Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy.

Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans. We report a tissue sampling approach with molecular biopsy using electroporation. This method, coined electroporation-based biopsy (e-biopsy), enables nondestructive nonthermal permeabilization of cells in the skin for vacuum-assisted extraction of biomolecules.

Proteome Expression Signatures: Differences between Orbital and Subcutaneous Abdominal Adipose Tissues.

Differences between orbital and subcutaneous abdominal fat in the same patient have been noted but not formally investigated, previously. The objective of this research was to compare the differential expression of protein profiles in subcutaneous abdominal and orbital adipose tissues. In this cross-sectional, observational study, orbital fat tissue was sampled from 10 patients who underwent blepharoplasty and agreed to provide a small sample of subcutaneous abdominal fat.

Treating Scars After Burns With Pulsed Electric Fields in the Rat Model.

Reducing scar size after severe burn injuries is an important and challenging medical, technological, and social problem. We have developed a battery-powered pulsed electric field (PEF) device and surface needle electrode applicator to deliver PEFs to the healing dorsal burn wound in rats. The pulsed electric field was used to treat residual burn wounds caused by metal contact in rats starting 10 days after the injury for 4 months every 11 or 22 days for 4 months using varying time applied voltages at 250-350 V range, 400 mA current, 40 pulses, 70 μs duration each, delivered at pulse repetition frequency 10 Hz at 5 locations inside the wound.

High-throughput lipidomic profiles sampled with electroporation-based biopsy differentiate healthy skin, cutaneous squamous cell carcinoma, and basal cell carcinoma.

Background: The incidence rates of cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) skin cancers are rising, while the current diagnostic process is time-consuming. We describe the development of a novel approach to high-throughput sampling of tissue lipids using electroporation-based biopsy, termed e-biopsy. We report on the ability of the e-biopsy technique to harvest large amounts of lipids from human skin samples.

Exploring multisite heterogeneity of human basal cell carcinoma proteome and transcriptome.

Basal cell carcinoma (BCC) is the most common type of skin cancer. Due to multiple, potential underlying molecular tumor aberrations, clinical treatment protocols are not well-defined. This study presents multisite molecular heterogeneity profiles of human BCC based on RNA and proteome profiling.

Electroporation-Based Biopsy Treatment Planning with Numerical Models and Tissue Phantoms.

Molecular sampling with vacuum-assisted tissue electroporation is a novel, minimally invasive method for molecular profiling of solid lesions. In this paper, we report on the design of the battery-powered pulsed electric field generator and electrode configuration for an electroporation-based molecular sampling device for skin cancer diagnostics. Using numerical models of skin electroporation corroborated by the potato tissue phantom model, we show that the electroporated tissue volume, which is the maximum volume for biomarker sampling, strongly depends on the electrode's geometry, needle electrode skin penetration depths, and the applied pulsed electric field protocol.

In vivo detection of bile duct pre-cancer with endoscopic light scattering spectroscopy.

Bile duct cancer is the second most common primary liver cancer, with most diagnoses occurring in the advanced stages. This leads to a poor survival rate, which means a technique capable of reliably detecting pre-cancer in the bile duct is urgently required. Unfortunately, radiological imaging lacks adequate accuracy for distinguishing dysplastic and benign biliary ducts, while endoscopic techniques, which can directly assess the bile duct lining, often suffer from insufficient sampling.

Nondestructive protein sampling with electroporation facilitates profiling of spatial differential protein expression in breast tumors in vivo.

Excision tissue biopsy, while central to cancer treatment and precision medicine, presents risks to the patient and does not provide a sufficiently broad and faithful representation of the heterogeneity of solid tumors. Here we introduce e-biopsy-a novel concept for molecular profiling of solid tumors using molecular sampling with electroporation. As e-biopsy provides access to the molecular composition of a solid tumor by permeabilization of the cell membrane, it facilitates tumor diagnostics without tissue resection.

Electroporation-based proteome sampling ex vivo enables the detection of brain melanoma protein signatures in a location proximate to visible tumor margins.

A major concern in tissue biopsies with a needle is missing the most lethal clone of a tumor, leading to a false negative result. This concern is well justified, since needle-based biopsies gather tissue information limited to needle size. In this work, we show that molecular harvesting with electroporation, e-biopsy, could increase the sampled tissue volume in comparison to tissue sampling by a needle alone.

Coherent confocal light scattering spectroscopic microscopy evaluates cancer progression and aggressiveness in live cells and tissue.

The observation of biological structures in live cells beyond the diffraction limit with super-resolution fluorescence microscopy is limited by the ability of fluorescence probes to permeate live cells and the effect of these probes, which are often toxic, on cellular behavior. Here we present a coherent confocal light scattering and absorption spectroscopic microscopy that for the first time enables the use of large numerical aperture optics to characterize structures in live cells down to 10 nm spatial scales, well beyond the diffraction limit. Not only does this new capability allow high resolution microscopy with light scattering contrast, but it can also be used with almost any light scattering spectroscopic application which employs lenses.

Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor.

Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly.

Spectroscopic label-free microscopy of changes in live cell chromatin and biochemical composition in transplantable organoids.

Organoids formed from human induced pluripotent stem cells (hiPSCs) could be a limitless source of functional tissue for transplantations in many organs. Unfortunately, fine-tuning differentiation protocols to form large quantities of hiPSC organoids in a controlled, scalable, and reproducible manner is quite difficult and often takes a very long time. Recently, we introduced a new approach of rapid organoid formation from dissociated hiPSCs and endothelial cells using microfabricated cell-repellent microwell arrays.

Distributed flux balance analysis simulations of serial biomass fermentation by two organisms.

Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms.

