Immunohistochemistry, histopathology and infrared spectral histopathology of colon cancer tissue sections

During the past years, many studies have shown that infrared spectral histopathology (SHP) can distinguish different tissue types and disease types independently of morphological criteria. In this manuscript, we report a comparison of immunohistochemical (IHC), histopathological and spectral histopathological results for colon cancer tissue sections. A supervised algorithm, based on the "random forest" methodology, was trained using classical histopathology, and used to automatically identify colon tissue types, and areas of colon adenocarcinoma. The SHP images subsequently were compared to IHC-based images. This comparison revealed excellent agreement between the methods, and demonstrated that label-free SHP detects compositional changes in tissue that are the basis of the sensitivity of IHC.

Evaluating different fixation protocols for spectral cytopathology, part 2: cultured cells

Spectral cytopathology (SCP) is a robust and reproducible diagnostic technique that employs infrared spectroscopy and multivariate statistical methods, such as principal component analysis to interrogate unstained cellular samples and discriminate changes on the biochemical level. In the past decade, SCP has taken considerable strides in its application for disease diagnosis. Cultured cell lines have proven to be useful model systems to provide detailed biological information to this field; however, the effects of sample fixation and storage of cultured cells are still not entirely understood in SCP. Conventional cytopathology utilizes fixation and staining methods that have been established and widely accepted for nearly a century and are focused on maintaining the morphology of a cell. Conversely, SCP practices must implement fixation protocols that preserve the sample's biochemical composition and maintain its spectral integrity so not to introduce spectral changes that may mask variance significant to disease. It is not only necessary to evaluate the effects on fixed exfoliated cells but also fixed cultured cells because although they are similar systems, they exhibit distinct differences. We report efforts to study the effects of fixation methodologies commonly used in traditional cytopathology and SCP including both fixed and unfixed routines applied to cultured HeLa cells, an adherent cervical cancer cell line. Data suggest parallel results to findings in Part 1 of this series for exfoliated cells, where the exposure time in fixative and duration of sample storage via desiccation contribute to minor spectral changes only. The results presented here reinforce observations from Part 1 indicating that changes induced by disease are much greater than changes observed as a result of alternate fixation methodologies. Principal component analysis of HeLa cells fixed via the same conditions and protocols as exfoliated cells (Part 1) yield nearly identical results. More importantly, the overall conclusion is that it is necessary that all samples subjected to comparative analysis should be prepared identically because although changes are minute, they are present.

Infrared spectral histopathology (SHP): a novel diagnostic tool for the accurate classification of lung cancer

We report results of a study utilizing a recently developed tissue diagnostic method, based on label-free spectral techniques, for the classification of lung cancer histopathological samples from a tissue microarray. The spectral diagnostic method allows reproducible and objective diagnosis of unstained tissue sections. This is accomplished by acquiring infrared hyperspectral data sets containing thousands of spectra, each collected from tissue pixels about 6 μm on edge; these pixel spectra contain an encoded snapshot of the entire biochemical composition of the pixel area. The hyperspectral data sets are subsequently decoded by methods of multivariate analysis, which reveal changes in the biochemical composition between tissue types, and between various stages and states of disease. In this study, a detailed comparison between classical and spectral histopathology (SHP) is presented, which suggests SHP can achieve levels of diagnostic accuracy that is comparable to that of multi-panel immunohistochemistry.

Identification of functionally relevant populations in enhanced biological phosphorus removal processes based on intracellular polymers profiles and insights into the metabolic diversity and heterogeneity

This study proposed and demonstrated the application of a new Raman microscopy-based method for metabolic state-based identification and quantification of functionally relevant populations, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), in enhanced biological phosphorus removal (EBPR) system via simultaneous detection of multiple intracellular polymers including polyphosphate (polyP), glycogen, and polyhydroxybutyrate (PHB). The unique Raman spectrum of different combinations of intracellular polymers within a cell at a given stage of the EBPR cycle allowed for its identification as PAO, GAO, or neither. The abundance of total PAOs and GAOs determined by Raman method were consistent with those obtained with polyP staining and fluorescence in situ hybridization (FISH). Different combinations and quantities of intracellular polymer inclusions observed in single cells revealed the distribution of different sub-PAOs groups among the total PAO populations, which exhibit phenotypic and metabolic heterogeneity and diversity. These results also provided evidence for the hypothesis that different PAOs may employ different extents of combination of glycolysis and TCA cycle pathways for anaerobic reducing power and energy generation and it is possible that some PAOs may rely on TCA cycle solely without glycolysis. Sum of cellular level quantification of the internal polymers associated with different population groups showed differentiated and distributed trends of glycogen and PHB level between PAOs and GAOs, which could not be elucidated before with conventional bulk measurements of EBPR mixed cultures.

