, the method allows not only the monitoring of material characteristics at a specific tissue age but also the kinetics of tissue maturation as well. The established reference Raman database will serve as sensitive tool to diagnose disturbances in material characteristics of pediatric bone biopsy samples.