Unintended CRISPR-Cas9 editing outcomes: a review of the detection and prevalence of structural variants generated by gene-editing in human cells.

Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) gene-editing system (CRISPR-Cas) is a valuable tool for fundamental and applied research applications. Significant improvements in editing efficacy have advanced genome editing strategies into phase 3 human clinical trials. However, recent studies suggest that our understanding of editing outcomes has lagged behind the developments made in generating the edits themselves. While many researchers have analyzed on- and off-target events through the lens of small insertions or deletions at predicted sites, screens for larger structural variants (SVs) and chromosomal abnormalities are not routinely performed. Full and comprehensive validation of on- and off-target effects is required to ensure reproducibility and to accurately assess the safety of future editing applications. Here we review SVs associated with CRISPR-editing in cells of human origin and highlight the methods used to detect and avoid them.

Epidermolysis Bullosa: A Review of the Tissue-Engineered Skin Substitutes Used to Treat Wounds.

Skin wound healing is a crucial process for regenerating healthy skin and avoiding the undesired consequences associated with open skin wounds. For epidermolysis bullosa (EB), a debilitating group of fragile skin disorders currently without a cure, skin blistering can often be severe and heal poorly, increasing susceptibility to life-threatening complications. To prevent these, investigational therapies have been exploring the use of tissue-engineered skin substitutes (TESSs) aimed at replacing damaged skin and promoting long-term wound closure. These products have either been developed in house or commercially sourced and are composed of allogeneic or autologous human skin cells, often with some form of bioscaffolding. They can be broadly classified based on their cellular composition: keratinocytes (epidermal substitutes), fibroblasts (dermal substitutes) or a combination of both (composite substitutes). Encouraging long-term wound healing has been achieved with epidermal substitutes. However, these substitutes have not demonstrated the same efficacy for all patients, which may be due to the molecular heterogeneity observed between EB subtypes. Autologous composite TESSs, which more closely resemble native human skin, are therefore being investigated and may hold promise for treating an extended range of patients. Additionally, future TESSs for EB are focused on using gene-corrected patient skin cells, which have already demonstrated remarkable long-term wound healing capabilities. In this review, we provide an overview of the different TESSs that have been investigated in clinical studies to treat patients with EB, as well as their long-term wound healing results. Where available, we describe the methods used to develop these products to inform future efforts in this field.

Multiplex assessment of serum biomarker concentrations in well-appearing children with inflicted traumatic brain injury.

Proper diagnosis of mild inflicted traumatic brain injury (ITBI) is difficult; children often present without a history of trauma and with nonspecific symptoms, such as vomiting. Previous studies suggest that biomarkers may be able to screen for brain injury in this population, but these studies focused on only a few biomarkers. We hypothesized that using multiplex bead technology we would be able to identify multiple differences in the serum biomarker profile between in children with ITBI and those without brain injury. We compared the concentrations of 44 serum biomarkers in 16 infants with mild ITBI and 20 infants without brain injury. There were significant group differences in the concentrations of nine of the 44 markers. Vascular cellular adhesion molecule (VCAM) (p < 0.00) and IL-6 (IL-6) (p < 0.00) had the most significant group differences; IL-6 was higher after ITBI, whereas VCAM was lower. Using VCAM and IL-6 in classification algorithms, we could discriminate the groups with a sensitivity and specificity of 87% and 90%, respectively. The results suggest significant changes in the serum biomarker profile after mild ITBI. Future research is needed to determine whether these biomarkers can screen for brain injury in infants with nonspecific symptoms.

Serum biomarker profiles and response to neoadjuvant chemotherapy for locally advanced breast cancer.

INTRODUCTION: Neoadjuvant chemotherapy has become the standard of care for the diverse population of women diagnosed with locally advanced breast cancer. Serum biomarker levels are increasingly being investigated for their ability to predict therapy response and aid in the development of individualized treatment regimens. Multianalyte profiles may offer greater predictive power for neoadjuvant treatment response than the individual biomarkers currently in use. METHODS: Serum samples were collected from 44 patients enrolled in a phase I-II, open-label study of liposomal doxorubicin and paclitaxel in combination with whole breast hyperthermia for the neoadjuvant treatment of locally advanced breast cancer (stage IIB or stage III). Samples were collected prior to each of four rounds of treatment and prior to definitive surgery. Samples were assayed by Luminex assay for 55 serum biomarkers, including cancer antigens, growth/angiogenic factors, apoptosis-related molecules, metastasis-related molecules, adhesion molecules, adipokines, cytokines, chemokines, hormones, and other proteins. RESULTS: Biomarker levels were compared retrospectively with clinical and pathologic treatment responses. Univariate analysis of the data identified several groups of biomarkers that differed significantly among treatment outcome groups early in the course of neoadjuvant chemotherapy. Multivariate statistical analysis revealed multibiomarker panels that could differentiate between treatment response groups with high sensitivity and specificity. CONCLUSION: We demonstrate here that serum biomarker profiles may offer predictive power concerning treatment response and outcome in the neoadjuvant setting. The continued development of these findings will be of considerable clinical utility in the design of treatment regimens for individual breast cancer patients. TRIAL REGISTRATION: #NCT00346229.

Development of multimarker panel for early detection of endometrial cancer. High diagnostic power of prolactin.

OBJECTIVE: Endometrial carcinoma is the most common gynecologic cancer. Although the prognosis for endometrial cancer is generally good, cancers identified at late stages are associated with high levels of morbidity and mortality. Therefore, prevention and early detection may further reduce the burden of this challenging disease. METHODS: A panel of 64 serum biomarkers was analyzed in sera of patients with stages I-III endometrial cancer and age-matched healthy women, utilizing a multiplex xMAP bead-based immunoassay. For multivariate analysis, four different statistical classification methods were used: logistic regression (LR), separating hyperplane (SHP), k nearest neighbors (KNN), and classification tree (CART). For each of these classifiers, a diagnostic model was created based on the cross-validation set consisting of sera from 115 patients with endometrial cancer and 135 healthy women. RESULTS: Our data have demonstrated that patients with endometrial cancer have significantly different expression patterns of several serum biomarkers as compared to healthy controls. Prolactin was the strongest discriminative biomarker for endometrial cancer providing 98.3% sensitivity and 98.0% specificity alone. Our results have revealed that serum concentration of cancer antigens, including CA 125, CA 15-3, and CEA are higher in patients with Stage III endometrial cancer as compared to those with Stage I. In addition, we have shown that the expression of CA 125, AFP, and ACTH is elevated in women with tumor grade 3 vs. grade 1. Furthermore, five-biomarker panel (prolactin, GH, Eotaxin, E-selectin, and TSH) identified in this study was able to discriminate endometrial cancer from ovarian and breast cancers with high sensitivity and specificity. CONCLUSIONS: The ability of prolactin to accurately discriminate between cancer and control groups indicates that this biomarker could potentially be used for development of blood-based test for the early detection of endometrial cancer in high-risk populations. Combining the information on multiple serum markers using flexible statistical methods allows for achieving high cancer selectivity.

Biological control does not imply paradox.

Is the classical predator-prey theory inherently pathological? Defenders of the theory are losing ground in the debate. We will demonstrate that detractors' main argument is based on a faulty model, and that the conceptual and predictive bases of the theory are fundamentally sound.