Raman microscopy for noninvasive imaging of pharmaceutical nanocarriers: intracellular distribution of cationic liposomes of different composition

Nanotechnology is playing an increasing role in targeted drug delivery into pathological tissues. Drug-loaded pharmaceutical nanocarriers can be delivered into diseased sites by passive targeting (spontaneous accumulation of nanocarriers in the areas with affected vasculature) or by active targeting (via site-specific ligands attached to the surface of drug-loaded nanocarriers). Subsequent level of targeting requires cellular internalization of nanocarriers and their specific association with certain individual cell organelles. The control over intracellular distribution of pharmaceutical nanocarriers requires effective and noninvasive methods of their visualization inside cells. In an attempt to enhance cellular internalization of pharmaceutical nanocarriers and their association with mitochondria specifically, we have prepared three types of cationic liposomes and investigated their intracellular distribution. The analysis was performed using Raman microspectroscopy in order to provide morphological information as well as biochemical signatures of the sample. It was demonstrated that Raman microscopy allows evaluation of the extent of mitochondrial association depending on the liposome composition.

Evaluating different fixation protocols for spectral cytopathology, part 1

Spectral cytopathology (SCP) is a novel approach for disease diagnosis that utilizes infrared spectroscopy to interrogate the biochemical components of cellular samples and multivariate statistical methods, such as principal component analysis, to analyze and diagnose spectra. SCP has taken vast strides in its application for disease diagnosis over the past decade; however, fixation-induced changes and sample handling methods are still not systematically understood. Conversely, fixation and staining methods in conventional cytopathology, typically involving protocols to maintain the morphology of cells, have been documented and widely accepted for nearly a century. For SCP, fixation procedures must preserve the biochemical composition of samples so that spectral changes significant to disease diagnosis are not masked. We report efforts to study the effects of fixation protocols commonly used in traditional cytopathology and SCP, including fixed and unfixed methods applied to exfoliated oral (buccal) mucosa cells. Data suggest that the length of time in fixative and duration of sample storage via desiccation contribute to minor spectral changes where spectra are nearly superimposable. These findings illustrate that changes influenced by fixation are negligible in comparison to changes induced by disease.

Impact of nano titanium dioxide exposure on cellular structure of Anabaena variabilis and evidence of internalization

The present study investigated the impact of nano titanium dioxide (nTiO(2) ) exposure on the cellular structures of the nitrogen-fixing cyanobacteria Anabaena variabilis. Results of the present study showed that nTiO(2) exposure led to observable alteration in various intracellular structures and induced a series of recognized stress responses, including production of reactive oxygen species (ROS), appearance and increase in the abundance of membrane crystalline inclusions, membrane mucilage layer formation, opening of intrathylakoidal spaces, and internal plasma membrane disruption. The production of total ROS in A. variabilis cells increased with increasing nTiO(2) doses and exposure time, and the intracellular ROS contributed to only a small fraction (<10%) of the total ROS measured. The percentage of cells with loss of thylakoids and growth of membrane crystalline inclusions increased as the nTiO(2) dose and exposure time increased compared with controls, suggesting their possible roles in stress response to nTiO(2) , as previously shown for metals. Algal cell surface morphology and mechanical properties were modified by nTiO(2) exposure, as indicated by the increase in cell surface roughness and shifts in cell spring constant determined by atomic force microscopy analysis. The change in cell surface structure and increase in the cellular turgor pressure likely resulted from the structural membrane damage mediated by the ROS production. Transmission electron microscopy (TEM) analysis of nTiO(2) aggregates size distribution seems to suggest possible disaggregation of nTiO(2) aggregates when in close contact with microbial cells, potentially as a result of biomolecules such as DNA excreted by organisms that may serve as a biodispersant. The present study also showed, for the first time, with both TEM and Raman imaging that internalization of nTiO(2) particles through multilayered membranes in algal cells is possible. Environ. Toxicol. Chem. 2011; 30:861-869. © 2010 SETAC.