Energy efficient dewatering of far offshore grown green macroalgae Ulva sp. biomass with pulsed electric fields and mechanical press.

Offshore macroalgae biomass production is a promising, yet challenging, pathway to provide feedstock for biorefineries. In this work, a device and a process for dewatering offshore grown biomass of the green macroalgae Ulva sp. using high-voltage pulsed electric fields (PEF) was developed.

Multispectral Endoscopy with Light Gating for Early Cancer Detection.

This paper reports the application of endoscopic light scattering spectroscopy (LSS) with light gating to detect malignancies in the biliary and pancreatic ducts, and also reviews the application of endoscopic LSS for differentiating cystic neoplasms in the pancreas and detecting invisible dysplasia in Barrett's esophagus. Information about tissue structure within the superficial epithelium where malignancy starts is present within the spectra of reflected light. Fortunately, this component of the reflected light is not yet randomized.

Multispectral light scattering endoscopic imaging of esophageal precancer.

Esophageal adenocarcinoma is the most rapidly growing cancer in America. Although the prognosis after diagnosis is unfavorable, the chance of a successful outcome increases tremendously if detected early while the lesion is still dysplastic. Unfortunately, the present standard-of-care, endoscopic surveillance, has major limitations, since dysplasia is invisible, often focal, and systematic biopsies typically sample less than one percent of the esophageal lining and therefore easily miss malignancies.

Picoanalysis of Drugs in Biofluids with Quantitative Label-Free Surface-Enhanced Raman Spectroscopy.

The enormous increase of Raman signal in the vicinity of metal nanoparticles allows surface-enhanced Raman spectroscopy (SERS) to be employed for label-free detection of substances at extremely low concentrations. However, the ultimate potential of label-free SERS to identify pharmaceutical compounds at low concentrations, especially in relation to biofluid sensing, is far from being fully realized. Opioids are a particular challenge for rapid clinical identification because their molecular structural similarities prevent their differentiation with immunolabeling approaches.

Genome-wide analysis of fitness data and its application to improve metabolic models.

Background: Synthetic biology and related techniques enable genome scale high-throughput investigation of the effect on organism fitness of different gene knock-downs/outs and of other modifications of genomic sequence.

Results: We develop statistical and computational pipelines and frameworks for analyzing high throughput fitness data over a genome scale set of sequence variants. Analyzing data from a high-throughput knock-down/knock-out bacterial study, we investigate differences and determinants of the effect on fitness in different conditions.

Design and Analysis of Offshore Macroalgae Biorefineries.

Displacing fossil fuels and their derivatives with renewables, and increasing sustainable food production are among the major challenges facing the world in the coming decades. A possible, sustainable direction for addressing this challenge is the production of biomass and the conversion of this biomass to the required products through a complex system coined biorefinery. Terrestrial biomass and microalgae are possible sources; however, concerns over net energy balance, potable water use, environmental hazards, and uncertainty in the processing technologies raise questions regarding their actual potential to meet the anticipated food, feed, and energy challenges in a sustainable way.

Light scattering spectroscopy identifies the malignant potential of pancreatic cysts during endoscopy.

Pancreatic cancers are usually detected at an advanced stage and have poor prognosis. About one fifth of these arise from pancreatic cystic lesions. Yet not all lesions are precancerous, and imaging tools lack adequate accuracy for distinguishing precancerous from benign cysts.

Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method.

Understanding the impact of all process parameters on the efficiency of biomass hydrolysis and on the final yield of products is critical to biorefinery design. Using Taguchi orthogonal arrays experimental design and Partial Least Square Regression, we investigated the impact of change and the comparative significance of thermochemical process temperature, treatment time, %Acid and %Solid load on carbohydrates release from green macroalgae from Ulva genus, a promising biorefinery feedstock. The average density of hydrolysate was determined using a new microelectromechanical optical resonator mass sensor.

Cancer exosomes perform cell-independent microRNA biogenesis and promote tumorigenesis.

Exosomes are secreted by all cell types and contain proteins and nucleic acids. Here, we report that breast cancer associated exosomes contain microRNAs (miRNAs) associated with the RISC-Loading Complex (RLC) and display cell-independent capacity to process precursor microRNAs (pre-miRNAs) into mature miRNAs. Pre-miRNAs, along with Dicer, AGO2, and TRBP, are present in exosomes of cancer cells.

Peer group normalization and urine to blood context in steroid metabolomics: the case of CAH and obesity.

Traditional interpretation of GC-MS output involved the semi-quantitative estimation of outstanding low or high specific metabolites and the ratio between metabolites. Here, we utilize a systems biology approach to steroid metabolomics of a complex steroid-related disorder, using an all-inclusive analysis of the steroidal pathway in the form of a subject steroidal fingerprint and disease signature, providing novel methods of normalization and visualization. The study compares 324 normal children to pure enzymatic deficiency in 27 untreated 21-hydroxylase CAH patients and to complex disease in 70 children with obesity.

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks.

Genome-scale metabolic network reconstructions are considered a key step in quantifying the genotype-phenotype relationship. We present a novel gap-filling approach, MetabolIc Reconstruction via functionAl GEnomics (MIRAGE), which identifies missing network reactions by integrating metabolic flux analysis and functional genomics data. MIRAGE's performance is demonstrated on the reconstruction of metabolic network models of E.

Spectral Imaging with Scattered Light: From Early Cancer Detection to Cell Biology.

This article reports the evolution of scanning spectral imaging techniques using scattered light for minimally invasive detection of early cancerous changes in tissue and cell biology applications. Optical spectroscopic techniques have shown promising results in the diagnosis of disease on a cellular scale. They do not require tissue removal, can be performed in vivo, and allow for real time diagnoses.