Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas.

Cancer is caused by germline and somatic mutations, which can share biological features such as amino acid change. However, integrated germline and somatic analysis remains uncommon. We present a framework that uses machine learning to learn features of recurrent somatic mutations to (1) predict somatic variants from tumor-only samples and (2) identify somatic-like germline variants for integrated analysis of tumor-normal DNA. Using data from 1769 patients from seven cancer types (bladder, glioblastoma, low-grade glioma, lung, melanoma, stomach, and pediatric glioma), we show that "somatic-like" germline variants are enriched for autosomal-dominant cancer-predisposition genes (p < 4.35 × 10-15), including TP53. Our framework identifies germline and somatic nonsense variants in BRCA2 and other Fanconi anemia genes in 11% (11/100) of bladder cancer cases, suggesting a potential genetic predisposition in these patients. The bladder carcinoma patients with Fanconi anemia nonsense variants display a BRCA-deficiency somatic mutation signature, suggesting treatment targeted to DNA repair.

Biomimetic tissue-engineered systems for advancing cancer research: NCI Strategic Workshop report.

Advanced technologies and biomaterials developed for tissue engineering and regenerative medicine present tractable biomimetic systems with potential applications for cancer research. Recently, the National Cancer Institute convened a Strategic Workshop to explore the use of tissue biomanufacturing for development of dynamic, physiologically relevant in vitro and ex vivo biomimetic systems to study cancer biology and drug efficacy. The workshop provided a forum to identify current progress, research gaps, and necessary steps to advance the field. Opportunities discussed included development of tumor biomimetic systems with an emphasis on reproducibility and validation of new biomimetic tumor models, as described in this report.

In vivo loading increases mechanical properties of scaffold by affecting bone formation and bone resorption rates.

A successful bone tissue engineering strategy entails producing bone-scaffold constructs with adequate mechanical properties. Apart from the mechanical properties of the scaffold itself, the forming bone inside the scaffold also adds to the strength of the construct. In this study, we investigated the role of in vivo cyclic loading on mechanical properties of a bone scaffold. We implanted PLA/ß-TCP scaffolds in the distal femur of six rats, applied external cyclic loading on the right leg, and kept the left leg as a control. We monitored bone formation at 7 time points over 35 weeks using time-lapsed micro-computed tomography (CT) imaging. The images were then used to construct micro-finite element models of bone-scaffold constructs, with which we estimated the stiffness for each sample at all time points. We found that loading increased the stiffness by 60% at 35 weeks. The increase of stiffness was correlated to an increase in bone volume fraction of 18% in the loaded scaffold compared to control scaffold. These changes in volume fraction and related stiffness in the bone scaffold are regulated by two independent processes, bone formation and bone resorption. Using time-lapsed micro-CT imaging and a newly-developed longitudinal image registration technique, we observed that mechanical stimulation increases the bone formation rate during 4-10 weeks, and decreases the bone resorption rate during 9-18 weeks post-operatively. For the first time, we report that in vivo cyclic loading increases mechanical properties of the scaffold by increasing the bone formation rate and decreasing the bone resorption rate.

In vivo assessment of local effects after application of bone screws delivering bisphosphonates into a compromised cancellous bone site.

BACKGROUND: The primary stability of cancellous screw is difficult to obtain in bone of compromised quality and failure of screw fixation is common. To overcome this problem, it is proposed to locally deliver bisphosphonate from the screw. An in vivo validation of the increase in fixation of the cancellous screw is then needed in compromised bone. METHODS: In this study, we used an overdrilling procedure, which enables consistent modeling of reduced screw stability comparable to compromised cancellous bone. Forty eight adult NZW rabbits were used in this study and all animals underwent bilateral femur implantation. One leg was implanted with the screw containing the bisphosphonate (biocoated group) while the other was used as control (control group) with the screw only. Mechanical testing and micro-CT imaging were used to assess the effect of local drug delivery of Zoledronate on screws fixation at 5 time points. FINDINGS: At the early time points (1, 5, and 10 days), no significant difference could be seen between the biocoated and control groups. At 6 weeks, the bone volume fraction was significantly higher in the trabecular region of the biocoated group. However, this increase did not have a significant effect on the pull-out force. At the last time point, 11 weeks, both the bone volume fraction and the pull-out force were significantly higher in the biocoated group. INTERPRETATION: The results of this study suggest that, in compromised bone, local delivery of bisphosphonate enhances the stability of bone screws.