Spectral Detection of Micro-Metastases and Individual Metastatic Cells in Lymph Node Histology

The detection of micro-metastases and individual metastatic cells in lymph node tissue by spectral methods is summarized. These methods are based on instrument-based acquisition of thousands of infrared spectra of individual tissue pixels from the tissue section, and analysis of the resulting spectral hypercube by multivariate algorithms. The method of infrared image acquisition, followed by multivariate analysis, is henceforth referred to as Spectral Histopathology (SHP). SHP produces pseudo-color images of tissue sections which reveal details that compare very favorably with images collected from hematoxylin/eosin (H & E) stained tissues in that the same tissue structures are detected. However, the infrared results are based on objective and reproducible measurements and do not depend on subjective interpretation. One of the major topics of this paper is the comparison of spectral patterns observed for the same cancer type from different patients. While this is easy in some tissue types, we found it to be difficult in tissues of very different cellularity, or tissue sections that exhibit high levels of inflammatory response. In both cases, spectral quality will be compromised due to confounding effects resulting from scattering effects. The correction of these effects now permits the direct comparison of different patient samples, and paves the way for diagnostic algorithms for cancer detection to be developed.

Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy

The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue.

Picosecond spectral coherent anti-Stokes Raman scattering imaging with principal component analysis of meibomian glands

The lipid distribution in the mouse meibomian gland was examined with picosecond spectral anti-Stokes Raman scattering (CARS) imaging. Spectral CARS data sets were generated by imaging specific localized regions of the gland within tissue sections at consecutive Raman shifts in the CH(2) stretching vibrational range. Spectral differences between the location specific CARS spectra obtained in the lipid-rich regions of the acinus and the central duct were observed, which were confirmed with a Raman microspectroscopic analysis, and attributed to meibum lipid modifications within the gland. A principal component analysis of the spectral data set reveals changes in the CARS spectrum when transitioning from the acini to the central duct. These results demonstrate the utility of picosecond spectral CARS imaging combined with multivariate analysis for assessing differences in the distribution and composition of lipids in tissues.

Confocal Raman microspectral imaging (CRMI) of murine stem cell colonies

Confocal Raman micro-spectral imaging (CRMI) is a relatively novel technique for the construction of label-free images of biological entities, such as cells or tissue sections. This method utilizes thousands of spatially resolved Raman spectra, and sophisticated image analysis algorithms, to construct images which are based strictly on the inherent biochemical abundance contrast afforded by Raman microscopy. Here, we apply this methodology to monitor the very early communication processes that occur in a growing stem cell colony, yielding information on biochemical composition during development processes of the early stages of embryogenesis.

Micro-Raman detection of nuclear membrane lipid fluctuations in senescent epithelial breast cancer cells

Originally identified in cultured cells, oncogenic cellular senescence is a growth-arrest mechanism which may inhibit tumor development by limiting the ability of cells to divide. However, literature shows that these cells secrete tumor-inducing and tumor-suppressing proteins leading to poor prognosis. Understanding the progression of oncogenic cellular senescence and associated mechanisms provides important implications for improving tumorigenesis therapeutic treatments. Micro-Raman spectroscopic imaging has grown in popularity as an imaging technique compared to the standard imaging predecessors and can be attributed to its numerous benefits such as no sample perturbation and the provision of direct chemical information. Through the use of label-free micro-Raman spectroscopy, control and senescent cells were noninvasively imaged. Resulting spectral images were processed using chemometric techniques, and average nuclei spectra from each sample set were compared. In turn, changes in the -cis and -trans unsaturated lipid isomer content were found to differ among proliferating and senescent cells. This may lead to increased nuclear fluidity and may contribute to the inability of senescent cells to complete the cell cycle. In the tumor environment, this detected increase in nuclear envelope fluidity could lead to downstream gene expression modifications and increased nucleo-cytoplasmic RNA translocation. Understanding nuclear envelope fluidity could provide insight into secretory profiles of senescent cells and their role in carcinogenesis, meriting further investigation into novel therapeutic technique development for oncogenic cellular senescence.

Single point vs. mapping approach for spectral cytopathology (SCP)

In this paper we describe the advantages of collecting infrared microspectral data in imaging mode opposed to point mode. Imaging data are processed using the PapMap algorithm, which co-adds pixel spectra that have been scrutinized for R-Mie scattering effects as well as other constraints. The signal-to-noise quality of PapMap spectra will be compared to point spectra for oral mucosa cells deposited onto low-e slides. Also the effects of software atmospheric correction will be discussed. Combined with the PapMap algorithm, data collection in imaging mode proves to be a superior method for spectral cytopathology.