Prediction of spatio-temporal bone formation in scaffold by diffusion equation.

Developing a successful bone tissue engineering strategy entails translation of experimental findings to clinical needs. A major leap forward toward this goal is developing a quantitative tool to predict spatial and temporal bone formation in scaffold. We hypothesized that bone formation in scaffold follows diffusion phenomenon. Subsequently, we developed an analytical formulation for bone formation, which had only three unknown parameters: C, the final bone volume fraction, α, the so-called scaffold osteoconduction coefficient, and h, the so-called peri-scaffold osteoinduction coefficient. The three parameters were estimated by identifying the model within vivo data of polymeric scaffolds implanted in the femoral condyle of rats. In vivo data were obtained by longitudinal micro-CT scanning of the animals. Having identified the three parameters, we used the model to predict the course of bone formation in two previously published in vivo studies. We found the predicted values to be consistent with the experimental ones. Bone formation into a scaffold can then adequately be described through diffusion phenomenon. This model allowed us to spatially and temporally predict the outcome of tissue engineering scaffolds with only 3 physically relevant parameters.

Surgical preparation of bone-scaffold interface is critical for bone regeneration inside tissue engineering scaffold.

The goal of this study was to investigate if the preparation of implantation site affects bone formation inside tissue engineering scaffolds. For this purpose, two different drilling techniques were used to create a hole in distal femurs of rats before the insertion of a bone scaffold: a manually driven wood drill bit and an electrically driven metal drill bit. The size and the position of the hole were identical for the two cases. The bone volume, bone mineral density, and callus formation were assessed noninvasively using micro-CT tomography at several time points after implantation. The formation of bone and soft tissue inside scaffold were evaluated by histology. The bone structure around the holes made by the two techniques was compared ex vivo. The long-term study of bone formation showed that when a wood drill bit was used, the bone formation is accelerated by 3 weeks compared to when a metal drill bit was used. The ex vivo studies suggest that this result is due to the drilling methods differentially affecting the structure of the bone surrounding the generated defects.

In vivo cyclic loading as a potent stimulatory signal for bone formation inside tissue engineering scaffold.

In clinical situations, bone defects are often located at load bearing sites. Tissue engineering scaffolds are future bone substitutes and hence they will be subjected to mechanical stimulation. The goal of this study was to test if cyclic loading can be used as stimulatory signal for bone formation in a bone scaffold. Poly(L-lactic acid) (PLA)/ 5% beta-tricalcium phosphate (beta-TCP) scaffolds were implanted in both distal femoral epiphyses of eight rats. Right knees were stimulated (10N, 4Hz, 5 min) five times, every two days, starting from the third day after surgery while left knees served as control. Finite element study of the in vivo model showed that the strain applied to the scaffold is similar to physiological strains. Using micro-computed tomography (CT), all knees were scanned five times after the surgery and the related bone parameters of the newly formed bone were quantified. Statistical modeling was used to estimate the evolution of these parameters as a function of time and loading. The results showed that mechanical stimulation had two effects on bone volume (BV): an initial decrease in BV at week 2, and a long-term increase in the rate of bone formation by 28%. At week 13, the BV was then significantly higher in the loaded scaffolds.

Biomechanical evaluation of porous biodegradable scaffolds for revision knee arthroplasty.

Tibial bone defect is a critical problem for revision knee arthroplasty. Instead of using metallic spacer or cement, biodegradable scaffolds could be an alternative solution. A numerical model of a revision knee arthroplasty was thus developed to estimate the mechanical resistance of the scaffold in this demanding situation. The tibia, scaffold, and prosthesis were represented by simplified parameterised geometries. The maximal gait cycle force was applied asymmetrically to simulate a critical loading. Several parameters were analysed: 1) inter-individual variability, 2) cortical bone stiffness, 3) cortical bone thickness, 4) prosthesis fixation quality, and 5) scaffold thickness. The calculated scaffold strain was compared to its experimental ultimate strain. Among the tested parameters, failure was only predicted with scaffold thickness below 5 mm. This study suggests that biodegradable bone scaffolds could be used to fill bone defects in revision knee arthroplasty, but scaffold size seems to be the limiting factor.