Two step resonant Mie scattering correction of infrared micro-spectral data: human lymph node tissue

In this manuscript, we report the application of EMSC to correct infrared micro-spectral data recorded from tissue that describe resonant Mie scattering contributions. Small breast micro-metastases previously undetectable using the raw measured spectra were provided clear contrast from the surrounding tissue after signal correction. The technique also proved transferrable, successfully correcting imaging data sets recorded from multiple patients. It is envisaged more robust methods of supervised analysis can now be constructed to automatically classify and diagnose tissue spectra.

Spectral cytopathology of cervical samples: detecting cellular abnormalities in cytologically normal cells

Spectral cytopathology (SCP) is a novel spectroscopic method for objective and unsupervised classification of individual exfoliated cells. The limitations of conventional cytopathology are well recognized within the pathology community. In SCP, cellular differentiation is made by observing molecular changes in the nucleus and the cytoplasm, which may or may not produce morphological changes detectable by conventional cytopathology. This proof of concept study shows SCP's potential as an enhancing tool for cytopathologists by aiding in the accurate and reproducible diagnosis of cells in all states of disease. Infrared spectra are collected from cervical cells deposited onto reflectively coated glass slides. Each cell has a corresponding infrared spectrum that describes its unique biochemical composition. Spectral data are processed and analyzed by an unsupervised chemometric algorithm, principal component analysis. In this blind study, cervical samples are classified by analyzing the spectra of morphologically normal looking squamous cells from normal samples and samples diagnosed by conventional cytopathology with low-grade squamous intraepithelial lesions. SCP discriminated cytopathological diagnoses amongst 12 different cervical samples with a high degree of specificity and sensitivity. SCP also correlated two samples with abnormal spectral changes: these samples had a normal cytopathological diagnosis but had a history of abnormal cervical cytology. The spectral changes observed in the morphologically normal looking cells are most likely because of an infection with human papillomavirus (HPV). HPV DNA testing was conducted on five additional samples, and SCP accurately differentiated these samples by their HPV status. SCP tracks biochemical variations in cells that are consistent with the onset of disease. HPV has been implicated as the cause of these changes detected spectroscopically. SCP does not depend on identifying the sparse number of morphologically abnormal cells within a large sample to make an accurate classification, as does conventional cytopathology. These findings suggest that the detection of cellular biochemical variations by SCP can serve as a new enhancing screening method that can identify earlier stages of disease.

Label-free Raman spectral imaging of intracellular delivery and degradation of polymeric nanoparticle systems

Novel optical imaging methods, such as Raman microspectroscopy, have been gaining recognition in their ability to obtain noninvasively the distribution of biochemical components of a sample. Raman spectroscopy in combination with optical microscopy provides a label-free method to assess and image cellular processes, without the use of extrinsic fluorescent dyes. The submicrometer resolution of the confocal Raman instrumentation allows us to image cellular organelles on the scale of conventional microscopy. We used the technique to monitor subcellular degradation patterns of two biodegradable nanocarrier systems-poly(epsilon-caprolactone) (PCL) and poly(lactic-co-glycolic acid) (PLGA). Our results suggest that both drug-delivery systems eventually are incorporated into Golgi-associated vesicles of late endosomes. These processes were monitored via the decrease of the molecule-characteristic peaks of PCL and PLGA. As the catabolic pathways proceed, shifts and variations in peak intensities and intensity ratios in the rendered Raman spectra unequivocally delineate their degradation patterns.

Evaluation of intracellular polyphosphate dynamics in enhanced biological phosphorus removal process using Raman microscopy

A Raman microscopy method was developed and successfully applied to evaluate the dynamics of intracellular polyphosphate in polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) processes. Distinctive Raman spectra of polyphosphates allowed for both identification of PAOs and quantification of intracellular polyphosphate during various metabolic phases in a lab-scale EBPR process. Observation of polyphosphate at individual cell level indicated thatthere are distributed states of cells in terms of polyphosphate content at any given time, suggesting that agent-based distributive modeling would more accurately reflect the behavior of an EBPR process than the traditional average-state based modeling. The results, for the first time, showed that the polyphosphate depletion or replenishment observed at the overall population level were collective results from shifts/transition in the distribution of abundance of PAOs with different amounts of polyphosphate inclusions during EBPR. Imaging construction based on simultaneous quantification of intracellular polyphosphate and protein revealed the spatial distribution of polyphosphate inside cells and showed that the polyphosphates accumulate in smaller or larger aggregates, rather than being evenly distributed within the cytoplasm. The results demonstated that Raman microscopy will allow for detailed cellular-level evaluation of polyphosphate metabolism and dynamics in EBPR processes and revealed mechanism insights, which otherwise would not be obtained using a traditional bulk measurement-based approach.